EP1597558A2 - Biomarqueurs et methodes de determination d'une sensibilite aux modulateurs du facteur de croissance epidermique - Google Patents
Biomarqueurs et methodes de determination d'une sensibilite aux modulateurs du facteur de croissance epidermiqueInfo
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- EP1597558A2 EP1597558A2 EP04700860A EP04700860A EP1597558A2 EP 1597558 A2 EP1597558 A2 EP 1597558A2 EP 04700860 A EP04700860 A EP 04700860A EP 04700860 A EP04700860 A EP 04700860A EP 1597558 A2 EP1597558 A2 EP 1597558A2
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- biomarkers
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
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- 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
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/74—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving hormones or other non-cytokine intercellular protein regulatory factors such as growth factors, including receptors to hormones and growth factors
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- 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
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2500/00—Screening for compounds of potential therapeutic value
- G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2800/00—Detection or diagnosis of diseases
- G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
Definitions
- the present invention relates generally to the field of pharmacogenomics, and more specifically to methods and procedures to determine sensitivity in patients to allow the development of individualized genetic profiles which aid in treating diseases and disorders based on patient response at a molecular level.
- Cancer is a disease with extensive histoclinical heterogeneity. Although conventional histological and clinical features have been correlated to prognosis, the same apparent prognostic type of tumors varies widely in its responsiveness to therapy and consequent survival of the patient.
- New prognostic and predictive markers which would facilitate an individualization of therapy for each patient, are needed to accurately predict patient response to treatments, such as small molecule or biological molecule drugs, in the clinic.
- the problem may be solved by the identification of new parameters that could better predict the patient's sensitivity to treatment.
- the classification of patient samples is a crucial aspect of cancer diagnosis and treatment.
- the association of a patient's response to a treatment with molecular and genetic markers can open up new opportunities for treatment development in non-responding patients, or distinguish a treatment's indication among other treatment choices because of higher confidence in the efficacy.
- the pre-selection of patients who are likely to respond well to a medicine, drug, or combination therapy may reduce the number of patients needed in a clinical study or accelerate the time needed to complete a clinical development program (M. Cockett et al., 2000, Current Opinion in Biotechnology, 11 : 602-609).
- the ability to predict drug sensitivity in patients is particularly challenging because drug responses reflect not only properties intrinsic to the target cells, but also a host's metabolic properties. Efforts to use genetic information to predict drug sensitivity have primarily focused on individual genes that have broad effects, such as the multidrug resistance genes, mdrl and mrpl (P. Sonneveld, 2000, J Intern. Med., 247:521-534).
- the invention provides methods and procedures for determining patient sensitivity to one or more Epidermal Growth Factor Receptor (EGFR) modulators.
- the invention also provides methods of determining or predicting whether an individual requiring therapy for a disease state such as cancer will or will not respond to treatment, prior to administration of the treatment, wherein the treatment comprises one or more EGFR modulators.
- the one or more EGFR modulators are compounds that can be selected from, for example, one or more EGFR specific ligands, one or more small molecule EGFR inhibitors, or one or more EGFR binding monoclonal antibodies.
- the invention provides a method for identifying a mammal that will respond therapeutically to a method of treating cancer comprising administering an EGFR modulator, wherein the method comprises: (a) measuring in the mammal the level of at least one biomarker selected from the biomarkers of Table 4; (b) exposing the mammal to the EGFR modulator; (c) following the exposing of step (b), measuring in the mammal the level of the at least one biomarker, wherein a difference in the level of the at least one biomarker measured in step (c) compared to the level of the at least one biomarker measured in step (a) indicates that the mammal will respond therapeutically to said method of treating cancer.
- respond therapeutically refers to the alleviation or abrogation of the cancer. This means that the life expectancy of an individual affected with the cancer will be increased or that one or more of the symptoms of the cancer will be reduced or ameliorated.
- the term encompasses a reduction in cancerous cell growth or tumor volume. Whether a mammal responds therapeutically can be measured by many methods well known in the art, such as PET imaging.
- the at least one biomarker can also be selected from the biomarkers of Table 5.
- the mammal can be, for example, a human, rat, mouse, dog rabbit, pig sheep, cow, horse, cat, primate, or monkey.
- the method of the invention can be, for example, an in vitro method and wherein the at least one biomarker is measured in at least one mammalian biological sample from the mammal.
- the biological sample can comprise, for example, at least one of whole fresh blood, peripheral blood mononuclear cells, frozen whole blood, fresh plasma, frozen plasma, urine, saliva, skin, hair follicle, or tumor tissue.
- the invention provides a method for identifying a mammal that will respond therapeutically to a method of treating cancer comprising administering an EGFR modulator, wherein the method comprises: (a) exposing the mammal to the EGFR modulator; (b) following the exposing of step (a), measuring in the mammal the level of the at least one biomarker selected from the biomarkers of Table 4, wherein a difference in the level of the at least one biomarker measured in step (b), compared to the level of the biomarker in a mammal that has not been exposed to said EGFR modulator, indicates that the mammal will respond therapeutically to said method of treating cancer.
- the invention provides a method for testing or predicting whether a mammal will respond therapeutically to a method of treating cancer comprising administering an EGFR modulator, wherein the method comprises: (a) measuring in the mammal the level of at least one biomarker selected from the biomarkers of Table 4; (b) exposing the mammal to the EGFR modulator; (c) following the exposing of step (b), measuring in the mammal the level of the at least one biomarker, wherein a difference in the level of the at least one biomarker measured in step (c) compared to the level of the at least one biomarker measured in step (a) indicates that the mammal will respond therapeutically to said method of treating cancer.
- the invention provides a method for determining whether a compound inhibits EGFR activity in a mammal, comprising: (a) exposing the mammal to the compound; and (b) following the exposing of step (a), measuring in the mammal the level of at least one biomarker selected from the biomarkers of Table 4, wherein a difference in the level of said biomarker measured in step (b), compared to the level of the biomarker in a mammal that has not been exposed to said compound, indicates that the compound inhibits EGFR activity in the mammal.
