US20150329643A1

US20150329643A1 - Identification and use of new tumor-promoting gene in hematological malignancies

Info

Publication number: US20150329643A1
Application number: US14/442,906
Authority: US
Inventors: Ulrich Steidl; Christian Steidl; Cynthia Ujunwa Okoye-Okafor
Original assignee: Albert Einstein College of Medicine
Current assignee: British Columbia Cancer Agency BCCA; Albert Einstein College of Medicine; Com Affiliation Inc
Priority date: 2012-11-16
Filing date: 2013-11-15
Publication date: 2015-11-19
Also published as: US20180371105A1; US10941209B2; WO2014078617A1

Abstract

Methods are provided for diagnosing and treating a blood cancer or a myelodysplastic syndrome in a subject. Associated compositions and kits therefor are also provided.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of U.S. Provisional Application No. 61/727,419, filed Nov. 16, 2012, and of U.S. Provisional Application No. 61/740,485, filed Dec. 21, 2012, the contents of each of which are hereby incorporated by reference.

BACKGROUND OF THE INVENTION

Throughout this application various publications are referred to. Full citations for these references may be found at the end of the specification. The disclosures of these publications, and of all patents, patent application publications and books referred to herein, are hereby incorporated by reference in their entirety into the subject application to more fully describe the art to which the subject invention pertains.
The hypothetical gene locus BX648577 (FLJ27352/hypothetical LOC145788) was recently identified as part of a gene fusion with Class II Transactivator (CIITA) in Hodgkin's lymphoma using whole-transcriptome paired-end sequencing (Steidl C. et al., Nature 2011). While CIITA has been extensively studied, it is not known whether BX648577 is a gene (whether it is transcribed and expressed physiologically as a protein and whether it has a biological function).
The present invention addresses the need for novel anti-leukemia treatments, antibodies useful in treating or diagnosing leukemias, and related assays based on discoveries disclosed herein regarding BX648577.

SUMMARY OF THE INVENTION

A method is provided of treating a cancer in a subject comprising administering to the subject an agent which inhibits expression of a BX648577 gene, or an agent which inhibits activity of an expression product of a BX648577 gene, so as to thereby treat the cancer.
Also provided is a method of diagnosing a subject as likely to develop a cancer or a myelodysplastic syndrome, or as susceptible to developing a cancer or a myelodysplastic syndrome, comprising determining whether a sample obtained from the subject expresses a BX648577 gene at a level in excess of a predetermined control level, wherein BX648577 gene expressed in the sample determined to be in excess of the predetermined control level indicates that the subject is likely to develop the cancer or is susceptible to developing the cancer, or is likely to develop the myelodysplastic syndrome or is susceptible to developing the myelodysplastic syndrome.
Also provided is a method of treating a cancer in a subject or inhibiting development of a cancer in a subject comprising determining whether a sample obtained from the subject expresses a BX648577 gene at a level in excess of a predetermined control level, wherein BX648577 gene expressed in the sample determined to be in excess of the predetermined control level identifies the subject as having the cancer or as likely to develop the cancer, and administering to a subject so-identified an anti-cancer therapy so as to thereby treat the cancer or inhibit development of a cancer.
An isolated antibody directed against the translocated in Hodgkin's lymphoma (TIHL) protein comprising SEQ ID NO:1 is also provided, as well as isolated antigen-binding fragments of such antibody, as are compositions comprising the isolated antibody. A cDNA encoding SEQ ID NO:1 is also provided.
Also provided is a kit comprising written instructions and reagents for determining TIHL levels or BX648577 gene (TIHL gene) expression levels in a biological sample obtained from a subject for determining the subject's susceptibility to a hematological malignancy.
An isolated protein is provided comprising consecutive amino acid residues having the sequence set forth in SEQ ID NO:1.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Confirmation of protein existence was performed by Western blot analysis of the 28 kilodalton protein. The protein encoded by the full length gene was given the name Translocated in Hodgkin's Lymphoma (TIHL) and the gene encoding it named TIHL.

FIG. 2: The TIHL sequence was determined, and was found to be highly conserved across species.

FIG. 3: Human TIHL was investigated for its genomic organization and predicted motifs. Potential roles were considered to be as an adaptor protein, signal transduction and/or localization regulation.

FIG. 4: The potential endogenous protein expression and localization was investigated. A TIHL specific antibody was generated to specifically probe its expression. Upon its overexpression by transfection using the lentiviral construct or knockdown shRNA constructs, we detect overexpression and downregulation of the endogenous proteins respectively in 293T cells. The antibody detects endogenous expression of the protein within various leukemia and lymphoma cell lines. Using immunofluorescence imaging coupled to confocal microscopy we detect both cytoplasmic and nuclear localization of the endogenous protein in NB4 and KG1a cells.

