WO2017087947A2 - Method of treatment of follicular lymphoma with a btk inhibitor - Google Patents

Method of treatment of follicular lymphoma with a btk inhibitor Download PDF

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WO2017087947A2
WO2017087947A2 PCT/US2016/063085 US2016063085W WO2017087947A2 WO 2017087947 A2 WO2017087947 A2 WO 2017087947A2 US 2016063085 W US2016063085 W US 2016063085W WO 2017087947 A2 WO2017087947 A2 WO 2017087947A2
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individual
dhrs7
sts
genes selected
ibrutinib
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PCT/US2016/063085
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French (fr)
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WO2017087947A3 (en
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Zhengyuang WANG
Betty Chang
Leo Cheung
Karl Eckert
Karl SCHWEIGHOFER
Shiquan Wu
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Pharmacyclics Llc
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • Bruton's tyrosine kinase (Btk), a member of the Tec family of non-receptor tyrosine kinases, is a key signaling enzyme expressed in all hematopoietic cells types except T
  • Btk plays an essential role in the B-cell signaling pathway linking cell surface B-cell receptor (BCR) stimulation to downstream intracellular responses.
  • BCR cell surface B-cell receptor
  • Follicular lymphoma FL
  • B-cell lymphoma B-cell lymphoma
  • NHL non-Hodgkin lymphoma
  • the lymphoma cells build up in lymph nodes.
  • the most common symptom is a painless swelling in the neck, armpit or groin.
  • a method of treating follicular lymphoma in an individual in need thereof wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
  • the individual has an overexpression of one or more genes selected from VCAM1, RPAl, and STS-1 (UBASH
  • a method for treating follicular lymphoma in an individual in need thereof comprising: (a) requesting a test providing the results of an analysis to determine whether the patient has an overexpression of one or more genes selected from
  • a method for selecting an individual having follicular lymphoma for treatment with ibrutinib comprising: (a) determining the expression level in the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7), and (b) administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof, if the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, T
  • a method of assessing an individual having follicular lymphoma for treatment with ibrutinib comprising: (a) determining the expression level the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7), and (b) determining that the individual is suitable for treatment or continued treatment with ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, V
  • a method for selecting an individual having follicular lymphoma for treatment with ibrutinib comprising: (a) determining the expression level in the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C
  • a method of optimizing the therapy of an individual receiving ibrutinib for treatment of follicular lymphoma comprising:
  • a method of monitoring response to ibrutinib of an individual receiving ibrutinib for treatment of follicular lymphoma comprising: (a) determining the expression level in the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7); and (b) and characterizing the individual as being responsive to the treatment with ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG
  • the method further comprising discontinue administration of ibrutinib to the individual.
  • kits useful in the methods disclosed herein comprising one or more reagents for determining the expression level of one or more genes selected from those disclosed herein in a sample.
  • the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising one or more genes disclosed herein.
  • a system useful in the methods described herein comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more genes described in a sample, and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a first software module configured to analyze the dataset to determine the expression level of one or more genes; and (ii) a second software module to assign the individual as a candidate for treatment with ibrutinib based on the expression level of the one or more biomarkers.
  • nucleic acid hybridization array comprising nucleic acid probes for detecting the genes described herein, wherein the nucleic acid probes hybridize to one or more genes disclosed herein.
  • ranges and amounts can be expressed as “about” a particular value or range. About also includes the exact amount. Hence “about 5 ⁇ _,” means “about 5 ⁇ _,” and also “5 ⁇ ..” Generally, the term “about” includes an amount that would be expected to be within experimental error, such as within ⁇ 10%, ⁇ 5% or ⁇ 1% of the stated value.
  • compositions and methods are intended to mean that the compositions and methods, etc., include the recited elements, but do not exclude others.
  • Consisting essentially of or its grammatic variants when used to define compositions and methods shall mean excluding other elements of any essential significance to the combination for the intended use, but not excluding elements that do not materially affect the characteristic(s) of the compositions or methods.
  • Consisting of or its grammatic variants shall mean excluding elements not specifically recited. Embodiments defined by each of these transition terms are within the scope of this invention. For example, when a formulation is described as comprising ingredients A, B and C, a formulation consisting essentially of A, B and C, and a formulation consisting of A, B and C are independently within the scope of this invention.
  • acceptable or “pharmaceutically acceptable”, with respect to a formulation, composition or ingredient, as used herein, means having no persistent detrimental effect on the general health of the subject being treated or does not abrogate the biological activity or properties of the compound, and is relatively nontoxic.
  • the terms "individual(s)", “subject(s)” and “patient(s)” mean any mammal.
  • the mammal is a human.
  • the mammal is a non-human. None of the terms require or are limited to situations characterized by the supervision (e.g. constant or intermittent) of a health care worker (e.g. a doctor, a registered nurse, a nurse practitioner, a physician's assistant, an orderly or a hospice worker).
  • a health care worker e.g. a doctor, a registered nurse, a nurse practitioner, a physician's assistant, an orderly or a hospice worker.
  • Ibrutinib is an inhibitor of Bruton's tyrosine kinase (Btk) having the chemical names of " 1 -((R)-3 -(4-amino-3 -(4-phenoxyphenyl)- lH-pyrazolo[3 ,4-d]pyrimidin- 1 -yl)piperidin- 1 - yl)prop-2-en- 1 -one" or " 1 - ⁇ (3R)-3 -[4-amino-3 -(4-phenoxyphenyl)- lH-pyrazolo[3 ,4- ⁇ i]pyrimidin-l-yl]piperidin-l-yl ⁇ prop-2-en-l-one" or "2-Propen-l-one, l-[(3R)-3-[4-amino-3-(4- phenoxyphenyl)-lH-pyrazolo[3,4- ⁇ i]pyrimidin-l-yl
  • compositions refers to a salt which does not cause significant irritation to a mammal to which it is administered and does not substantially abrogate the biological activity and properties of the compound.
  • Pharmaceutically acceptable salt may include acid addition salts of a compound formed with an organic acid, which include aliphatic mono- and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxyl alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and aromatic sulfonic acids, amino acids, acetic acid, trifluoroacetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic
  • Solvates refer to a complex of a compound formed with either stoichiometric or non- stoichiometric amounts of a solvent, for example, pharmaceutically acceptable solvents such as water, ethanol, methanol, methyl tert-butyl ether (MTBE), diisopropyl ether (DIPE), ethyl acetate, isopropyl acetate, isopropyl alcohol, methyl isobutyl ketone (MIBK), methyl ethyl ketone (MEK), acetone, nitromethane, tetrahydrofuran (THF), dichloromethane (DCM), dioxane, heptanes, toluene, anisole, acetonitrile, and the like.
  • solvents for example, pharmaceutically acceptable solvents such as water, ethanol, methanol, methyl tert-butyl ether (MTBE), diisopropyl ether (DIPE),
  • solvates of ibrutinib are anhydrous.
  • ibrutinib, or pharmaceutically acceptable salts thereof exist in unsolvated form.
  • ibrutinib, or pharmaceutically acceptable salts thereof exist in unsolvated form and are anhydrous.
  • ibrutinib, or a pharmaceutically acceptable salt thereof is prepared in various forms, including but not limited to, amorphous phase, crystalline forms, milled forms and nano-particulate forms.
  • ibrutinib, or a pharmaceutically acceptable salt thereof is amorphous.
  • ibrutinib, or a pharmaceutically acceptable salt thereof is amorphous and anhydrous.
  • ibrutinib, or a pharmaceutically acceptable salt thereof is crystalline.
  • ibrutinib, or a pharmaceutically acceptable salt thereof is crystalline and anhydrous.
  • ibrutinib or a pharmaceutically acceptable salt thereof is a crystalline form, alone or with a conformer, described in, e.g., WO2016141068, WO2016160598 and WO2016160604, all of which are incorporated by reference in their entirety.
  • Bruton's tyrosine kinase refers to B niton's tyrosine kinase from Homo sapiens, as disclosed in, e.g., U.S. Patent No. 6,326,469 (GenBank Accession No. NP_000052).
  • "treating" and like terms refer to reducing the severity and/or frequency of symptoms of a disease, such as FL, eliminating the symptoms and/or the underlying cause of said symptoms, reducing the frequency or likelihood of the symptoms and/or their underlying cause, and improving or remediating damage caused, directly or indirectly, by the disease, such as FL. include alleviating, abating or ameliorating a disease or condition, or symptoms thereof; managing a disease or condition, or symptoms thereof; preventing additional symptoms;
  • ameliorating or preventing the underlying metabolic causes of symptoms inhibiting the disease or condition, e.g., arresting the development of the disease or condition; relieving the disease or condition; causing regression of the disease or condition, relieving a condition caused by the disease or condition; or stopping the symptoms of the disease or condition.
  • an “effective amount” or “therapeutically effective amount,” as used herein, refer to a sufficient amount of an agent or a compound being administered which will relieve to some extent one or more of the symptoms of the disease or condition being treated. The result can be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system.
  • an “effective amount” for therapeutic uses is the amount of compound required to provide a clinically significant decrease in disease symptoms without undue adverse side effects.
  • therapeutically effective amount includes, for example, a prophylactically effective amount.
  • an effect amount or "a therapeutically effective amount” can vary from subject to subject, due to variation in metabolism of the compound, age, weight, general condition of the subject, the condition being treated, the severity of the condition being treated, and the judgment of the prescribing physician.
  • therapeutically effective amounts may be determined by routine experimentation, including but not limited to a dose escalation clinical trial.
  • biological sample refers to any sample from a patient that contains, or can contain, the biomarkers of interest or an encoded peptide thereof, including, for example, tumor, blood, serum, or plasma.
  • the sample is a tumor biopsy sample.
  • nucleic acid refers to deoxyribonucleotides, deoxyribonucleosides, ribonucleosides, or ribonucleotides and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides which have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless specifically limited otherwise, the term also refers to oligonucleotide analogs including PNA (peptidonucleic acid), analogs of DNA used in antisense technology (e.g., phosphorothioates, phosphoroamidates). Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (including but not limited to, degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated.
  • PNA peptidonucleic acid
  • degenerate codon substitutions are achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al. ( ⁇ 99 ⁇ )Nucleic Acid Res. 19:5081; Ohtsuka et al. (1985) J. Biol. Chem. 260:2605-2608; and Cassol et al. ( ⁇ 992)Mol. Cell. Probes 6, 327-331; and Rossolini et al. (1994) Mol. Cell. Probes 8:91-98).
  • the nucleic acid or a fragment thereof encodes a protein.
  • polypeptide peptide
  • protein protein
  • the terms apply to naturally occurring amino acid polymers as well as amino acid polymers in which one or more amino acid residues is a non- naturally occurring amino acid, e.g., an amino acid analog.
  • the terms encompass amino acid chains of any length, including full length proteins, wherein the amino acid residues are linked by covalent peptide bonds.
  • Gene expression level refers to the measurable quantity (such as number of molecules or concentration) of a particular gene or a gene product (including any of DNA, cDNA, RNA, transcript, or a polypeptide encoded by the gene) in an individual or a sample taken from the individual. In some embodiments, expression level refers to the amount of RNA of the particular gene. In some embodiments, expression level refers to the amount of a particular gene in a sample from individual, such as a tumor sample, blood sample, serum sample, etc., and can, for example, be detected de novo or correspond to a previous determination.
  • Normal expression refers to an expression level of a gene in an individual (or in tumor cells of the individual) that is comparable to control, such as within ⁇ 25%, ⁇ 20% or ⁇ 10% of control or has no statistically significant difference as compared with control.
  • Overexpression refers to an increase in the expression level of a gene in an individual (or in tumor cells of the individual) relative to control or presence of a gene which is absent in control. In some embodiments, overexpression means that the expression level of the gene has an increase of at least 20%, 50%, 100% or 200% relative to control. In some embodiments, overexpression means that the increase in expression level of the gene relative to control is statistically significant.
  • Underexpression refers to a decrease in the expression level of a gene in an individual (or in tumor cells of the individual) relative to control or absence of a gene that is expressed in control. In some embodiments, underexpression means that the expression level of the gene is no more than 90%, 80%, 75%, 50%, 20%, or 10%, or less relative to control. In some embodiments, underexpression means that the decrease in expression level of the gene relative to control is statistically significant.
  • control refers to any reference standard suitable to provide a comparison to the expression products in the test sample.
  • the control comprises obtaining a "control sample” from which expression product levels are detected and compared to the expression product levels from the test sample.
  • Such a control sample may comprise any suitable sample, including but not limited to a sample from a control cancer patient (can be stored sample or previous sample measurement) with a known outcome; normal tissue or cells isolated from a subject, such as a normal patient or the cancer patient, cultured primary cells/tissues isolated from a subject such as a normal subject or the cancer patient, adjacent normal cells/tissues obtained from the same organ or body location of the cancer patient, a tissue or cell sample isolated from a normal subject, or a primary cells/tissues obtained from a depository.
  • a sample from a control cancer patient can be stored sample or previous sample measurement
  • normal tissue or cells isolated from a subject such as a normal patient or the cancer patient
  • cultured primary cells/tissues isolated from a subject such as a normal subject or the cancer patient
  • adjacent normal cells/tissues obtained from the same organ or body location of the cancer patient a tissue or cell sample isolated from a normal subject, or a primary cells/tissues obtained from a depository.
  • control may comprise a reference standard expression product level from any suitable source, including but not limited to housekeeping genes, an expression product level range from normal tissue (or other previously analyzed control sample), a previously determined expression product level range within a test sample from a group of patients, or a set of patients with a certain outcome (for example, survival for one, two, three, four years, etc.) or receiving a certain treatment (for example, standard of care cancer therapy). It will be understood by those of skill in the art that such control samples and reference standard expression product levels can be used in combination as controls.
  • the control may comprise normal or noncancerous cell/tissue sample.
  • control may comprise an expression level for a set of patients, such as a set of cancer patients, or for a set of cancer patients receiving a certain treatment, or for a set of patients with one outcome versus another outcome.
  • the specific expression product level of each patient can be assigned to a percentile level of expression, or expressed as either higher or lower than the mean or average of the reference standard expression level.
  • the control may comprise normal cells, cells from patients treated with combination chemotherapy, and cells from patients having benign cancer.
  • the control may also comprise a measured value for example, average level of expression of a particular gene in a population compared to the level of expression of a housekeeping gene in the same population.
  • control comprises a ratio transformation of expression product levels, including but not limited to determining a ratio of expression product levels of two genes in the test sample and comparing it to any suitable ratio of the same two genes in a reference standard; determining expression product levels of the two or more genes in the test sample and determining a difference in expression product levels in any suitable control; and determining expression product levels of the two or more genes in the test sample, normalizing their expression to expression of housekeeping genes in the test sample, and comparing to any suitable control.
  • control comprises a control sample which is of the same lineage and/or type as the test sample.
  • control may comprise expression product levels grouped as percentiles within or based on a set of patient samples, such as all patients with cancer.
  • a control expression product level is established wherein higher or lower levels of expression product relative to, for instance, a particular percentile, are used as the basis for predicting outcome.
  • a control expression product level is established using expression product levels from cancer control patients with a known outcome, and the expression product levels from the test sample are compared to the control expression product level as the basis for predicting outcome.
  • the control can be the background gene expression level of follicular lymphoma patients, or a predetermined gene expression level, e.g., an average or medium of historical expression levels of follicular lymphoma patients.
  • the control is the expression levels of one or more of the biomarker disclosed herein in a follicular lymphoma patient or a group of patients who are not insensitive toward ibrutinib.
  • the control is the expression levels of one or more of the biomarkers disclosed herein in a follicular lymphoma patient or a group of patients who have not been treated with ibrutinib.
  • the control is the expression levels of one or more of the biomarkers disclosed herein in a follicular lymphoma patient or a group of patients who have not been treated for follicular lymphoma.
  • probe refers to a nucleic acid molecule that comprises a sequence of nucleotides (such as 10 or more, 15 or more, 20 or more, or 10-25, 26-50, 51-75, 76- 100, or 101-500 bases or nucleotides) that will hybridize specifically to a target nucleic acid sequence, such as a gene disclosed herein.
  • nucleotides such as 10 or more, 15 or more, 20 or more, or 10-25, 26-50, 51-75, 76- 100, or 101-500 bases or nucleotides
  • primer refers to a nucleic acid sequence, whether occurring naturally as in a purified restriction digest or produced synthetically, that is capable of acting as a point of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand is induced (e.g. in the presence of nucleotides and an inducing agent such as DNA polymerase and at a suitable temperature and pH).
  • Non-Hodgkin's lymphoma is a cancer that starts in lymphocytes.
  • the non-Hodgkin's lymphoma is Burkitt lymphoma, chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, mantle cell lymphoma, marginal zone B-cell lymphomas, Waldenstrom's
  • lymphoplasmacytic lymphoma hairy cell leukemia, mediastinal large B-cell lymphoma, cutaneous lymphomas, mycosis fungoides, anaplastic large cell lymphoma, peripheral T-cell lymphomas, enteropathy associated T cell lymphoma (EATL), hepatosplenic gamma delta T cell lymphoma, or precursor T-lymphoblastic lymphoma.
  • TTL enteropathy associated T cell lymphoma
  • hepatosplenic gamma delta T cell lymphoma or precursor T-lymphoblastic lymphoma.
  • the non-Hodgkin's lymphoma is Burkitt lymphoma, chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, mantle cell lymphoma, marginal zone B-cell lymphomas, Waldenstrom's macroglobulinemia,
  • CLL chronic lymphocytic leukemia
  • SLL small lymphocytic lymphoma
  • DLBCL diffuse large B-cell lymphoma
  • FL follicular lymphoma
  • immunoblastic large cell lymphoma precursor B-lymphoblastic lymphoma
  • mantle cell lymphoma mantle cell lymphoma
  • marginal zone B-cell lymphomas Waldenstrom's macroglobulinemia
  • the non-Hodgkin's lymphoma is DLBCL. In some embodiments, the non- Hodgkin's lymphoma is FL. In some embodiments, the non-Hodgkin's lymphoma is previously treated with another anticancer agent. In some embodiments, the non-Hodgkin's lymphoma is a relapsed or refractory non-Hodgkin's lymphoma. In some embodiments, the relapsed or refractory non-Hodgkin's lymphoma is a relapsed or refractory FL. In some embodiments, the FL is treatment naive FL, i.e., previously untreated FL. In some embodiments, the FL is currently being or was previously treated with only ibrutinib.
  • Anticancer therapies refer to therapeutic agents or treatment useful or commonly used for treating a cancer, such as a Non-Hodgkin's lymphoma, and in particular follicular lymphoma. Such therapies include anticancer agents, radiation therapy, and surgical procedures, etc. In some embodiments, anticancer agents include chemotherapeutic agents, steroids, immunotherapeutic agents, targeted therapeutic agents, or a combination thereof.
  • anticancer agents include chlorambucil, ifosphamide, doxorubicin, mesalazine, thalidomide, lenalidomide, pomalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, obinutuzumab, rituximab, dexamethasone, prednisone, idelalisib, ibritumomab, tositumomab, bortezomib, pentostatin, endostatin, carfilzomib, or a combination thereof, such as R- Bendamustine (rituximab and bendamustine), R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone), and R-CVP (rituximab,
  • biomarkers useful in identifying follicular lymphoma patients suitable for treatment or continued treatment with ibrutinib, or in predicting or assessing response of follicular lymphoma patients to treatment with ibrutinib are biomarkers useful in identifying follicular lymphoma patients suitable for treatment or continued treatment with ibrutinib, or in predicting or assessing response of follicular lymphoma patients to treatment with ibrutinib.
  • biomarkers include CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299 (see, e.g., US 2015/0010514), TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5,
  • Biomarkers include the genes described herein, orthologs thereof, the nucleic acid (DNA or RNA) molecules comprising the genes, or proteins encoded by the genes. In some embodiments, the biomarkers described herein are present in humans. Detailed description of the genes can be found from National Center for Biotechnology
  • NCBI National Library of Medicine
  • the biomarkers are:
  • FILIP1 filamin A interacting protein 1 ; 27145 filamin-A-interacting protein 1
  • GCET2 GCSAM germinal center 257144 germinal center-associated associated signaling and signaling and motility protein motility; HGAL; GCAT2;
  • DNASE1L1 deoxyribonuclease 1 like 1; XIB; 1774 deoxyribonuclease- 1 -like 1
  • nucleoporin C nucleoporin C
  • POM121-2 membrane protein POM 121C LOC100131972
  • OSBPL2 oxysterol binding protein like; 9885 oxysterol-binding protein- ORP2; ORP-2; DFNA67; related protein 2
  • NT5C1B 5 '-nucleotidase, cytosolic IB; 93034 cytosolic 5 '-nucleotidase IB
  • OSBPL2 oxysterol binding protein like 2; 9885 oxysterol-binding protein- ORP2; ORP-2; DFNA67; related protein 2
  • KDM1B lysine demethylase IB; AOF1; 221656 lysine-specific histone
  • PCDHB3 protocadherin beta 3
  • PCDH- 56132 protocadherin beta-3
  • ZBTB39 zinc finger and BTB domain 9880 zinc finger and BTB domain- containing 39; ZNF922 containing protein 39
  • PAIP2 poly(A) binding protein 51247 polyadenylate-binding protein- interacting protein 2; PAIP-2; interacting protein 2
  • ALG2 ALG2 alpha- 1,3/1, 6- 85365 alpha- 1,3/ 1,6- mannosyltransferase; CDGIi; mannosyltransferase ALG2 CMS 14; NET38; CMSTA3;
  • SPOl l 1, initiator of meiotic 23626 meiotic recombination protein double stranded breaks; CT35; SPOl l
  • MIR24-1 microRNA 24-l MIR189; 407012
  • MIRN24-l miR-24-l
  • CTGF connective tissue growth factor 1490 connective tissue growth factor
  • PLA2G2A phospholipase A2 group IIA; 5320 phospholipase A2, membrane
  • the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675.
  • the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108,
  • the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108,
  • the individual has an overexpression of one or more (e.g., at least one, two, three or four) genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM
  • C170RF48 and FILIP1, and/or a normal expression or underexpression of one or more (e.g., at least one, two, three or four) genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
  • one or more e.g., at least one, two, three or four genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
  • the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
  • the individual has a normal expression of one or more genes selected from CERCAM, POM121C
  • the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
  • the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or a normal expression or underexpression of CERCAM or DHRS7.
  • the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B).
  • the individual has a normal expression of CERCAM or DHRS7.
  • the individual has an underexpression of CERCAM or DHRS7.
  • the individual has an overexpression of RPAl or STS-1 (UBASH3B), and/or a normal expression or underexpression of DHRS7.
  • the individual has an overexpression of RPAl or STS-1 (UBASH3B).
  • the individual has a normal expression of DHRS7.
  • the individual has an underexpression of DHRS7.
  • the individual has an increase in the expression level of one or more (e.g., at least one, two, three or four) genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, and/or an absence of an increase (e.g., decrease) in the expression level of one or more (e.g., at least one, two, three or four) genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • CALB2RY11 PPAN- P2RY11
  • DNAJC8 TTC19
  • VCAMl CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (
  • the individual has an increase in the expression level of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or an absence of an increase in the expression level of CERCAM or DHRS7. In some embodiments, the individual has an increase in the expression level of RPAl or STS-1 (UBASH3B), and/or an absence of an increase in the expression level of DHRS7.
  • follicular lymphoma FL
  • one or more biomarkers selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3,
  • LOC644248, C90RF169, SLC45A2, and LOC100128675 and/or a normal expression or underexpression or an absence of an increase in the expression level of one or more (e.g., at least one, two, three or four) biomarkers selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418,
  • follicular lymphoma FL
  • C170RF48 and FILIP1 and/or a normal expression or underexpression of one or more (e.g., at least one, two, three or four) biomarkers selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
  • one or more e.g., at least one, two, three or four biomarkers selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7
  • method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
  • the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or a normal expression or underexpression of CERCAM or DHRS7. In some embodiments, the individual has an overexpression of RPAl or STS-1
  • a method of treating follicular lymphoma in an individual in need thereof who has an increase in the expression level of one or more (e.g., at least one, two, three or four) biomarkers selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, and/or an absence of an increase (e.g., decrease) of one or more (e.g., at least one, two, three or four) biomarkers selected from CERCAM, POM121C
  • the individual has an increase in the expression level of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or an absence of an increase in the expression level of CERCAM or DHRS7. In some embodiments, the individual has an increase in the expression level of RPAl or STS-1 (UBASH3B), and/or an absence of an increase of DHRS7.
  • the individual has a decrease in the expression level of CERCAM or DHRS7.
  • a method of selecting an individual having a non- Hodgkin's lymphoma for treatment or for continuing treatment with ibrutinib comprising:
  • a method of selecting an individual having a non-Hodgkin's lymphoma for treatment or for continuing treatment with ibrutinib comprising: (a) determining the expression level of one or more of the biomarkers selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM
  • LOC 100131972 PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1,
  • the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, and/or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
  • CALB2RY11 PPAN- P2RY11
  • DNAJC8 TTC19
  • VCAMl CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1
  • CERCAM CERCAM
  • the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or a normal expression or underexpression of CERCAM or DHRS7.
  • the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
  • the non-Hodgkin's lymphoma is follicular lymphoma.
  • a method for selecting an individual having follicular lymphoma (FL) for treatment or for continuing treatment with ibrutinib comprising: (a) determining the expression level of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7, and (b) administering to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof, if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19,
  • the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7.
  • the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
  • a method for selecting an individual having follicular lymphoma (FL) for treatment or for continuing treatment with ibrutinib comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435,
  • a method for selecting an individual having follicular lymphoma (FL) for treatment with ibrutinib comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is a presence or absence of modifications in the one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN.
  • a method of monitoring whether an individual receiving ibrutinib for treatment of FL has developed or is likely to develop resistance to the therapy comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl,
  • LOCI 00132299, STS-1, and CRYGN characterizing the individual as resistant or is likely to become resistant to therapy with ibrutinib if the individual has modifications in the one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN.
  • a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN; and (b) modifying, discontinuing, or continuing the treatment based on the presence or absence of modifications in the one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN.
  • the method further comprises determining the presence or absence of a modification in two or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN.
  • the presence or absence of a modification in all 9 genes is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in all 9 genes.
  • the presence or absence of a modification in at least 8 of the following genes is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 8 of the genes.
  • a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 8 of the genes.
  • the presence or absence of a modification in at least 7 of the following genes ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl,
  • LOCI 00132299, STS-1, CRYGN is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 7 of the genes.
  • the presence or absence of a modification in at least 6 of the genes is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 6 of the genes.
  • the presence or absence of a modification in at least 5 of the genes is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 5 of the genes.