- the invention provides a method for determining whether a mammal has been exposed to a compound that inhibits EGFR activity, comprising (a) exposing the mammal to the compound; and (b) following the exposing of step (a), measuring in the mammal the level of at least one biomarker selected from the biomarkers of Table 4, wherein a difference in the level of said biomarker measured in step (b), compared to the level of the biomarker in a mammal that has not been exposed to said compound, indicates that the mammal has been exposed to a compound that inhibits EGFR activity.
- the invention provides a method for determining whether a mammal is responding to a compound that inhibits EGFR activity, comprising (a) exposing the mammal to the compound; and (b) following the exposing of step (a), measuring in the mammal the level of at least one biomarker selected from the biomarkers of Table 4, wherein a difference in the level of said biomarker measured in step (b), compared to the level of the biomarker in a mammal that has not been exposed to said compound, indicates that the mammal is responding to the compound that inhibits EGFR activity.
- responding encompasses responding by way of a biological and cellular response, as well as a clinical response (such as improved symptoms, a therapeutic effect, or an adverse event), in a mammal
- the invention also provides an isolated biomarker selected from the biomarkers of Table 4.
- the biomarkers of the invention comprise sequences selected from the nucleotide and amino acid sequences provided in Table 4 and the Sequence Listing, as well as fragments and variants thereof.
- the invention also provides a biomarker set comprising two or more biomarkers selected from the biomarkers of Table 4.
- kits for determining or predicting whether a patient would be susceptible or resistant to a treatment that comprises one or more EGFR modulators may have a cancer or tumor such as, for example, a colon cancer or tumor.
- the kit comprises a suitable container that comprises one or more specialized microarrays of the invention, one or more EGFR modulators for use in testing cells from patient tissue specimens or patient samples, and instructions for use.
- the kit may further comprise reagents or materials for monitoring the expression of a biomarker set at the level of mRNA or protein.
- the invention provides a kit comprising two or more biomarkers selected from the biomarkers of Table 4.
- the invention provides a kit comprising at least one of an antibody and a nucleic acid for detecting the presence of at least one of the biomarkers selected from the biomarkers of Table 4.
- the kit further comprises instructions for determining whether or not a mammal will respond therapeutically to a method of treating cancer comprising administering a compound that inhibits EGFR activity.
- the instructions comprise the steps of (a) measuring in the mammal the level of at least one biomarker selected from the biomarkers of Table 4, (b) exposing the mammal to the compound, (c) followmg the exposing of step (b), measuring in the mammal the level of the at least one biomarker, wherein a difference in the level of the at least one biomarker measured in step (c) compared to the level of the at least one biomarker measured in step (a) indicates that the mammal will respond therapeutically to said method of treating cancer.
- the invention also provides screening assays for determining if a patient will be susceptible or resistant to treatment with one or more EGFR modulators.
- the invention also provides a method of monitoring the treatment of a patient having a disease treatable by one or more EGFR modulators.
- the invention also provides individualized genetic profiles which are necessary to treat diseases and disorders based on patient response at a molecular level.
- the invention also provides specialized microarrays, e.g., oligonucleotide microarrays or cDNA microarrays, comprising one or more biomarkers having expression profiles that correlate with either sensitivity or resistance to one or more EGFR modulators.
- specialized microarrays e.g., oligonucleotide microarrays or cDNA microarrays, comprising one or more biomarkers having expression profiles that correlate with either sensitivity or resistance to one or more EGFR modulators.
- the invention also provides antibodies, including polyclonal or monoclonal, directed against one or more biomarkers of the invention.
- FIG. 1 illustrates a EGFR biomarker identification and prioritization strategy.
- FIG. 2A illustrates the RT-PCR results for EGFR in thirty one colon cancer cell lines to identify cell lines which do not have significant mRNA expression of EGFR
- FIG. 2B illustrates the IC50 profile for twenty two colon cancer cell lines with an EGFR inhibitor compound, and determination of sensitive and resistant cell lines.
- DETAILED DESCRIPTION OF THE INVENTION The invention provides biomarkers that respond to the modulation of a specific signal transduction pathway and also correlate with EGFR modulator sensitivity or resistance. These biomarkers can be employed for predicting response to one or more EGFR modulators.
- the biomarkers of the invention are those provided in Table 4 and the Sequence Listing, including both polynucleotide and polypeptide sequences.
- the biomarkers were determined by an in vitro assay employing microarray technology to monitor simultaneously the expression pattern of thousands of discrete genes in untreated cells, whose response to the modulation of a signal transduction pathway, in particular the EGFR pathway, was tested on untreated cells whose sensitivity to EGFR modulators was tested.
- the biomarkers have expression levels in the cells that are dependent on the activity of the EFGR signal transduction pathway and that are also highly correlated with EGFR modulator sensitivity exhibited by the cells.
- Biomarkers serve as useful molecular tools for predicting a response to EGFR modulators, preferably biological molecules, small molecules, and the like that affect EGFR kinase activity via direct or indirect inhibition or antagonism of EGFR kinase function or activity.
- EGFR modulator is intended to mean a compound or drug that is a biological molecule or a small molecule that directly or indirectly modulates EGFR activity or the EGFR signal transduction pathway.
- compounds or drugs as used herein is intended to include both small molecules and biological molecules.
- Direct or indirect modulation includes activation or inhibition of EGFR activity or the EGFR signal transduction pathway.
- inhibition refers to inhibition of the binding of EGFR to an EGFR ligand such as, for example, EGF.
- inhibition refers to inhibition of the kinase activity of EGFR.
- EGFR modulators include, for example, EGFR specific ligands, small molecule EGFR inhibitors, and EGFR monoclonal antibodies.
- the EGFR modulators include, for example, EGFR specific ligands, small molecule EGFR inhibitors, and EGFR monoclonal antibodies.
- the EGFR modulators include, for example, EGFR specific ligands, small molecule EGFR
- the EGFR modulator inhibits EGFR activity and/or inhibits the EGFR signal transduction pathway.
- the EGFR modulator is an EGFR antibody that inhibits EGFR activity and/or inhibits the EGFR signal transduction pathway.
- EGFR modulators include biological molecules or small molecules.
- Biological molecules include all lipids and polymers of monosaccharides, amino acids, and nucleotides having a molecular weight greater than 450.
- biological molecules include, for example, oligosaccharides and polysaccharides; oligopeptides, polypeptides, peptides, and proteins; and oligonucleotides and polynucleotides.