FIG. 5: TIHL mRNA expression was investigated in hematopoietic cells from human and murine bone marrow.

FIG. 6: TIHL mRNA expression profiles in leukemia and lymphoma cell lines were determined using realtime PCR primers specific to wild-type BX648577 expression.

FIG. 7: Significant overexpression of TIHL was identified in patients with AML having translocation 15; 17 (and in myelodysplastic syndromes (MDS)) compared to healthy controls and other AMLs.

FIG. 8: Functional consequences of TIHL knockdown were investigated. Knockdown of TIHL in myeloid leukemia NB4 and KG1a cells inhibits cell growth.

FIG. 9: Knockdown of TIHL in myeloid leukemia cells leads to decreased clonogenicity.

FIG. 10: Decreased cell cycle shown as decreased EdU incorporation and increased apoptosis with TIHL knockdown was observed in KG1a and NB4 cells.

FIG. 11: Overexpression of Wildtype TIHL in human NB4 cells and murine HPC-7 cells. FACS plot of sorted cells and real time PCR show overexpression of TIHL RNA and protein (GFP).

FIG. 12: TIHL overexpression confers a growth advantage in myeloid leukemia NB4 cells. Red arrow depicts a dividing cell.

FIG. 13: TIHL overexpression leads to increased clonogenicity in human myeloid leukemia NB4 cells and murine HPC-7 cells.

FIG. 14: TIHL overexpression leads increased cell cycling in both human myeloid leukemia NB4 and murine HPC-7 cells.

DETAILED DESCRIPTION OF THE INVENTION

A method is provided of treating a cancer in a subject comprising administering to the subject an agent which inhibits expression of a BX648577 gene, or an agent which inhibits activity of an expression product of a BX648577 gene, so as to thereby treat the cancer.
Also provided is a method of diagnosing a subject as likely to develop a cancer or a myelodysplastic syndrome, or as susceptible to developing a cancer or a myelodysplastic syndrome, comprising determining whether a sample obtained from the subject expresses a BX648577 gene at a level in excess of a predetermined control level, wherein BX648577 gene expressed in the sample determined to be in excess of the predetermined control level indicates that the subject is likely to develop the cancer or is susceptible to developing the cancer, or is likely to develop the myelodysplastic syndrome or is susceptible to developing the myelodysplastic syndrome. In an embodiment, the method is for diagnosing a subject as likely to develop a cancer. In an embodiment, the method is for diagnosing a subject as susceptible to developing a cancer. In an embodiment, the method is for diagnosing a subject as likely to develop a myelodysplastic syndrome. In an embodiment, the method is for diagnosing a subject as susceptible to developing a myelodysplastic syndrome. In an embodiment, the cancer is a hematological cancer.
Also provided is a method of treating a cancer in a subject or inhibiting development of a cancer in a subject comprising determining whether a sample obtained from the subject expresses a BX648577 gene at a level in excess of a predetermined control level, wherein BX648577 gene expressed in the sample determined to be in excess of the predetermined control level identifies the subject as having the cancer or as likely to develop the cancer, and administering to a subject so-identified an anti-cancer therapy so as to thereby treat the cancer or inhibit development of a cancer. In an embodiment, the method is of treating a cancer in a subject and the subject has the cancer. In an embodiment, the method is of inhibiting development of a cancer in a subject and the subject does not yet have the cancer.
In an embodiment of the methods, the cancer is a hematological malignancy. In an embodiment of the methods, the hematological malignancy is an acute myeloid leukemia.
In an embodiment of the methods, the anti-cancer therapy is an anti-acute myeloid leukemia therapy. In an embodiment of the methods, the anti-cancer therapy is agent which inhibits expression of a BX648577 gene, or an agent which inhibits activity of an expression product of a BX648577 gene. In an embodiment of the methods, the agent comprises an anti-translocated in Hodgkin's lymphoma protein (TIHL) antibody or an antigen-binding fragment of an anti-TIHL antibody.
In an embodiment of the methods, determining the level of expression of the BX648577 gene is effected by quantifying gene RNA transcript levels. In an embodiment, RNA transcript levels are quantified using quantitative reverse transcriptase PCR. In an embodiment, the agent is an siRNA directed to the BX648577 gene or an shRNA directed to the BX648577 gene. In an embodiment, the agent is an siRNA directed to a nucleic acid encoding BX648577 gene product or a transcript thereof or a shRNA directed to a nucleic acid encoding BX648577 gene product or a transcript thereof.
In an embodiment of the methods, the BX648577 gene encodes an mRNA encoding SEQ ID NO:1.
In an embodiment of the methods, the sample comprises a blood sample, a sample derived from blood, a bone marrow sample, or a stem cell.
Also provided is an isolated antibody directed against the THIL comprising SEQ ID NO:1. Also provided is an isolated antigen-binding fragment of antibody directed against the THIL comprising SEQ ID NO:1. The isolated antigen-binding fragment binds to THIL comprising SEQ ID NO:1. Also provided is a cDNA encoding SEQ ID NO:1.
In an embodiment, the antibody is a monoclonal antibody. In an embodiment, the antibody is a human antibody, a humanized antibody or a chimeric antibody. In an embodiment, the antibody fragment is a fragment of a human antibody, a humanized antibody or a chimeric antibody.
Also provided is a composition comprising any of the instant antibodies or fragments. In an embodiment, the composition comprises a physiological carrier. In an embodiment, the composition comprises a pharmaceutically acceptable carrier. In an embodiment, the composition comprises the isolated antibody conjugated to a cyotoxin, a radioisotope, a chemotherapeutic or an imaging label or comprises the isolated antigen-binding fragment of the antibody conjugated to a cyotoxin, a radioisotope, a chemotherapeutic or an imaging label. Imaging labels are well known in the art and include fluorophores and fluorescent dyes and radio-opaque dyes.
Also provided is a kit comprising written instructions and reagents for determining THIL levels or BX648577 gene expression levels in a biological sample obtained from a subject for determining the subject's susceptibility to a hematological malignancy. In an embodiment, the hematological malignancy is a leukemia. In an embodiment, the hematological malignancy is AML. In an embodiment, the hematological malignancy is myelodysplastic syndrome.
In an embodiment, the kit comprises a microarray having (i) an antibody specific for THIL or (ii) a nucleic acid probe thereon specific for a transcript of an BX648577 gene.
In an embodiment, the kit comprises a set of forward and reverse PCR primers specific for a region of the BX648577 gene comprising a portion encoding a transcript of the BX648577 gene for which the nucleic acid probe is specific.
An isolated protein is provided comprising consecutive amino acid residues having the sequence set forth in SEQ ID NO:1. In an embodiment, the isolated protein consists of amino acid residues having the sequence set forth in SEQ ID NO:1.
In an embodiment in humans TIHL comprises the sequence:

(SEQ ID NO: 1)

MTDRNRDKKSTSPSNSDTEMKSEQLPPCVNPGNPVFSCMLDPKTLQTATS

LSKPQQMIMYKTNSSHYGEFLPIPQFFPCNYTPKEQVFSSHIRATGFYQN

NTLNTAPDRTRTLDFPPNIQHTL.

A cDNA encoding SEQ ID NO:1 is also provided.
In an embodiment of the methods, RNA transcript levels are quantified using quantitative reverse transcriptase PCR.
In an embodiment of the methods, the cancer is an acute myeloid leukemia. In an embodiment, the aggressive anti-cancer therapy is an anti-acute myeloid leukemia therapy. In an embodiment, the subject has been diagnosed as being of intermediate cytogenetic risk for AML. An aggressive anti-cancer therapy is determined by those of skill in the art, such as physicians, based on the cancer, and means that a less-aggressive anti-cancer therapy is available. For example, aggressive anti-cancer therapy in AML could comprise a stem-cell transplantation. For example, an aggressive anti-cancer therapy in could comprise an aggressive chemotherapy.
In an embodiment of the methods, the sample comprises a blood sample, a bone marrow sample, or a stem cell.
In an embodiment, the kits comprise a plurality of sets of forward and reverse PCR primers, each set specific for a region of one of the recited genes comprising a portion encoding a transcript of the gene for which the nucleic acid probe is specific.
In an embodiment, an siRNA (small interfering RNA) used as an agent in the methods or compositions described herein is directed to BX648577 gene (which encodes TIHL) and comprises a portion which is complementary to an mRNA sequence corresponding to the following:

(SEQ ID NO: 2)

acttccagttgctatggttacgagttgcaacctccagaaagaattcgtgg

tttcacccgggaaaacagctccccggattaaacggataggtttacacata

ctgatccacccagctattcatcttctgtttgctgctttaattgggtgcgg

ttaaaaggccacgtccctaggcgttcaccggctttcttgccatctgctgc

atgaaaactgactttgccgaaaaaattaacaaagaagagcgaaaatgaca

gaccgcaaccgggataagaaaagtacttcaccttcaaattcagacacaga

aatgaaatctgaacaactgcctccttgtgtgaaccctggcaatcctgtgt

tttcatgtatgttggatccaaagacactccagacagccacctcactatca

aaacctcaaatgattatgtataaaaccaattcaagtcattatggtgaatt

tctacctattccacagtttttcccctgcaattatactccaaaggagcaag

tattttcaagccatatcagagcaactggattttatcaaaataacactcta

aatactgcacctgacagaaccagaactcttgattttcctaatattcaaca

cactctatgaaaatatattcctttgtatattgaagagaaaatatactcgg

gaaaaatgagtgttaaatctaagggtagaatacctaataaagaagataaa

aagttttgaatcaatttttaaaataagttaaataaagtatttcaactgat

aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

and the siRNA is effective to inhibit expression of TIHL.