  • the presence or absence of a modification in at least 4 of the genes is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 4 of the genes.
  • the presence or absence of a modification in at least 3 of the genes is
  • a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 3 of the genes.
  • the presence or absence of a modification in at least 2 of the genes is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 2 of the genes.
  • the one or more biomarker genes are selected from one or more of those disclosed herein.
  • the one or more biomarker genes are selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN and combinations thereof.
  • the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof.
  • the genes disclosed herein comprise one or more modifications in each gene.
  • the modification associated with one or more of the genes disclosed herein results in modifications in the corresponding proteins.
  • the method further comprises testing a sample containing nucleic acid molecules encoding the biomarker genes selected from those disclosed herein and obtained from the individual, and determining whether each of the genes selected from those disclosed herein contains one or more
  • the follicular lymphoma is previously treated with another anticancer agent.
  • the follicular lymphoma is a relapsed or refractory follicular lymphoma.
  • the follicular lymphoma is treatment naive follicular lymphoma, i.e., previously untreated follicular lymphoma.
  • the follicular lymphoma is currently being or was previously treated with only ibrutinib.
  • ibrutinib is administered according to a method described herein. In some embodiments, ibrutinib is administered once a day, two times per day, three times per day, four times per day, or five times per day. In some embodiments, ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments, ibrutinib is administered at a dosage of about 140 mg/day, 280 mg/day, 420 mg/day, 560 mg/day, 840 mg/day or about 1000 mg/day. In some embodiments, ibrutinib is administered orally. In some embodiments, ibrutinib is administered in a pharmaceutical formulation comprising ibrutinib or a pharmaceutically acceptable salt or solvate thereof and a
  • the method further comprises administering an additional therapeutic agent.
  • the additional therapeutic agent is selected from a chemotherapeutic agent and radiation therapeutic agent.
  • the chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide,
  • ibrutinib is administered simultaneously, sequentially or intermittently with the additional therapeutic agent.
  • ibrutinib and the additional therapeutic agent are administered in one dosage form.
  • ibrutinib and the additional therapeutic agent are
  • the expression level of the biomarker increases or decreases by 0.5-fold, 1-fold, 1.5-fold, 2-fold, 2.5-fold, 3-fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6- fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9-fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50- fold, or more compared to the control.
  • the overexpression, normal expression, underexpression, increase or decrease in the expression levels of the biomarkers described herein is found a lymphoma tumor sample of the individual or a sample of the individual having tumor cells.
  • a method of assessing an individual having FL for treatment with ibrutinib comprising: (a) determining the expression level of at least one biomarker gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1,
  • a method of assessing an individual having FL for treatment with ibrutinib comprising: (a) determining the expression level of at least one biomarker gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, and (b) determining that the individual is suitable for treatment with ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1; and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or decrease in expression level in at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834,
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1 and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is a decrease in expression level in at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1,
  • LOC652640 DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1 relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPAl, LOC100132299, DHRS7, THBS4, Z F514, AFF2, HS.493947, CST1, C R1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB 1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B), and
  • biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPAl, LOC100132299, DHRS7, THBS4, Z F514, AFF2, HS.493947, CST1, C R1, FAM167A, HSD
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPAl,
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least two biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or decrease in expression level in at least two biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase in expression level in at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOC100132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is a decrease in expression level in at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOC100132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least three biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least three biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least four biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least four biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least five biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least five biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least six biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least six biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least seven biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least seven biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of at least eight biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least eight biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
  • a method of assessing an individual having FL for treatment comprising: (a) determining the expression level of all of the following biomarker genes: ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS- 1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in all of nine of the biomarker genes (i.e., ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN) relative to a control.
  • biomarker genes i.e., ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN
  • methods of assessing sensitivity of an individual for treatment with a Btk inhibitor are provided by determining the expression levels of one or more of the biomarkers as described herein.
  • a Btk inhibitor i.e., ibrutinib (alone or in combination with rituximab )/responsiveness to treatment with ibrutinib (alone or in combination with rituximab)
  • the individual has treatment naive follicular lymphoma. In embodiments, the individual has relapsed/refractory follicular lymphoma.
  • methods of determining identifying an individual for treatment with a Btk inhibitor i.e., ibrutinib (alone or in combination with rituximab )/responsiveness to treatment with ibrutinib (alone or in combination with rituximab)] by determining the expression levels of one or more of the biomarkers as described herein.
  • the individual has treatment naive follicular lymphoma.
  • the individual has relapsed/refractory follicular lymphoma.
  • the expression level of the at least one biomarker selected from those disclosed herein increase or decrease by 0.5-fold, 1-fold, 1.5-fold, 2-fold, 2.5-fold, 3-fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6-fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9- fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50-fold, or more compared to the control.
  • ibrutinib is administered once a day, two times per day, three times per day, four times per day, or five times per day. In some embodiments, ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments, ibrutinib is administered at a dosage of about 140 mg/day, 280 mg/day, 420 mg/day,
  • ibrutinib is administered orally. In some embodiments, ibrutinib is administered in a pharmaceutical formulation comprising ibrutinib or a pharmaceutically acceptable salt or solvate thereof and a
  • the method further comprises administering an additional therapeutic agent.
  • the additional therapeutic agent is selected from a chemotherapeutic agent and radiation therapeutic agent.
  • the chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, ofatumumab, rituximab, dexamethasone, prednisone, CAL- 101, ibritumomab, tositumomab, bortezomib, pentostatin, and endostatin, or a combination thereof.
  • ibrutinib is administered simultaneously, sequentially or intermittently with the additional therapeutic agent. In some embodiments, ibrutinib and the additional therapeutic agent are administered in one dosage form. In some embodiments, ibrutinib and the additional therapeutic agent are administered in separate dosage forms.
  • the FL is a treatment naive FL. In some embodiments, the FL is a relapsed or refractory FL.
  • a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL comprising: (a) determining the expression level in the individual of one or more biomarker genes selected from those disclosed herein (e.g., CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15,
  • biomarker genes selected from those disclosed herein (e.g., CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15,
  • LOC644248 C90RF169, SLC45A2, and LOC100128675, or discontinue administering ibrutinib to the individual if there is an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY
  • ibrutinib treatment is continued if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
  • ibrutinib treatment is continued if there is an overexpression of one or more genes selected from VCAM1, RPA1, and STS-1 (UBASH3B).
  • ibrutinib treatment is continued if there is an overexpression of one or more genes selected from RPA1 or STS-1 (UBASH3B).
  • ibrutinib treatment is discontinued if there is an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • POM121C LOC 100131972
  • PPP1R3D PPP1R3D
  • PLOD2 PPP1R3D
  • SDHA SDHAP3
  • OSBPL2 HCFC1R1
  • DHRS7 DHRS7
  • ibrutinib treatment is discontinued if there is an overexpression of DHRS7.
  • a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1,
  • biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7,
  • the method further comprises determining the presence or absence of a modification in two or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPA1, LOC100132299, and STS-1.
  • a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from those disclosed herein (e.g., BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, ZNF514, AFF2,
  • the one or more biomarker genes are selected from one or more of those disclosed herein.
  • the one or more biomarker genes are selected from BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, ZNF514, AFF2, HS.493947, CST1, CNR1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERNl, C90RF164, PLEKHBl, S100A8, SEPT5, PDK4, DDX60, INDO, and INPP4B and combinations thereof.
  • the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof.
  • the genes disclosed herein comprise one or more modifications in each gene.
  • the modification associated with one or more of the genes disclosed herein results in
  • the modification associated with the BCL-2 gene results in modifications in the BCL-2 protein.
  • a method of monitoring the development of insensitivity to ibrutinib treatment in an individual having a non-Hodgkin's lymphoma comprising: (a) determining the expression level of one or more biomarkers disclosed herein; and (b) characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an overexpression of CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC64
  • the individual is characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • POM121C LOC 100131972
  • PPP1R3D PPP1R3D
  • PLOD2 PPP1R3D
  • SDHA SDHAP3
  • OSBPL2 HCFC1R1R1
  • DHRS7 DHRS7
  • the individual is characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an
  • the individual is characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an overexpression of DHRS7.
  • a method of monitoring disease progression in an individual having a non-Hodgkin's lymphoma being treated with ibrutinib comprising:
  • LOC 100131972 PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1,
  • the individual is characterizing the individual as having disease progression or likely to develop disease progression if the individual shows an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7. In some embodiments, the individual is characterizing the individual as having disease progression or likely to develop disease progression if the individual shows an overexpression of CERCAM or DHRS7. In some embodiments, the individual is characterizing the individual as having disease progression or likely to develop disease progression if the individual shows an overexpression of DHRS7.
  • a method of monitoring the disease progression in an individual having FL comprising: (a) determining the expression level of at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, Z F514, AFF2, HS.493947, CSTl, CNRl, FAM167A, HSD17B 14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B; and (b) characterizing the individual as having a stable FL if the individual shows an increase in expression level or a decrease in expression level in at least one biomarker gene selected from those disclosed herein (e.g.,, but not limited to, BCL2, STS-1, RPA1, LOC100132299, DHRS
  • a method of monitoring whether an individual receiving ibrutinib for treatment of FL has developed or is likely to develop resistance to the therapy comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from those disclosed herein (e.g., BCL2, STS-1, RPAl,
  • LOC389816 LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B).
  • a method of monitoring the disease progression in an individual having FL comprising: (a) determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPA1,
  • LOCI 00132299, and STS-1 characterizing the individual as having a stable FL if the individual shows an increase in expression level or a decrease in expression level in at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPA1, LOC100132299, and STS-1 relative to a control.
  • biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6,
  • a method of monitoring the disease progression in an individual having FL comprising: (a) determining the expression level of at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN); and (b) characterizing the individual as having a stable FL if the individual shows an increase in expression level or a decrease in expression level in at least one biomarker gene selected from at least one of ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOC100132299, STS-1, and CRYGN relative to a control.
  • the expression level of the biomarker increases by 0.5-fold, 1- fold, 1.5-fold, 2-fold, 2.5-fold, 3-fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6-fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9-fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50-fold, or more compared to the control.
  • the non-Hodgkin's lymphoma is follicular lymphoma.
  • the follicular lymphoma is previously treated with another anticancer agent.
  • the follicular lymphoma is a relapsed or refractory follicular lymphoma.
  • the follicular lymphoma is treatment naive follicular lymphoma, i.e., previously untreated follicular lymphoma.
  • the follicular lymphoma is not previously treated with any non-ibrutinib agent.
  • the expression level of the at least one biomarker gene selected from those disclosed herein increase or decrease by 0.5-fold, 1-fold, 1.5-fold, 2-fold, 2.5-fold, 3- fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6-fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9-fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50-fold, or more compared to the control.
  • Ibrutinib may be administered as according to a dosing and in a dosage form known in the art.
  • ibrutinib is administered once a day, two times per day, three times per day, four times per day, or five times per day. In some embodiments, ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments, ibrutinib is administered at a dosage of about 140 mg/day, 280 mg/day, 420 mg/day,
  • ibrutinib is administered orally.
  • ibrutinib is administered in a pharmaceutical formulation comprising ibrutinib or a pharmaceutically acceptable salt or solvate thereof and a pharmaceutically acceptable excipient, such as a formulation described in e.g., WO2013184572, WO2016022942, and WO2016141068, which are incorporated by reference in their entirety.
  • the invention relates to any of the methods described herein, wherein the method comprises ibrutinib or its use; and the unit dosage of ibrutinib is a capsule comprising 140 mg of ibrutinib.
  • the unit dosage of ibrutinib is a capsule comprising 140 mg of ibrutinib, croscarmellose sodium, magnesium stearate, microcrystalline cellulose, and sodium lauryl sulfate.
  • the invention relates to any of the methods described herein, wherein the method comprises ibrutinib or its use; and the unit dosage of ibrutinib is a tablet comprising 140 mg, 280 mg, 420 mg or 560 mg of ibrutinib.
  • the ibrutinib is administered with an additional therapeutic agent. In some embodiments, ibrutinib is administered simultaneously, sequentially or intermittently with the additional therapeutic agent. In some embodiments, ibrutinib and the additional therapeutic agent are administered in one dosage form. In some embodiments, ibrutinib and the additional therapeutic agent are administered in separate dosage forms. In some embodiments, ibrutinib and the additional therapeutic agent are administered in one dosage form. In some embodiments, ibrutinib and the additional therapeutic agent are administered in separate dosage forms.
  • the additional therapeutic agent is selected from a
  • the chemotherapeutic agent and radiation therapeutic agent.
  • the radiation therapeutic agent In some embodiments, the
  • chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, ofatumumab, rituximab, dexamethasone, prednisone, CAL-101, ibritumomab, tositumomab, bortezomib, pentostatin, and endostatin, or a combination thereof.
  • the additional therapeutic agent is a CD79A inhibitor, a CD79B inhibitor, a CD 19 inhibitor, a Lyn inhibitor, a Syk inhibitor, a PI3K inhibitor, a Blnk inhibitor, a PLCy inhibitor, a PKCP inhibitor, or a combination thereof.
  • the additional therapeutic agent is an antibody, B cell receptor signaling inhibitor, a PI3K inhibitor, an IAP inhibitor, an mTOR inhibitor, a radioimmunotherapeutic, a DNA damaging agent, a proteosome inhibitor, a histone deacetylase inhibitor, a protein kinase inhibitor, a hedgehog inhibitor, an Hsp90 inhibitor, a telomerase inhibitor, a Bcl-2 inhibitor, a Jakl/2 inhibitor, a protease inhibitor, a PKC inhibitor, a PARP inhibitor, or a combination thereof.
  • the additional therapeutic agent is an inhibitor of LYN, SYK, JAK, PI3K, PLCy, MAPK, HDAC, NF K B, or MEK.
  • the additional therapeutic agent is selected from a chemotherapeutic agent, a biologic agent, radiation therapy, bone marrow transplant and surgery.
  • the additional therapeutic agent is selected from a
  • the chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, ofatumumab, rituximab, cari lzomib, dexamethasone, prednisone, idelalisib, ibritumomab, tositumomab, bortezomib, venetoclax, pentostatin, and endostatin, or a combination thereof.
  • the additional therapeutic agent comprises an agent selected from: bendamustine, bortezomib, lenalidomide, idelalisib, vorinostat, everolimus, panobinostat, temsirolimus, romidepsin, vorinostat, fludarabine, cyclophosphamide, mitoxantrone,
  • the additional therapeutic agent is rituximab.
  • rituximab is further administered as a maintenance therapy.
  • the additional therapeutic agent is bendamustine.
  • bortezomib is administered in combination with rituximab.
  • the additional therapeutic agent is bortezomib.
  • bendamustine is administered in combination with rituximab.
  • the additional therapeutic agent is lenalidomide.
  • lenalidomide is administered in combination with rituximab.
  • the additional therapeutic agent is a multi-agent therapeutic regimen.
  • the additional therapeutic agent comprises the HyperCVAD regimen (cyclophosphamide, vincristine, doxorubicin, dexamethasone alternating with methotrexate and cytarabine).
  • the HyperCVAD regimen is administered in combination with rituximab.
  • the additional therapeutic agent comprises the R-CHOP regiment
  • the additional therapeutic agent comprises bortezomib and rituximab.
  • the additional therapeutic agent comprises cladribine and rituximab.
  • the additional therapeutic agent comprises the FCR regimen (fludarabine, cyclophosphamide, rituximab).
  • the additional therapeutic agent comprises the FCMR regimen (fludarabine, cyclophosphamide, mitoxantrone, rituximab).
  • the additional therapeutic agent comprises the FMR regimen (fludarabine, mitoxantrone, rituximab).
  • the additional therapeutic agent comprises the PCR regimen (pentostatin, cyclophosphamide, rituximab).
  • the additional therapeutic agent comprises the PEPC regimen (prednisone, etoposide, procarbazine, cyclophosphamide).
  • the additional therapeutic agent comprises radioimmunotherapy with 90 Y-ibritumomab tiuxetan or 131 I-tositumomab.
  • the additional therapeutic agent is an autologous stem cell transplant.
  • the additional therapeutic agent is selected from: Nitrogen Mustards such as for example, bendamustine, chlorambucil, chlormethine, cyclophosphamide, ifosfamide, melphalan, prednimustine, trofosfamide; Alkyl Sulfonates like busulfan,
  • mannosulfan, treosulfan Ethylene Imines like carboquone, thiotepa, triaziquone; Nitrosoureas like carmustine, fotemustine, lomustine, nimustine, ranimustine, semustine, streptozocin;
  • Epoxides such as for example, etoglucid; Other Alkylating Agents such as for example dacarbazine, mitobronitol, pipobroman, temozolomide; Folic Acid Analogues such as for example methotrexate, permetrexed, pralatrexate, raltitrexed; Purine Analogs such as for example cladribine, clofarabine, fludarabine, mercaptopurine, nelarabine, tioguanine; Pyrimidine Analogs such as for example azacitidine, capecitabine, carmofur, cytarabine, decitabine, fluorouracil, gemcitabine, tegafur; Vinca Alkaloids such as for example vinblastine, vincristine, vindesine, vinflunine, vinorelbine; Podophyllotoxin Derivatives such as for example etoposide, teniposide; Colchicine derivatives
  • Antracyclines such as for example aclarubicin, daunorubicin, doxorubicin, epirubicin, idarubicin, mitoxantrone, pirarubicin, valrubicin, zorubincin;
  • Other Cytotoxic Antibiotics such as for example bleomycin, ixabepilone, mitomycin, plicamycin;
  • Platinum Compounds such as for example carboplatin, cisplatin, oxaliplatin, satraplatin; Methylhydrazines such as for example procarbazine;
  • Sensitizers such as for example aminolevulinic acid, efaproxiral, methyl aminolevulinate, porfimer sodium, temoporfin; Protein Kinase Inhibitors such as for example dasatinib, erlotinib, everolimus, gefitinib, imatinib, lapatinib, nilotin
  • Progestogens such as for example gestonorone, medroxyprogesterone, megestrol; Gonadotropin Releasing Hormone Analogs such as for example buserelin, goserelin, leuprorelin, triptorelin; Anti-Estrogens such as for example fulvestrant, tamoxifen, toremifene; Anti-Androgens such as for example bicalutamide, flutamide, nilutamide, , Enzyme Inhibitors, aminoglutethimide, anastrozole, exemestane, formestane, letrozole, vorozole; Other Hormone Antagonists such as for example abarelix, degarelix; Immunostimulants such as for example histamine
  • Immunosuppressants such as for example everolimus, gusperimus, leflunomide, mycophenolic acid, sirolimus; Calcineurin Inhibitors such as for example ciclosporin, tacrolimus; Other Immunosuppressants such as for example azathioprine, lenalidomide, methotrexate, thalidomide; and Radiopharmaceuticals such as for example, iobenguane.
  • the additional therapeutic agent is selected from: interferons, interleukins, Tumor Necrosis Factors, Growth Factors, and the like.
  • the additional therapeutic agent is selected from: ancestim, filgrastim, lenograstim, molgramostim, pegfilgrastim, sargramostim; Interferons such as for example interferon alfa natural, interferon alfa-2a, interferon alfa-2b, interferon alfacon-1, interferon alfa-nl, interferon beta natural, interferon beta-la, interferon beta-lb, interferon gamma, peginterferon alfa-2a, peginterferon alfa-2b; Interleukins such as for example aldesleukin, oprelvekin; Other Immunostimulants such as for example BCG vaccine, glatiramer acetate, histamine dihydrochloride, immunocyanin, lentinan, melanoma vaccine, mifamurtide, pegademase, pidotimod, plerixafor,
  • Interferons such as
  • Immunosuppressants such as for example azathioprine, lenalidomide, methotrexate, thalidomide.
  • the additional therapeutic agent is selected from: Adalimumab, Alemtuzumab, Basiliximab, Bevacizumab, Cetuximab, Certolizumab pegol, Daclizumab, Eculizumab, Efalizumab, Gemtuzumab, Ibritumomab tiuxetan, Infliximab, Muromonab-CD3, Natalizumab, Panitumumab, Ranibizumab, Rituximab, Tositumomab, Trastuzumab, and the like, or a combination thereof.
  • the additional therapeutic agent is selected from: Monoclonal Antibodies such as for example alemtuzumab, bevacizumab, catumaxomab, cetuximab, edrecolomab, gemtuzumab, panitumumab, rituximab, trastuzumab; Immunosuppressants, eculizumab, efalizumab, muromab-CD3, natalizumab; TNF alpha Inhibitors such as for example adalimumab, afelimomab, certolizumab pegol, golimumab, infliximab; Interleukin Inhibitors, basiliximab, canakinumab, daclizumab, mepolizumab, tocilizumab, ustekinumab;
  • Radiopharmaceuticals ibritumomab tiuxetan, tositumomab; Others Monoclonal Antibodies such as for example abagovomab, adecatumumab, alemtuzumab, anti-CD30 monoclonal antibody Xmab2513, anti-MET monoclonal antibody MetMab, apolizumab, apomab, arcitumomab, basiliximab, bispecific antibody 2B1, blinatumomab, brentuximab vedotin, capromab pendetide, cixutumumab, claudiximab, conatumumab, dacetuzumab, denosumab, eculizumab, epratuzumab, epratuzumab, ertumaxomab, etaracizumab, figitumumab, fre
  • ramacurimab ranibizumab, siplizumab, sonepcizumab, tanezumab, tositumomab, trastuzumab, tremelimumab, tucotuzumab celmoleukin, veltuzumab, visilizumab, volociximab, and zalutumumab.
  • the additional therapeutic agent is selected from: agents that affect the tumor micro-environment such as cellular signaling network (e.g. phosphatidylinositol 3-kinase (PI3K) signaling pathway, signaling from the B-cell receptor and the IgE receptor).
  • PI3K phosphatidylinositol 3-kinase
  • the additional therapeutic agent is a PI3K signaling inhibitor or a syc kinase inhibitor.
  • the syk inhibitor is R788.
  • is a PKOy inhibitor such as by way of example only, enzastaurin.
  • agents that affect the tumor micro-environment include PI3K signaling inhibitor, syc kinase inhibitor, Protein Kinase Inhibitors such as for example dasatinib, erlotinib, everolimus, gefitinib, imatinib, lapatinib, nilotinib, pazonanib, sorafenib, sunitinib, temsirolimus; Other Angiogenesis Inhibitors such as for example GT-111, JI- 101, R1530; Other Kinase Inhibitors such as for example AC220, AC480, ACE-041, AMG 900, AP24534, Any-614, AT7519, AT9283, AV-951, axitinib, AZD1152, AZD7762, AZD8055, AZD8931, bafetinib, BAY 73-4506, BGJ398, BGT226, BI 811283, BI6727
  • the additional therapeutic agent is selected from: inhibitors of mitogen-activated protein kinase signaling, e.g., U0126, PD98059, PD184352, PD0325901, ARRY-142886, SB239063, SP600125, BAY 43-9006, wortmannin, or LY294002; Syk inhibitors; mTOR inhibitors; and antibodies (e.g., rituxan).
  • inhibitors of mitogen-activated protein kinase signaling e.g., U0126, PD98059, PD184352, PD0325901, ARRY-142886, SB239063, SP600125, BAY 43-9006, wortmannin, or LY294002
  • Syk inhibitors e.g., mTOR inhibitors
  • mTOR inhibitors e.g., rituxan
  • the additional therapeutic agent is selected from: Adriamycin, Dactinomycin, Bleomycin, Vinblastine, Cisplatin, acivicin; aclarubicin; acodazole
  • hydrochloride acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan;
  • cactinomycin calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; daunorubicin hydrochloride; decitabine;
  • dexormaplatin dezaguanine; dezaguanine mesylate; diaziquone; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin;
  • edatrexate eflornithine hydrochloride
  • elsamitrucin enloplatin
  • enpromate epipropidine
  • epirubicin hydrochloride erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole
  • hydrochloride megestrol acetate; melengestrol acetate; melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin;
  • mitocromin mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone
  • hydrochloride mycophenolic acid; nocodazoie; nogalamycin; ormaplatin; oxisuran;
  • pegaspargase peliomycin; pentamustine; peplomycin sulfate; perfosfamide; pipobroman;
  • piposulfan piroxantrone hydrochloride
  • plicamycin plicamycin
  • plomestane porfimer sodium
  • porfiromycin prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; pumprazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; sulofenur; talisomycin; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine;
  • thiotepa tiazofurin; tirapazamine; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine sulfate; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate;
  • vinrosidine sulfate vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride.
  • the additional therapeutic agent is selected from: 20-epi-l, 25 dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; aclarubicin; acylfulvene; adecypenol;
  • adozelesin aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox; amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole; andrographolide;
  • angiogenesis inhibitors antagonist D; antagonist G; antarelix; anti-dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen; antineoplaston; antisense
  • oligonucleotides oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators;
  • apurinic acid ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin; azatyrosine; baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists; benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate;
  • combretastatin A4 combretastatin analogue
  • conagenin crambescidin 816
  • crisnatol
  • cryptophycin 8 cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine;
  • dehydrodidemnin B deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone; didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; 9- dioxamycin; diphenyl spiromustine; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol;
  • duocarmycin SA duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur; epirubicin; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists;
  • etanidazole etoposide phosphate; exemestane; fadrozole; trasrabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fiuorodaunorunicin hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin; gallium nitrate;
  • galocitabine ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; hepsulfam; heregulin; hexamethylene bisacetamide; hypericin; ibandronic acid; idarubicin; idoxifene;
  • idramantone ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-such as for example growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol, 4-; iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor;
  • leukocyte alpha interferon leuprolide+estrogen+progesterone; leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin;
  • loxoribine lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maitansine; mannostatin A; marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; MIF inhibitor; mifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol;
  • mitomycin analogues mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin;
  • oligonucleotides onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer;
  • ormaplatin osaterone; oxaliplatin; oxaunomycin; palauamine; palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine; pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol;
  • phenazinomycin phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B; plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor; protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins;
  • pyrazoloacridine pyridoxylated hemoglobin polyoxyethylerie conjugate; raf antagonists;
  • raltitrexed ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B l; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A; sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen-binding protein; sizofiran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparf
  • spicamycin D spiromustine; splenopentin; spongistatin 1; squalamine
  • stem cell inhibitor stem- cell division inhibitors; stipiamide; stromelysin inhibitors; sulfinosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans; tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide;
  • tetrachlorodecaoxide tetrazomine; thaliblastine; thiocoraline; thrombopoietin; thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpunn; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine; triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors; tyrphostins; UBC inhibitors; ubenimex;
  • urogenital sinus-derived growth inhibitory factor urokinase receptor antagonists
  • vapreotide variolin B
  • vector system erythrocyte gene therapy
  • velaresol veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; and zinostatin stimalamer.