- Oligonucleotides and polynucleotides include, for example, DNA and RNA.
- Biological molecules further include derivatives of any of the molecules described above.
- derivatives of biological molecules include lipid and glycosylation derivatives of oligopeptides, polypeptides, peptides, and proteins.
- Derivatives of biological molecules further include lipid derivatives of oligosaccharides and polysaccharides, e.g., lipopolysaccharides.
- biological molecules are antibodies, or functional equivalents of antibodies. Functional equivalents of antibodies have binding characteristics comparable to those of antibodies, and inhibit the growth of cells that express EGFR. Such functional equivalents include, for example, chimerized, humanized, and single chain antibodies as well as fragments thereof.
- Functional equivalents of antibodies also include polypeptides with amino acid sequences substantially the same as the amino acid sequence of the variable or hypervariable regions of the antibodies.
- An amino acid sequence that is substantially the same as another sequence, but that differs from the other sequence by means of one or more substitutions, additions, and/or deletions, is considered to be an equivalent sequence.
- Preferably, less than 50%, more preferably less than 25%, and still more preferably less than 10%, of the number of amino acid residues in a sequence are substituted for, added to, or deleted from the protein.
- the functional equivalent of an antibody is preferably a chimerized or humanized antibody.
- a chimerized antibody comprises the variable region of a non- human antibody and the constant region of a human antibody.
- a humanized antibody comprises the hypervariable region (CDRs) of a non-human antibody.
- the variable region other than the hypervariable region, e.g., the framework variable region, and the constant region of a humanized antibody are those of a human antibody.
- Suitable variable and hypervariable regions of non-human antibodies may be derived from antibodies produced by any non-human mammal in which monoclonal antibodies are made. Suitable examples of mammals other than humans include, for example, rabbits, rats, mice, horses, goats, or primates.
- Functional equivalents further include fragments of antibodies that have binding characteristics that are the same as, or are comparable to, those of the whole antibody.
- Suitable fragments of the antibody include any fragment that comprises a sufficient portion of the hypervariable (i.e., complementarity determining) region to bind specifically, and with sufficient affinity, to EGFR tyrosine kinase to inhibit growth of cells that express such receptors.
- Such fragments may, for example, contain one or both Fab fragments or the F(ab') 2 fragment.
- the antibody fragments contain all six complementarity determining regions of the whole antibody, although functional fragments containing fewer than all of such regions, such as three, four, or five CDRs, are also included.
- the fragments are single chain antibodies, or Fv fragments.
- Single chain antibodies are polypeptides that comprise at least the variable region of the heavy chain of the antibody linked to the variable region of the light chain, with or without an interconnecting linker.
- Fv fragment comprises the entire antibody combining site.
- These chains may be produced in bacteria or in eukaryotic cells.
- the antibodies and functional equivalents may be members of any class of immunoglobulins, such as IgG, IgM, IgA, IgD, or IgE, and the subclasses thereof. In one aspect, the antibodies are members of the IgGl subclass.
- the functional equivalents may also be equivalents of combinations of any of the above classes and subclasses.
- EGFR antibodies can be selected from chimerized, humanized, fully human, and single chain antibodies derived from the murine antibody 225 described in U.S. Patent No. 4,943,533 to Mendelsohn et al.
- the 225 derived antibodies have the following hypervariable (CDR) regions of the light and heavy chain, wherein the amino acid sequences are indicated below the nucleotide sequences:
- AACTATGGTGTACAC (SEQ IDNO: 179) NYGVH (SEQ IDNO: 180) CDR2 GTGATATGGAGTGGTGGAAACACAGACTATAATACACCTTTCACATCC (SEQ IDNO: 181)
- the EGFR antibody can be selected from the antibodies described in U.S. Patent No.6,235,883 to Jakobovits et al., U.S. Patent No.5,558,864 to Bendi et al, and U.S. Patent No.5,891 ,996 to Mateo de Acosta del Rio et al.
- the EGFR modulators useful in the invention may also be small molecules. Any molecule that is not a biological molecule is considered herein to be a small molecule. Some examples of small molecules include organic compounds, organometallic compounds, salts of organic and organometallic compounds, saccharides, amino acids, and nucleotides. Small molecules further include molecules that would otherwise be considered biological molecules, except their molecular weight is not greater than 450. Thus, small molecules may be lipids, oligosaccharides, oligopeptides, and oligonucleotides and their derivatives, having a molecular weight of 450 or less.
- small molecules can have any molecular weight. They are merely called small molecules because they typically have molecular weights less than 450. Small molecules include compounds that are found in nature as well as synthetic compounds.
- the EGFR modulator is a small molecule that inhibits the growth of tumor cells that express EGFR. In another embodiment, the EGFR modulator is a small molecule that inhibits the growth of refractory tumor cells that express EGFR. Numerous small molecules have been described as being useful to inhibit
- U.S. Patent No. 5,656,655 to Spada et al. discloses styryl substituted heteroaryl compounds that inhibit EGFR.
- the heteroaryl group is a monocyclic ring with one or two heteroatoms, or a bicyclic ring with 1 to about 4 heteroatoms, the compound being optionally substituted or polysubstituted.
- U.S. Patent No. 5,646,153 to Spada et al. discloses bis mono and/or bicyclic aryl heteroaryl, carbocyclic, and heterocarbocyclic compounds that inhibit EGFR.
- U.S. Patent No. 5,679,683 to Bridges et al. discloses tricyclic pyrimidine compounds that inhibit the EGFR. The compounds are fused heterocyclic pyrimidine derivatives described at column 3, line 35 to column 5, line 6.
- U.S. Patent No. 5,616,582 to Barker discloses quinazoline derivatives that have receptor tyrosine kinase inhibitory activity.
- Osherov et al. disclose tyrphostins that inhibit EGFR/HER1 and HER 2, particularly those in Tables I, II, III, and IV.
- U.S. Patent No. 5,196,446 to Levitzki et al. discloses heteroarylethenediyl or heteroarylethendeiylaryl compounds that inhibit EGFR, particularly from column 2, line 42 to column 3, line 40.
- PD166285 is identified as 6-(2,6- dicMorophenyl)-2-(4-(2-diethylaminoethyoxy)phenylamino)-8-methyl-8H- pyrido(2,3-d)pyrimidin-7-one having the structure shown in Figure 1 on page 1436.