In an embodiment, the siRNA comprises a double-stranded portion (duplex). In an embodiment, the siRNA is 20-25 nucleotides in length. In an embodiment the siRNA comprises a 19-21 core RNA duplex with a one or 2 nucleotide 3′ overhang on, independently, either one or both strands. In an embodiment, the overhang is UU. The siRNA can be 5′ phosphorylated or not and may be modified with any of the known modifications in the art to improve efficacy and/or resistance to nuclease degradation. In a non-limiting embodiment, the siRNA can be administered such that it is transfected into one or more cells.
In one embodiment, a siRNA of the invention comprises a double-stranded RNA comprising a first and second strand, wherein one strand of the RNA is 80, 85, 90, 95 or 100% complementary to a portion of an RNA transcript of a gene encoding TIHL. Thus, in an embodiment, the invention encompasses an siRNA comprising a 19, 20 or 21 nucleotide first RNA strand which is 80, 85, 90, 95 or 100% complementary to a 19, 20 or 21 nucleotide portion, respectively, of an RNA transcript of an TIHL-encoding gene. In an embodiment, the second RNA strand of the double-stranded RNA is also 19, 20 or 21 nucleotides, respectively, a 100% complementary to the first strand. In another embodiment, a siRNA of the invention comprises a double-stranded RNA wherein one strand of the RNA comprises a portion having a sequence the same as a portion of 18-25 consecutive nucleotides of an RNA transcript of a gene encoding Homo sapiens TIHL. In yet another embodiment, a siRNA of the invention comprises a double-stranded RNA wherein both strands of RNA are connected by a non-nucleotide linker. Alternately, a siRNA of the invention comprises a double-stranded RNA wherein both strands of RNA are connected by a nucleotide linker, such as a loop or stem loop structure.
In one embodiment, a single strand component of a siRNA of the invention is from 14 to 50 nucleotides in length. In another embodiment, a single strand component of a siRNA of the invention is 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 nucleotides in length. In yet another embodiment, a single strand component of a siRNA of the invention is 21 nucleotides in length. In yet another embodiment, a single strand component of a siRNA of the invention is 22 nucleotides in length. In yet another embodiment, a single strand component of a siRNA of the invention is 23 nucleotides in length. In one embodiment, a siRNA of the invention is from 28 to 56 nucleotides in length.
In another embodiment, an siRNA of the invention comprises at least one 2′-sugar modification. In another embodiment, an siRNA of the invention comprises at least one nucleic acid base modification. In another embodiment, an siRNA of the invention comprises at least one phosphate backbone modification.
In one embodiment, RNAi inhibition of TIHL is effected by an agent which is a short hairpin RNA (“shRNA”). The shRNA is introduced into the cell by transduction with a vector. In an embodiment, the vector is a lentiviral vector. In an embodiment, the vector comprises a promoter. In an embodiment, the promoter is a U6 or H1 promoter. In an embodiment the shRNA encoded by the vector is a first nucleotide sequence ranging from 19-29 nucleotides complementary to the target gene, in the present case TIHL. In an embodiment the shRNA encoded by the vector also comprises a short spacer of 4-15 nucleotides (a loop, which does not hybridize) and a 19-29 nucleotide sequence that is a reverse complement of the first nucleotide sequence. In an embodiment the siRNA resulting from intracellular processing of the shRNA has overhangs of 1 or 2 nucleotides. In an embodiment the siRNA resulting from intracellular processing of the shRNA overhangs has two 3′ overhangs. In an embodiment the overhangs are UU.
In one embodiment, inhibition of TIHL is effected by an agent which is an antibody or by a fragment of an antibody. As used herein, the term “antibody” refers to complete, intact antibodies, “antigen-binding fragment of an antibody” refers to Fab, Fab′, F(ab)₂, and other fragments thereof, or an ScFv, which bind the antigen of interest, in this case TIHL. Complete, intact antibodies include, but are not limited to, monoclonal antibodies such as murine monoclonal antibodies, polyclonal antibodies, chimeric antibodies, human antibodies, and humanized antibodies.
Various forms of antibodies may be produced using standard recombinant DNA techniques (Winter and Milstein, Nature 349: 293-99, 1991). For example, “chimeric” antibodies may be constructed, in which the antigen binding domain from an animal antibody is linked to a human constant domain (an antibody derived initially from a nonhuman mammal in which recombinant DNA technology has been used to replace all or part of the hinge and constant regions of the heavy chain and/or the constant region of the light chain, with corresponding regions from a human immunoglobulin light chain or heavy chain) (see, e.g., Cabilly et al., U.S. Pat. No. 4,816,567; Morrison et al., Proc. Natl. Acad. Sci. 81: 6851-55, 1984). Chimeric antibodies reduce the immunogenic responses elicited by animal antibodies when used in human clinical treatments. In addition, recombinant “humanized” antibodies may be synthesized. Humanized antibodies are antibodies initially derived from a nonhuman mammal in which recombinant DNA technology has been used to substitute some or all of the amino acids not required for antigen binding with amino acids from corresponding regions of a human immunoglobulin light or heavy chain. That is, they are chimeras comprising mostly human immunoglobulin sequences into which the regions responsible for specific antigen-binding have been inserted (see, e.g., PCT patent application WO 94/04679). Animals are immunized with the desired antigen, the corresponding antibodies are isolated and the portion of the variable region sequences responsible for specific antigen binding are removed. The animal-derived antigen binding regions are then cloned into the appropriate position of the human antibody genes in which the antigen binding regions have been deleted. Humanized antibodies minimize the use of heterologous (inter-species) sequences in antibodies for use in human therapies, and are less likely to elicit unwanted immune responses. Primatized antibodies can be produced similarly.
Another embodiment of the antibodies employed in the compositions and methods of the invention is a human antibody directed against TIHL, or a fragment of such antibody, which can be produced in nonhuman animals, such as transgenic animals harboring one or more human immunoglobulin transgenes. Such animals may be used as a source for splenocytes for producing hybridomas, for example as is described in U.S. Pat. No. 5,569,825.
Fragments of the antibodies described herein and univalent antibodies may also be used in the methods and compositions of this invention. Univalent antibodies comprise a heavy chain/light chain dimer bound to the Fc (or stem) region of a second heavy chain. “Fab region” refers to those portions of the chains which are roughly equivalent, or analogous, to the sequences which comprise the Y branch portions of the heavy chain and to the light chain in its entirety, and which collectively (in aggregates) have been shown to exhibit antibody activity. A Fab protein includes aggregates of one heavy and one light chain (commonly known as Fab′), as well as tetramers which correspond to the two branch segments of the antibody Y, (commonly known as F(ab)₂), whether any of the above are covalently or non-covalently aggregated, so long as the aggregation is capable of specifically reacting with a particular antigen or antigen family.