  • the additional therapeutic agent is selected from: alkylating agents, antimetabolites, natural products, and hormones, e.g., nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, etc.), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, ete.), or triazenes (decarbazine, etc.).
  • nitrogen mustards e.g., mechloroethamine, cyclophosphamide, chlorambucil, etc.
  • alkyl sulfonates e.g., busulfan
  • nitrosoureas e.g., carmustine, lomusitne, ete.
  • triazenes decarbazine, etc.
  • antimetabolites include but are not limited to folic acid analogs (e.g., methotrexate), or pyrimidine analogs (e.g., Cytarabine), or purine analogs (e.g., mercaptopurine, thioguanine, pentostatin).
  • folic acid analogs e.g., methotrexate
  • pyrimidine analogs e.g., Cytarabine
  • purine analogs e.g., mercaptopurine, thioguanine, pentostatin
  • the additional therapeutic agent is selected from: nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, meiphalan, etc.), ethylenimine and methylmelamines (e.g., hexamethlymelamine, thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, semustine, streptozocin, etc.), and triazenes (decarbazine, ete.).
  • nitrogen mustards e.g., mechloroethamine, cyclophosphamide, chlorambucil, meiphalan, etc.
  • ethylenimine and methylmelamines e.g., hexamethlymelamine, thiotepa
  • alkyl sulfonates e.g., bus
  • antimetabolites include, but are not limited to folic acid analogs (e.g., methotrexate), or pyrimidine analogs (e.g., fluorouracil, floxouridine, Cytarabine), or purine analogs (e.g., mercaptopurine, thioguanine, pentostatin.
  • folic acid analogs e.g., methotrexate
  • pyrimidine analogs e.g., fluorouracil, floxouridine, Cytarabine
  • purine analogs e.g., mercaptopurine, thioguanine, pentostatin.
  • the additional therapeutic agent is selected from: agents which act by arresting cells in the G2-M phases due to stabilized microtubules, e.g., Erbulozole (also known as R-55104), Dolastatin 10 (also known as DLS-10 and NSC-376128), Mivobulin isethionate (also known as CI-980), Vincristine, NSC-639829, Discodermolide (also known as NVP-XX-A-296), ABT-751 (Abbott, also known as E-7010), Altorhyrtins (such as Altorhyrtin A and Altorhyrtin C), Spongistatins (such as Spongistatin 1, Spongistatin 2, Spongistatin 3, Spongistatin 4, Spongistatin 5, Spongistatin 6, Spongistatin 7, Spongistatin 8, and Spongistatin 9), Cemadotin hydrochloride (also known as LU-10),
  • Epothilone E Epothilone F, Epothilone B N-oxide, Epothilone A N-oxide, 16-aza-epothilone B, 21-aminoepothilone B (also known as BMS-310705), 21 -hydroxy epothilone D (also known as Desoxyepothilone F and dEpoF), 26-fluoroepothilone), Auristatin PE (also known as NSC- 654663), Soblidotin (also known as TZT-1027), LS-4559-P (Pharmacia, also known as LS- 4577), LS-4578 (Pharmacia, also known as LS-477-P), LS-4477 (Pharmacia), LS-4559
  • ibrutinib is administered continuously, e.g., when the patient is determined to be suitable for treatment of continued treatment with ibrutinib, or is responsive to ibrutinib according to methods described herein.
  • ibrutinib is administered in multiple cycles.
  • a cycle of administration is one month, 2 months, 3 months, 4 months, 6 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months or longer.
  • a cycle of administration comprises administration of a single therapeutic dosage of ibrutinib over the cycle.
  • a cycle of administration comprises two or more different dosages of ibrutinib over the cycle.
  • the dosage of ibrutinib differs over consecutive cycles.
  • the dosage of ibrutinib increases over consecutive cycles.
  • the dosage of ibrutinib is the same over consecutive cycles.
  • the expression levels of the biomarkers can be determined by methods known in the art. In some embodiments, the expression levels of the biomarkers are determined by testing a sample containing nucleic acid molecules obtained from the individual. In some embodiments, the sample is a sample obtained prior to the first administration of ibrutinib. In some
  • the sample is a sample obtained periodically during administration of ibrutinib.
  • the sample is a sample obtained at 1 week, 2 weeks, 3 weeks, 8 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, 14 months, 16 months, 18 months, 20 months, 22 months, or 24 months following the first administration of ibrutinib.
  • the sample is obtained 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 times over the course of treatment with ibrutinib.
  • the sample is a tumor biopsy sample, a blood sample, a serum sample, a lymph sample or a bone marrow aspirate.
  • the sample is a tissue biopsy and is obtained, for example, by needle biopsy, CT-guided needle biopsy, aspiration biopsy, endoscopic biopsy, bronchoscopic biopsy, bronchial lavage, incisional biopsy, excisional biopsy, punch biopsy, shave biopsy, skin biopsy, bone marrow biopsy, and the Loop Electrosurgical Excision Procedure (LEEP).
  • LEEP Loop Electrosurgical Excision Procedure
  • a non-necrotic, sterile biopsy or specimen is obtained that is greater than 100 mg, but which can be smaller, such as less than 100 mg, 50 mg or less, 10 mg or less or 5 mg or less; or larger, such as more than 100 mg, 200 mg or more, or 500 mg or more, 1 gm or more, 2 gm or more, 3 gm or more, 4 gm or more or 5 gm or more.
  • the sample size to be extracted for the assay depends on a number of factors including, but not limited to, the number of assays to be performed, the health of the tissue sample, the type of cancer, and the condition of the patient.
  • the tissue is placed in a sterile vessel, such as a sterile tube or culture plate, and is optionally immersed in an appropriate media.
  • a sterile vessel such as a sterile tube or culture plate
  • the cells are dissociated into cell suspensions by mechanical means and/or enzymatic treatment as is well known in the art.
  • the cells are collected and then subjected to standard procedures for the isolation of nucleic acid for the assay.
  • the sample contains one or more tumor cells of the individual. In some embodiments, the sample contains circulating tumor DNA (ctDNA). In some
  • the nucleic acid molecule is RNA. In some embodiments, the nucleic acid molecule is DNA. In some embodiments, the DNA is genomic DNA.
  • the method for determining expression levels comprises detecting the nucleic acid molecules using a microarray. In some embodiments, the method further comprises isolating the nucleic acid molecules. In some embodiments, the method further comprises amplifying the nucleic acid molecules. In some embodiments, amplification is by isothermal amplification or polymerase chain reaction (PCR). In some embodiments,
  • amplification is by PCR.
  • testing comprises using allele specific PCR.
  • single nucleotide changes are detectable PCR using PCR- based cleaved amplified polymorphic sequences (CAPS) markers which create restriction sites in the mutant sequences (Michaels et al (1998) Plant J. 14(3):381-5) or sequence specific hairpin probes attached to detectable moieties, such as, but not limited to, a fluorophore (Mhlanga and Malmberg (2001) Methods 25:463-471).
  • CAPS PCR- based cleaved amplified polymorphic sequences
  • the method comprises contacting nucleic acids with sequence specific nucleic acid probes, wherein the sequence specific nucleic acid probes bind to the genes selected from those disclosed herein.
  • testing comprises PCR
  • the sequence specific probe is conjugated to a detectable molecule, such as a fluorescent label, a bioluminescent label, a chemiluminescent label, a radiolabel, an enzyme label, a detectable substrate, or a peptide or molecule that binds to a second detectable molecule.
  • a detectable molecule such as a fluorescent label, a bioluminescent label, a chemiluminescent label, a radiolabel, an enzyme label, a detectable substrate, or a peptide or molecule that binds to a second detectable molecule.
  • the method for determining expression levels comprises sequencing the nucleic acid molecules.
  • Exemplary sequencing methods are well known in the art and include, but are not limited to, dideoxy or chain termination methods, Maxam-Gilbert sequencing, massively parallel signature sequencing (or MPSS), polony sequencing,
  • the method comprises using a microarray for detecting the genes described herein.
  • the oligonucleotide array is contained on a microchip.
  • the use of the array comprises: (a) determining the expression level of the biomarker genes in a sample; (b) comparing the expression levels of the biomarker genes to a control; and (c) characterizing the individual as having a stable FL, partial response (PR), or complete response (CR) if the individual shows an increase or decrease in expression level in at least one biomarker genes disclosed herein relative to a control.
  • kits for carrying out the methods disclosed herein comprising one or more reagents for determining the expression levels of one or more biomarker genes selected from those disclosed herein in the sample.
  • the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising one or more of the biomarkers disclosed herein.
  • kits for carrying out the methods disclosed herein comprising one or more reagents for determining the expression level of at least one biomarker genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASEILI, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345,
  • the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, or DHRS7.
  • CALB2RY11 PPAN-P2RY11
  • DNAJC8 TTC19
  • VCAMl CSAG3, GP1BA
  • RPAl RSC1A1, STS-1
  • UASH3B UASH3B
  • ADPRM C170RF48
  • FILIPl FILIPl
  • CERCAM CERCAM
  • POM121C LOD2, SDHA (SDHAP3)
  • the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising VCAMl, RPAl, STS-1 (UBASH3B), CERCAM or DHRS7. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising RPAl, STS-1 (UBASH3B), or DHRS7.
  • the kit comprises an antibody that binds to a protein encoded by the genes described herein.
  • the kit comprises an antibody that binds to a protein encoded by a gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASEILI, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418
  • the kit comprises an antibody that binds to a protein encoded by a gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
  • the kit comprises an antibody that binds to a protein encoded by a gene selected from VCAM1, RPA1, STS-1 (UBASH3B), CERCAM and DHRS7.
  • the kit comprises an antibody that binds to a protein encoded by RPAl, STS-1 (UBASH3B), or DHRS7.
  • kits for carrying out the methods disclosed herein comprising one or more reagents for determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFCIRI, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl,
  • the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules encoding PAIP2, LOC730200,
  • KDM1B KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1,
  • LOC652640 DHRS7, LOC100132535, LOC647435, HCFCIRI, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, or STS-1.
  • the kit comprises an antibody that binds to a protein encoded by PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFCIRI, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, or STS-1.
  • the kit comprises one or more reagents for determining the expression level of at least one biomarker gene selected from ODF4,
  • the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules encoding ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC 100132299, STS-1, or CRYGN.
  • the kit comprises an antibody that binds to a protein encoded by ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl,
  • kits for carrying out the methods disclosed herein comprising one or more reagents for determining the presence or absence of a modification in one or more biomarker genes selected from those disclosed herein in the sample.
  • the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules encoding one or more of the genes disclosed herein.
  • nucleic acid hybridization array comprising nucleic acid probes useful in the methods described herein, wherein nucleic acid probes hybridize to biomarker genes selected from those disclosed herein. In some embodiments, at least one of the nucleic acid probes hybridizes to a biomarker gene selected from those disclosed herein.
  • the kit comprises a hybridization array.
  • kits include a carrier, package, or container that are compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in a method described herein.
  • Suitable containers include, for example, bottles, vials, syringes, and test tubes.
  • the containers are formed from a variety of materials such as glass or plastic.
  • a kit typically includes labels listing contents and/or instructions for use, and package inserts with instructions for use. A set of instructions will also typically be included.
  • a label is on or associated with the container.
  • a label is on a container when letters, numbers or other characters forming the label are attached, molded or etched into the container itself; a label is associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert.
  • the label also indicates directions for use of the contents, such as in the methods described herein.
  • a system useful in the methods described herein comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes described herein in the sample; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a first software module configured to analyze the dataset to determine the expression level in one or more biomarker genes; and (ii) a second software module to assign the individual as a candidate for treatment with ibrutinib according to the expression level of the one or more biomarker genes according to the methods described herein.
  • the first software module is configured to also analyze the dataset to determine the presence or absence of a modification in one or more biomarker genes.
  • the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof.
  • the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device.
  • the analytical device performs microarray analysis.
  • the digital processing device is connected to a computer network.
  • the second software module further generates a report, wherein the second software module is executed by the digital processing device.
  • the second software module further transmits the report to an end- user, wherein the second software module is executed by the digital processing device.
  • a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of those disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a third software module configured to analyze the dataset to determine the expression level of one or more biomarker genes; (ii) a forth software module configured to match the expression level of one or more biomarker genes to a control; and (iii) a fifth software module to assign the individual as a candidate to treatment with ibrutinib if there is an increase in expression level in the one or more biomarker genes relative to the control.
  • the system further comprises an analytical device configured to provide biomark
  • the digital processing device is connected to a computer network.
  • the fifth software module further generates a report, wherein the fifth software module is executed by the digital processing device.
  • the fifth software module further transmits the report to an end-user, wherein the fifth software module is executed by the digital processing device.
  • nucleic acid hybridization array comprising nucleic acid probes for evaluating whether an individual having FL has a stable FL or has a change in tumor size (i.e., as disclosed in the figures, referred to as "SPD" which refers to "longest overall tumor diameter and longest diameter perpendicular to the longest overall diameter), consisting essentially of nucleic acid probes which hybridize to biomarker genes selected from the group consisting of one or more of the biomarkers disclosed herein.
  • the use of the array comprises: (a) determining the expression level of the biomarker genes in a sample; (b) comparing the expression levels of the biomarker genes to a control; and (c) characterizing the individual as having a stable FL, partial response (PR), or complete response (CR) if the individual shows an increase or decrease in expression level in at least one biomarker genes disclosed herein relative to a control.
  • the use of the array comprises of determining the presence or absence of modifications in one or more biomarker genes in a sample obtained from the individual; and characterizing the individual as resistant or is likely to become resistant to therapy with ibrutinib if the individual has
  • suitable digital processing devices include, by way of non-limiting examples, server computers, desktop computers, laptop computers, notebook computers, sub-notebook computers, netbook computers, netpad computers, set-top computers, media streaming devices, handheld computers, Internet appliances, mobile smartphones, tablet computers, personal digital assistants, video game consoles, and vehicles.
  • server computers desktop computers, laptop computers, notebook computers, sub-notebook computers, netbook computers, netpad computers, set-top computers, media streaming devices, handheld computers, Internet appliances, mobile smartphones, tablet computers, personal digital assistants, video game consoles, and vehicles.
  • smartphones are suitable for use in the system described herein.
  • Suitable tablet computers include those with booklet, slate, and convertible configurations, known to those of skill in the art.
  • the digital processing device includes an operating system configured to perform executable instructions.
  • the operating system is, for example, software, including programs and data, which manages the device's hardware and provides services for execution of applications.
  • suitable server operating systems include, by way of non-limiting examples, FreeBSD, OpenBSD, NetBSD ® , Linux, Apple ® Mac OS X Server ® , Oracle ® Solaris ® , Windows Server ® , and Novell ® NetWare ® .
  • suitable personal computer operating systems include, by way of non-limiting examples, Microsoft ® Windows ® , Apple ® Mac OS X ® , UNIX ® , and UNIX- like operating systems such as GNU/Linux ® .
  • the operating system is provided by cloud computing.
  • suitable mobile smart phone operating systems include, by way of non-limiting examples, Nokia ® Symbian ® OS, Apple ® iOS ® , Research In Motion ® BlackBerry OS ® , Google ® Android ® , Microsoft ® Windows Phone ® OS, Microsoft ® Windows Mobile ® OS, Linux ® , and Palm ® WebOS ® .
  • suitable media streaming device operating systems include, by way of non-limiting examples, Apple TV ® , Roku ® , Boxee ® , Google TV ® , Google Chromecast ® , Amazon Fire ® , and Samsung ® HomeSync ® .
  • suitable video game console operating systems include, by way of non-limiting examples, Sony ® PS3 ® , Sony ® PS4 ® , Microsoft ® Xbox 360 ® , Microsoft Xbox One, Nintendo ® Wii ® , Nintendo ® Wii U ® , and Ouya ® .
  • the device includes a storage and/or memory device.
  • the storage and/or memory device is one or more physical apparatuses used to store data or programs on a temporary or permanent basis.
  • the device is volatile memory and requires power to maintain stored information.
  • the device is non-volatile memory and retains stored information when the digital processing device is not powered.
  • the non-volatile memory comprises flash memory.
  • the non-volatile memory comprises dynamic random-access memory (DRAM).
  • the non-volatile memory comprises ferroelectric random access memory (FRAM).
  • the non-volatile memory comprises phase-change random access memory (PRAM).
  • the device is a storage device including, by way of non-limiting examples, CD-ROMs, DVDs, flash memory devices, magnetic disk drives, magnetic tapes drives, optical disk drives, and cloud computing based storage.
  • the storage and/or memory device is a combination of devices such as those disclosed herein.
  • the digital processing device includes a display to send visual information to a user.
  • the display is a cathode ray tube (CRT).
  • the display is a liquid crystal display (LCD).
  • the display is a thin film transistor liquid crystal display (TFT-LCD).
  • the display is an organic light emitting diode (OLED) display.
  • OLED organic light emitting diode
  • on OLED display is a passive-matrix OLED (PMOLED) or active-matrix OLED (AMOLED) display.
  • the display is a plasma display.
  • the display is a video projector.
  • the display is a combination of devices such as those disclosed herein.
  • the digital processing device includes an input device to receive information from a user.
  • the input device is a keyboard.
  • the input device is a pointing device including, by way of non-limiting examples, a mouse, trackball, track pad, joystick, game controller, or stylus.
  • the input device is a touch screen or a multi-touch screen.
  • the input device is a microphone to capture voice or other sound input.
  • the input device is a video camera or other sensor to capture motion or visual input.
  • the input device is a KinectTM, Leap MotionTM, or the like.
  • the input device is a combination of devices such as those disclosed herein.
  • Non-transitory computer readable storage medium
  • the systems and methods disclosed herein include one or more non-transitory computer readable storage media encoded with a program including instructions executable by the operating system of an optionally networked digital processing device.
  • a computer readable storage medium is a tangible component of a digital processing device.
  • a computer readable storage medium is optionally removable from a digital processing device.
  • a computer readable storage medium includes, by way of non-limiting examples, CD-ROMs, DVDs, flash memory devices, solid state memory, magnetic disk drives, magnetic tape drives, optical disk drives, cloud computing systems and services, and the like.
  • the program and instructions are permanently, substantially permanently, semi-permanently, or non-transitorily encoded on the media.
  • the systems and methods disclosed herein include at least one computer program, or use of the same.
  • a computer program includes a sequence of instructions, executable in the digital processing device's CPU, written to perform a specified task.
  • computer readable instructions are implemented as program modules, such as functions, objects, Application Programming Interfaces (APIs), data structures, and the like, that perform particular tasks or implement particular abstract data types.
  • APIs Application Programming Interfaces
  • a computer program in certain embodiments, is written in various versions of various languages.
  • a computer program comprises one sequence of instructions. In some embodiments, a computer program comprises a plurality of sequences of instructions. In some embodiments, a computer program is provided from one location. In other embodiments, a computer program is provided from a plurality of locations. In various embodiments, a computer program includes one or more software modules. In various embodiments, a computer program includes, in part or in whole, one or more web applications, one or more mobile applications, one or more standalone applications, one or more web browser plug-ins, extensions, add-ins, or add-ons, or combinations thereof.
  • a computer program includes a web application.
  • a web application in various embodiments, utilizes one or more software frameworks and one or more database systems.
  • a web application is created upon a software framework such as Microsoft ® .NET or Ruby on Rails (RoR).
  • a web application utilizes one or more database systems including, by way of non-limiting examples, relational, non-relational, object oriented, associative, and XML database systems.
  • suitable relational database systems include, by way of non-limiting examples, Microsoft ® SQL Server, mySQLTM, and Oracle ® .
  • a web application in various embodiments, is written in one or more versions of one or more languages.
  • a web application is written in one or more markup languages, presentation definition languages, client-side scripting languages, server-side coding languages, database query languages, or combinations thereof.
  • a web application is written to some extent in a markup language such as Hypertext Markup Language (HTML), Extensible Hypertext Markup Language (XHTML), or extensible Markup Language (XML).
  • a web application is written to some extent in a presentation definition language such as Cascading Style Sheets (CSS).
  • CSS Cascading Style Sheets
  • a web application is written to some extent in a client-side scripting language such as Asynchronous Javascript and XML (AJAX), Flash Actionscript, Javascript, or Silverlight .
  • AJAX Asynchronous Javascript and XML
  • a web application is written to some extent in a server-side coding language such as Active Server Pages (ASP), ColdFusion ® , Perl, JavaTM, JavaServer Pages (JSP), Hypertext Preprocessor (PHP), PythonTM, Ruby, Tel, Smalltalk, WebDNA ® , or Groovy.
  • a web application is written to some extent in a database query language such as Structured Query Language (SQL).
  • SQL Structured Query Language
  • a web application integrates enterprise server products such as IBM ® Lotus Domino ® .
  • a web application includes a media player element.
  • a media player element utilizes one or more of many suitable multimedia technologies including, by way of non-limiting examples, Adobe ® Flash ® , HTML 5, Apple ® QuickTime ® , Microsoft ® Silverlight ® , JavaTM, and Unity ® .
  • a computer program includes a mobile application provided to a mobile digital processing device.
  • the mobile application is provided to a mobile digital processing device at the time it is manufactured.
  • the mobile application is provided to a mobile digital processing device via the computer network described herein.
  • a mobile application is created by techniques known to those of skill in the art using hardware, languages, and development environments known to the art. Those of skill in the art will recognize that mobile applications are written in several languages. Suitable programming languages include, by way of non-limiting examples, C, C++, C#, Objective-C, JavaTM, Javascript, Pascal, Object Pascal, PythonTM, Ruby, VB.NET, WML, and XHTML/HTML with or without CSS, or combinations thereof.
  • Suitable mobile application development environments are available from several sources. Commercially available development environments include, by way of non-limiting examples, AirplaySDK, alcheMo, Appcelerator ® , Celsius, Bedrock, Flash Lite, .NET Compact Framework, Rhomobile, and WorkLight Mobile Platform. Other development environments are available without cost including, by way of non-limiting examples, Lazarus, MobiFlex, MoSync, and Phonegap. Also, mobile device manufacturers distribute software developer kits including, by way of non-limiting examples, iPhone and iPad (iOS) SDK, AndroidTM SDK, BlackBerry ® SDK, BREW SDK, Palm ® OS SDK, Symbian SDK, webOS SDK, and Windows ® Mobile SDK.
  • iOS iPhone and iPad
  • a computer program includes a standalone application, which is a program that is run as an independent computer process, not an add-on to an existing process, e.g., not a plug-in.
  • standalone applications are often compiled.
  • a compiler is a computer program(s) that transforms source code written in a programming language into binary object code such as assembly language or machine code. Suitable compiled programming languages include, by way of non-limiting examples, C, C++, Objective-C, COBOL, Delphi, Eiffel, JavaTM, Lisp, PythonTM, Visual Basic, and VB .NET, or combinations thereof. Compilation is often performed, at least in part, to create an executable program.
  • a computer program includes one or more executable complied applications.
  • the computer program includes a web browser plug-in.
  • a plug-in is one or more software components that add specific functionality to a larger software application. Makers of software applications support plug-ins to enable third- party developers to create abilities which extend an application, to support easily adding new features, and to reduce the size of an application. When supported, plug-ins enable customizing the functionality of a software application. For example, plug-ins are commonly used in web browsers to play video, generate interactivity, scan for viruses, and display particular file types. Those of skill in the art will be familiar with several web browser plug-ins including, Adobe ® Flash ® Player, Microsoft ® Silverlight ® , and Apple ® QuickTime ® .
  • the toolbar comprises one or more web browser extensions, add-ins, or add-ons. In some embodiments, the toolbar comprises one or more explorer bars, tool bands, or desk bands.
  • plug-in frameworks are available that enable development of plug-ins in various programming languages, including, by way of non-limiting examples, C++, Delphi, JavaTM, PHP, PythonTM, and VB .NET, or combinations thereof.
  • Web browsers are software applications, designed for use with network-connected digital processing devices, for retrieving, presenting, and traversing information resources on the World Wide Web. Suitable web browsers include, by way of non- limiting examples, Microsoft ® Internet Explorer ® , Mozilla ® Firefox ® , Google ® Chrome, Apple ® Safari ® , Opera Software ® Opera ® , and KDE Konqueror. In some embodiments, the web browser is a mobile web browser.
  • Mobile web browsers are designed for use on mobile digital processing devices including, by way of non-limiting examples, handheld computers, tablet computers, netbook computers, subnotebook computers, smartphones, music players, personal digital assistants (PDAs), and handheld video game systems.
  • Suitable mobile web browsers include, by way of non-limiting examples, Google ® Android ® browser, RIM BlackBerry ® Browser, Apple ® Safari ® , Palm ® Blazer, Palm ® WebOS ® Browser, Mozilla ® Firefox ® for mobile, Microsoft ® Internet Explorer ® Mobile, Amazon ® Kindle ® Basic Web, Nokia ® Browser, Opera Software ® Opera ® Mobile, and Sony ® PSPTM browser.
  • the systems and methods disclosed herein include software, server, and/or database modules, or use of the same.
  • software modules are created by techniques known to those of skill in the art using machines, software, and languages known to the art.
  • the software modules disclosed herein are
  • a software module comprises a file, a section of code, a programming object, a programming structure, or combinations thereof.
  • a software module comprises a plurality of files, a plurality of sections of code, a plurality of programming objects, a plurality of programming structures, or combinations thereof.
  • the one or more software modules comprise, by way of non-limiting examples, a web application, a mobile application, and a standalone application.
  • software modules are in one computer program or application.
  • software modules are in more than one computer program or application.
  • software modules are hosted on one machine.
  • software modules are hosted on more than one machine.
  • software modules are hosted on cloud computing platforms.
  • software modules are hosted on one or more machines in one location. In other embodiments, software modules are hosted on one or more machines in more than one location.
  • the methods and systems disclosed herein include one or more databases, or use of the same.
  • suitable databases include, by way of non- limiting examples, relational databases, non-relational databases, object oriented databases, object databases, entity-relationship model databases, associative databases, and XML databases.
  • a database is internet-based.
  • a database is web- based.
  • a database is cloud computing-based.
  • a database is based on one or more local computer storage devices.
  • a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of one or more of the genes disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a first software module configured to analyze the dataset to determine the presence or absence of modifications in one or more biomarker genes; and (ii) a second software module to assign the individual as a candidate for treatment with ibrutinib if there is a presence or absence of modifications in the one or more biomarker genes.
  • the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof.
  • the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device.
  • the analytical device performs microarray analysis.
  • the digital processing device is connected to a computer network.
  • the second software module further generates a report, wherein the second software module is executed by the digital processing device.
  • the second software module further transmits the report to an end-user, wherein the second software module is executed by the digital processing device.