- BIOMARKERS AND BIOMARKER SETS The invention includes individual biomarkers and biomarker sets having both diagnostic and prognostic value in disease areas in which signaling through EGFR or the EGFR pathway is of importance, e.g., in cancers or tumors, in immunological disorders, conditions or dysfunction, or in disease states in which cell signaling and/or cellular proliferation controls are abnormal or aberrant.
- the biomarker sets comprise a plurality of biomarkers such as, for example, a plurality of the biomarkers provided in Table 4 below, that highly correlate with resistance or sensitivity to one or more EGFR modulators.
- the biomarker sets of the invention enable one to predict or reasonably foretell the likely effect of one or more EGFR modulators in different biological systems or for cellular responses.
- the biomarker sets can be used in in vitro assays of EGFR modulator response by test cells to predict in vivo outcome.
- the various biomarker sets described herein, or the combination of these biomarker sets with other biomarkers or markers can be used, for example, to predict how patients with cancer might respond to therapeutic intervention with one or more EGFR modulators.
- a biomarker set of cellular gene expression patterns correlating with sensitivity or resistance of cells following exposure of the cells to one or more EGFR modulators provides a useful tool for screening one or tumor samples before treatment with the EGFR modulator.
- the screening allows a prediction of cells of a tumor sample exposed to one or more EGFR modulators, based on the expression results of the biomarker set, as to whether or not the tumor, and hence a patient harboring the tumor, will or will not respond to treatment with the EGFR modulator.
- biomarker or biomarker set can also be used as described herein for monitoring the progress of disease treatment or therapy in those patients undergoing treatment for a disease involving an EGFR modulator.
- the biomarkers serve as targets for the development of therapies for disease treatment. Such targets may be particularly applicable to treatment of breast disease, such as breast cancers or tumors. Indeed, because these biomarkers are differentially expressed in sensitive and resistant cells, their expression patterns are correlated with relative intrinsic sensitivity of cells to treatment with EGFR modulators. Accordingly, the biomarkers highly expressed in resistant cells may serve as targets for the development of new therapies for the tumors which are resistant to EGFR modulators, particularly EGFR inhibitors.
- the invention also includes specialized microarrays, e.g., oligonucleotide microarrays or cDNA microarrays, comprising one or more biomarkers, showing expression profiles that correlate with either sensitivity or resistance to one or more EGFR modulators.
- microarrays can be employed in in vitro assays for assessing the expression level of the biomarkers in the test cells from tumor biopsies, and determining whether these test cells are likely to be resistant or sensitive to EGFR modulators.
- a specialized microarray can be prepared using all the biomarkers, or subsets thereof, as described herein and shown in Table 4. Cells from a tissue or organ biopsy can be isolated and exposed to one or more of the EGFR modulators.
- the pattern of gene expression of the tested cells can be determined and compared with that of the biomarker pattern from the control panel of cells used to create the biomarker set on the microarray. Based upon the gene expression pattern results from the cells that underwent testing, it can be determined if the cells show a resistant or a sensitive profile of gene expression. Whether or not the tested cells from a tissue or organ biopsy will respond to one or more of the EGFR modulators and the course of treatment or therapy can then be determined or evaluated based on the information gleaned from the results of the specialized microarray analysis.
- the invention also includes antibodies, including polyclonal or monoclonal, directed against one or more of the polypeptide biomarkers.
- antibodies can be used in a variety of ways, for example, to purify, detect, and target the biomarkers of the invention, including both in vitro and in vivo diagnostic, detection, screening, and/or therapeutic methods.
- kits for determining or predicting whether a patient would be susceptible or resistant to a treatment that comprises one or more EGFR modulators may have a cancer or tumor such as, for example, a breast cancer or tumor.
- kits would be useful in a clinical setting for use in testing a patient's biopsied tumor or cancer samples, for example, to determine or predict if the patient's tumor or cancer will be resistant or sensitive to a given treatment or therapy with an EGFR modulator.
- the kit comprises a suitable container that comprises: one or more microarrays, e.g., oligonucleotide microarrays or cDNA microarrays, that comprise those biomarkers that correlate with resistance and sensitivity to EGFR modulators, particularly EGFR inhibitors; one or more EGFR modulators for use in testing cells from patient tissue specimens or patient samples; and instructions for use.
- one or more microarrays e.g., oligonucleotide microarrays or cDNA microarrays, that comprise those biomarkers that correlate with resistance and sensitivity to EGFR modulators, particularly EGFR inhibitors
- one or more EGFR modulators for use in testing cells from patient tissue specimens or patient samples
- instructions for use e.g., instructions for use.
- kits contemplated by the invention can further include, for example, reagents or materials for monitoring the expression of biomarkers of the invention at the level of mRNA or protein, using other techniques and systems practiced in the art such as, for example, RT-PCR assays, which employ primers designed on the basis of one or more of the biomarkers described herein, immunoassays, such as enzyme linked immunosorbent assays (ELIS As), immunoblotting, e.g., Western blots, or in situ hybridization, and the like, as further described herein.
- reagents or materials for monitoring the expression of biomarkers of the invention at the level of mRNA or protein using other techniques and systems practiced in the art such as, for example, RT-PCR assays, which employ primers designed on the basis of one or more of the biomarkers described herein, immunoassays, such as enzyme linked immunosorbent assays (ELIS As), immunoblotting, e.g., Western blots, or in situ hybridization
- Biomarkers and biomarker sets may be used in different applications.
- Biomarker sets can be built from any combination of biomarkers listed in Table 4 to make predictions about the likely effect of any EGFR modulator in different biological systems.
- the various biomarkers and biomarker sets described herein can be used, for example, as diagnostic or prognostic indicators in disease management, to predict how patients with cancer might respond to therapeutic intervention with compounds that modulate the EGFR, and to predict how patients might respond to therapeutic intervention that modulates signaling through the entire EGFR regulatory pathway.
- biomarkers While the data described herein were generated in cell lines that are routinely used to screen and identify compounds that have potential utility for cancer therapy, the biomarkers have both diagnostic and prognostic value in other diseases areas in which signaling through EGFR or the EGFR pathway is of importance, e.g., in immunology, or in cancers or tumors in which cell signaling and/or proliferation controls have gone awry.