In an embodiment, the agents of the invention as described herein are administered in the form of a composition comprising the agent and a carrier. The term “carrier” is used in accordance with its art-understood meaning, to refer to a material that is included in a pharmaceutical composition but does not abrogate the biological activity of pharmaceutically active agent(s) that are also included within the composition. Typically, carriers have very low toxicity to the animal to which such compositions are to be administered. In some embodiments, carriers are inert.
In one embodiment of the methods, the TIHL expression level is detected using a detectable agent. As used herein, a “detectable agent” is any agent that binds to BX648577 gene or to TIHL and which can be detected or observed, when bound, by methods known in the art. In non-limiting examples, the detectable agent can be an antibody or a fragment of an antibody, which is itself detectable, e.g. by a secondary antibody, or which is labeled with a detectable marker such as a radioisotope, a fluorophore, a dye etc. permitting detection of the presence of the bound agent by the appropriate machine, or optionally in the case of visually detectable agents, with the human eye. In an embodiment, the amount of detectable agent can be quantified.
As used herein, a “cancer” is a disease state characterized by the presence in a subject of cells demonstrating abnormal uncontrolled replication. In a preferred embodiment, the cancer is a leukemia. In a most preferred embodiment, the cancer is acute myeloid leukemia. As used herein, “treating” a cancer, or a grammatical equivalent thereof, means effecting a reduction of, amelioration of, or prevention of further development of one or more symptoms of the disease, or placing the cancer in a state of remission, or maintaining it in a state of remission.
As used herein a “leukemia” is an art-recognized cancer of the blood or bone marrow characterized by an abnormal increase of immature white blood cells called “blasts”. The specific condition of acute myeloid leukemia (AML) is a cancer of the myeloid line of blood cells, characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells.
In an embodiment, the stem cell obtained from the subject is obtained by obtaining a sample from the subject. As used herein, a “sample” of a cancer or of a tumor is a portion of the cancer or of the tumor, respectively, for example as obtained by a biopsy. In the case of a leukemia, or AML, the preferred sample is bone marrow, or is derived from bone marrow, or is blood or is derived from blood. In an embodiment, the sample is, or comprises, a stem cell or a progenitor cell. As used herein a “sample derived from blood” or a “sample derived from bone marrow” is a sample which has been treated chemically and/or mechanically, but in such a manner not to alter TIHL expression levels or activity levels which might be contained therein.
In an embodiment, the microarray comprises probes attached via surface engineering to a solid surface by a covalent bond to a chemical matrix (via, in non-limiting examples, epoxy-silane, amino-silane, lysine, polyacrylamide). Suitable solid surface can be, in non-limiting examples, glass or a silicon chip, a solid bead forms of, for example, polystyrene. As used herein, unless otherwise specified, a microarray includes both solid-phase microarrays and bead microarrays. In an embodiment, the microarray is a solid-phase microarray. In an embodiment, the microarray is a plurality of beads microarray. In an embodiment, the microarray is a spotted microarray. In an embodiment, the microarray is an oligonucleotide microarray. The nucleic acid probes (e.g. oligonucleotide probes) of the microarray may be of any convenient length necessary for unique discrimination (is specific for) of target gene transcripts. In non-limiting examples, the probes are 20 to 30 nucleotides in length, 31 to 40 nucleotides in length, 41 to 50 nucleotides in length, 51 to 60 nucleotides in length, 61 to 70 nucleotides in length, or 71 to 80 nucleotides in length. In an embodiment, the target sample (e.g. gene mRNA transcripts), or nucleic acids derived from the target sample, such as cDNA, are contacted with a detectable marker, such as one or more fluorophores, under conditions permitting the detectable marker to attach to the target sample or nucleic acids derived from the target sample. Such fluorophores are well known in the art, for example cyanine 3, cyanine 5. In an embodiment, the target hybridized to the probe can be detected by conductance, mass spectrometry (including MALDI-TOF), or electrophoresis. The microarray can be manufactured by any method known in the art including by photolithography, pipette, drop-touch, piezoelectric (ink-jet), and electric techniques.
If desired, mRNA in the sample can be enriched with respect to other cellular RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA). Most mRNAs contain a poly(A) tail at their 3′ end. This allows them to be enriched by affinity chromatography, for example, using oligo(dT) or poly(U) coupled to a solid support, such as cellulose or Sephadex™ (see Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, vol. 2, Current Protocols Publishing, New York (1994), hereby incorporated by reference). In a non-limiting example, once bound, poly(A)+mRNA is eluted from the affinity column using 2 mM EDTA/0.1% SDS. Methods for preparing total and poly(A)+RNA are well known and are described generally in Sambrook et al., MOLECULAR CLONING—A LABORATORY MANUAL (2ND ED.), Vols. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)) and Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, vol. 2, Current Protocols Publishing, New York (1994)), the contents of both of which are incorporated herein. RNA may be isolated from samples of eukaryotic cells by procedures that involve lysis of the cells and denaturation of the proteins contained therein. Additional steps may be employed to remove DNA. Cell lysis may be accomplished with a nonionic detergent, followed by microcentrifugation to remove the nuclei and hence the bulk of the cellular DNA. In one embodiment, RNA is extracted from cells of the various types of interest using guanidinium thiocyanate lysis followed by CsCl centrifugation to separate the RNA from DNA (Chirgwin et al., Biochemistry 18:5294-5299 (1979) hereby incorporated by reference). Poly(A)+RNA can be selected by selection with oligo-dT cellulose (see Sambrook et al, MOLECULAR CLONING—A LABORATORY MANUAL (2ND ED.), Vols. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989). Alternatively, separation of RNA from DNA can be accomplished by organic extraction, for example, with hot phenol or phenol/chloroform/isoamyl alcohol. If desired, RNase inhibitors may be added to the lysis buffer. Likewise, for certain cell types, it may be desirable to add a protein denaturation/digestion step to the protocol.
In an embodiment of the methods and compositions the BX648577 gene is human. n an embodiment of the methods and compositions the BX648577 gene product is human.
As used herein “likely” in describing an occurrence means more likely than not. As used herein, “susceptible to” in describing a condition means more likely to develop the condition in a situation than a majority of the population from which the subject is drawn.
As used herein a “predetermined level” with regard to a quantity is the level of the quantity determined from one or more suitable control(s). In an embodiment the suitable control is a subject who does not have the relevant cancer and/or is not susceptible to the relevant cancer, or is a tissue or cell of such a subject. In an embodiment, the cancer that the subject does not have and/or is not susceptible to is acute myeloid leukemia.
All combinations of the various elements described herein are within the scope of the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
This invention will be better understood from the Experimental Details, which follow. However, one skilled in the art will readily appreciate that the specific methods and results discussed are merely illustrative of the invention as described more fully in the claims that follow thereafter.