  • a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of those disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a third software module configured to analyze the dataset to determine the expression level of one or more biomarker genes; (ii) a forth software module configured to match the expression level of one or more biomarker genes to a control; and (iii) a fifth software module to assign the individual as a candidate to treatment with ibrutinib if there is an increase in expression level in the one or more biomarker genes relative to the control.
  • a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of those disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a third software module configured to analyze the dataset to determine the expression level of one or more biomarker genes; (ii) a forth software module configured to match the expression level of one or more biomarker genes to a control; and (iii) a fifth software module to assign the individual as a candidate to treatment with ibrutinib if there is an increase in expression level in the one or more biomarker genes relative to the control.
  • the system further comprises an analytical device configured to provide biomark
  • the digital processing device is connected to a computer network.
  • the fifth software module further generates a report, wherein the fifth software module is executed by the digital processing device.
  • the fifth software module further transmits the report to an end-user, wherein the fifth software module is executed by the digital processing device.
  • the method further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device.
  • the analytical device performs microarray analysis.
  • the digital processing device is connected to a computer network.
  • the second software module further generates a report, wherein the second software module is executed by the digital processing device.
  • the second software module further transmits the report to an end-user, wherein the second software module is executed by the digital processing device.
  • the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device.
  • the analytical device performs microarray analysis.
  • the digital processing device is connected to a computer network.
  • the fifth software module further generates a report, wherein the fifth software module is executed by the digital processing device.
  • the fifth software module further transmits the report to an end-user, wherein the fifth software module is executed by the digital processing device.
  • Embodiment 1 A method of treating a non-Hodgkin' s lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418
  • Embodiment 2 The method of Embodiment 1, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and
  • Embodiment 3 The method of Embodiment 1 or Embodiment 2, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC64
  • Embodiment 4 The method of Embodiment 1 or Embodiment 2, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC6477
  • Embodiment 5 The method of any one of Embodiments 1-4, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • CALB2RY11 PPAN- P2RY11
  • DNAJC8 TTC19
  • VCAMl CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1
  • CERCAM CERCAM
  • POM121C LOC
  • Embodiment 6 The method of any one of Embodiments 1-5, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
  • Embodiment 7 The method of any one of Embodiments 1-6, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • Embodiment 8 The method of any one of Embodiments 1-6, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • Embodiment 9 The method of any one of Embodiments 1-8, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7.
  • Embodiment 10 The method of any one of Embodiments 1-9, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B).
  • Embodiment 11 The method of any one of Embodiments 1-10, wherein the individual has a normal expression of CERCAM or DHRS7.
  • Embodiment 12 The method of any one of Embodiments 1-10, wherein the individual has an underexpression of CERCAM or DHRS7.
  • Embodiment 13 The method of any one of Embodiments 1-12, wherein the individual has an overexpression of RPA1 or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
  • Embodiment 14 The method of any one of Embodiments 1-13, wherein the individual has an overexpression of RPA1 or STS-1 (UBASH3B).
  • Embodiment 15 The method of any one of Embodiments 1-14, wherein the individual has a normal expression of DHRS7.
  • Embodiment 16 The method of any one of Embodiments 1-14, wherein the individual has an underexpression of DHRS7.
  • Embodiment 17 A method of treating a follicular lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, L
  • Embodiment 18 The method of Embodiment 17, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675.
  • CALB2RY11 PPAN-P2RY11
  • DNAJC8 TTC19
  • VCAM1 CSAG3, GP1BA
  • RPA1, RSC1A1, STS-1 UASH3B
  • ADPRM C170RF48
  • FILIPl FILIPl
  • LOC653297 IL15
  • Embodiment 19 The method of Embodiment 17 or Embodiment 18, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC64
  • Embodiment 20 The method of Embodiment 17 or Embodiment 18, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC64
  • Embodiment 21 A method of treating a follicular lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
  • CALB2RY11 PPAN-P2RY11
  • DNAJC8 TTC19
  • VCAM1 CSAG3, GP1BA RPA1, RSC1A1,
  • Embodiment 22 The method of Embodiment 21, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
  • Embodiment 23 The method of Embodiment 21 or Embodiment 22, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • Embodiment 24 The method of Embodiment 21 or Embodiment 22, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
  • Embodiment 25 The method of any one of Embodiments 21-24, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7.
  • Embodiment 26 The method of any one of Embodiments 21-25, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B).
  • Embodiment 27 The method of any one of Embodiments 21-26, wherein the individual has a normal expression of CERCAM or DHRS7.
  • Embodiment 28 The method of any one of Embodiments 21-26, wherein the individual has an underexpression of CERCAM or DHRS7.
  • Embodiment 29 The method of any one of Embodiments 21-28, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
  • Embodiment 30 The method of any one of Embodiments 21-29, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B).
  • Embodiment 31 The method of any one of Embodiments 21-30, wherein the individual has a normal expression of DHRS7.
  • Embodiment 32 The method of any one of Embodiments 21-30, wherein the individual has an underexpression of DHRS7.
  • Embodiment 33 The method of any one of Embodiments 1-32, wherein the individual has not been previously treated for lymphoma.
  • Embodiment 34 The method of any one of Embodiments 1-32, wherein the individual has not been previously treated with ibrutinib for lymphoma.
  • Embodiment 35 The method of any one of Embodiments 1-32, wherein the individual has been previously treated for lymphoma with an anticancer therapy other than ibrutinib.
  • Embodiment 36 The method of Embodiment 35, wherein the lymphoma is relapsed or refractory.
  • Embodiment The method of any one of Embodiments 1-32, wherein the individual has been previously treated for lymphoma with ibrutinib and administration of ibrutinib is continued.
  • Embodiment 38 The method of any one of Embodiments 1-37, wherein ibrutinib is administered with another therapeutic agent.
  • Embodiment 39 The method of any one of Embodiments 1-38, wherein ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day.
  • Illumina HT12 v4 BeadArray Microarray gene expression probe-level data were background corrected and normalized by Pharmacyclics bioinformatics beadarray data processing pipeline as follows: first the "ID AT" files (of probe intensity) of all samples (arrays) were taken as input to a pipeline and the R package "beadarray” was used, and then the "neqc” normalization program was used to generate the final normalized gene expression levels for downstream statistical analyses.
  • the "neqc” normalization is a method combining the normal- exponential background correction procedure with the quantile normalization procedure.
  • the Pearson correlation coefficient R is a measure of linear dependence between 2 variables: one variable is the gene expression value at the probe level, and the other variable is the percent change in the sum of the perpendicular diameters (SPD) of index lesions from baseline to the end of the 8 weeks of ibrutinib treatment.
  • the Pearson correlation coefficient R ranges from -1 to 1.
  • a value of 1 implies that a positive linear relationship between gene expression value and percent change in the SPD perfectly, with all data points lying on a line for which one variable increases as the other variable increases.
  • a value of -1 implies that all data points lie on a line for which one variable decreases as the other variable increases.
  • a value of 0 implies that there is no linear correlation between the variables.
  • the False Discovery Rate (FDR) is one way of
  • ILMN_1653856 STS- 1 UBASH3B 0.000013 -0.839817688 0.079

Abstract

Disclosed herein are methods of treating follicular lymphoma in an individual in need thereof wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.

Description

METHODS OF TREATMENT OF FOLLICULAR LYMPHOMA WITH A BTK
INHIBITOR
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] The present application claims the benefit of priority from U.S. Provisional Patent Application No. 62/257,563, filed November 19, 2015, and U.S. Provisional Patent Application No. 62/280,562, filed January 19, 2016, the contents of both of which are herein incorporated by reference in their entirety.
BACKGROUND
[0002] Bruton's tyrosine kinase (Btk), a member of the Tec family of non-receptor tyrosine kinases, is a key signaling enzyme expressed in all hematopoietic cells types except T
lymphocytes and natural killer cells. Btk plays an essential role in the B-cell signaling pathway linking cell surface B-cell receptor (BCR) stimulation to downstream intracellular responses.
[0003] Follicular lymphoma (FL), a B-cell lymphoma, is the most common indolent (slow- growing) form of non-Hodgkin lymphoma (NHL). The lymphoma cells build up in lymph nodes. The most common symptom is a painless swelling in the neck, armpit or groin.
SUMMARY
[0004] Disclosed herein, in one aspect, is a method of treating follicular lymphoma in an individual in need thereof wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof. In some embodiments, the individual has an overexpression of one or more genes selected from VCAM1, RPAl, and STS-1 (UBASH3B), or a normal expression or
underexpression of CERCAM or DHRS7. In some embodiments, the individual has an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7. [0005] Disclosed herein, in another aspect, is a method for treating follicular lymphoma in an individual in need thereof comprising: (a) requesting a test providing the results of an analysis to determine whether the patient has an overexpression of one or more genes selected from
CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSCl Al, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, and/or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7; and (b) administering or continuing to administer to the individual ibrutinib if the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, and/or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
[0006] In another aspect, disclosed herein is a method for selecting an individual having follicular lymphoma for treatment with ibrutinib, comprising: (a) determining the expression level in the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7), and (b) administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof, if the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
[0007] In still another aspect, disclosed herein is a method of assessing an individual having follicular lymphoma for treatment with ibrutinib, comprising: (a) determining the expression level the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7), and (b) determining that the individual is suitable for treatment or continued treatment with ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7, and administering to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[0008] In another aspect, disclosed is a method for selecting an individual having follicular lymphoma for treatment with ibrutinib, comprising: (a) determining the expression level in the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C
(LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7), and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
[0009] Further disclosed herein, in still another aspect, is a method of optimizing the therapy of an individual receiving ibrutinib for treatment of follicular lymphoma, comprising:
(a) determining the expression level in the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7); and (b) continuing the treatment with ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
[0010] Further disclosed herein, in still another aspect, is a method of monitoring response to ibrutinib of an individual receiving ibrutinib for treatment of follicular lymphoma, comprising: (a) determining the expression level in the individual of one or more genes selected from those disclosed herein (e.g., but not limited to, CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7); and (b) and characterizing the individual as being responsive to the treatment with ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7.
[0011] Also disclosed herein, in still another aspect, is a method of monitoring the disease progression in an individual having follicular lymphoma, comprising: (a) determining the expression level of one or more genes selected from those disclosed herein; and (b)
characterizing the individual as having a disease progression if there is an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7. In some embodiments, the method further comprising discontinue administration of ibrutinib to the individual.
[0012] Disclosed herein, in still another aspect, is a kit useful in the methods disclosed herein, comprising one or more reagents for determining the expression level of one or more genes selected from those disclosed herein in a sample. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising one or more genes disclosed herein.
[0013] Disclosed herein, in still another aspect, is a system useful in the methods described herein comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more genes described in a sample, and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a first software module configured to analyze the dataset to determine the expression level of one or more genes; and (ii) a second software module to assign the individual as a candidate for treatment with ibrutinib based on the expression level of the one or more biomarkers.
[0014] Disclosed herein, in certain embodiments, is a nucleic acid hybridization array comprising nucleic acid probes for detecting the genes described herein, wherein the nucleic acid probes hybridize to one or more genes disclosed herein.
[0015] This and other aspects are described in more details in the text that follows.
DETAILED DESCRIPTION
Certain Terminology
[0016] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the claimed subject matter belongs. It is to be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of any subject matter claimed. In this application, the use of the singular includes the plural unless specifically stated otherwise. It must be noted that, as used in the specification and the appended claims, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise. In this application, the use of "or" means "and/or" unless stated otherwise.
Furthermore, use of the term "including" as well as other forms, such as "include", "includes," and "included," is not limiting.
[0017] As used herein, ranges and amounts can be expressed as "about" a particular value or range. About also includes the exact amount. Hence "about 5 μΙ_," means "about 5 μΙ_," and also "5 μΐ.." Generally, the term "about" includes an amount that would be expected to be within experimental error, such as within ±10%, ±5% or ±1% of the stated value.
[0018] As used herein, the term "comprising" or its grammatic variants is intended to mean that the compositions and methods, etc., include the recited elements, but do not exclude others. "Consisting essentially of or its grammatic variants when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination for the intended use, but not excluding elements that do not materially affect the characteristic(s) of the compositions or methods. "Consisting of or its grammatic variants shall mean excluding elements not specifically recited. Embodiments defined by each of these transition terms are within the scope of this invention. For example, when a formulation is described as comprising ingredients A, B and C, a formulation consisting essentially of A, B and C, and a formulation consisting of A, B and C are independently within the scope of this invention.
[0019] The term "acceptable" or "pharmaceutically acceptable", with respect to a formulation, composition or ingredient, as used herein, means having no persistent detrimental effect on the general health of the subject being treated or does not abrogate the biological activity or properties of the compound, and is relatively nontoxic.
[0020] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
[0021] As used herein, the terms "individual(s)", "subject(s)" and "patient(s)" mean any mammal. In some embodiments, the mammal is a human. In some embodiments, the mammal is a non-human. None of the terms require or are limited to situations characterized by the supervision (e.g. constant or intermittent) of a health care worker (e.g. a doctor, a registered nurse, a nurse practitioner, a physician's assistant, an orderly or a hospice worker).
[0022] Ibrutinib is an inhibitor of Bruton's tyrosine kinase (Btk) having the chemical names of " 1 -((R)-3 -(4-amino-3 -(4-phenoxyphenyl)- lH-pyrazolo[3 ,4-d]pyrimidin- 1 -yl)piperidin- 1 - yl)prop-2-en- 1 -one" or " 1 - { (3R)-3 -[4-amino-3 -(4-phenoxyphenyl)- lH-pyrazolo[3 ,4- <i]pyrimidin-l-yl]piperidin-l-yl}prop-2-en-l-one" or "2-Propen-l-one, l-[(3R)-3-[4-amino-3-(4- phenoxyphenyl)-lH-pyrazolo[3,4-<i]pyrimidin-l-yl]-l-piperidinyl-" or any other suitable name and the following structure:
Figure imgf000007_0001
[0023] The term "pharmaceutically acceptable salts" refers to a salt which does not cause significant irritation to a mammal to which it is administered and does not substantially abrogate the biological activity and properties of the compound. Pharmaceutically acceptable salt may include acid addition salts of a compound formed with an organic acid, which include aliphatic mono- and dicarboxylic acids, phenyl-substituted alkanoic acids, hydroxyl alkanoic acids, alkanedioic acids, aromatic acids, aliphatic and aromatic sulfonic acids, amino acids, acetic acid, trifluoroacetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like; inorganic acids, which include hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, hydroiodic acid, hydrofluoric acid, phosphorous acid, and the like.
[0024] Solvates refer to a complex of a compound formed with either stoichiometric or non- stoichiometric amounts of a solvent, for example, pharmaceutically acceptable solvents such as water, ethanol, methanol, methyl tert-butyl ether (MTBE), diisopropyl ether (DIPE), ethyl acetate, isopropyl acetate, isopropyl alcohol, methyl isobutyl ketone (MIBK), methyl ethyl ketone (MEK), acetone, nitromethane, tetrahydrofuran (THF), dichloromethane (DCM), dioxane, heptanes, toluene, anisole, acetonitrile, and the like. In some embodiments, solvates of ibrutinib are anhydrous. In some embodiments, ibrutinib, or pharmaceutically acceptable salts thereof, exist in unsolvated form. In some embodiments, ibrutinib, or pharmaceutically acceptable salts thereof, exist in unsolvated form and are anhydrous.
[0025] In yet other embodiments, ibrutinib, or a pharmaceutically acceptable salt thereof, is prepared in various forms, including but not limited to, amorphous phase, crystalline forms, milled forms and nano-particulate forms. In some embodiments, ibrutinib, or a pharmaceutically acceptable salt thereof, is amorphous. In some embodiments, ibrutinib, or a pharmaceutically acceptable salt thereof, is amorphous and anhydrous. In some embodiments, ibrutinib, or a pharmaceutically acceptable salt thereof, is crystalline. In some embodiments, ibrutinib, or a pharmaceutically acceptable salt thereof, is crystalline and anhydrous. In some embodiments, ibrutinib or a pharmaceutically acceptable salt thereof, is a crystalline form, alone or with a conformer, described in, e.g., WO2016141068, WO2016160598 and WO2016160604, all of which are incorporated by reference in their entirety.
[0026] The term "Bruton's tyrosine kinase," as used herein, refers to B niton's tyrosine kinase from Homo sapiens, as disclosed in, e.g., U.S. Patent No. 6,326,469 (GenBank Accession No. NP_000052). [0027] As used herein, "treating" and like terms refer to reducing the severity and/or frequency of symptoms of a disease, such as FL, eliminating the symptoms and/or the underlying cause of said symptoms, reducing the frequency or likelihood of the symptoms and/or their underlying cause, and improving or remediating damage caused, directly or indirectly, by the disease, such as FL. include alleviating, abating or ameliorating a disease or condition, or symptoms thereof; managing a disease or condition, or symptoms thereof; preventing additional symptoms;
ameliorating or preventing the underlying metabolic causes of symptoms; inhibiting the disease or condition, e.g., arresting the development of the disease or condition; relieving the disease or condition; causing regression of the disease or condition, relieving a condition caused by the disease or condition; or stopping the symptoms of the disease or condition.
[0028] The terms "effective amount" or "therapeutically effective amount," as used herein, refer to a sufficient amount of an agent or a compound being administered which will relieve to some extent one or more of the symptoms of the disease or condition being treated. The result can be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. For example, an "effective amount" for therapeutic uses is the amount of compound required to provide a clinically significant decrease in disease symptoms without undue adverse side effects. The term "therapeutically effective amount" includes, for example, a prophylactically effective amount. It is understood that "an effect amount" or "a therapeutically effective amount" can vary from subject to subject, due to variation in metabolism of the compound, age, weight, general condition of the subject, the condition being treated, the severity of the condition being treated, and the judgment of the prescribing physician. By way of example only, therapeutically effective amounts may be determined by routine experimentation, including but not limited to a dose escalation clinical trial.
[0029] The term "biological sample" refers to any sample from a patient that contains, or can contain, the biomarkers of interest or an encoded peptide thereof, including, for example, tumor, blood, serum, or plasma. In some embodiments, the sample is a tumor biopsy sample.
[0030] The term "nucleic acid" refers to deoxyribonucleotides, deoxyribonucleosides, ribonucleosides, or ribonucleotides and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides which have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless specifically limited otherwise, the term also refers to oligonucleotide analogs including PNA (peptidonucleic acid), analogs of DNA used in antisense technology (e.g., phosphorothioates, phosphoroamidates). Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (including but not limited to, degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated.
Specifically, degenerate codon substitutions are achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al. (\99\)Nucleic Acid Res. 19:5081; Ohtsuka et al. (1985) J. Biol. Chem. 260:2605-2608; and Cassol et al. (\992)Mol. Cell. Probes 6, 327-331; and Rossolini et al. (1994) Mol. Cell. Probes 8:91-98). In some embodiments, the nucleic acid or a fragment thereof encodes a protein.
[0031] The terms "polypeptide", peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to naturally occurring amino acid polymers as well as amino acid polymers in which one or more amino acid residues is a non- naturally occurring amino acid, e.g., an amino acid analog. The terms encompass amino acid chains of any length, including full length proteins, wherein the amino acid residues are linked by covalent peptide bonds.
[0032] Gene expression level refers to the measurable quantity (such as number of molecules or concentration) of a particular gene or a gene product (including any of DNA, cDNA, RNA, transcript, or a polypeptide encoded by the gene) in an individual or a sample taken from the individual. In some embodiments, expression level refers to the amount of RNA of the particular gene. In some embodiments, expression level refers to the amount of a particular gene in a sample from individual, such as a tumor sample, blood sample, serum sample, etc., and can, for example, be detected de novo or correspond to a previous determination.
[0033] Normal expression refers to an expression level of a gene in an individual (or in tumor cells of the individual) that is comparable to control, such as within ± 25%, ± 20% or ± 10% of control or has no statistically significant difference as compared with control. Overexpression refers to an increase in the expression level of a gene in an individual (or in tumor cells of the individual) relative to control or presence of a gene which is absent in control. In some embodiments, overexpression means that the expression level of the gene has an increase of at least 20%, 50%, 100% or 200% relative to control. In some embodiments, overexpression means that the increase in expression level of the gene relative to control is statistically significant. Underexpression refers to a decrease in the expression level of a gene in an individual (or in tumor cells of the individual) relative to control or absence of a gene that is expressed in control. In some embodiments, underexpression means that the expression level of the gene is no more than 90%, 80%, 75%, 50%, 20%, or 10%, or less relative to control. In some embodiments, underexpression means that the decrease in expression level of the gene relative to control is statistically significant.
[0034] The term "control" refers to any reference standard suitable to provide a comparison to the expression products in the test sample. In one embodiment, the control comprises obtaining a "control sample" from which expression product levels are detected and compared to the expression product levels from the test sample. Such a control sample may comprise any suitable sample, including but not limited to a sample from a control cancer patient (can be stored sample or previous sample measurement) with a known outcome; normal tissue or cells isolated from a subject, such as a normal patient or the cancer patient, cultured primary cells/tissues isolated from a subject such as a normal subject or the cancer patient, adjacent normal cells/tissues obtained from the same organ or body location of the cancer patient, a tissue or cell sample isolated from a normal subject, or a primary cells/tissues obtained from a depository. In another embodiment, the control may comprise a reference standard expression product level from any suitable source, including but not limited to housekeeping genes, an expression product level range from normal tissue (or other previously analyzed control sample), a previously determined expression product level range within a test sample from a group of patients, or a set of patients with a certain outcome (for example, survival for one, two, three, four years, etc.) or receiving a certain treatment (for example, standard of care cancer therapy). It will be understood by those of skill in the art that such control samples and reference standard expression product levels can be used in combination as controls. In one embodiment, the control may comprise normal or noncancerous cell/tissue sample. In another embodiment, the control may comprise an expression level for a set of patients, such as a set of cancer patients, or for a set of cancer patients receiving a certain treatment, or for a set of patients with one outcome versus another outcome. In the former case, the specific expression product level of each patient can be assigned to a percentile level of expression, or expressed as either higher or lower than the mean or average of the reference standard expression level. In another embodiment, the control may comprise normal cells, cells from patients treated with combination chemotherapy, and cells from patients having benign cancer. In another embodiment, the control may also comprise a measured value for example, average level of expression of a particular gene in a population compared to the level of expression of a housekeeping gene in the same population. Such a population may comprise normal subjects, cancer patients who have not undergone any treatment (i.e., treatment naive), cancer patients undergoing standard of care therapy, or patients having benign cancer. In another embodiment, the control comprises a ratio transformation of expression product levels, including but not limited to determining a ratio of expression product levels of two genes in the test sample and comparing it to any suitable ratio of the same two genes in a reference standard; determining expression product levels of the two or more genes in the test sample and determining a difference in expression product levels in any suitable control; and determining expression product levels of the two or more genes in the test sample, normalizing their expression to expression of housekeeping genes in the test sample, and comparing to any suitable control. In particular embodiments, the control comprises a control sample which is of the same lineage and/or type as the test sample. In another embodiment, the control may comprise expression product levels grouped as percentiles within or based on a set of patient samples, such as all patients with cancer. In one embodiment a control expression product level is established wherein higher or lower levels of expression product relative to, for instance, a particular percentile, are used as the basis for predicting outcome. In another embodiment, a control expression product level is established using expression product levels from cancer control patients with a known outcome, and the expression product levels from the test sample are compared to the control expression product level as the basis for predicting outcome. For example, the control can be the background gene expression level of follicular lymphoma patients, or a predetermined gene expression level, e.g., an average or medium of historical expression levels of follicular lymphoma patients. In some embodiments, the control is the expression levels of one or more of the biomarker disclosed herein in a follicular lymphoma patient or a group of patients who are not insensitive toward ibrutinib. In some embodiments, the control is the expression levels of one or more of the biomarkers disclosed herein in a follicular lymphoma patient or a group of patients who have not been treated with ibrutinib. In some embodiments, the control is the expression levels of one or more of the biomarkers disclosed herein in a follicular lymphoma patient or a group of patients who have not been treated for follicular lymphoma.
[0035] The term "probe" as used herein refers to a nucleic acid molecule that comprises a sequence of nucleotides (such as 10 or more, 15 or more, 20 or more, or 10-25, 26-50, 51-75, 76- 100, or 101-500 bases or nucleotides) that will hybridize specifically to a target nucleic acid sequence, such as a gene disclosed herein.
[0036] The term "primer" as used herein refers to a nucleic acid sequence, whether occurring naturally as in a purified restriction digest or produced synthetically, that is capable of acting as a point of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand is induced (e.g. in the presence of nucleotides and an inducing agent such as DNA polymerase and at a suitable temperature and pH).
[0037] Non-Hodgkin's lymphoma, NHL, is a cancer that starts in lymphocytes. In some embodiments, the non-Hodgkin's lymphoma is Burkitt lymphoma, chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, mantle cell lymphoma, marginal zone B-cell lymphomas, Waldenstrom's
macroglobulinemia, lymphoplasmacytic lymphoma, hairy cell leukemia, mediastinal large B-cell lymphoma, cutaneous lymphomas, mycosis fungoides, anaplastic large cell lymphoma, peripheral T-cell lymphomas, enteropathy associated T cell lymphoma (EATL), hepatosplenic gamma delta T cell lymphoma, or precursor T-lymphoblastic lymphoma. In some embodiments, the non-Hodgkin's lymphoma is Burkitt lymphoma, chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, mantle cell lymphoma, marginal zone B-cell lymphomas, Waldenstrom's macroglobulinemia,
lymphoplasmacytic lymphoma, hairy cell leukemia, or mediastinal large B-cell lymphoma. In some embodiments, the non-Hodgkin's lymphoma is DLBCL. In some embodiments, the non- Hodgkin's lymphoma is FL. In some embodiments, the non-Hodgkin's lymphoma is previously treated with another anticancer agent. In some embodiments, the non-Hodgkin's lymphoma is a relapsed or refractory non-Hodgkin's lymphoma. In some embodiments, the relapsed or refractory non-Hodgkin's lymphoma is a relapsed or refractory FL. In some embodiments, the FL is treatment naive FL, i.e., previously untreated FL. In some embodiments, the FL is currently being or was previously treated with only ibrutinib.
[0038] Anticancer therapies refer to therapeutic agents or treatment useful or commonly used for treating a cancer, such as a Non-Hodgkin's lymphoma, and in particular follicular lymphoma. Such therapies include anticancer agents, radiation therapy, and surgical procedures, etc. In some embodiments, anticancer agents include chemotherapeutic agents, steroids, immunotherapeutic agents, targeted therapeutic agents, or a combination thereof. In some embodiments, anticancer agents include chlorambucil, ifosphamide, doxorubicin, mesalazine, thalidomide, lenalidomide, pomalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, obinutuzumab, rituximab, dexamethasone, prednisone, idelalisib, ibritumomab, tositumomab, bortezomib, pentostatin, endostatin, carfilzomib, or a combination thereof, such as R- Bendamustine (rituximab and bendamustine), R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone), and R-CVP (rituximab, cyclophosphamide, vincristine, and prednisone).