- the biomarkers of the invention are expected to have both diagnostic and prognostic value for other compounds that ⁇ dulate EGFR or the EGFR signaling pathways.
- the described biomarkers are expected to have utility for predicting drug sensitivity or resistance to compounds that interact with or inhibit the EGFR activity in cells from other tissues or organs associated with a disease state, or cancers or tumors derived from other tissue types.
- Non-limiting examples of such cells, tissues and organs include breast, colon, lung, prostate, testes, ovaries, cervix, esophagus, pancreas, spleen, liver, kidney, stomach, lymphocytic and brain, thereby providing a broad and advantageous applicability to the biomarkers described herein.
- Cells for analysis can be obtained by conventional procedures as known in the art, for example, tissue biopsy, aspiration, sloughed cells, e.g., colonocytes, clinical or medical tissue or cell sampling procedures.
- cells from a patient tissue sample e.g., a tumor or cancer biopsy
- a patient tissue sample e.g., a tumor or cancer biopsy
- test cells e.g., tumor or cancer biopsy
- test cells show a biomarker expression profile which corresponds to that of the biomarkers in the control panel of cells which are sensitive to the EGFR modulator, it is highly likely or predicted that the individual's cancer or tumor will respond favorably to treatment with the EGFR modulator.
- test cells show a biomarker expression pattern corresponding to that of the biomarkers of the control panel of cells which are resistant to the EGFR modulator, it is highly likely or predicted that the individual's cancer or tumor will not respond to treatment with the EGFR modulator.
- the invention also provides a method of monitoring the treatment of a patient having a disease treatable by one or more EGFR modulators.
- the isolated test cells from the patient's tissue sample e.g., a tumor biopsy or tumor sample, can be assayed to determine the expression pattern of one or more biomarkers before and after exposure to an EGFR modulator wherein, preferably, the EGFR modulator is an EGFR inhibitor.
- the resulting biomarker expression profile of the test cells before and after treatment is compared with that of one or more biomarkers as described and shown herein to be highly expressed in the control panel of cells that are either resistant or sensitive to an EGFR modulator.
- the patient's treatment prognosis can be qualified as favorable and treatment can continue.
- the test cells don't show a change in the biomarker expression profile corresponding to the control panel of cells that are sensitive to the EGFR modulator, it can serve as an indicator that the current treatment should be modified, changed, or even discontinued.
- This monitoring process can indicate success or failure of a patient's treatment with an EGFR modulator and such monitoring processes can be repeated as necessary or desired.
- the biomarkers of the invention can be used to predict an outcome prior to having any knowledge about a biological system. Essentially, a biomarker can be considered to be a statistical tool. Biomarkers are useful primarily in predicting the phenotype that is used to classify the biological system. In an embodiment of the invention, the goal of the prediction is to classify cancer cells as having an active or inactive EGFR pathway. Cancer cells with an inactive EGFR pathway can be considered resistant to treatment with an EGFR modulator.
- An inactive EGFR pathway is defined herein as a non-significant expression of the EGFR or by a classification as "resistant” or “sensitive” based on the IC 50 value of each colon cell line to a compound (EGFR inhibitor compound BMS-461453) exemplified herein.
- a number of the biomarker described herein are known to be regulated by EGFR, e.g., mucin 2 (J Biol Chem. 2002 Aug 30;277(35):32258-67).
- Another biomarker, betacellulin is know to be an EGFR ligand (Biochem Biophys Res Commun. 2002 Jun 28;294(5): 1040-6).
- a functional relationship of the top biomarkers to the EGFR is expected, since biomarkers that contribute to high biomarker accuracy are likely to play a functional role in the pathway that is being modulated.
- Perception therapy i.e., antibody that binds to the Her2 receptor and prevents function via internalization
- the Her2 gene is overexpressed. It is unlikely that a therapy will have any therapeutic effect if the target enzyme is not expressed.
- biomarkers are not currently known, some of the biomarkers are likely to be directly or indirectly involved in the EGFR signaling pathway. In addition, some of the biomarkers may function in the metabolic or other resistance pathways specific to the EGFR modulators tested. Notwithstanding, knowledge about the function of the biomarkers is not a requisite for determining the accuracy of a biomarker according to the practice of the invention.
- biomarkers were identified whose expression patterns, in a subset of cell lines, correlated to and can be used as an in vitro marker of cellular response to treatment or therapy with one compound, or with a combination or series of compounds, that are known to inhibit or activate the function of a protein, enzyme, or molecule (e.g., a receptor) that is directly or indirectly involved in cell proliferation, cell responses to external stimuli, (such as ligand binding), or signal transduction, e.g., a receptor tyrosine kinase.
- a protein, enzyme, or molecule e.g., a receptor
- FIG. 1 illustrates the EGFR biomarker identification and prioritization strategy.
- the mRNA expression level of EGFR was used to identify six colon cancer cell lines with, inferred from the mRNA expression level, no significant presence of the EGFR protein and hence no significant activity of the EGFR pathway (FIG. 2A).
- biomarkers were identified that had no significant mRNA expression level in the six cell lines and no inferred presence of the EGFR protein. Further, it was required that these biomarkers would have a significant mRNA expression level in at least six other cell lines.
- an EGFR specific tyrosine kinase inhibitor compound was used to determine compound sensitivity in a panel of twenty two colon cancer cell lines following exposure of the cells to the compound. Some of the cell lines were determined to be resistant to treatment with the inhibitor compound, while others were determined to be sensitive to the inhibitor (FIG. 2B). A subset of the cell lines examined provided an expression pattern or profile of biomarkers that correlated to a response by the cells to the EGFR inhibitor compound as well as the absence of significant EGFR expression as thus could serve as biomarkers.
- the invention advantageously focuses on cell-intrinsic properties that are exposed in cell culture to identify biomarkers that predict compound sensitivity and resistance.
- the discovery and identification of biomarkers in tumor cells and cell lines assayed in vitro can be used to predict responses to one or more EGFR modulators in vivo and, thus, can be extended to clinical situations in which the same biomarkers are used to predict patients' responses to one or more EGFR modulators and treatments comprising one or more EGFR modulators.