EXPERIMENTAL DETAILS

Initial comparative analysis of the 13-16 kDa predicted BX648577 (TIHL) protein sequences in various species revealed high evolutionary conservation (≧54%), including in invertebrates (e.g. Saccoglossus kowalevskii). A TIHL (BX648577)-specific antibody generated was used to identify endogenous protein expression of TIHL by western blot analysis in several cell lines, including 293T cells, and myeloid NB4 and KG1a cells. Expression analysis was performed in several leukemia and lymphoma cell lines by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). It was found that TIHL mRNA was widely and variably expressed, with particularly high expression in malignant hematopoietic cells including 5 fold increase in NB4 cells (p=0.0057) and 9 fold higher in THP-1 cells (p=8.66e-6, when compared to healthy donor peripheral blood CD14+ monocytes. In addition, TIHL mRNA expression was detectable in sorted, primary human and murine bone marrow derived hematopoietic stem cells (Lin-CD34+CD38− (human) or Lin-c-Kit+Sca-1+ (mouse)) and progenitor cells (Lin-CD34+CD38+ (human) or Lin-c-Kit+Sca-1− (mouse)), as well as human healthy donor mature peripheral blood mononuclear cells with the most prominent expression in Glycophorin A and CD56 positive cells by qRT-PCR.
Utilizing murine HPC-7 cells as well as acute myeloid leukemia cell lines (NB4, KG1a), the biological consequences of modulating TIHL expression was assessed. Knockdown of TIHL by two independent shRNAs with greater than 50% knockdown efficiencies, led to significantly decreased leukemic cell growth in suspension culture. Additionally we observed decreased clonogenic capacity in both cell lines when the cells were transduced with either TIHL sh#1 or sh#2, with 72% (p=1.19e-3) and 77% (p=8.36e-4) inhibition in clonogenicity in NB4 cells when compared to cells transduced with a non-silencing control vector. Similarly, 72% (p=7.13e-4) and 63% (p=7.78e-4) inhibition of clonogenicity was observed in KG1a cells. In addition, knockdown of TIHL led to decreased cell cycling with less EdU incorporation in KG1a and NB4 cells, as well as increased cell death. No changes indicative of differentiation were found when cellular morphology and surface protein expression was analyzed. Cloning of the full length cDNA of human TIHL into a lentiviral expression vector was performed. While ectopic expression of human or murine TIHL in sorted Lin-c-Kit+ cells did not lead to a change in clonogenicity when compared to the empty control vector, we observed a 1.5 fold (p=0.0161) and 2 fold (p=0.0039) increase in colony forming capacity in NB4 and murine HPC-7 cells respectively upon TIHL overexpression. For Empty or TIHL overexpressing NB4 cells grown in suspension culture, we observed approximately a 2 fold increase in cell growth (p<0.001). Finally, in silico domain analysis suggests that TIHL may function as an adaptor protein and may be involved in facilitating previously established signal transduction pathways.
With regard to the figures herein: initially, BX648577 was identified as part of a novel hypothetical gene fusion in Hodgkin's Lymphoma cell line KM-H2. It was identified as co-localized CIITA and BX648577 on chromosome 16. Confirmation was performed by Western blot analysis of the 28 kilodalton fusion protein (see FIG. 1). The Wildtype full length BX648577 protein was given the name Translocated in Hodgkin's Lymphoma (TIHL). Subsequently, its actual physiological expression was investigated as well as any possible biological function. Both normal and malignant hematopoietic cells were used for this investigation. Its sequence was determined, and was found to be highly conserved across species (FIG. 2). Human TIHL was investigated for its genomic organization and predicted motifs (see FIG. 3). Potential roles were considered to be as an adaptor protein, signal transduction and/or regulated localization.
The potential endogenous protein expression and localization was investigated (FIG. 4). In investigating its possible role in hematopoiesis, the following questions were considered: is TIHL expressed in immature stem and progenitor cells of the bone marrow? (human & mouse) and in human peripheral blood mature cells; and is BX648577 aberrantly expressed in leukemias or lymphomas? Also investigated was the functional consequences of TIHL overexpression or knockdown in human hematopoietic cells.
TIHL mRNA expression was investigated in hematopoietic cells (FIG. 5). Then, TIHL mRNA expression profiles in leukemia and lymphoma cell lines were determined (FIG. 6) using real-time PCR primers specific to wild-type BX648577 expression. In addition, significant overexpression of BX648577 was identified in patients with AML having translocation 15; 17 (and in MDS) compared to healthy controls and other AMLs (FIG. 7).
Functional consequences of TIHL knockdown or overexpression were investigated. Knockdown of TIHL in myeloid leukemia NB4 and KG1a cells inhibits cell growth (FIG. 8). Knockdown of TIHL in myeloid leukemia cells also leads to decreased clonogenicity (FIG. 9). In TIHL knockdown in NB4 cells, no differences in colony morphology or size. Decreased EdU incorporation and increased apoptosis was observed with TIHL knockdown in KG1a and NB4 cells (FIG. 10).
The effect of the overexpression of wildtype TIHL on NB4 and HPC-7 cells was also evaluated (FIG. 11). TIHL overexpression confers a growth advantage in myeloid leukemia NB4 cells (FIG. 12). TIHL overexpression also leads to increased clonogenicity in myeloid leukemia NB4 cells and murine HPC-7 cells (FIG. 13). TIHL overexpression also leads increased cell cycling (FIG. 14).