Biomarkers
[0039] Disclosed herein, in one aspect, are biomarkers useful in identifying follicular lymphoma patients suitable for treatment or continued treatment with ibrutinib, or in predicting or assessing response of follicular lymphoma patients to treatment with ibrutinib. The
biomarkers include CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299 (see, e.g., US 2015/0010514), TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5,
LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070 (e.g., Probe Set ID: ILMN 1723094), PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CTLP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B. Biomarkers include the genes described herein, orthologs thereof, the nucleic acid (DNA or RNA) molecules comprising the genes, or proteins encoded by the genes. In some embodiments, the biomarkers described herein are present in humans. Detailed description of the genes can be found from National Center for Biotechnology
Information (NCBI), U. S. National Library of Medicine, e.g., at
https://www.ncbi.nlm.nih.gov/gene/.
[0040] In some embodiments, the biomarkers are:
Figure imgf000015_0001
Gene symbol Alternative names Gene ID Encoding protein
ADPRM ADP-ribose/CDP-alcohol 56985 manganese -dependent ADP- diphosphatase, manganese ribose/CDP-alcohol dependent; C170RF48; diphosphatase
MDS006; NBLA03831
FILIP1 filamin A interacting protein 1 ; 27145 filamin-A-interacting protein 1
FILIP
LOC653297 similar to CSAG family, 653297 similar to CSAG family, member 2 member 2
IL15 interleukin 15 3600 interleukin- 15
NR2E3 nuclear receptor subfamily 2 10002 photoreceptor-specific nuclear group E member 3; PNR; RNR; receptor rd7; ESCS; RP37
TTTY11 testis-specific transcript, Y- 83866
linked 11 (non-protein coding)
GCET2 GCSAM; germinal center 257144 germinal center-associated associated signaling and signaling and motility protein motility; HGAL; GCAT2;
OR1C1 olfactory receptor family 1 26188 olfactory receptor 1C1
subfamily C member 1; OR 1-42;
ORL211; TPCR27; HSTPCR27;
OR1.5.10
DNASE1L1 deoxyribonuclease 1 like 1; XIB; 1774 deoxyribonuclease- 1 -like 1
G4.8; DNL1L; DNASEX;
DNAS1L1
LOC100127891 100127891
CRYGN crystallin gamma N 155051 gamma-crystallin N
LOC644248 644248
C90RF169 CYSRT1; cysteine rich tail 1 375791 cysteine-rich tail protein 1
SLC45A2 solute carrier family 45 member 51151 membrane-associated
2; 1A1; AIM1; MATP; OCA4; transporter protein
SHEP5 Gene symbol Alternative names Gene ID Encoding protein
LOC100128675 HPN-AS 1 HPN antisense RNA 100128675
1
CERCAM cerebral endothelial cell 51148 probable inactive
adhesion molecule; CEECAMl; glycosyltransferase 25 family GLT25D3 member 3
POM121C POM 121 transmembrane 100101267 nuclear envelope pore
nucleoporin C; POM121-2; membrane protein POM 121C LOC100131972
PPP1R3D protein phosphatase 1 regulatory 5509 protein phosphatase 1
subunit 3D; PPP1R6 regulatory subunit 3D
PLOD2 procollagen-lysine,2- 5352 procollagen-lysine,2- oxoglutarate 5-dioxygenase 2; oxoglutarate 5-dioxygenase 2 LH2; TLH; BRKS2
SDHA succinate dehydrogenase 6389 succinate dehydrogenase complex flavoprotein subunit A; [ubiquinone] flavoprotein FP; PGL5; SDH1; SDH2; subunit, mitochondrial SDHF; CMD1GG
SDHAP3 succinate dehydrogenase 728609
complex flavoprotein subunit A
pseudogene 3; SDHAL;
SDHACL
OSBPL2 oxysterol binding protein like; 9885 oxysterol-binding protein- ORP2; ORP-2; DFNA67; related protein 2
DNFA67
HCFC1R1 host cell factor CI regulator 1; 54985 host cell factor C 1 regulator 1
HPIP
DHRS7 dehydrogenase/reductase 7; 51635 dehydrogenase/reductase SDR
CGI-86; SDR34C1; retDSR4; family member 7 retSDR4
LOC652418 652418
LOC440345 NPIPB4 440345
LOC647435 647435 Gene symbol Alternative names Gene ID Encoding protein
KRTHB6 keratin 86; HB6; Hbl; K86; 3892 keratin, type II cuticular Hb6
MNX; KRTHB1; KRT86
TH1L NELFCD; negative elongation 51497 negative elongation factor C/D factor complex member C/D;
TH1; NELF-C; NELF-D;
HSPC130
BBS5 Bardet-Biedl syndrome 5 129880 Bardet-Biedl syndrome 5 protein
LOC100128935 100128935
NT5C1B 5 '-nucleotidase, cytosolic IB; 93034 cytosolic 5 '-nucleotidase IB
AIRP; CN1B; CN-IB
LOC653234 AGAP10P ArfGAP with 653234
GTPase domain, ankyrin repeat
and PH domain 10 pseudogene
LOC392506 392506
PPEF2 protein phosphatase with EF- 5470 serine/threonine-protein hand domain 2; PPP7CB phosphatase with EF-hands 2
LOC100134108 100134108
LOC392100 PSMC1P3; proteasome 26S 392100
subunit, ATPase 1 pseudogene 3
LOC100132535 100132535
OSBPL2 oxysterol binding protein like 2; 9885 oxysterol-binding protein- ORP2; ORP-2; DFNA67; related protein 2
DNFA67
LOC643341 643341
LOC284379 284379
ARPC2 actin related protein 2/3 complex 10109 actin-related protein 2/3 subunit 2; ARC34; PR02446; complex subunit 2 p34-Arc; PNAS-139
KDM1B lysine demethylase IB; AOF1; 221656 lysine-specific histone
LSD2; C6orfl93; bA204B7.3; demethylase IB
dJ298J15.2 Gene symbol Alternative names Gene ID Encoding protein
SEZ6L seizure related 6 homolog like; 23544 seizure 6-like protein
LOC729251 729251
PCDHB3 protocadherin beta 3; PCDH- 56132 protocadherin beta-3
BETA3
LOC644473 644473
LOC646357 646357
TMEM22 744962 transmembrane protein 22
LOC730200 730200
ZBTB39 zinc finger and BTB domain 9880 zinc finger and BTB domain- containing 39; ZNF922 containing protein 39
TTTY17A testis-specific transcript, Y- 252949
linked 17A (non-protein coding);
TTTY17; NCR A00140
PAIP2 poly(A) binding protein 51247 polyadenylate-binding protein- interacting protein 2; PAIP-2; interacting protein 2
PAIP2A
KBTBD9 KLHL29; kelch like family 114818 kelch-like protein 29
member 29
LOC647788 647788
ALG2 ALG2, alpha- 1,3/1, 6- 85365 alpha- 1,3/ 1,6- mannosyltransferase; CDGIi; mannosyltransferase ALG2 CMS 14; NET38; CMSTA3;
hALPG2
ELOVL2 ELOVL fatty acid elongase 2; 54898 elongation of very long chain
SSC2 fatty acids protein 2
RFX4 regulatory factor X4; NYD-SP10 5992 transcription factor RFX4
CILP cartilage intermediate layer 8483 cartilage intermediate layer protein; CILP-1; HsT18872 protein 1
COMP cartilage oligomeric matrix 1311 cartilage oligomeric matrix protein; MED; EDM1; EPD1; protein
TSP5; PSACH; THBS5
LOC100134540 100134540 Gene symbol Alternative names Gene ID Encoding protein
CYP4Z1 cytochrome P450 family 4 199974 cytochrome P450 4Z1
subfamily Z member 1 ;
CYP4A20
LOC100129434 100129434
GALNT9 polypeptide N- 50614 polypeptide N- acetylgalactosaminyltransferase acetylgalactosaminyltransferase 9; GALNACT9; GALNAC-T9 9
NBPF7 neuroblastoma breakpoint family 343505 putative neuroblastoma
member 7 breakpoint family member 7
MTUS1 microtubule associated tumor 57509 microtubule-associated tumor suppressor 1 suppressor 1
ODF4 outer dense fiber of sperm tails 146852 outer dense fiber protein 4
4; CT134; CT136; OPPOl
LOC652640 652640
LOC642978 642978
LOC440402 440402
SPOl l SPOl 1, initiator of meiotic 23626 meiotic recombination protein double stranded breaks; CT35; SPOl l
TOPVIA; SPATA43
PLOD2 procollagen-lysine,2- 5352 procollagen-lysine,2- oxoglutarate 5-dioxygenase 2; oxoglutarate 5-dioxygenase 2 LH2; TLH; BRKS2
MIR24-1 microRNA 24-l; MIR189; 407012
MIRN24-l; miR-24-l;
miR A24-l
LOC648164 648164
CTGF connective tissue growth factor; 1490 connective tissue growth factor
CCN2; NOV2; HCS24; IGFBP8
LOC390834 FEM1AP2; fem-1 homolog A 390834
pseudogene 2
COL8A1 collagen type VIII alpha 1 chain; 1295 collagen alpha- 1 (VIII) chain
C3orf7 Gene symbol Alternative names Gene ID Encoding protein
PTGIS prostaglandin 12 synthase; 5740 prostacyclin synthase
CYP8; PGIS; PTGI; CYP8A1
PLA2G2A phospholipase A2 group IIA; 5320 phospholipase A2, membrane
MOM1; PLA2; PLA2B; PLA2L; associated
PLA2S; PLAS l; sPLA2
LOC644763 644763 similar to erythrocyte
membrane protein band 4.1 like 4B isoform 2
BTBD7 BTB domain containing 7 55727 BTB/POZ domain-containing protein 7
LOC644038 644038
LOC100131972 100131972
LOC651231 651231
LOC650677 650677
CSRP2BP PET117 PET117 homolog 100303755 protein PET117 homolog,
mitochondrial
CSRP2BP KAT14; lysine acetyltransferase 57325 cysteine-rich protein 2-binding
14; ATAC2; CRP2BP; protein
CSRP2BP; PRO 1194;
dJ717M23.1
CDKN2B cyclin dependent kinase inhibitor 1030 cyclin-dependent kinase 4
2B; P15; MTS2; TP 15; CDK4I; inhibitor B
INK4B; pl5INK4b
Methods of Treatment
[0041] Disclosed herein, in one aspect, is a method of treating a non-Hodgkin's lymphoma in an individual in need thereof who has an overexpression or an increase in the expression level of one or more (e.g., at least one, two, three or four) genes selected from CALB2, P2RY1 1 (PPAN- P2RY1 1), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C 1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, and/or a normal expression or underexpression or an absence of an increase (e.g., decrease) in the expression level of one or more (e.g., at least one, two, three or four) genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108,
LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, which method comprises administering or continuing administering to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[0042] In certain embodiments, the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675.
[0043] In certain embodiments, the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108,
LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
[0044] In certain embodiments, the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108,
LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDMIB, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
[0045] In some embodiments, the individual has an overexpression of one or more (e.g., at least one, two, three or four) genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM
(C170RF48) and FILIP1, and/or a normal expression or underexpression of one or more (e.g., at least one, two, three or four) genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7. In some
embodiments, the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1. In some embodiments, the individual has a normal expression of one or more genes selected from CERCAM, POM121C
(LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7. In some embodiments, the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7. In some embodiments, the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or a normal expression or underexpression of CERCAM or DHRS7. In some embodiments, the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B). In some embodiments, the individual has a normal expression of CERCAM or DHRS7. In some embodiments, the individual has an underexpression of CERCAM or DHRS7. In some embodiments, the individual has an overexpression of RPAl or STS-1 (UBASH3B), and/or a normal expression or underexpression of DHRS7. In some embodiments, the individual has an overexpression of RPAl or STS-1 (UBASH3B). In some embodiments, the individual has a normal expression of DHRS7. In some embodiments, the individual has an underexpression of DHRS7.
[0046] In some embodiments, the individual has an increase in the expression level of one or more (e.g., at least one, two, three or four) genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, and/or an absence of an increase (e.g., decrease) in the expression level of one or more (e.g., at least one, two, three or four) genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7. In some embodiments, the individual has an increase in the expression level of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or an absence of an increase in the expression level of CERCAM or DHRS7. In some embodiments, the individual has an increase in the expression level of RPAl or STS-1 (UBASH3B), and/or an absence of an increase in the expression level of DHRS7.
[0047] In some embodiments, disclosed herein is a method of treating follicular lymphoma (FL) in an individual in need thereof who has an overexpression or an increase in the expression level of one or more (e.g., at least one, two, three or four) biomarkers selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3,
LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN,
LOC644248, C90RF169, SLC45A2, and LOC100128675, and/or a normal expression or underexpression or an absence of an increase in the expression level of one or more (e.g., at least one, two, three or four) biomarkers selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418,
LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[0048] In some embodiments, disclosed herein is a method of treating follicular lymphoma (FL) in an individual in need thereof who has an overexpression of one or more (e.g., at least one, two, three or four) biomarkers selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM
(C170RF48) and FILIP1, and/or a normal expression or underexpression of one or more (e.g., at least one, two, three or four) biomarkers selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof. In some
embodiments, the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or a normal expression or underexpression of CERCAM or DHRS7. In some embodiments, the individual has an overexpression of RPAl or STS-1
(UBASH3B), and/or a normal expression or underexpression of DHRS7.
[0049] In some embodiments, disclosed herein is a method of treating follicular lymphoma in an individual in need thereof who has an increase in the expression level of one or more (e.g., at least one, two, three or four) biomarkers selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, and/or an absence of an increase (e.g., decrease) of one or more (e.g., at least one, two, three or four) biomarkers selected from CERCAM, POM121C
(LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof. In some embodiments, the individual has an increase in the expression level of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or an absence of an increase in the expression level of CERCAM or DHRS7. In some embodiments, the individual has an increase in the expression level of RPAl or STS-1 (UBASH3B), and/or an absence of an increase of DHRS7. In some embodiments, the individual has a decrease in the expression level of CERCAM or DHRS7. [0050] Disclosed herein, in another aspect, is a method of selecting an individual having a non- Hodgkin's lymphoma for treatment or for continuing treatment with ibrutinib, comprising:
(a) determining the expression level of one or more of the biomarkers disclosed herein, and
(b) administering to the individual a therapeutically effective amount of ibrutinib or a
pharmaceutically acceptable salt or solvate thereof if there is no increased expression, an increase in expression level, or a decrease in expression level in one or more of the biomarkers disclosed herein relative to a control. In some embodiments, disclosed is a method of selecting an individual having a non-Hodgkin's lymphoma for treatment or for continuing treatment with ibrutinib, comprising: (a) determining the expression level of one or more of the biomarkers selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C
(LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1,
LOC100129434, GALNT9, NBPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, and (b) administering to the individual a therapeutically effective amount of ibrutinib or a
pharmaceutically acceptable salt or solvate thereof if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, NR2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, and/or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418,
LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B. In some embodiments, the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, and/or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7. In some embodiments, the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), and/or a normal expression or underexpression of CERCAM or DHRS7. In some embodiments, the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7. In some embodiments, the non-Hodgkin's lymphoma is follicular lymphoma.
[0051] In another aspect, disclosed herein is a method for selecting an individual having follicular lymphoma (FL) for treatment or for continuing treatment with ibrutinib, comprising: (a) determining the expression level of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7, and (b) administering to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof, if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, and/or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7. In some embodiments, the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7. In some embodiments, the individual is administered ibrutinib or a pharmaceutically acceptable salt or solvate thereof if there is an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
[0052] Disclosed herein, in certain embodiments, is a method for selecting an individual having follicular lymphoma (FL) for treatment or for continuing treatment with ibrutinib, comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435,
HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1 and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is a presence or absence of modifications in the one or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOCI 00132535, LOC647435, HCFC1R1, KRTHB6,
LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1.
[0053] Disclosed herein, in certain embodiments, is a method for selecting an individual having follicular lymphoma (FL) for treatment with ibrutinib, comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is a presence or absence of modifications in the one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN. Also disclosed herein, in certain embodiments, is a method of monitoring whether an individual receiving ibrutinib for treatment of FL has developed or is likely to develop resistance to the therapy, comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl,
LOCI 00132299, STS-1, and CRYGN and (b) characterizing the individual as resistant or is likely to become resistant to therapy with ibrutinib if the individual has modifications in the one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN. Further disclosed herein, in some embodiments, is a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL, comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN; and (b) modifying, discontinuing, or continuing the treatment based on the presence or absence of modifications in the one or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN. In some embodiments, the method further comprises determining the presence or absence of a modification in two or more biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN.
[0054] In some embodiments, the presence or absence of a modification in all 9 genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN) is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in all 9 genes. In some embodiments, the presence or absence of a modification in at least 8 of the following genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, CRYGN) is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 8 of the genes. In some embodiments, the presence or absence of a modification in at least 7 of the following genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl,
LOCI 00132299, STS-1, CRYGN) is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 7 of the genes. In some embodiments, the presence or absence of a modification in at least 6 of the genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, CRYGN) is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 6 of the genes. In some embodiments, the presence or absence of a modification in at least 5 of the genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, CRYGN) is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 5 of the genes. In some embodiments, the presence or absence of a modification in at least 4 of the genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, CRYGN) is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 4 of the genes. In some embodiments, the presence or absence of a modification in at least 3 of the genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, CRYGN) is
determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 3 of the genes. In some embodiments, the presence or absence of a modification in at least 2 of the genes (ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, CRYGN) is determined, and a therapeutically effective amount of ibrutinib is administered if there is a presence or absence of a modification in at least 2 of the genes.
[0055] In some embodiments, the one or more biomarker genes are selected from one or more of those disclosed herein. In some embodiments, the one or more biomarker genes are selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN and combinations thereof. In some embodiments, the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof. In some embodiments, the genes disclosed herein comprise one or more modifications in each gene. In some embodiments, the modification associated with one or more of the genes disclosed herein results in modifications in the corresponding proteins. In some embodiments, the method further comprises testing a sample containing nucleic acid molecules encoding the biomarker genes selected from those disclosed herein and obtained from the individual, and determining whether each of the genes selected from those disclosed herein contains one or more
modifications.
[0056] In some embodiments, the follicular lymphoma is previously treated with another anticancer agent. In some embodiments, the follicular lymphoma is a relapsed or refractory follicular lymphoma. In some embodiments, the follicular lymphoma is treatment naive follicular lymphoma, i.e., previously untreated follicular lymphoma. In some embodiments, the follicular lymphoma is currently being or was previously treated with only ibrutinib.
[0057] In some embodiments, ibrutinib is administered according to a method described herein. In some embodiments, ibrutinib is administered once a day, two times per day, three times per day, four times per day, or five times per day. In some embodiments, ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments, ibrutinib is administered at a dosage of about 140 mg/day, 280 mg/day, 420 mg/day, 560 mg/day, 840 mg/day or about 1000 mg/day. In some embodiments, ibrutinib is administered orally. In some embodiments, ibrutinib is administered in a pharmaceutical formulation comprising ibrutinib or a pharmaceutically acceptable salt or solvate thereof and a
pharmaceutically acceptable excipient, such as a formulation described in e.g., WO2013184572, WO2016022942, and WO2016141068, which are incorporated by reference in their entirety. In some embodiments, the method further comprises administering an additional therapeutic agent. In some embodiments, the additional therapeutic agent is selected from a chemotherapeutic agent and radiation therapeutic agent. In some embodiments, the chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide,
temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, ofatumumab, rituximab, dexamethasone, prednisone, CAL-101, ibritumomab, tositumomab, bortezomib, pentostatin, and endostatin, or a combination thereof. In some embodiments, ibrutinib is administered simultaneously, sequentially or intermittently with the additional therapeutic agent. In some embodiments, ibrutinib and the additional therapeutic agent are administered in one dosage form. In some embodiments, ibrutinib and the additional therapeutic agent are
administered in separate dosage forms.
[0058] In some embodiments, the expression level of the biomarker increases or decreases by 0.5-fold, 1-fold, 1.5-fold, 2-fold, 2.5-fold, 3-fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6- fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9-fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50- fold, or more compared to the control.
[0059] In some embodiments, the overexpression, normal expression, underexpression, increase or decrease in the expression levels of the biomarkers described herein is found a lymphoma tumor sample of the individual or a sample of the individual having tumor cells. Methods of Assessment to Treatment
[0060] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment with ibrutinib, comprising: (a) determining the expression level of at least one biomarker gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1,
LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B; and (b) determining that the individual is suitable for ibrutinib treatment if the individual a therapeutically effective amount of ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418,
LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, NBPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, and administering to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[0061] In another aspect, disclosed herein is a method of assessing an individual having FL for treatment with ibrutinib, comprising: (a) determining the expression level of at least one biomarker gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, and (b) determining that the individual is suitable for treatment with ibrutinib if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, and administering to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[0062] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1; and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or decrease in expression level in at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834,
CYP4Z1, LOC652640, DHRS7, LOC 100132535, LOC647435, HCFC1R1, KRTHB6,
LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1 relative to a control.
[0063] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1 and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is a decrease in expression level in at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1,
LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1 relative to a control.
[0064] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPAl, LOC100132299, DHRS7, THBS4, Z F514, AFF2, HS.493947, CST1, C R1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB 1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B), and
(b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase in expression level in at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPAl, LOC100132299, DHRS7, THBS4, Z F514, AFF2, HS.493947, CST1, C R1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW,
LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B relative to a control.
[0065] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPAl,
LOC100132299, DHRS7, THBS4, ZNF514, AFF2, HS.493947, CST1, CNR1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB 1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B) and
(b) administering to the individual a therapeutically effective amount of ibrutinib if there is a decrease in expression level in at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPAl, LOC100132299, DHRS7, THBS4, ZNF514, AFF2, HS.493947, CST1, CNR1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW,
LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B relative to a control.
[0066] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least two biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or decrease in expression level in at least two biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
[0067] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase in expression level in at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOC100132299, STS-1, and CRYGN relative to a control.
[0068] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is a decrease in expression level in at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOC100132299, STS-1, and CRYGN relative to a control.
[0069] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least three biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least three biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN relative to a control.
[0070] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least four biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least four biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN relative to a control.
[0071] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least five biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least five biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
[0072] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least six biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least six biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
[0073] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least seven biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least seven biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
[0074] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of at least eight biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in at least eight biomarker genes selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOCI 00132299, STS-1, and CRYGN relative to a control.
[0075] Disclosed herein, in certain embodiments, is a method of assessing an individual having FL for treatment, comprising: (a) determining the expression level of all of the following biomarker genes: ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS- 1, and CRYGN, and (b) administering to the individual a therapeutically effective amount of ibrutinib if there is an increase or a decrease in expression level in all of nine of the biomarker genes (i.e., ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN) relative to a control. [0076] In some embodiments, methods of assessing sensitivity of an individual for treatment with a Btk inhibitor [i.e., ibrutinib (alone or in combination with rituximab )/responsiveness to treatment with ibrutinib (alone or in combination with rituximab)] are provided by determining the expression levels of one or more of the biomarkers as described herein. In some
embodiments, the individual has treatment naive follicular lymphoma. In embodiments, the individual has relapsed/refractory follicular lymphoma.
[0077] In some embodiments, methods of determining identifying an individual for treatment with a Btk inhibitor [i.e., ibrutinib (alone or in combination with rituximab )/responsiveness to treatment with ibrutinib (alone or in combination with rituximab)] by determining the expression levels of one or more of the biomarkers as described herein. In some embodiments, the individual has treatment naive follicular lymphoma. In embodiments, the individual has relapsed/refractory follicular lymphoma.
[0078] In some embodiments, the expression level of the at least one biomarker selected from those disclosed herein increase or decrease by 0.5-fold, 1-fold, 1.5-fold, 2-fold, 2.5-fold, 3-fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6-fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9- fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50-fold, or more compared to the control.
[0079] In some embodiments, ibrutinib is administered once a day, two times per day, three times per day, four times per day, or five times per day. In some embodiments, ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments, ibrutinib is administered at a dosage of about 140 mg/day, 280 mg/day, 420 mg/day,
560 mg/day, 840 mg/day or about 1000 mg/day. In some embodiments, ibrutinib is administered orally. In some embodiments, ibrutinib is administered in a pharmaceutical formulation comprising ibrutinib or a pharmaceutically acceptable salt or solvate thereof and a
pharmaceutically acceptable excipient, such as a formulation described in e.g., WO2013184572, WO2016022942, and WO2016141068. In some embodiments, the method further comprises administering an additional therapeutic agent. In some embodiments, the additional therapeutic agent is selected from a chemotherapeutic agent and radiation therapeutic agent. In some embodiments, the chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, ofatumumab, rituximab, dexamethasone, prednisone, CAL- 101, ibritumomab, tositumomab, bortezomib, pentostatin, and endostatin, or a combination thereof. In some embodiments, ibrutinib is administered simultaneously, sequentially or intermittently with the additional therapeutic agent. In some embodiments, ibrutinib and the additional therapeutic agent are administered in one dosage form. In some embodiments, ibrutinib and the additional therapeutic agent are administered in separate dosage forms.
[0080] In some embodiments, the FL is a treatment naive FL. In some embodiments, the FL is a relapsed or refractory FL.
Methods for Optimizing Treatment
[0081] Further disclosed herein, in some embodiments, is a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL, comprising: (a) determining the expression level in the individual of one or more biomarker genes selected from those disclosed herein (e.g., CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15,
R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418,
LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B); and (b) continue to administer ibrutinib to the individual if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN,
LOC644248, C90RF169, SLC45A2, and LOC100128675, or discontinue administering ibrutinib to the individual if there is an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOCI 00134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B. In some embodiments, ibrutinib treatment is continued if there is an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1. In some embodiments, ibrutinib treatment is continued if there is an overexpression of one or more genes selected from VCAM1, RPA1, and STS-1 (UBASH3B).In some embodiments, ibrutinib treatment is continued if there is an overexpression of one or more genes selected from RPA1 or STS-1 (UBASH3B). In some embodiments, ibrutinib treatment is discontinued if there is an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7. In some
embodiments, ibrutinib treatment is discontinued if there is an overexpression of DHRS7.
[0082] Further disclosed herein, in some embodiments, is a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL, comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1,
LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPA1, LOC100132299, and STS-1; and (b) modifying,
discontinuing, or continuing the treatment based on the presence or absence of modifications in the one or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7,
LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, and STS-1. In some embodiments, the method further comprises determining the presence or absence of a modification in two or more biomarker genes selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPA1, LOC100132299, and STS-1.