- oligonucleotide microarrays were used to measure the expression levels of over 44,792 probe sets in a panel of thirty one untreated colon cancer cell lines for which the expression status of the EGFR and the drug sensitivity to EGFR inhibitor compounds was determined. This analysis was performed to determine whether the gene expression signatures of untreated cells were sufficient for the prediction of sensitivity of the disease to inhibition of the EGFR by small molecule or biological molecule compounds. Through data analysis, biomarkers were identified whose expression levels were found to be highly counter- correlated with the status of the EGFR and correlated with the drug sensitivity. In addition, the treatment of cells with a small molecule EGFR inhibitor also provided gene expression signatures predictive of sensitivity to the compound.
- FIG. 2B represents the resistance/sensitivity classifications of the twenty- two colon cell lines to the small molecule EGFR inhibitor. Five cell lines were classified as sensitive and seventeen cell lines as resistant.
- Biomarkers were discovered based on two criteria: (i) the correlation of their mRNA expression level to the expression of EGFR in cell lines with insignificant EGFR expression and (ii) the correlation of the IC 50 values for the small molecule EGFR inhibitor BMS-461453 with gene expression levels.
- probe sets that appeared in both EGFR-A and IC-50 B were selected (Biomarker Probe Set List A, Table 2) and probe sets that appeared in both EGFR-B and IC-50-A were selected (Biomarker Probe Set List B, Table 3).
- RT-PCR expression data for EGFR were obtained from thirty one colon cancer cell lines and six cell lines with a significantly lower expression level of EGFR compared to the other cell lines were identified as described in Example 1 below. (FIG. 2 A).
- Expression profiling data of 44,792 probe sets represented on the HG- U133 array set for all thirty one untreated colon cancer cell lines were obtained and analyzed for the identification of probe sets which would be correlated with the above described six cell lines with no significant mRNA expression of EGFR.
- For the discovery probe set list EGFR-A all probe sets which were judged to be absent by the Affymetrix Mas 5.0 software in six of the six colon cancer cell lines with significantly lower expression of EGFR were identified.
- the discovery probe set list EGFR-B was generated by selecting all probe sets which were judged to be absent by the Affymetrix Mas 5.0 software in five of the six colon cancer cell lines with significantly lower expression of EGFR and which would be present in at least six cell lines of the twenty five cell lines classified as having significant mRNA expression of the EGFR.
- Discovery probe set list EGR-B contains 1,852 probe sets (U133A: 876; U133B: 976). Identifying Genes that Significantly Correlate with Drug Resistance/Sensitivity Classification
- Expression profiling data of 44,792 probe sets represented on the HG-U133 array set for twenty two untreated colon cell lines were obtained and preprocessed as described in Example 1 below. These data were analyzed using the Student's TTEST to identify genes whose expression patterns were strongly correlated with the drug resistance/sensitivity classification.
- Table 1 provides the resistance/sensitivity phenotype classification of the twenty two colon cell lines for the EGFR antagonist BMS-461453 based on the IC 50 results.
- the mean IC 0 values along with standard deviations (SD) were calculated from 2 to 5 individual determinations for each cell line as shown.
- the mean ICso across the twenty two colon cell lines for BMS-461453 was calculated and used to normalize the IC 50 data for each cell line. All cell lines with at least a 1.75 fold lower IC 50 than the most resistant cell lines were considered to be sensitive to treatment with BMS-461453.
- the cell lines designated with an asterisk are defined as being sensitive to the drug treatment.
- An "idealized expression pattern” corresponds to a gene that is uniformly high in one class (e.g., sensitive) and uniformly low in the other (e.g., resistant).
- a Student TTEST was performed in which a T value was obtained for each probe set.
- T value was generated, its corresponding confidence value (P) was found on a standard table of significance.
- T(g,c) represents the T value between expression for gene g and the sensitivity/resistance classification c;
- Xi represents mean gene expression level of samples in class 1 ;
- Discovery probe set list IC-50-B contains 5,050 probe sets (U133A: 2,498; U133B: 2,552).
- Discovery probe set list IC-50-A was generated using the Pearson correlation coefficient (a dimensionless index that ranges from -1.0 to 1.0). This value was calculated by treating the IC 50 data as continuous variables and by utilizing a linear regression model to correlate gene expression levels with IC 50 values for twenty-two colon cell lines. Probe sets with a correlation coefficient less than -0.5 were selected
- biomarker probe set lists A and B were generated, biomarker probe set lists A and B, by identifying probe sets which were present in EGFR-A and
- the biomarker probe set list A (Table 2) contains a total of 74 probe sets
- the biomarker probe set list B (Table 3) contains 95 probe sets (U133A: 47; U133B 48).
- the biomarker probe set list B contains polynucleotides identified to be biomarkers of EGFR antagonist sensitivity employing strategy B.
- strategy B polynucleotides were required to satisfy a stringent criteria for correlation to IC 50 values and a less stringent condition for EGFR status coregulation. Namely, the polynucleotides had to have a Pearsons correlation of -0.5 or less with respect to IC 50 and be called absent by the Affymetrix software in 5 out of the 6 cell lines with lowest expression of EGFR.
- the two biomarker probe sets A and B were then combined, a total of 161 different probe sets, and the redundant polynucleotides were removed, representing 125 unique polynucleotides which are provided below in Table 4.
- the Table 4 polynucleotides are biomarkers of the invention.
- Biomarker Candidates Modulation of Expression by Treatment with Ligands for EGFR or by Treatment with Inhibitors for EGFR
- Genes inhibited by EGFR antagonists were identified by treating cells in the presence of 10% serum with 0.5uM of BMS-461453 or lug/ml or 5ug/ml of C225 for 6 and 24 hours. Cells exposed to 0.05% DMSO were used as the experimental control. Expression profiling was performed, and data were analyzed using
- the gene expression of the inhibitor or EGFR treated cell lines was compared pair-wise to the untreated controls.
- Polynucleotides from the biomarker list in which expression was increased two fold with EGFR exposure or decreased two fold with EGFR inhibitor treatment compared to the untreated controls, were considered to be modulated by EGFR.
- These biomarkers are provided in Table 4. Examples of the biomarkers include EphAl, B-cell translocation gene 2, prostaglandin-endoperoxide synthase 2 and serine (or cysteine) proteinase inhibitor (clade B), which are highly expressed in sensitive cells and up regulated by treatment with EGFR.