Claims

1. A method of treating a cancer in a subject comprising administering to the subject an amount of an agent which inhibits expression of a BX648577 gene, or an amount of an agent which inhibits activity of an expression product of a BX648577 gene, so as to thereby treat the cancer.

2. (canceled)

3. A method of treating a cancer in a subject or inhibiting development of a cancer in a subject comprising determining whether a sample obtained from the subject expresses a BX648577 gene at a level in excess of a predetermined control level, wherein BX648577 gene expressed in the sample determined to be in excess of the predetermined control level identifies the subject as having the cancer or as likely to develop the cancer, and administering to a subject so-identified an anti-cancer therapy so as to thereby treat the cancer or inhibit development of a cancer.

4. The method of claim 3, wherein the method is of treating a cancer in a subject and the subject has the cancer.

5. The method of claim 3, wherein the method is of inhibiting development of a cancer in a subject and the subject does not yet have the cancer.

6. The method of claim 1, wherein the cancer is a hematological malignancy.

7. The method of claim 6, wherein the hematological malignancy is an acute myeloid leukemia.

8. The method of claim 3, wherein the anti-cancer therapy is an anti-acute myeloid leukemia therapy.

9. The method of claim 3, wherein the anti-cancer therapy is agent which inhibits expression of a BX648577 gene, or an agent which inhibits activity of an expression product of a BX648577 gene.

10. The method of claim 9, wherein the agent comprises an anti-translocated in Hodgkin's lymphoma protein (TIHL) antibody or an antigen-binding fragment of an anti-TIHL antibody.

11. The method of claim 3, wherein determining the level of expression of the BX648577 gene is effected by quantifying BX648577 gene RNA transcript levels.

12. The method of claim 11, wherein RNA transcript levels are quantified using quantitative reverse transcriptase PCR.

13. The method of claim 9, wherein the agent is an siRNA directed to a BX648577 gene or a transcript thereof, an shRNA directed to a BX648577 gene or a transcript thereof.

14. The method of claim 1, wherein the BX648577 gene encodes an mRNA encoding SEQ ID NO: 1.

15. The method of claim 3, wherein the sample comprises a blood sample, a sample derived from blood, a bone marrow sample, or a stem cell.

16-17. (canceled)

18. An isolated antibody directed against the translocated in Hodgkin's lymphoma protein (THIL) comprising SEQ ID NO:1 or an isolated antigen-binding fragment of such antibody.

19. The antibody or fragment of claim 18, wherein the antibody is a monoclonal antibody.

20. The antibody or fragment of claim 18, wherein the antibody is a human antibody, a humanized antibody or a chimeric antibody.

21. A composition comprising the antibody of claim 18.

22. The composition of claim 21, wherein the composition comprises the isolated antibody.

23-24. (canceled)

25. The composition of claim 21, wherein the isolated antibody or isolated antigen-binding fragment of the antibody is conjugated to a cyotoxin, a radioisotope, a chemotherapeutic or an imaging label.

26-33. (canceled)