[0083] Further disclosed herein, in some embodiments, is a method of optimizing the therapy of an individual receiving ibrutinib for treatment of FL, comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from those disclosed herein (e.g., BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, ZNF514, AFF2,
HS.493947, CST1, CNR1, FAM167A, HSD17B 14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERNl, C90RF164, PLEKHBl, S100A8, SEPT 5, PDK4, DDX60, INDO, and/or INPP4B); and (b) modifying, discontinuing, or continuing the treatment based on the presence or absence of modifications in the one or more biomarker genes selected from those disclosed herein (e.g., BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, ZNF514, AFF2, HS.493947, CST1, CNR1, FAM167A, HSD17B 14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERNl, C90RF164, PLEKHBl, S100A8, SEPT 5, PDK4, DDX60, INDO, and/or INPP4B).
[0084] In some embodiments, the one or more biomarker genes are selected from one or more of those disclosed herein. In some embodiments, the one or more biomarker genes are selected from BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, ZNF514, AFF2, HS.493947, CST1, CNR1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERNl, C90RF164, PLEKHBl, S100A8, SEPT5, PDK4, DDX60, INDO, and INPP4B and combinations thereof.
[0085] In some embodiments, the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof. In some embodiments, the genes disclosed herein comprise one or more modifications in each gene. In some embodiments, the modification associated with one or more of the genes disclosed herein results in
modifications in the corresponding proteins. In some embodiments, the modification associated with the BCL-2 gene results in modifications in the BCL-2 protein.
Methods for Monitoring Disease Progression or Resistance
[0086] Disclosed herein, in certain embodiments, is a method of monitoring the development of insensitivity to ibrutinib treatment in an individual having a non-Hodgkin's lymphoma, comprising: (a) determining the expression level of one or more biomarkers disclosed herein; and (b) characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an overexpression of CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUSl, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B. In some embodiments, the individual is characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7. In some
embodiments, the individual is characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an
overexpression of CERCAM or DHRS7. In some embodiments, the individual is characterizing the individual as developed an insensitivity to ibrutinib or likely to develop an insensitivity to ibrutinib if the individual shows an overexpression of DHRS7.
[0087] Disclosed herein, in another aspect, is a method of monitoring disease progression in an individual having a non-Hodgkin's lymphoma being treated with ibrutinib, comprising:
(a) determining the expression level of one or more biomarkers disclosed herein; and
(b) characterizing the individual as having disease progression or likely to develop disease progression if the individual shows an overexpression of CERCAM, POM121C
(LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1,
LOC100129434, GALNT9, BPF7, MTUSl, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, or CDKN2B. In some embodiments, the individual is characterizing the individual as having disease progression or likely to develop disease progression if the individual shows an overexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7. In some embodiments, the individual is characterizing the individual as having disease progression or likely to develop disease progression if the individual shows an overexpression of CERCAM or DHRS7. In some embodiments, the individual is characterizing the individual as having disease progression or likely to develop disease progression if the individual shows an overexpression of DHRS7.
[0088] Also disclosed herein, in certain embodiments, is a method of monitoring the disease progression in an individual having FL, comprising: (a) determining the expression level of at least one biomarker gene selected from those disclosed herein (e.g., but not limited to, BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, Z F514, AFF2, HS.493947, CSTl, CNRl, FAM167A, HSD17B 14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B; and (b) characterizing the individual as having a stable FL if the individual shows an increase in expression level or a decrease in expression level in at least one biomarker gene selected from those disclosed herein (e.g.,, but not limited to, BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, ZNF514, AFF2, HS.493947, CSTl, CNRl, FAM167A, HSD17B 14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B relative to a control.
[0089] Also disclosed herein, in certain embodiments, is a method of monitoring whether an individual receiving ibrutinib for treatment of FL has developed or is likely to develop resistance to the therapy, comprising: (a) determining the presence or absence of a modification in one or more biomarker genes selected from those disclosed herein (e.g., BCL2, STS-1, RPAl,
LOC100132299, DHRS7, THBS4, ZNF514, AFF2, HS.493947, CSTl, CNRl, FAM167A, HSD17B14, FCN3, SNORA57, CTSW, LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB 1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B) and
(b) characterizing the individual as resistant or is likely to become resistant to therapy with ibrutinib if the individual has modifications in the one or more biomarker genes selected from those disclosed herein (e.g., BCL2, STS-1, RPA1, LOC100132299, DHRS7, THBS4, Z F514, AFF2, HS.493947, CST1, C R1, FAM167A, HSD17B14, FCN3, SNORA57, CTSW,
LOC389816, LRRC26, MNDA, CD300A, ERN1, C90RF164, PLEKHB1, S100A8, SEPT5, PDK4, DDX60, INDO, and/or INPP4B).
[0090] Also disclosed herein, in certain embodiments, is a method of monitoring the disease progression in an individual having FL, comprising: (a) determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPA1,
LOCI 00132299, and STS-1; and (b) characterizing the individual as having a stable FL if the individual shows an increase in expression level or a decrease in expression level in at least one biomarker gene selected from PAIP2, LOC730200, KDMIB, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFC1R1, KRTHB6, LOC653234, LOC100127891, CRYGN, RPA1, LOC100132299, and STS-1 relative to a control.
[0091] Also disclosed herein, in certain embodiments, is a method of monitoring the disease progression in an individual having FL, comprising: (a) determining the expression level of at least one biomarker gene selected from ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOCI 00132299, STS-1, and CRYGN); and (b) characterizing the individual as having a stable FL if the individual shows an increase in expression level or a decrease in expression level in at least one biomarker gene selected from at least one of ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPA1, LOC100132299, STS-1, and CRYGN relative to a control.
[0092] In some embodiments, the expression level of the biomarker increases by 0.5-fold, 1- fold, 1.5-fold, 2-fold, 2.5-fold, 3-fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6-fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9-fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50-fold, or more compared to the control.
[0093] In some embodiments, the non-Hodgkin's lymphoma is follicular lymphoma. In some embodiments, the follicular lymphoma is previously treated with another anticancer agent. In some embodiments, the follicular lymphoma is a relapsed or refractory follicular lymphoma. In some embodiments, the follicular lymphoma is treatment naive follicular lymphoma, i.e., previously untreated follicular lymphoma. In some embodiments, the follicular lymphoma is not previously treated with any non-ibrutinib agent.
[0094] In some embodiments, the expression level of the at least one biomarker gene selected from those disclosed herein increase or decrease by 0.5-fold, 1-fold, 1.5-fold, 2-fold, 2.5-fold, 3- fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6-fold, 6.5-fold, 7-fold, 7.5-fold, 8-fold, 8.5-fold, 9-fold, 9.5-fold, 10-fold, 15-fold, 20-fold, 50-fold, or more compared to the control.
Administration of Ibrutinib
[0095] Ibrutinib may be administered as according to a dosing and in a dosage form known in the art.
[0096] In some embodiments, ibrutinib is administered once a day, two times per day, three times per day, four times per day, or five times per day. In some embodiments, ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day. In some embodiments, ibrutinib is administered at a dosage of about 140 mg/day, 280 mg/day, 420 mg/day,
560 mg/day, 840 mg/day or about 1000 mg/day.
[0097] In some embodiments, ibrutinib is administered orally. In some embodiments, ibrutinib is administered in a pharmaceutical formulation comprising ibrutinib or a pharmaceutically acceptable salt or solvate thereof and a pharmaceutically acceptable excipient, such as a formulation described in e.g., WO2013184572, WO2016022942, and WO2016141068, which are incorporated by reference in their entirety.
[0098] In certain embodiments, the invention relates to any of the methods described herein, wherein the method comprises ibrutinib or its use; and the unit dosage of ibrutinib is a capsule comprising 140 mg of ibrutinib. In certain embodiments, the unit dosage of ibrutinib is a capsule comprising 140 mg of ibrutinib, croscarmellose sodium, magnesium stearate, microcrystalline cellulose, and sodium lauryl sulfate. In certain embodiments, the invention relates to any of the methods described herein, wherein the method comprises ibrutinib or its use; and the unit dosage of ibrutinib is a tablet comprising 140 mg, 280 mg, 420 mg or 560 mg of ibrutinib.
[0099] In some embodiments, the ibrutinib is administered with an additional therapeutic agent. In some embodiments, ibrutinib is administered simultaneously, sequentially or intermittently with the additional therapeutic agent. In some embodiments, ibrutinib and the additional therapeutic agent are administered in one dosage form. In some embodiments, ibrutinib and the additional therapeutic agent are administered in separate dosage forms. In some embodiments, ibrutinib and the additional therapeutic agent are administered in one dosage form. In some embodiments, ibrutinib and the additional therapeutic agent are administered in separate dosage forms.
[00100] In some embodiments, the additional therapeutic agent is selected from a
chemotherapeutic agent and radiation therapeutic agent. In some embodiments, the
chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, ofatumumab, rituximab, dexamethasone, prednisone, CAL-101, ibritumomab, tositumomab, bortezomib, pentostatin, and endostatin, or a combination thereof.
[00101] In some embodiments, the additional therapeutic agent is a CD79A inhibitor, a CD79B inhibitor, a CD 19 inhibitor, a Lyn inhibitor, a Syk inhibitor, a PI3K inhibitor, a Blnk inhibitor, a PLCy inhibitor, a PKCP inhibitor, or a combination thereof. In some embodiments, the additional therapeutic agent is an antibody, B cell receptor signaling inhibitor, a PI3K inhibitor, an IAP inhibitor, an mTOR inhibitor, a radioimmunotherapeutic, a DNA damaging agent, a proteosome inhibitor, a histone deacetylase inhibitor, a protein kinase inhibitor, a hedgehog inhibitor, an Hsp90 inhibitor, a telomerase inhibitor, a Bcl-2 inhibitor, a Jakl/2 inhibitor, a protease inhibitor, a PKC inhibitor, a PARP inhibitor, or a combination thereof. In some embodiments, the additional therapeutic agent is an inhibitor of LYN, SYK, JAK, PI3K, PLCy, MAPK, HDAC, NFKB, or MEK. In some embodiments, the additional therapeutic agent is selected from a chemotherapeutic agent, a biologic agent, radiation therapy, bone marrow transplant and surgery.
[00102] In some embodiments, the additional therapeutic agent is selected from a
chemotherapeutic agent, a biologic agent, radiation therapy, bone marrow transplant and surgery. In some embodiments, the chemotherapeutic agent is selected from chlorambucil, ifosfamide, doxorubicin, mesalazine, thalidomide, lenalidomide, temsirolimus, everolimus, fludarabine, fostamatinib, paclitaxel, docetaxel, ofatumumab, rituximab, cari lzomib, dexamethasone, prednisone, idelalisib, ibritumomab, tositumomab, bortezomib, venetoclax, pentostatin, and endostatin, or a combination thereof.
[00103] In some embodiments, the additional therapeutic agent comprises an agent selected from: bendamustine, bortezomib, lenalidomide, idelalisib, vorinostat, everolimus, panobinostat, temsirolimus, romidepsin, vorinostat, fludarabine, cyclophosphamide, mitoxantrone,
pentostatine, prednisone, etopside, procarbazine, and thalidomide. [00104] In some embodiments, the additional therapeutic agent is rituximab. In some embodiments, rituximab is further administered as a maintenance therapy.
[00105] In some embodiments the additional therapeutic agent is bendamustine. In some embodiments, bortezomib is administered in combination with rituximab.
[00106] In some embodiments, the additional therapeutic agent is bortezomib. In some embodiments, bendamustine is administered in combination with rituximab.
[00107] In some embodiments, the additional therapeutic agent is lenalidomide. In some embodiments, lenalidomide is administered in combination with rituximab.
[00108] In some embodiments, the additional therapeutic agent is a multi-agent therapeutic regimen. In some embodiments the additional therapeutic agent comprises the HyperCVAD regimen (cyclophosphamide, vincristine, doxorubicin, dexamethasone alternating with methotrexate and cytarabine). In some embodiments, the HyperCVAD regimen is administered in combination with rituximab.
[00109] In some embodiments the additional therapeutic agent comprises the R-CHOP regiment
(rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone).
[00110] In some embodiments the additional therapeutic agent comprises bortezomib and rituximab.
[00111] In some embodiments the additional therapeutic agent comprises cladribine and rituximab.
[00112] In some embodiments the additional therapeutic agent comprises the FCR regimen (fludarabine, cyclophosphamide, rituximab).
[00113] In some embodiments the additional therapeutic agent comprises the FCMR regimen (fludarabine, cyclophosphamide, mitoxantrone, rituximab).
[00114] In some embodiments the additional therapeutic agent comprises the FMR regimen (fludarabine, mitoxantrone, rituximab).
[00115] In some embodiments the additional therapeutic agent comprises the PCR regimen (pentostatin, cyclophosphamide, rituximab).
[00116] In some embodiments the additional therapeutic agent comprises the PEPC regimen (prednisone, etoposide, procarbazine, cyclophosphamide).
[00117] In some embodiments the additional therapeutic agent comprises radioimmunotherapy with 90Y-ibritumomab tiuxetan or 131I-tositumomab. [00118] In some embodiments, the additional therapeutic agent is an autologous stem cell transplant.
[00119] In some embodiments, the additional therapeutic agent is selected from: Nitrogen Mustards such as for example, bendamustine, chlorambucil, chlormethine, cyclophosphamide, ifosfamide, melphalan, prednimustine, trofosfamide; Alkyl Sulfonates like busulfan,
mannosulfan, treosulfan; Ethylene Imines like carboquone, thiotepa, triaziquone; Nitrosoureas like carmustine, fotemustine, lomustine, nimustine, ranimustine, semustine, streptozocin;
Epoxides such as for example, etoglucid; Other Alkylating Agents such as for example dacarbazine, mitobronitol, pipobroman, temozolomide; Folic Acid Analogues such as for example methotrexate, permetrexed, pralatrexate, raltitrexed; Purine Analogs such as for example cladribine, clofarabine, fludarabine, mercaptopurine, nelarabine, tioguanine; Pyrimidine Analogs such as for example azacitidine, capecitabine, carmofur, cytarabine, decitabine, fluorouracil, gemcitabine, tegafur; Vinca Alkaloids such as for example vinblastine, vincristine, vindesine, vinflunine, vinorelbine; Podophyllotoxin Derivatives such as for example etoposide, teniposide; Colchicine derivatives such as for example demecolcine; Taxanes such as for example docetaxel, paclitaxel, paclitaxel poliglumex; Other Plant Alkaloids and Natural Products such as for example trabectedin; Actinomycines such as for example dactinomycin;
Antracyclines such as for example aclarubicin, daunorubicin, doxorubicin, epirubicin, idarubicin, mitoxantrone, pirarubicin, valrubicin, zorubincin; Other Cytotoxic Antibiotics such as for example bleomycin, ixabepilone, mitomycin, plicamycin; Platinum Compounds such as for example carboplatin, cisplatin, oxaliplatin, satraplatin; Methylhydrazines such as for example procarbazine; Sensitizers such as for example aminolevulinic acid, efaproxiral, methyl aminolevulinate, porfimer sodium, temoporfin; Protein Kinase Inhibitors such as for example dasatinib, erlotinib, everolimus, gefitinib, imatinib, lapatinib, nilotinib, pazonanib, sorafenib, sunitinib, temsirolimus; Other Antineoplastic Agents such as for example alitretinoin, altretamine, amzacrine, anagrelide, arsenic trioxide, asparaginase, bexarotene, bortezomib, celecoxib, denileukin diftitox, estramustine, hydroxycarbamide, irinotecan, lonidamine, masoprocol, miltefosein, mitoguazone, mitotane, oblimersen, pegaspargase, pentostatin, romidepsin, sitimagene ceradenovec, tiazofurine, topotecan, tretinoin, vorinostat; Estrogens such as for example diethylstilbenol, ethinylestradiol, fosfestrol, polyestradiol phosphate;
Progestogens such as for example gestonorone, medroxyprogesterone, megestrol; Gonadotropin Releasing Hormone Analogs such as for example buserelin, goserelin, leuprorelin, triptorelin; Anti-Estrogens such as for example fulvestrant, tamoxifen, toremifene; Anti-Androgens such as for example bicalutamide, flutamide, nilutamide, , Enzyme Inhibitors, aminoglutethimide, anastrozole, exemestane, formestane, letrozole, vorozole; Other Hormone Antagonists such as for example abarelix, degarelix; Immunostimulants such as for example histamine
dihydrochloride, mifamurtide, pidotimod, plerixafor, roquinimex, thymopentin;
Immunosuppressants such as for example everolimus, gusperimus, leflunomide, mycophenolic acid, sirolimus; Calcineurin Inhibitors such as for example ciclosporin, tacrolimus; Other Immunosuppressants such as for example azathioprine, lenalidomide, methotrexate, thalidomide; and Radiopharmaceuticals such as for example, iobenguane.
[00120] In some embodiments, the additional therapeutic agent is selected from: interferons, interleukins, Tumor Necrosis Factors, Growth Factors, and the like.
[00121] In some embodiments, the additional therapeutic agent is selected from: ancestim, filgrastim, lenograstim, molgramostim, pegfilgrastim, sargramostim; Interferons such as for example interferon alfa natural, interferon alfa-2a, interferon alfa-2b, interferon alfacon-1, interferon alfa-nl, interferon beta natural, interferon beta-la, interferon beta-lb, interferon gamma, peginterferon alfa-2a, peginterferon alfa-2b; Interleukins such as for example aldesleukin, oprelvekin; Other Immunostimulants such as for example BCG vaccine, glatiramer acetate, histamine dihydrochloride, immunocyanin, lentinan, melanoma vaccine, mifamurtide, pegademase, pidotimod, plerixafor, poly I:C, poly ICLC, roquinimex, tasonermin, thymopentin; Immunosuppressants such as for example abatacept, abetimus, alefacept, antilymphocyte immunoglobulin (horse), antithymocyte immunoglobulin (rabbit), eculizumab, efalizumab, everolimus, gusperimus, leflunomide, muromab-CD3, mycophenolic acid, natalizumab, sirolimus; TNF alpha Inhibitors such as for example adalimumab, afelimomab, certolizumab pegol, etanercept, golimumab, infliximab; Interleukin Inhibitors such as for example anakinra, basiliximab, canakinumab, daclizumab, mepolizumab, rilonacept, tocilizumab, ustekinumab; Calcineurin Inhibitors such as for example ciclosporin, tacrolimus; and Other
Immunosuppressants such as for example azathioprine, lenalidomide, methotrexate, thalidomide.
[00122] In some embodiments, the additional therapeutic agent is selected from: Adalimumab, Alemtuzumab, Basiliximab, Bevacizumab, Cetuximab, Certolizumab pegol, Daclizumab, Eculizumab, Efalizumab, Gemtuzumab, Ibritumomab tiuxetan, Infliximab, Muromonab-CD3, Natalizumab, Panitumumab, Ranibizumab, Rituximab, Tositumomab, Trastuzumab, and the like, or a combination thereof.
[00123] In some embodiments, the additional therapeutic agent is selected from: Monoclonal Antibodies such as for example alemtuzumab, bevacizumab, catumaxomab, cetuximab, edrecolomab, gemtuzumab, panitumumab, rituximab, trastuzumab; Immunosuppressants, eculizumab, efalizumab, muromab-CD3, natalizumab; TNF alpha Inhibitors such as for example adalimumab, afelimomab, certolizumab pegol, golimumab, infliximab; Interleukin Inhibitors, basiliximab, canakinumab, daclizumab, mepolizumab, tocilizumab, ustekinumab;
Radiopharmaceuticals, ibritumomab tiuxetan, tositumomab; Others Monoclonal Antibodies such as for example abagovomab, adecatumumab, alemtuzumab, anti-CD30 monoclonal antibody Xmab2513, anti-MET monoclonal antibody MetMab, apolizumab, apomab, arcitumomab, basiliximab, bispecific antibody 2B1, blinatumomab, brentuximab vedotin, capromab pendetide, cixutumumab, claudiximab, conatumumab, dacetuzumab, denosumab, eculizumab, epratuzumab, epratuzumab, ertumaxomab, etaracizumab, figitumumab, fresolimumab, galiximab, ganitumab, gemtuzumab ozogamicin, glembatumumab, ibritumomab, inotuzumab ozogamicin, ipilimumab, lexatumumab, lintuzumab, lintuzumab, lucatumumab, mapatumumab, matuzumab, milatuzumab, monoclonal antibody CC49, necitumumab, nimotuzumab, oregovomab, pertuzumab,
ramacurimab, ranibizumab, siplizumab, sonepcizumab, tanezumab, tositumomab, trastuzumab, tremelimumab, tucotuzumab celmoleukin, veltuzumab, visilizumab, volociximab, and zalutumumab.
[00124] In some embodiments, the additional therapeutic agent is selected from: agents that affect the tumor micro-environment such as cellular signaling network (e.g. phosphatidylinositol 3-kinase (PI3K) signaling pathway, signaling from the B-cell receptor and the IgE receptor). In some embodiments, the additional therapeutic agent is a PI3K signaling inhibitor or a syc kinase inhibitor. In one embodiment, the syk inhibitor is R788. In another embodiment is a PKOy inhibitor such as by way of example only, enzastaurin.
[00125] Examples of agents that affect the tumor micro-environment include PI3K signaling inhibitor, syc kinase inhibitor, Protein Kinase Inhibitors such as for example dasatinib, erlotinib, everolimus, gefitinib, imatinib, lapatinib, nilotinib, pazonanib, sorafenib, sunitinib, temsirolimus; Other Angiogenesis Inhibitors such as for example GT-111, JI- 101, R1530; Other Kinase Inhibitors such as for example AC220, AC480, ACE-041, AMG 900, AP24534, Any-614, AT7519, AT9283, AV-951, axitinib, AZD1152, AZD7762, AZD8055, AZD8931, bafetinib, BAY 73-4506, BGJ398, BGT226, BI 811283, BI6727, BIBF 1120, BIBW 2992, BMS-690154, BMS-777607, BMS-863233, BSK-461364, CAL-101, CEP-11981, CYC116, DCC-2036, dinaciclib, dovitinib lactate, E7050, EMD 1214063, ENMD-2076, fostamatinib disodium, GSK2256098, GSK690693, INCB 18424, INNO-406, JNJ-26483327, JX-594, KX2-391, linifanib, LY2603618, MGCD265, MK-0457, MK1496, MLN8054, MLN8237, MP470, NMS- 1116354, MS-1286937, ON 01919.Na, OSI-027, OSI-930, Btk inhibitor, PF-00562271, PF- 02341066, PF-03814735, PF-04217903, PF-04554878, PF-04691502, PF-3758309, PHA- 739358, PLC3397, progenipoietin, R547, R763, ramucirumab, regorafenib, R05185426, SAR103168, SCH 727965, SGI-1176, SGX523, SNS-314, TAK-593, TAK-901, TKI258, TLN- 232, TTP607, XL147, XL228, XL281R05126766, XL418, XL765.
[00126] In some embodiments, the additional therapeutic agent is selected from: inhibitors of mitogen-activated protein kinase signaling, e.g., U0126, PD98059, PD184352, PD0325901, ARRY-142886, SB239063, SP600125, BAY 43-9006, wortmannin, or LY294002; Syk inhibitors; mTOR inhibitors; and antibodies (e.g., rituxan).
[00127] In some embodiments, the additional therapeutic agent is selected from: Adriamycin, Dactinomycin, Bleomycin, Vinblastine, Cisplatin, acivicin; aclarubicin; acodazole
hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan;
cactinomycin; calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; daunorubicin hydrochloride; decitabine;
dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin;
edatrexate; eflornithine hydrochloride; elsamitrucin; enloplatin; enpromate; epipropidine;
epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole
hydrochloride; fazarabine; fenretinide; floxuridine; fludarabine phosphate; fluorouracil;
flurocitabine; fosquidone; fostriecin sodium; gemcitabine; gemcitabine hydrochloride; hydroxyurea; idarubicin hydrochloride; ifosfamide; iimofosine; interleukin II (including recombinant interleukin II, or rlL2), interferon alfa-2a; interferon alfa-2b; interferon alfa-nl; interferon alfa-n3; interferon beta-1 a; interferon gamma-1 b; iproplatin; irinotecan hydrochloride; lanreotide acetate; letrozole; leuprolide acetate; liarozole hydrochloride; lometrexol sodium; lomustine; losoxantrone hydrochloride; masoprocol; maytansine; mechlorethamine
hydrochloride; megestrol acetate; melengestrol acetate; melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin;
mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone
hydrochloride; mycophenolic acid; nocodazoie; nogalamycin; ormaplatin; oxisuran;
pegaspargase; peliomycin; pentamustine; peplomycin sulfate; perfosfamide; pipobroman;
piposulfan; piroxantrone hydrochloride; plicamycin; plomestane; porfimer sodium;
porfiromycin; prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; simtrazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; sulofenur; talisomycin; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine;
thiotepa; tiazofurin; tirapazamine; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine sulfate; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate;
vinrosidine sulfate; vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride.
[00128] In some embodiments, the additional therapeutic agent is selected from: 20-epi-l, 25 dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; aclarubicin; acylfulvene; adecypenol;
adozelesin; aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox; amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole; andrographolide;
angiogenesis inhibitors; antagonist D; antagonist G; antarelix; anti-dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen; antineoplaston; antisense
oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators;
apurinic acid; ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin; azatyrosine; baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists; benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate;
bropirimine; budotitane; buthionine sulfoximine; calcipotriol; calphostin C; camptothecin derivatives; canarypox IL-2; capecitabine; carboxamide-amino-triazole; carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropin B; cetrorelix; chlorlns; chloroquinoxaline sulfonamide; cicaprost; cis- porphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B;
combretastatin A4; combretastatin analogue; conagenin; crambescidin 816; crisnatol;
cryptophycin 8; cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine;
dehydrodidemnin B; deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone; didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; 9- dioxamycin; diphenyl spiromustine; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol;
duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur; epirubicin; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists;
etanidazole; etoposide phosphate; exemestane; fadrozole; fazarabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fiuorodaunorunicin hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin; gallium nitrate;
galocitabine; ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; hepsulfam; heregulin; hexamethylene bisacetamide; hypericin; ibandronic acid; idarubicin; idoxifene;
idramantone; ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-such as for example growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol, 4-; iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor;
leukocyte alpha interferon; leuprolide+estrogen+progesterone; leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin;
loxoribine; lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maitansine; mannostatin A; marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; MIF inhibitor; mifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol;
mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin;
monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1 -based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N-substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; neridronic acid; neutral endopeptidase; nilutamide; nisamycin; nitric oxide modulators; nitroxide antioxidant; nitrullyn; 06-benzylguanine; octreotide; okicenone;
oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer;
ormaplatin; osaterone; oxaliplatin; oxaunomycin; palauamine; palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine; pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol;
phenazinomycin; phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B; plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor; protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins;
pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylerie conjugate; raf antagonists;
raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B l; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A; sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen-binding protein; sizofiran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid;
spicamycin D; spiromustine; splenopentin; spongistatin 1; squalamine; stem cell inhibitor; stem- cell division inhibitors; stipiamide; stromelysin inhibitors; sulfinosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans; tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide;
tetrachlorodecaoxide; tetrazomine; thaliblastine; thiocoraline; thrombopoietin; thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpunn; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine; triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors; tyrphostins; UBC inhibitors; ubenimex;
urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; and zinostatin stimalamer.