- spondin 1, talin 2 and nuclear receptor subfamily 3 are genes whose expression levels correlate with sensitivity or resistance of colon cancer cell lines and are consistently down regulated by treatment with EGFR inhibitors BMS-461453 and C225. It appears that these biomarkers are likely to be directly or indirectly involved in the EGFR signaling pathway, based on their expression modulation by EGF or EGFR inhibitor treatment.
- betacellulin showed counter regulation with EGFR expression as defined for the EGFR-A list but had just a p value of 0.04 in the Student's TTest for correlation with IC 50 . It was still selected as a top biomarker for the strong literature support, as betacellulin is one of the published ligands of EGFR.
- Polynucleotides that correlate to a specific property of a biological system can be used to make predictions about that biological system and other biological systems.
- the invention includes single biomarkers including, for example, the fourteen top biomarkers which were tested in a voting scheme.
- the mean expression value was calculated for all fourteen biomarkers. Colon cancer cell lines which showed an expression level above the mean were then voted to be sensitive, and colon cancer cell lines with expression levels below the mean were voted to be resistant. After this procedure, the voting was compared to the actual sensitivity/resistance status according to the definition based on ICso (see above) and an error rate was calculated.
- the error rates of the fourteen top biomarkers are shown in Table 6.
- biomarkers talin, the Cystic fibrosis conductance regulator (CFTR), and mucin 3 were the best single biomarkers with error rates below 12%.
- EGFR inhibitor eriotinib HCl
- BMS-461453 A small molecule EGFR inhibitor, eriotinib HCl (BMS-461453), was tested for cytoxicity in vitro against a panel of twenty-two human colon cancer cell lines available from the American Type Culture Collection. Cytotoxicity was assessed in cells by MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4- sulphenyl)-2H-tetrazolium, inner salt) assay (T.L. Riss et al., 1992, Mol. Biol. Cell, 3 (Suppl.):184a).
- MTS 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4- sulphenyl)-2H-tetrazolium, inner salt
- the colon cells were plated at 4,000 cell/well in 96 well microtiter plates and 24 hours later serial diluted drugs were added.
- the concentration range for the EGFR inhibitor was from 5 ⁇ g/ml to 0.0016 ⁇ g/ml (roughly 10 ⁇ M to 0.0032 ⁇ M).
- the cells were incubated at 37 °C for 72 hours at which time the tetrazolium dye MTS (333 ⁇ g/ml final concentration) in combination with the electron coupling agent phenazine methosulfate (25 ⁇ M final concentration) was added.
- a dehydrogenase enzyme in live cells reduces the MTS to a form that absorbs light at 492 nm that can be quantified spectrophotometrically.
- the results were expressed as an IC 50 , which is the drug concentration required to inhibit cell proliferation (i.e., absorbance at 450 nm) to 50% of that of untreated control cells.
- the mean IC 50 and standard deviation (SD) from multiple tests for each cell line were calculated.
- the cell lines with IC 50 below 6 ⁇ M were defined as sensitive to the EGFR inhibitor, whereas those with IC 50 above 6 ⁇ M were considered to be resistant.
- the resistant/sensitive classification are shown above in Table 1, with five cell lines classified as sensitive and seventeen cell lines classified as resistant.
- RNA from each cell line was used to prepare biotinylated probe according to the Affymetrix Genechip® Expression Analysis Technical Manual, 2001.
- Targets were hybridized to Affymetrix high density oligonucleotide array human HG-U133 set chips (Affymetrix, Santa Clara, California). Arrays were then washed, and stained using the GeneChip Fluidies station according to the manufacture's instructions.
- the HG-U133 set consisting of two GeneChip® arrays contains nearly 45,000 probe sets representing more than 39,000 transcripts derived from approximately 33,000 well- substantiated human genes.
- the five colon cell lines and one lung cell line indicated with asterisks in Table 1 were used in the drug induction study.
- Three of the colon cell lines express EGFR and are sensitive to the EGFR inhibitor BMS-461453.
- the SW480 cell line, while expressing EGFR is insensitive to the EGFR inhibitor, and the COLO320_DM does not express EGFR and is EGFR inhibitor resistant.
- the lung cancer cell line H292 expresses EGFR, but its sensitivity status is unknown. Cells were seeded in a 10 cm culture plate with the medium described above and cultured for 24 hours.
- H292 cell line were washed 2X PBS, and the media was changed to RPMI without serum. The next day the cells were treated with 20 ng/ml EGF, and eventually lysed I for RNA isolation 0.5, 6 and 18 hours post treatment. Gene expression was profiled as described below.
- EGFR inhibition studies were conducted on the colon cell lines GEO, CCD33- CO, SW480 and COLO320DM.
- the expression profiling was performed as described above and data was analyzed using GeneChip® Expression Analysis software MAS 5.0.
- the expression data of EGFR inhibitor treated cell lines were compared pair- ise to that of untreated same cell line. A change was considered significant if a two fold difference in expression was demonstrated between the treated and the untreated control. Analysis was done for all four cell lines to compare the gene expression with or without EGFR inhibitor treatment.
- RNA quantification was performed using the SYBR Green real-time PCR.
- the SYBR Green real-time PCR assay is one of the most precise methods for assaying the concentration of nucleic acid templates .
- RNA can be prepared using standard methods, preferably, employing the RNeasy Kit commercially available from Qiagen (Valencia, California).
- cDNA template for real-time PCR can be generated using the SuperscriptTM First Strand Synthesis system for RT-PCR.
- SYBR Green real-time PCR reactions are prepared as follows: the reaction mix contains 20 ng first strand cDNA; 50 nM Forward Primer; 50 nM Reverse Primer; 0.75X SYBR Green I (Sigma); IX SYBR Green PCR Buffer (50mMTris-HCl pH 8.3, 75 mM KC1); 10% DMSO; 3 mM MgCl 2 ; 300 ⁇ M each dATP, dGTP, dTTP, dCTP; 1 U Platinum® Taq DNA Polymerase High Fidelity (Cat# 11304-029; Life Technologies; Rockville, Maryland).
- Real-time PCR is performed using an Applied Biosystems 5700 Sequence Detection System.