[00129] In some embodiments, the additional therapeutic agent is selected from: alkylating agents, antimetabolites, natural products, and hormones, e.g., nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, etc.), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, ete.), or triazenes (decarbazine, etc.). Examples of antimetabolites include but are not limited to folic acid analogs (e.g., methotrexate), or pyrimidine analogs (e.g., Cytarabine), or purine analogs (e.g., mercaptopurine, thioguanine, pentostatin).
[00130] In some embodiments, the additional therapeutic agent is selected from: nitrogen mustards (e.g., mechloroethamine, cyclophosphamide, chlorambucil, meiphalan, etc.), ethylenimine and methylmelamines (e.g., hexamethlymelamine, thiotepa), alkyl sulfonates (e.g., busulfan), nitrosoureas (e.g., carmustine, lomusitne, semustine, streptozocin, etc.), and triazenes (decarbazine, ete.). Examples of antimetabolites include, but are not limited to folic acid analogs (e.g., methotrexate), or pyrimidine analogs (e.g., fluorouracil, floxouridine, Cytarabine), or purine analogs (e.g., mercaptopurine, thioguanine, pentostatin.
[00131] In some embodiments, the additional therapeutic agent is selected from: agents which act by arresting cells in the G2-M phases due to stabilized microtubules, e.g., Erbulozole (also known as R-55104), Dolastatin 10 (also known as DLS-10 and NSC-376128), Mivobulin isethionate (also known as CI-980), Vincristine, NSC-639829, Discodermolide (also known as NVP-XX-A-296), ABT-751 (Abbott, also known as E-7010), Altorhyrtins (such as Altorhyrtin A and Altorhyrtin C), Spongistatins (such as Spongistatin 1, Spongistatin 2, Spongistatin 3, Spongistatin 4, Spongistatin 5, Spongistatin 6, Spongistatin 7, Spongistatin 8, and Spongistatin 9), Cemadotin hydrochloride (also known as LU-103793 and NSC-D-669356), Epothilones (such as Epothilone A, Epothilone B, Epothilone C (also known as desoxyepothilone A or dEpoA), Epothilone D (also referred to as KOS-862, dEpoB, and desoxyepothilone B ),
Epothilone E, Epothilone F, Epothilone B N-oxide, Epothilone A N-oxide, 16-aza-epothilone B, 21-aminoepothilone B (also known as BMS-310705), 21 -hydroxy epothilone D (also known as Desoxyepothilone F and dEpoF), 26-fluoroepothilone), Auristatin PE (also known as NSC- 654663), Soblidotin (also known as TZT-1027), LS-4559-P (Pharmacia, also known as LS- 4577), LS-4578 (Pharmacia, also known as LS-477-P), LS-4477 (Pharmacia), LS-4559
(Pharmacia), RPR-112378 (Aventis), Vincristine sulfate, DZ-3358 (Daiichi), FR-182877 (Fujisawa, also known as WS-9885B), GS-164 (Takeda), GS-198 (Takeda), KAR-2 (Hungarian Academy of Sciences), BSF-223651 (BASF, also known as ILX-651 and LU-223651 ), SAH- 49960 (Lilly/Novartis), SDZ-268970 (Lilly/Novartis), AM-97 (Armad/Kyowa Hakko), AM-132 (Armad), AM-138 (Armad/Kyowa Hakko), IDN-5005 (Indena), Cryptophycin 52 (also known as LY-355703), AC-7739 (Ajinomoto, also known as AVE-8063A and CS-39.HCI), AC-7700 (Ajinomoto, also known as AVE-8062, AVE-8062A, CS-39-L-Ser.HCI, and RPR-258062A), Vitilevuamide, Tubulysin A, Canadensol, Centaureidin (also known as NSC-106969), T-138067 (Tularik, also known as T-67, TL-138067 and TI-138067), COBRA-1 (Parker Hughes Institute, also known as DDE-261 and WHI-261), H10 (Kansas State University), HI 6 (Kansas State University), Oncocidin Al (also known as BTO-956 and DIME), DDE-313 (Parker Hughes Institute), Fijianolide B, Laulimalide, SPA-2 (Parker Hughes Institute), SPA-1 (Parker Hughes Institute, also known as SPIKET-P), 3-IAABU (Cytoskeleton/Mt. Sinai School of Medicine, also known as MF-569), Narcosine (also known as NSC-5366), Nascapine, D-24851 (Asta Medica), A-105972 (Abbott), Hemiasterlin, 3-BAABU (Cytoskeleton/Mt. Sinai School of Medicine, also known as MF-191), TMPN (Arizona State University), Vanadocene acetylacetonate, T- 138026 (Tularik), Monsatrol, Inanocine (also known as NSC-698666), 3-lAABE (Cytoskeleton/Mt. Sinai School of Medicine), A-204197 (Abbott), T-607 (Tuiarik, also known as T-900607), RPR- 115781 (Aventis), Eleutherobins (such as Desmethyleleutherobin, Desaetyleleutherobin, lsoeleutherobin A, and Z-Eleutherobin), Caribaeoside, Caribaeolin, Halichondrin B, D-64131 (Asta Medica), D-68144 (Asta Medica), Diazonamide A, A-293620 (Abbott), NPI-2350
(Nereus), Taccalonolide A, TUB-245 (Aventis), A-259754 (Abbott), Diozostatin, (-)- Phenylahistin (also known as NSCL-96F037), D-68838 (Asta Medica), D-68836 (Asta Medica), Myoseverin B, D-43411 (Zentaris, also known as D-81862), A-289099 (Abbott), A-318315 (Abbott), HTI-286 (also known as SPA- 110, trifluoroacetate salt) (Wyeth), D-82317 (Zentaris), D-82318 (Zentaris), SC-12983 (NCI), Resverastatin phosphate sodium, BPR-OY-007 (National Health Research Institutes), and SSR-250411 (Sanofi).
[00132] In some embodiments, ibrutinib is administered continuously, e.g., when the patient is determined to be suitable for treatment of continued treatment with ibrutinib, or is responsive to ibrutinib according to methods described herein. In some embodiments, ibrutinib is administered in multiple cycles. In some embodiments, a cycle of administration is one month, 2 months, 3 months, 4 months, 6 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months or longer. In some embodiments, a cycle of administration comprises administration of a single therapeutic dosage of ibrutinib over the cycle. In some embodiments, a cycle of administration comprises two or more different dosages of ibrutinib over the cycle. In some embodiments, the dosage of ibrutinib differs over consecutive cycles. In some embodiments, the dosage of ibrutinib increases over consecutive cycles. In some embodiments, the dosage of ibrutinib is the same over consecutive cycles.
Determination of the Expression Levels of Biomarkers
[00133] The expression levels of the biomarkers can be determined by methods known in the art. In some embodiments, the expression levels of the biomarkers are determined by testing a sample containing nucleic acid molecules obtained from the individual. In some embodiments, the sample is a sample obtained prior to the first administration of ibrutinib. In some
embodiments, the sample is a sample obtained periodically during administration of ibrutinib. In some embodiments, the sample is a sample obtained at 1 week, 2 weeks, 3 weeks, 8 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months, 14 months, 16 months, 18 months, 20 months, 22 months, or 24 months following the first administration of ibrutinib. In some embodiments, the sample is obtained 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 times over the course of treatment with ibrutinib.
[00134] In some embodiments, the sample is a tumor biopsy sample, a blood sample, a serum sample, a lymph sample or a bone marrow aspirate. In some embodiments, the sample is a tissue biopsy and is obtained, for example, by needle biopsy, CT-guided needle biopsy, aspiration biopsy, endoscopic biopsy, bronchoscopic biopsy, bronchial lavage, incisional biopsy, excisional biopsy, punch biopsy, shave biopsy, skin biopsy, bone marrow biopsy, and the Loop Electrosurgical Excision Procedure (LEEP). Typically, a non-necrotic, sterile biopsy or specimen is obtained that is greater than 100 mg, but which can be smaller, such as less than 100 mg, 50 mg or less, 10 mg or less or 5 mg or less; or larger, such as more than 100 mg, 200 mg or more, or 500 mg or more, 1 gm or more, 2 gm or more, 3 gm or more, 4 gm or more or 5 gm or more. The sample size to be extracted for the assay depends on a number of factors including, but not limited to, the number of assays to be performed, the health of the tissue sample, the type of cancer, and the condition of the patient. In some embodiments, the tissue is placed in a sterile vessel, such as a sterile tube or culture plate, and is optionally immersed in an appropriate media. Typically, the cells are dissociated into cell suspensions by mechanical means and/or enzymatic treatment as is well known in the art. Typically, the cells are collected and then subjected to standard procedures for the isolation of nucleic acid for the assay.
[00135] In some embodiments, the sample contains one or more tumor cells of the individual. In some embodiments, the sample contains circulating tumor DNA (ctDNA). In some
embodiments, the nucleic acid molecule is RNA. In some embodiments, the nucleic acid molecule is DNA. In some embodiments, the DNA is genomic DNA.
[00136] In some embodiments, the method for determining expression levels comprises detecting the nucleic acid molecules using a microarray. In some embodiments, the method further comprises isolating the nucleic acid molecules. In some embodiments, the method further comprises amplifying the nucleic acid molecules. In some embodiments, amplification is by isothermal amplification or polymerase chain reaction (PCR). In some embodiments,
amplification is by PCR. In some embodiments of the methods, testing comprises using allele specific PCR. In some embodiments, single nucleotide changes are detectable PCR using PCR- based cleaved amplified polymorphic sequences (CAPS) markers which create restriction sites in the mutant sequences (Michaels et al (1998) Plant J. 14(3):381-5) or sequence specific hairpin probes attached to detectable moieties, such as, but not limited to, a fluorophore (Mhlanga and Malmberg (2001) Methods 25:463-471).
[00137] In some embodiments, the method comprises contacting nucleic acids with sequence specific nucleic acid probes, wherein the sequence specific nucleic acid probes bind to the genes selected from those disclosed herein. In some embodiments, testing comprises PCR
amplification using the sequence specific nucleic acid probes. In some embodiments, the sequence specific probe is conjugated to a detectable molecule, such as a fluorescent label, a bioluminescent label, a chemiluminescent label, a radiolabel, an enzyme label, a detectable substrate, or a peptide or molecule that binds to a second detectable molecule.
[00138] In some embodiments, the method for determining expression levels comprises sequencing the nucleic acid molecules. Exemplary sequencing methods are well known in the art and include, but are not limited to, dideoxy or chain termination methods, Maxam-Gilbert sequencing, massively parallel signature sequencing (or MPSS), polony sequencing,
pyrosequencing, Illumina dye sequencing, SOLiD (or sequencing by ligation) sequencing, ion semiconductor sequencing, DNA nanoball sequencing, heliscope sequencing, single molecule real time (SMRT) sequencing, Roche 454 sequencing, and Ion torrent: Proton / PGM
sequencing.
[00139] In some embodiments, the method comprises using a microarray for detecting the genes described herein. In some embodiments, the oligonucleotide array is contained on a microchip.
[00140] In some embodiments, the use of the array comprises: (a) determining the expression level of the biomarker genes in a sample; (b) comparing the expression levels of the biomarker genes to a control; and (c) characterizing the individual as having a stable FL, partial response (PR), or complete response (CR) if the individual shows an increase or decrease in expression level in at least one biomarker genes disclosed herein relative to a control.
Kits and Systems
[00141] Disclosed herein, in certain embodiments, is a kit for carrying out the methods disclosed herein, comprising one or more reagents for determining the expression levels of one or more biomarker genes selected from those disclosed herein in the sample. In some
embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising one or more of the biomarkers disclosed herein.
[00142] Disclosed herein, in certain embodiments, is a kit for carrying out the methods disclosed herein, comprising one or more reagents for determining the expression level of at least one biomarker genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASEILI, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOCI 00134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B in a sample. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, or DHRS7. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising VCAMl, RPAl, STS-1 (UBASH3B), CERCAM or DHRS7. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules comprising RPAl, STS-1 (UBASH3B), or DHRS7.
[00143] In some embodiments, the kit comprises an antibody that binds to a protein encoded by the genes described herein. In some embodiments, the kit comprises an antibody that binds to a protein encoded by a gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GP1BA, RPAl, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASEILI, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, LOC100128675, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1, LOC100129434, GALNT9, NBPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B. In some embodiments, the kit comprises an antibody that binds to a protein encoded by a gene selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFCIRI, and DHRS7. In some embodiments, the kit comprises an antibody that binds to a protein encoded by a gene selected from VCAM1, RPA1, STS-1 (UBASH3B), CERCAM and DHRS7. In some embodiments, the kit comprises an antibody that binds to a protein encoded by RPAl, STS-1 (UBASH3B), or DHRS7.
[00144] Disclosed herein, in certain embodiments, is a kit for carrying out the methods disclosed herein, comprising one or more reagents for determining the expression level of at least one biomarker gene selected from PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFCIRI, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl,
LOC100132299, and STS-1 in the sample. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules encoding PAIP2, LOC730200,
KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1,
LOC652640, DHRS7, LOC100132535, LOC647435, HCFCIRI, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, or STS-1. In some embodiments, the kit comprises an antibody that binds to a protein encoded by PAIP2, LOC730200, KDM1B, ARPC2, BBS5, PTGIS, COL8A1, ODF4, COMP, LOC390834, CYP4Z1, LOC652640, DHRS7, LOC100132535, LOC647435, HCFCIRI, KRTHB6, LOC653234, LOC100127891, CRYGN, RPAl, LOC100132299, or STS-1.
[00145] Disclosed herein, in certain embodiments, the kit comprises one or more reagents for determining the expression level of at least one biomarker gene selected from ODF4,
LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC100132299, STS-1, and CRYGN in the sample. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules encoding ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl, LOC 100132299, STS-1, or CRYGN. In some embodiments, the kit comprises an antibody that binds to a protein encoded by ODF4, LOC652640, DHRS7, CYP4Z1, PAIP2, RPAl,
LOC100132299, STS-1, or CRYGN.
[00146] Disclosed herein, in certain embodiments, is a kit for carrying out the methods disclosed herein, comprising one or more reagents for determining the presence or absence of a modification in one or more biomarker genes selected from those disclosed herein in the sample. In some embodiments, the kit comprises nucleic acid probes or primers that bind to the nucleic acid molecules encoding one or more of the genes disclosed herein.
[00147] Disclosed herein, in certain embodiments, is a nucleic acid hybridization array comprising nucleic acid probes useful in the methods described herein, wherein nucleic acid probes hybridize to biomarker genes selected from those disclosed herein. In some embodiments, at least one of the nucleic acid probes hybridizes to a biomarker gene selected from those disclosed herein.
[00148] In some instances, the kit comprises a hybridization array.
[00149] In some embodiments, the kits include a carrier, package, or container that are compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in a method described herein. Suitable containers include, for example, bottles, vials, syringes, and test tubes. In one embodiment, the containers are formed from a variety of materials such as glass or plastic.
[00150] A kit typically includes labels listing contents and/or instructions for use, and package inserts with instructions for use. A set of instructions will also typically be included.
[00151] In one embodiment, a label is on or associated with the container. In one embodiment, a label is on a container when letters, numbers or other characters forming the label are attached, molded or etched into the container itself; a label is associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert. The label also indicates directions for use of the contents, such as in the methods described herein.
[00152] Disclosed herein, in certain embodiments, is a system useful in the methods described herein, comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes described herein in the sample; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a first software module configured to analyze the dataset to determine the expression level in one or more biomarker genes; and (ii) a second software module to assign the individual as a candidate for treatment with ibrutinib according to the expression level of the one or more biomarker genes according to the methods described herein. In some embodiments, the first software module is configured to also analyze the dataset to determine the presence or absence of a modification in one or more biomarker genes. In some embodiments, the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof. In some embodiments, the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device. In some embodiments, the analytical device performs microarray analysis. In some embodiments, the digital processing device is connected to a computer network. In some embodiments, the second software module further generates a report, wherein the second software module is executed by the digital processing device. In some embodiments, the second software module further transmits the report to an end- user, wherein the second software module is executed by the digital processing device.
[00153] Disclosed herein, in certain embodiments, is a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of those disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a third software module configured to analyze the dataset to determine the expression level of one or more biomarker genes; (ii) a forth software module configured to match the expression level of one or more biomarker genes to a control; and (iii) a fifth software module to assign the individual as a candidate to treatment with ibrutinib if there is an increase in expression level in the one or more biomarker genes relative to the control. In some embodiments, the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device. In some embodiments, the analytical device performs microarray analysis. In some
embodiments, the digital processing device is connected to a computer network. In some embodiments, the fifth software module further generates a report, wherein the fifth software module is executed by the digital processing device. In some embodiments, the fifth software module further transmits the report to an end-user, wherein the fifth software module is executed by the digital processing device.
[00154] Disclosed herein, in certain embodiments, is a nucleic acid hybridization array comprising nucleic acid probes for evaluating whether an individual having FL has a stable FL or has a change in tumor size (i.e., as disclosed in the figures, referred to as "SPD" which refers to "longest overall tumor diameter and longest diameter perpendicular to the longest overall diameter), consisting essentially of nucleic acid probes which hybridize to biomarker genes selected from the group consisting of one or more of the biomarkers disclosed herein. In some embodiments, the use of the array comprises: (a) determining the expression level of the biomarker genes in a sample; (b) comparing the expression levels of the biomarker genes to a control; and (c) characterizing the individual as having a stable FL, partial response (PR), or complete response (CR) if the individual shows an increase or decrease in expression level in at least one biomarker genes disclosed herein relative to a control. In some embodiments, the use of the array comprises of determining the presence or absence of modifications in one or more biomarker genes in a sample obtained from the individual; and characterizing the individual as resistant or is likely to become resistant to therapy with ibrutinib if the individual has
modifications in the one or more biomarker genes.
[00155] In accordance with the description herein, suitable digital processing devices include, by way of non-limiting examples, server computers, desktop computers, laptop computers, notebook computers, sub-notebook computers, netbook computers, netpad computers, set-top computers, media streaming devices, handheld computers, Internet appliances, mobile smartphones, tablet computers, personal digital assistants, video game consoles, and vehicles. Those of skill in the art will recognize that many smartphones are suitable for use in the system described herein. Those of skill in the art will also recognize that select televisions, video players, and digital music players with optional computer network connectivity are suitable for use in the system described herein. Suitable tablet computers include those with booklet, slate, and convertible configurations, known to those of skill in the art.
[00156] In some embodiments, the digital processing device includes an operating system configured to perform executable instructions. The operating system is, for example, software, including programs and data, which manages the device's hardware and provides services for execution of applications. Those of skill in the art will recognize that suitable server operating systems include, by way of non-limiting examples, FreeBSD, OpenBSD, NetBSD®, Linux, Apple® Mac OS X Server®, Oracle® Solaris®, Windows Server®, and Novell® NetWare®. Those of skill in the art will recognize that suitable personal computer operating systems include, by way of non-limiting examples, Microsoft® Windows®, Apple® Mac OS X®, UNIX®, and UNIX- like operating systems such as GNU/Linux®. In some embodiments, the operating system is provided by cloud computing. Those of skill in the art will also recognize that suitable mobile smart phone operating systems include, by way of non-limiting examples, Nokia® Symbian® OS, Apple® iOS®, Research In Motion® BlackBerry OS®, Google® Android®, Microsoft® Windows Phone® OS, Microsoft® Windows Mobile® OS, Linux®, and Palm® WebOS®. Those of skill in the art will also recognize that suitable media streaming device operating systems include, by way of non-limiting examples, Apple TV®, Roku®, Boxee®, Google TV®, Google Chromecast®, Amazon Fire®, and Samsung® HomeSync®. Those of skill in the art will also recognize that suitable video game console operating systems include, by way of non-limiting examples, Sony® PS3®, Sony® PS4®, Microsoft® Xbox 360®, Microsoft Xbox One, Nintendo® Wii®, Nintendo® Wii U®, and Ouya®.
[00157] In some embodiments, the device includes a storage and/or memory device. The storage and/or memory device is one or more physical apparatuses used to store data or programs on a temporary or permanent basis. In some embodiments, the device is volatile memory and requires power to maintain stored information. In some embodiments, the device is non-volatile memory and retains stored information when the digital processing device is not powered. In further embodiments, the non-volatile memory comprises flash memory. In some embodiments, the non-volatile memory comprises dynamic random-access memory (DRAM). In some embodiments, the non-volatile memory comprises ferroelectric random access memory (FRAM). In some embodiments, the non-volatile memory comprises phase-change random access memory (PRAM). In other embodiments, the device is a storage device including, by way of non-limiting examples, CD-ROMs, DVDs, flash memory devices, magnetic disk drives, magnetic tapes drives, optical disk drives, and cloud computing based storage. In further embodiments, the storage and/or memory device is a combination of devices such as those disclosed herein.
[00158] In some embodiments, the digital processing device includes a display to send visual information to a user. In some embodiments, the display is a cathode ray tube (CRT). In some embodiments, the display is a liquid crystal display (LCD). In further embodiments, the display is a thin film transistor liquid crystal display (TFT-LCD). In some embodiments, the display is an organic light emitting diode (OLED) display. In various further embodiments, on OLED display is a passive-matrix OLED (PMOLED) or active-matrix OLED (AMOLED) display. In some embodiments, the display is a plasma display. In other embodiments, the display is a video projector. In still further embodiments, the display is a combination of devices such as those disclosed herein.
[00159] In some embodiments, the digital processing device includes an input device to receive information from a user. In some embodiments, the input device is a keyboard. In some embodiments, the input device is a pointing device including, by way of non-limiting examples, a mouse, trackball, track pad, joystick, game controller, or stylus. In some embodiments, the input device is a touch screen or a multi-touch screen. In other embodiments, the input device is a microphone to capture voice or other sound input. In other embodiments, the input device is a video camera or other sensor to capture motion or visual input. In further embodiments, the input device is a Kinect™, Leap Motion™, or the like. In still further embodiments, the input device is a combination of devices such as those disclosed herein.
Non-transitory computer readable storage medium
[00160] In some embodiments, the systems and methods disclosed herein include one or more non-transitory computer readable storage media encoded with a program including instructions executable by the operating system of an optionally networked digital processing device. In further embodiments, a computer readable storage medium is a tangible component of a digital processing device. In still further embodiments, a computer readable storage medium is optionally removable from a digital processing device. In some embodiments, a computer readable storage medium includes, by way of non-limiting examples, CD-ROMs, DVDs, flash memory devices, solid state memory, magnetic disk drives, magnetic tape drives, optical disk drives, cloud computing systems and services, and the like. In some cases, the program and instructions are permanently, substantially permanently, semi-permanently, or non-transitorily encoded on the media.
Computer program
[00161] In some embodiments, the systems and methods disclosed herein include at least one computer program, or use of the same. A computer program includes a sequence of instructions, executable in the digital processing device's CPU, written to perform a specified task. In some embodiments, computer readable instructions are implemented as program modules, such as functions, objects, Application Programming Interfaces (APIs), data structures, and the like, that perform particular tasks or implement particular abstract data types. In light of the disclosure provided herein, those of skill in the art will recognize that a computer program, in certain embodiments, is written in various versions of various languages.
[00162] In some embodiments, the functionality of the computer readable instructions are combined or distributed as desired in various environments. In some embodiments, a computer program comprises one sequence of instructions. In some embodiments, a computer program comprises a plurality of sequences of instructions. In some embodiments, a computer program is provided from one location. In other embodiments, a computer program is provided from a plurality of locations. In various embodiments, a computer program includes one or more software modules. In various embodiments, a computer program includes, in part or in whole, one or more web applications, one or more mobile applications, one or more standalone applications, one or more web browser plug-ins, extensions, add-ins, or add-ons, or combinations thereof.
Web application
[00163] In some embodiments, a computer program includes a web application. In light of the disclosure provided herein, those of skill in the art will recognize that a web application, in various embodiments, utilizes one or more software frameworks and one or more database systems. In some embodiments, a web application is created upon a software framework such as Microsoft® .NET or Ruby on Rails (RoR). In some embodiments, a web application utilizes one or more database systems including, by way of non-limiting examples, relational, non-relational, object oriented, associative, and XML database systems. In further embodiments, suitable relational database systems include, by way of non-limiting examples, Microsoft® SQL Server, mySQL™, and Oracle®. Those of skill in the art will also recognize that a web application, in various embodiments, is written in one or more versions of one or more languages. In some embodiments, a web application is written in one or more markup languages, presentation definition languages, client-side scripting languages, server-side coding languages, database query languages, or combinations thereof. In some embodiments, a web application is written to some extent in a markup language such as Hypertext Markup Language (HTML), Extensible Hypertext Markup Language (XHTML), or extensible Markup Language (XML). In some embodiments, a web application is written to some extent in a presentation definition language such as Cascading Style Sheets (CSS). In some embodiments, a web application is written to some extent in a client-side scripting language such as Asynchronous Javascript and XML (AJAX), Flash Actionscript, Javascript, or Silverlight . In some embodiments, a web application is written to some extent in a server-side coding language such as Active Server Pages (ASP), ColdFusion®, Perl, Java™, JavaServer Pages (JSP), Hypertext Preprocessor (PHP), Python™, Ruby, Tel, Smalltalk, WebDNA®, or Groovy. In some embodiments, a web application is written to some extent in a database query language such as Structured Query Language (SQL). In some embodiments, a web application integrates enterprise server products such as IBM® Lotus Domino®. In some embodiments, a web application includes a media player element. In various further embodiments, a media player element utilizes one or more of many suitable multimedia technologies including, by way of non-limiting examples, Adobe® Flash®, HTML 5, Apple® QuickTime®, Microsoft® Silverlight®, Java™, and Unity®.
Mobile application
[00164] In some embodiments, a computer program includes a mobile application provided to a mobile digital processing device. In some embodiments, the mobile application is provided to a mobile digital processing device at the time it is manufactured. In other embodiments, the mobile application is provided to a mobile digital processing device via the computer network described herein.