- Conditions are 95 °C for 10 minutes (denaturation and activation of Platinum® Taq DNA Polymerase), 40 cycles of PCR (95 °C for 15 seconds, 60 °C for 1 minute).
- PCR products are analyzed for uniform melting using an analysis algorithm built into the 5700 Sequence Detection System.
- cDNA quantification used in the normalization of template quantity is performed using SYBR Green real-time PCR. Expression of EGFR is normalized to GAPDH expression as described below.
- the sequences for the GAPDH oligonucleotides used in the SYBR Green realtime PCR reactions are:
- GAPDH-F 5'-AGCCGAGCCACATCGCT-3' (SEQ ID NO: 191)
- GAPDH-R 5'-GTGACCAGGCGCCCAATAC-3' (SEQ ID NO: 192)
- SEQ ID NO: 192 The sequences for the EGFR oligonucleotides used in the SYBR Green realtime PCR reactions are:
- EGFR-F 5'- GCGTCTCTTGCCGGAATGT-3' (SEQ ID NO: 193)
- EGFR-R 5'- AGCCGAGGCAGGGAATGCGTG-3' (SEQ ID NO: 194)
- the Sequence Detection System generates a Ct (threshold cycle) value that is used to calculate a concentration for each input cDNA template.
- cDNA levels for each gene of interest are normalized to GAPDH cDNA levels to compensate for variations in total cDNA quantity in the input sample. This is done by generating GAPDH Ct values for each cell line.
- Ct values for the gene of interest and GAPDH are inserted into a modified version of the ⁇ Ct equation (Applied Biosystems Prism® 5700 Sequence Detection System User Manual) which is used to calculate a GAPDH normalized relative cDNA level for each specific cDNA.
- Antibodies against the biomarkers can be prepared by a variety of methods. For example, cells expressing an biomarker polypeptide can be administered to an animal to induce the production of sera containing polyclonal antibodies directed to the expressed polypeptides.
- the biomarker protein is prepared and isolated or otherwise purified to render it substantially free of natural contaminants, using techniques commonly practiced in the art. Such a preparation is then introduced into an animal in order to produce polyclonal antisera of greater specific activity for the expressed and isolated polypeptide.
- the antibodies of the invention are monoclonal antibodies (or protein binding fragments thereof).
- Cells expressing the biomarker polypeptide can be cultured in any suitable tissue culture medium, however, it is preferable to culture cells in Earle's modified Eagle's medium supplemented to contain 10% fetal bovine serum (inactivated at about 56 °C), and supplemented to contain about 10 g/1 nonessential amino acids, about 1,00 U/ml penicillin, and about 100 ⁇ g/ml streptomycin.
- the splenocytes of immunized (and boosted) mice can be extracted and fused with a suitable myeloma cell line.
- a suitable myeloma cell line can be employed in accordance with the invention, however, it is preferable to employ the parent myeloma cell line (SP2/0), available from the ATCC.
- SP2/0 parent myeloma cell line
- the resulting hybridoma cells are selectively maintained in HAT medium, and then cloned by limiting dilution as described by Wands et al. (1981, Gastroenterology, 80:225-232).
- the hybridoma cells obtained through such a selection are then assayed to identify those cell clones that secrete antibodies capable of binding to the polypeptide immunogen, or a portion thereof.
- additional antibodies capable of binding to the biomarker polypeptide can be produced in a two-step procedure using anti-idiotypic antibodies.
- a method makes use of the fact that antibodies are themselves antigens and, therefore, it is possible to obtain an antibody that binds to a second antibody.
- protein specific antibodies can be used to immunize an animal, preferably a mouse.
- the splenocytes of such an immunized animal are then used to produce hybridoma cells, and the hybridoma cells are screened to identify clones that produce an antibody whose ability to bind to the protein-specific antibody can be blocked by the polypeptide.
- Such antibodies comprise anti-idiotypic antibodies to the protein-specific antibody and can be used to immunize an animal to induce the formation of further protein-specific antibodies.
- the following immunofluorescence protocol may be used, for example, to verify EGFR biomarker protein expression on cells or, for example, to check for the presence of one or more antibodies that bind EGFR biomarkers expressed on the surface of cells.
- Lab-Tek II chamber slides are coated overnight at 4 °C with 10 micrograms/milliliter ( ⁇ g/ml) of boyine collagen Type II in DPBS containing calcium and magnesium (DPBS++). The slides are then washed twice with cold DPBS++ and seeded with 8000 CHO-CCR5 or CHO ⁇ C4 transfected cells in a total volume of 125 ⁇ l and incubated at 37 °C in the presence of 95% oxygen / 5% carbon dioxide.
- the culture medium is gently removed by aspiration and the adherent cells are washed twice with DPBS++ at ambient temperature.
- the slides are blocked with DPBS++ containing 0.2% BSA (blocker) at 0-4 °C for one hour.
- the blocking solution is gently removed by aspiration, and 125 ⁇ l of antibody containing solution (an antibody containing solution may be, for example, a hybridoma culture supernatant which is usually used undiluted, or serum/plasma which is usually diluted, e.g., a dilution of about 1/100 dilution).
- the slides are incubated for 1 hour at 0-4 °C.
- Antibody solutions are then gently removed by aspiration and the cells are washed five times with 400 ⁇ l of ice cold blocking solution. Next, 125 ⁇ l of 1 ⁇ g/ml rhodamine labeled secondary antibody (e.g., anti-human IgG) in blocker solution is added to the cells. Again, cells are incubated for 1 hour at 0-4 °C.
- rhodamine labeled secondary antibody e.g., anti-human IgG
- the secondary antibody solution is then gently removed by aspiration and the cells are washed three times with 400 ⁇ l of ice cold blocking solution, and five times with cold DPBS++.
- the cells are then fixed with 125 ⁇ l of 3.7% formaldehyde in DPBS++ for 15 minutes at ambient temperature. Thereafter, the cells are washed five times with 400 ⁇ l of DPBS++ at ambient temperature. Finally, the cells are mounted in 50% aqueous glycerol and viewed in a fluorescence microscope using rhodamine filters.
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WO2004063709A2 (fr) | 2004-07-29 |
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WO2004063709A8 (fr) | 2005-03-31 |
CA2512536A1 (fr) | 2004-07-29 |
WO2004063709A3 (fr) | 2008-05-15 |
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