[00165] In view of the disclosure provided herein, a mobile application is created by techniques known to those of skill in the art using hardware, languages, and development environments known to the art. Those of skill in the art will recognize that mobile applications are written in several languages. Suitable programming languages include, by way of non-limiting examples, C, C++, C#, Objective-C, Java™, Javascript, Pascal, Object Pascal, Python™, Ruby, VB.NET, WML, and XHTML/HTML with or without CSS, or combinations thereof.
[00166] Suitable mobile application development environments are available from several sources. Commercially available development environments include, by way of non-limiting examples, AirplaySDK, alcheMo, Appcelerator®, Celsius, Bedrock, Flash Lite, .NET Compact Framework, Rhomobile, and WorkLight Mobile Platform. Other development environments are available without cost including, by way of non-limiting examples, Lazarus, MobiFlex, MoSync, and Phonegap. Also, mobile device manufacturers distribute software developer kits including, by way of non-limiting examples, iPhone and iPad (iOS) SDK, Android™ SDK, BlackBerry® SDK, BREW SDK, Palm® OS SDK, Symbian SDK, webOS SDK, and Windows® Mobile SDK. [00167] Those of skill in the art will recognize that several commercial forums are available for distribution of mobile applications including, by way of non-limiting examples, Apple® App Store, Android™ Market, BlackBerry® App World, App Store for Palm devices, App Catalog for webOS, Windows® Marketplace for Mobile, Ovi Store for Nokia® devices, Samsung® Apps, and Nintendo® DSi Shop.
Standalone application
[00168] In some embodiments, a computer program includes a standalone application, which is a program that is run as an independent computer process, not an add-on to an existing process, e.g., not a plug-in. Those of skill in the art will recognize that standalone applications are often compiled. A compiler is a computer program(s) that transforms source code written in a programming language into binary object code such as assembly language or machine code. Suitable compiled programming languages include, by way of non-limiting examples, C, C++, Objective-C, COBOL, Delphi, Eiffel, Java™, Lisp, Python™, Visual Basic, and VB .NET, or combinations thereof. Compilation is often performed, at least in part, to create an executable program. In some embodiments, a computer program includes one or more executable complied applications.
Web browser plug-in
[00169] In some embodiments, the computer program includes a web browser plug-in. In computing, a plug-in is one or more software components that add specific functionality to a larger software application. Makers of software applications support plug-ins to enable third- party developers to create abilities which extend an application, to support easily adding new features, and to reduce the size of an application. When supported, plug-ins enable customizing the functionality of a software application. For example, plug-ins are commonly used in web browsers to play video, generate interactivity, scan for viruses, and display particular file types. Those of skill in the art will be familiar with several web browser plug-ins including, Adobe® Flash® Player, Microsoft® Silverlight®, and Apple® QuickTime®. In some embodiments, the toolbar comprises one or more web browser extensions, add-ins, or add-ons. In some embodiments, the toolbar comprises one or more explorer bars, tool bands, or desk bands.
[00170] In view of the disclosure provided herein, those of skill in the art will recognize that several plug-in frameworks are available that enable development of plug-ins in various programming languages, including, by way of non-limiting examples, C++, Delphi, Java™, PHP, Python™, and VB .NET, or combinations thereof.
[00171] Web browsers (also called Internet browsers) are software applications, designed for use with network-connected digital processing devices, for retrieving, presenting, and traversing information resources on the World Wide Web. Suitable web browsers include, by way of non- limiting examples, Microsoft® Internet Explorer®, Mozilla® Firefox®, Google® Chrome, Apple® Safari®, Opera Software® Opera®, and KDE Konqueror. In some embodiments, the web browser is a mobile web browser. Mobile web browsers (also called mircrobrowsers, mini-browsers, and wireless browsers) are designed for use on mobile digital processing devices including, by way of non-limiting examples, handheld computers, tablet computers, netbook computers, subnotebook computers, smartphones, music players, personal digital assistants (PDAs), and handheld video game systems. Suitable mobile web browsers include, by way of non-limiting examples, Google® Android® browser, RIM BlackBerry® Browser, Apple® Safari®, Palm® Blazer, Palm® WebOS® Browser, Mozilla® Firefox® for mobile, Microsoft® Internet Explorer® Mobile, Amazon® Kindle® Basic Web, Nokia® Browser, Opera Software® Opera® Mobile, and Sony® PSP™ browser.
Software modules
[00172] In some embodiments, the systems and methods disclosed herein include software, server, and/or database modules, or use of the same. In view of the disclosure provided herein, software modules are created by techniques known to those of skill in the art using machines, software, and languages known to the art. The software modules disclosed herein are
implemented in a multitude of ways. In various embodiments, a software module comprises a file, a section of code, a programming object, a programming structure, or combinations thereof. In further various embodiments, a software module comprises a plurality of files, a plurality of sections of code, a plurality of programming objects, a plurality of programming structures, or combinations thereof. In various embodiments, the one or more software modules comprise, by way of non-limiting examples, a web application, a mobile application, and a standalone application. In some embodiments, software modules are in one computer program or application. In other embodiments, software modules are in more than one computer program or application. In some embodiments, software modules are hosted on one machine. In other embodiments, software modules are hosted on more than one machine. In further embodiments, software modules are hosted on cloud computing platforms. In some embodiments, software modules are hosted on one or more machines in one location. In other embodiments, software modules are hosted on one or more machines in more than one location.
Databases
[00173] In some embodiments, the methods and systems disclosed herein include one or more databases, or use of the same. In view of the disclosure provided herein, those of skill in the art will recognize that many databases are suitable for storage and retrieval of analytical information described elsewhere herein. In various embodiments, suitable databases include, by way of non- limiting examples, relational databases, non-relational databases, object oriented databases, object databases, entity-relationship model databases, associative databases, and XML databases. In some embodiments, a database is internet-based. In further embodiments, a database is web- based. In still further embodiments, a database is cloud computing-based. In other embodiments, a database is based on one or more local computer storage devices.
[00174] Disclosed herein, in certain embodiments, is a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of one or more of the genes disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a first software module configured to analyze the dataset to determine the presence or absence of modifications in one or more biomarker genes; and (ii) a second software module to assign the individual as a candidate for treatment with ibrutinib if there is a presence or absence of modifications in the one or more biomarker genes. In some embodiments, the modification is base substitution, insertion, deletion, DNA rearrangement, copy number alteration, or a combination thereof. In some embodiments, the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device. In some embodiments, the analytical device performs microarray analysis. In some embodiments, the digital processing device is connected to a computer network. In some embodiments, the second software module further generates a report, wherein the second software module is executed by the digital processing device. In some embodiments, the second software module further transmits the report to an end-user, wherein the second software module is executed by the digital processing device.
[00175] Disclosed herein, in certain embodiments, is a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of those disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a third software module configured to analyze the dataset to determine the expression level of one or more biomarker genes; (ii) a forth software module configured to match the expression level of one or more biomarker genes to a control; and (iii) a fifth software module to assign the individual as a candidate to treatment with ibrutinib if there is an increase in expression level in the one or more biomarker genes relative to the control.
[00176] Disclosed herein, in certain embodiments, is a system of assessing an individual having FL for treatment comprising: (a) a digital processing device comprising an operating system configured to perform executable instructions, and an electronic memory; (b) a dataset stored in the electronic memory, wherein the dataset comprises data for one or more biomarker genes in a sample, wherein the biomarker genes are selected from the group consisting of those disclosed herein; and (c) a computer program including instructions executable by the digital processing device to create an application comprising: (i) a third software module configured to analyze the dataset to determine the expression level of one or more biomarker genes; (ii) a forth software module configured to match the expression level of one or more biomarker genes to a control; and (iii) a fifth software module to assign the individual as a candidate to treatment with ibrutinib if there is an increase in expression level in the one or more biomarker genes relative to the control. In some embodiments, the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device. In some embodiments, the analytical device performs microarray analysis. In some
embodiments, the digital processing device is connected to a computer network. In some embodiments, the fifth software module further generates a report, wherein the fifth software module is executed by the digital processing device. In some embodiments, the fifth software module further transmits the report to an end-user, wherein the fifth software module is executed by the digital processing device.
[00177] In some embodiments, the method further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device. In some embodiments, the analytical device performs microarray analysis. In some
embodiments, the digital processing device is connected to a computer network. In some embodiments, the second software module further generates a report, wherein the second software module is executed by the digital processing device. In some embodiments, the second software module further transmits the report to an end-user, wherein the second software module is executed by the digital processing device.
[00178] In some embodiments, the system further comprises an analytical device configured to provide biomarker data; wherein the analytical device is coupled to the digital processing device. In some embodiments, the analytical device performs microarray analysis. In some
embodiments, the digital processing device is connected to a computer network. In some embodiments, the fifth software module further generates a report, wherein the fifth software module is executed by the digital processing device. In some embodiments, the fifth software module further transmits the report to an end-user, wherein the fifth software module is executed by the digital processing device.
Exemplary Embodiments
[00179] Embodiment 1. A method of treating a non-Hodgkin' s lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108,
LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[00180] Embodiment 2. The method of Embodiment 1, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and
LOC100128675.
[00181] Embodiment 3. The method of Embodiment 1 or Embodiment 2, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1,
LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
[00182] Embodiment 4. The method of Embodiment 1 or Embodiment 2, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
[00183] Embodiment 5. The method of any one of Embodiments 1-4, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
[00184] Embodiment 6. The method of any one of Embodiments 1-5, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
[00185] Embodiment 7. The method of any one of Embodiments 1-6, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
[00186] Embodiment 8. The method of any one of Embodiments 1-6, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
[00187] Embodiment 9. The method of any one of Embodiments 1-8, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7.
[00188] Embodiment 10. The method of any one of Embodiments 1-9, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B).
[00189] Embodiment 11. The method of any one of Embodiments 1-10, wherein the individual has a normal expression of CERCAM or DHRS7.
[00190] Embodiment 12. The method of any one of Embodiments 1-10, wherein the individual has an underexpression of CERCAM or DHRS7. [00191] Embodiment 13. The method of any one of Embodiments 1-12, wherein the individual has an overexpression of RPA1 or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
[00192] Embodiment 14. The method of any one of Embodiments 1-13, wherein the individual has an overexpression of RPA1 or STS-1 (UBASH3B).
[00193] Embodiment 15. The method of any one of Embodiments 1-14, wherein the individual has a normal expression of DHRS7.
[00194] Embodiment 16. The method of any one of Embodiments 1-14, wherein the individual has an underexpression of DHRS7.
[00195] Embodiment 17. A method of treating a follicular lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108,
LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[00196] Embodiment 18. The method of Embodiment 17, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675.
[00197] Embodiment 19. The method of Embodiment 17 or Embodiment 18, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1,
LOC100129434, GALNT9, BPF7, MTUSl, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
[00198] Embodiment 20. The method of Embodiment 17 or Embodiment 18, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC 100134540, CYP4Z1,
LOC100129434, GALNT9, BPF7, MTUSl, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
[00199] Embodiment 21. A method of treating a follicular lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIPl, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
[00200] Embodiment 22. The method of Embodiment 21, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
[00201] Embodiment 23. The method of Embodiment 21 or Embodiment 22, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
[00202] Embodiment 24. The method of Embodiment 21 or Embodiment 22, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
[00203] Embodiment 25. The method of any one of Embodiments 21-24, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7.
[00204] Embodiment 26. The method of any one of Embodiments 21-25, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B).
[00205] Embodiment 27. The method of any one of Embodiments 21-26, wherein the individual has a normal expression of CERCAM or DHRS7.
[00206] Embodiment 28. The method of any one of Embodiments 21-26, wherein the individual has an underexpression of CERCAM or DHRS7.
[00207] Embodiment 29. The method of any one of Embodiments 21-28, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
[00208] Embodiment 30. The method of any one of Embodiments 21-29, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B).
[00209] Embodiment 31. The method of any one of Embodiments 21-30, wherein the individual has a normal expression of DHRS7.
[00210] Embodiment 32. The method of any one of Embodiments 21-30, wherein the individual has an underexpression of DHRS7. [00211] Embodiment 33. The method of any one of Embodiments 1-32, wherein the individual has not been previously treated for lymphoma.
[00212] Embodiment 34. The method of any one of Embodiments 1-32, wherein the individual has not been previously treated with ibrutinib for lymphoma.
[00213] Embodiment 35. The method of any one of Embodiments 1-32, wherein the individual has been previously treated for lymphoma with an anticancer therapy other than ibrutinib.
[00214] Embodiment 36. The method of Embodiment 35, wherein the lymphoma is relapsed or refractory.
[00215] Embodiment The method of any one of Embodiments 1-32, wherein the individual has been previously treated for lymphoma with ibrutinib and administration of ibrutinib is continued.
[00216] Embodiment 38. The method of any one of Embodiments 1-37, wherein ibrutinib is administered with another therapeutic agent.
[00217] Embodiment 39. The method of any one of Embodiments 1-38, wherein ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day.
EXAMPLE
[00218] The following specific and non-limiting example is to be construed as merely illustrative, and do not limit the present disclosure in any way whatsoever. Without further elaboration, it is believed that one skilled in the art can, based on the description herein, utilize the present disclosure to its fullest extent. All publications cited herein are hereby incorporated by reference in their entirety. Where reference is made to a URL or other such identifier or address, it is understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.
Example: Effect of ibrutinib treatment on gene expression levels in follicular lymphoma patients
[00219] In a clinical study, eligible patients were treated with 560 mg ibrutinib per day orally as a single agent for eight weeks.
Eligibility
• Ages Eligible for Study: 18 Years and older (Adult, Senior) • Genders Eligible for Study: Both
• Accepts Healthy Volunteers: No
Key Inclusion criteria:
• Histologically documented FL (Grade 1, 2 and 3 A)
• Not previously treated with prior anti-cancer therapy for FL
• Stage II, III or IV disease
• At least one measurable lesion > 2 cm in longest diameter by CT and/or MRI scan
• Men and women > 18 years of age
• Eastern Cooperative Oncology Group (ECOG) performance status of < 2
Key Exclusion criteria:
• Medically apparent central nervous system lymphoma or leptomeningeal disease
• FL with evidence of large cell transformation
• Any prior history of other hematologic malignancy besides FL or myelodysplasia
• History of other malignancies, except
• Malignancy treated with curative intent and with no known active disease present for >5 years before the first dose of study drug and felt to be at low risk for recurrence by treating physician.
• Adequately treated non-melanoma skin cancer or lentigomaligna without evidence of disease.
• Adequately treated carcinoma in situ without evidence of disease.
• Currently active, clinically significant cardiovascular disease or myocardial infarction within 6 months of screening
• Known anaphylaxis or IgE-mediated hypersensitivity to murine proteins or to any
component of rituximab (Rituxan®)
• Requires anti-coagulation with warfarin or a vitamin K antagonist.
• Requires treatment with strong CYP3 A inhibitors.
• Known bleeding diathesis or hemophilia
[00220] The baseline tumor tissue samples of 20 of the patients were collected, processed and analyzed by MD Anderson Cancer Center using Illumina HT12 v4 BeadArray based technology arrays for whole-genome gene expression analysis.
[00221] Illumina HT12 v4 BeadArray Microarray gene expression probe-level data were background corrected and normalized by Pharmacyclics bioinformatics beadarray data processing pipeline as follows: first the "ID AT" files (of probe intensity) of all samples (arrays) were taken as input to a pipeline and the R package "beadarray" was used, and then the "neqc" normalization program was used to generate the final normalized gene expression levels for downstream statistical analyses. The "neqc" normalization is a method combining the normal- exponential background correction procedure with the quantile normalization procedure.
Specifically, it 1) estimates the signal for each probe based on the probe fluorescence intensity by treating the intensities as the mixtures from a normally distributed background noise and an exponentially distributed true signal, and 2) does a quantile normalization based on the estimated (corrected) signals across different arrays. To increase statistical power to detect significant expression patterns, Pearson correlation analyses were performed to test for correlation between the tumor shrinkage measurements and the normalized gene expression levels of 18 of the 20 patients from the study (NOTE: only 18 of the 20 patients have tumor shrinkage
measurements for the 8 weeks of ibrutinib treatment). Tumor shrinkage was used as an efficacy outcome and was calculated as the percent change in the sum of the perpendicular diameters (SPD) of index lesions from baseline to the end of the 8 weeks of ibrutinib treatment. The genes with statistical significant results are summarized in Table 1. In the Table, the Pearson correlation coefficient R is a measure of linear dependence between 2 variables: one variable is the gene expression value at the probe level, and the other variable is the percent change in the sum of the perpendicular diameters (SPD) of index lesions from baseline to the end of the 8 weeks of ibrutinib treatment. The Pearson correlation coefficient R ranges from -1 to 1. A value of 1 implies that a positive linear relationship between gene expression value and percent change in the SPD perfectly, with all data points lying on a line for which one variable increases as the other variable increases. A value of -1 implies that all data points lie on a line for which one variable decreases as the other variable increases. A value of 0 implies that there is no linear correlation between the variables. The False Discovery Rate (FDR) is one way of
conceptualizing the rate of errors in hypothesis testing when conducting multiple comparisons. Typically, scientists define results to be very strongly statistically significant when FDR < 0.10.
[00222] Three genes (2 probes for the gene RPA1, one probe for the gene STS-1/UBASH3B, one probe for the gene DFIRS7) in Table 1 had the strongest statistically significant correlation to the change in tumor measurement (SPD) from baseline to the end of 8 weeks of ibrutinib treatment. In particular, increasing in gene expression of RPA1 and/or STS-1/UBASH3B was strongly correlated to decreasing in tumor measurement, hence more tumor shrinkage; however increasing in gene expression of DHRS7 was strongly correlated to increasing in tumor measurement, hence less tumor shrinkage.
[00223] Seventeen genes in Table 1 had strong statistically significant correlation to the change in tumor measurement from baseline to the end of the 8 weeks of ibrutinib treatment. In particular, increasing in gene expression of any of the 10 genes: VCAM1, CSAG3, GP1BA, RSClAl, P2RY1 1/PPAN-P2RY1 1, FILIPl, TTC19, CALB2, ADPRM/C170RF48, and DNAJC8 was strongly correlated to decreasing in tumor measurement, hence more tumor shrinkage; however increasing in gene expression of any of the 7 genes: CERCAM, PPP1R3D, POM121C/LOC100131972, HCFC IRI, SDHA/SDHAP3, OSBPL2, and PLOD2 was strongly correlated to increasing in tumor measurement, hence less tumor shrinkage.
Table 1
Figure imgf000081_0001
Pearson Correlation False Discovery
Probe_Set_ID Gene Symbol P-Value Coefficient R Rate (FDR)
P2RY1 1/PPAN-
ILMN_1752226 P2RY1 1 0.000663296 -0.725024793 0.818
ILMN_1726704 RSC 1A1 0.000660388 -0.72519641 1 0.818
ILMN_1753575 GP1BA 0.000639761 -0.726432166 0.818
ILMN_1803852 CSAG3 0.000345564 -0.74919997 0.818
ILMN_2325763 VCAM1 0.000324411 -0.751410296 0.818
ILMN_3249261 RPA1 0.0000174 -0.833417362 0.079
ILMN_1653856 STS- 1 UBASH3B 0.000013 -0.839817688 0.079
ILMN_1795719 RPA1 0.00001 1 -0.843424618 0.079

Claims

WHAT IS CLAIMED IS:
1. A method of treating a non-Hodgkin' s lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN- P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5,
LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39,
TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP,
LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
2. The method of claim 1, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1,
LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675.
3. The method of claim 1 or claim 2, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345,
LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
4. The method of claim 1 or claim 2, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345,
LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
5. The method of claim 1, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
6. The method of claim 5, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
7. The method of claim 5 or claim 6, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
8. The method of claim 5 or claim 6, wherein the individual has an underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
9. The method of claim 1, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7.
10. The method of claim 9, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B).
11. The method of claim 9 or claim 10, wherein the individual has a normal expression of CERCAM or DHRS7.
12. The method of claim 9 or claim 10, wherein the individual has an underexpression of CERCAM or DHRS7.
13. The method of claim 1, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
14. The method of claim 13, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B).
15. The method of claim 13 or claim 14, wherein the individual has a normal expression of DHRS7.
16. The method of claim 13 or claim 14, wherein the individual has an
underexpression of DHRS7.
17. A method of treating a follicular lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48), FILIPl, LOC653297, IL15, R2E3, LOC100132299, TTTYl l, GCET2, OR1C1, DNASE1L1, LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and
LOC100128675, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418, LOC440345, LOC647435, KRTHB6, TH1L, BBS5,
LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDMIB, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39,
TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP,
LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUSl, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
18. The method of claim 17, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAM1, CSAG3, GP1BA, RPA1, RSC1A1, STS-1 (UBASH3B), ADPRM (C170RF48), FILIP1, LOC653297, IL15, R2E3, LOC100132299, TTTY11, GCET2, OR1C1, DNASE1L1,
LOC100127891, CRYGN, LOC644248, C90RF169, SLC45A2, and LOC100128675.
19. The method of claim 17 or claim 18, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418,
LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
20. The method of claim 17 or claim 18, wherein the individual has an
underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, DHRS7, LOC652418,
LOC440345, LOC647435, KRTHB6, TH1L, BBS5, LOC100128935, NT5C1B, LOC653234, LOC392506, PPEF2, LOC100134108, LOC392100, LOC100132535, OSBPL2, LOC643341, LOC284379, ARPC2, KDM1B, SEZ6L, LOC729251, LOC645070, PCDHB3, LOC644473, LOC646357, TMEM22, LOC730200, ZBTB39, TTTY17A, PAIP2, KBTBD9, LOC647788, ALG2, ELOVL2, RFX4, CILP, COMP, LOC100134540, CYP4Z1, LOC100129434, GALNT9, BPF7, MTUS1, ODF4, LOC652640, LOC642978, LOC440402, SPOl l, PLOD2, MIR24-1, LOC648164, CTGF, LOC390834, COL8A1, PTGIS, PLA2G2A, LOC644763, BTBD7, LOC644038, LOC651231, LOC650677, CSRP2BP, and CDKN2B.
21. A method of treating a follicular lymphoma in an individual in need thereof who has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1, or a normal expression or underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7, which method comprises administering or continuing to administer to the individual a therapeutically effective amount of ibrutinib or a pharmaceutically acceptable salt or solvate thereof.
22. The method of claim 21, wherein the individual has an overexpression of one or more genes selected from CALB2, P2RY11 (PPAN-P2RY11), DNAJC8, TTC19, VCAMl, CSAG3, GPIBA, RPAl, RSClAl, STS-1 (UBASH3B), ADPRM (C170RF48) and FILIP1.
23. The method of claim 21 or claim 22, wherein the individual has a normal expression of one or more genes selected from CERCAM, POM121C (LOC 100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
24. The method of claim 21 or claim 22, wherein the individual has an
underexpression of one or more genes selected from CERCAM, POM121C (LOC100131972), PPP1R3D, PLOD2, SDHA (SDHAP3), OSBPL2, HCFC1R1, and DHRS7.
25. The method of claim 21, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B), or a normal expression or underexpression of CERCAM or DHRS7.
26. The method of claim 25, wherein the individual has an overexpression of one or more genes selected from VCAMl, RPAl, and STS-1 (UBASH3B).
27. The method of claim 25 or claim 26, wherein the individual has a normal expression of CERCAM or DHRS7.
28. The method of claim 25 or claim 26, wherein the individual has an
underexpression of CERCAM or DHRS7.
29. The method of claim 21, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B), or a normal expression or underexpression of DHRS7.
30. The method of claim 29, wherein the individual has an overexpression of RPAl or STS-1 (UBASH3B).
31. The method of claim 29 or claim 30, wherein the individual has a normal expression of DHRS7.
32. The method of claim 29 or claim 30, wherein the individual has an
underexpression of DHRS7.
33. The method of any one of claims 1-32, wherein the individual has not been previously treated for lymphoma.
34. The method of any one of claims 1-32, wherein the individual has not been previously treated with ibrutinib for lymphoma.
35. The method of any one of claims 1-32, wherein the individual has been previously treated for lymphoma with an anticancer therapy other than ibrutinib.
36. The method of claim 35, wherein the lymphoma is relapsed or refractory.
37. The method of any one of claims 1-32, wherein the individual has been previously treated for lymphoma with ibrutinib and administration of ibrutinib is continued.
38. The method of any one of claims 1-37, wherein ibrutinib is administered with another therapeutic agent.
39. The method of any one of claims 1-38, wherein ibrutinib is administered at a dosage of about 40 mg/day to about 1000 mg/day.
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WO2020112761A1 (en) * 2018-11-30 2020-06-04 Janssen Biotech, Inc. Methods of treating follicular lymphoma
CN111481666A (en) * 2019-01-28 2020-08-04 中国科学院大连化学物理研究所 Application of inhibitor capable of inhibiting CA L B2 protein expression and liver cancer drug
US10954567B2 (en) 2012-07-24 2021-03-23 Pharmacyclics Llc Mutations associated with resistance to inhibitors of Bruton's Tyrosine Kinase (BTK)
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Family Cites Families (2)

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US7622260B2 (en) * 2001-09-05 2009-11-24 The Brigham And Women's Hospital, Inc. Diagnostic and prognostic tests
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US10478439B2 (en) 2010-06-03 2019-11-19 Pharmacyclics Llc Use of inhibitors of bruton's tyrosine kinase (Btk)
US10653696B2 (en) 2010-06-03 2020-05-19 Pharmacyclics Llc Use of inhibitors of bruton's tyrosine kinase (BTK)
US10751342B2 (en) 2010-06-03 2020-08-25 Pharmacyclics Llc Use of inhibitors of Bruton's tyrosine kinase (Btk)
US11672803B2 (en) 2010-06-03 2023-06-13 Pharmacyclics Llc Use of inhibitors of Brutons tyrosine kinase (Btk)
US10954567B2 (en) 2012-07-24 2021-03-23 Pharmacyclics Llc Mutations associated with resistance to inhibitors of Bruton's Tyrosine Kinase (BTK)
WO2020112761A1 (en) * 2018-11-30 2020-06-04 Janssen Biotech, Inc. Methods of treating follicular lymphoma
CN113164782A (en) * 2018-11-30 2021-07-23 詹森生物科技公司 Method for treating follicular lymphoma
CN111481666A (en) * 2019-01-28 2020-08-04 中国科学院大连化学物理研究所 Application of inhibitor capable of inhibiting CA L B2 protein expression and liver cancer drug
WO2023105119A1 (en) * 2021-12-07 2023-06-15 Sartar Therapeutics Oy Synergistic compositions for use in the treatment of cancer

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