Biological markers predictive of anti-cancer response to epidermal growth factor receptor kinase inhibitors

Abstract

The present invention provides diagnostic and prognostic methods for predicting the effectiveness of treatment of a cancer patient with an EGFR kinase inhibitor. Methods are provided for predicting the sensitivity of tumor cell growth to inhibition by an EGFR kinase inhibitor, comprising assessing whether the tumor cell has undergone an epithelial to mesenchymal transition (EMT), by determining the expression level of epithelial and/or mesenchymal biomarkers, wherein tumor cells that have undergone an EMT are substantially less sensitive to inhibition by EGFR kinase inhibitors. Improved methods for treating cancer patients with EGFR kinase inhibitors that incorporate the above methodology are also provided. Additionally, methods are provided for the identification of new biomarkers that are predictive of responsiveness of tumors to EGFR kinase inhibitors. Furthermore, methods for the identification of agents that restore the sensitivity of tumor cells that have undergone EMT to inhibition by EGFR kinase inhibitors are also provided.

1 - 16 . (canceled) 
     
     
         17 . A method for treating human non-small cell lung cancer tumors in a patient, comprising:
 diagnosing a patient's likely responsiveness to the EGFR kinase inhibitor erlotinib by the steps of:   assessing the level of an epithelial biomarker expressed by cells of the tumor relative to the expression level of said biomarker in a control cell sample that is either an epithelial tumor cell or a mesenchymal-like tumor cell that has undergone an epithelial-to-mesenchymal transition; and   determining whether said level is more similar to the high level of the biomarker in a tumor epithelial cell, or low level in a tumor mesenchymal-like cell that has undergone an epithelial-to-mesenchymal transition; and   predicting if the tumor will respond effectively to treatment with the EGFR kinase inhibitor, wherein high expression levels of tumor cell epithelial biomarkers correlate with a tumor that will respond effectively to treatment with the EGFR kinase inhibitor,   wherein the epithelial biomarker is one of phospho-14-3-3 epsilon, 14-3-3 sigma (Stratifin), phospho-serine/threonine phosphatase 2A, 4F2hc(CD98 antigen), adenine nucleotide translocator 2, annexin A3, ATP synthase beta chain, phospho-insulin receptor substrate p53/p54, Basigin (CD 147 antigen), phospho-CRK-associated substrate (p130Cas), Bcl-X, phospho-P-cadherin, phospho-calmodulin (CAM), Calpain-2 catalytic subunit, Cathepsin D, Cofilin-1, Calpain small subunit 1, Catenin beta-1, Catenin delta-1 (p 120 catenin), Cystatin B, phospho-DAZ-associated protein 1, Carbonyl reductase [NADPH], Diaphanous-related formin 1 (DRF 1), Desmoglein-2, Elongation factor 1-delta, Ezrin (p81), phospho-focal adhesion kinase 1, phospho-GRB2-associated binding protein 1, phospho-GRB2, GRP 78, Glutathione S-transferase P, 3-hydroxyacyl-CoA dehydrogenase, HSP70-1, elF3 p 110, Leukocyte elastase inhibitor, Importin-4, Integrin alpha-6, Integrin beta-4, phospho-Cytokeratin 17, Cytokeratin 19, Casein kinase I alpha, Protein kinase C delta, phospho-Erbin, LIM and SH3 domain protein 1 (LASP-1), 4F21c (CD98 light chain), L-lactate dehydrogenase A chain, phospho-LIN-7 homolog C, MAP (APC-binding protein EB 1), phospho-Met tyrosine kinase (HGF receptor), Mixed-lineage leukemia protein 2, Monocarboxylate transporter 4, Myosin-9, Myosin light polypeptide 6, Nicotinamide phosphoribosyltransferase, Niban-like protein (Meg-3), Ornithine aminotransferase, phospho-Occludin, Ubiquitin thiolesterase, PAF acetylhydrolase IB beta subunit, phospho-partitioning-defective 3 (PAR-3), phospho-programmed cell death 6-interacting protein, phospho-Programmed cell death protein 6, phospho-plakophilin-2, phospho-plakophilin-3, Protein phosphatase 1, Peroxiredoxin 5, Proteasome activator complex subunit 1, RuvB-like 1, S-100P, S-100L, Calcyclin, S100C, phospho-Sec23A, phospho-Sec23B,  Lysosome  membrane protein II (LIMP II), phospho-Amplaxin (EMS 1), SLP-2, Tumor calcium signal transducer 1, Transgelin-2, Transaldolase, Translationally controlled (TCTP), Tissue transglutaminase, Transmembrane protein Tmp21, Ubiquitin-conjugating enzyme E2 N, UDP-glucosyltransferase 1, phospho-p61-Yes, or phospho-Tight junction protein ZO-1; and   administering to said patient a therapeutically effective amount of the EGFR kinase inhibitor erlotinib if the patient is identified as one who is predicted to respond effectively to treatment with the EGFR kinase inhibitor.   
     
     
         18 . A method for treating human non-small cell lung cancer tumors in a patient, comprising:
 diagnosing a patient's likely responsiveness to the EGFR kinase inhibitor erlotinib by the steps of:   assessing the level of two or more epithelial biomarkers expressed by a sample of tumor cells relative to the expression level of said biomarkers in a control cell sample that is either an epithelial carcinoma cell or a mesenchymal-like carcinoma cell, to determine whether the epithelial biomarker expression is more similar to that of an epithelial carcinoma cell or a mesenchymal-like carcinoma cell; and   predicting the sensitivity of tumor cell growth to inhibition by the EGFR kinase inhibitor, wherein simultaneous high expression levels of the two or more tumor cell epithelial biomarkers, as observed in epithelial carcinoma cells, correlates with high sensitivity of tumor cell growth to inhibition by the EGFR kinase inhibitor,   wherein the two or more epithelial biomarkers are selected from the group consisting of 14-3-3 sigma (Stratifin), 4F2hc(CD98 antigen), adenine nucleotide translocator 2, annexin A3, ATP synthase beta chain, Basigin (CD 147 antigen), Bcl-X, Calpain-2 catalytic subunit, Cathepsin D, Cofilin-1, Calpain small subunit 1, Catenin beta-1, Catenin delta-1 (p 120 catenin), Cystatin B, Carbonyl reductase [NADPH], Diaphanous-related formin 1 (DRF 1), Desmoglein-2, Elongation factor 1-delta, Ezrin (p81), GRP 78, Glutathione S-transferase P, 3-hydroxyacyl-CoA dehydrogenase, HSP70-1, elF3 p 110, Leukocyte elastase inhibitor, Importin-4, Integrin alpha-6, Integrin beta-4, Cytokeratin 19, Casein kinase I alpha, Protein kinase C delta, LIM and SH3 domain protein 1 (LASP-1), 4F21c (CD98 light chain), L-lactate dehydrogenase A chain, MAP (APC-binding protein EB 1), Mixed-lineage leukemia protein 2, Monocarboxylate transporter 4, Myosin-9, Myosin light polypeptide 6, Nicotinamide phosphoribosyltransferase, Niban-like protein (Meg-3), Ornithine aminotransferase, Ubiquitin thiolesterase, PAF acetylhydrolase IB beta subunit, Protein phosphatase 1, Peroxiredoxin 5, Proteasome activator complex subunit 1, RuvB-like 1, S-100P, S-100L, Calcyclin, S100C,  Lysosome  membrane protein II (LIMP II), SLP-2, Tumor calcium signal transducer 1, Transgelin-2, Transaldolase, Translationally controlled (TCTP), Tissue transglutaminase, Transmembrane protein Tmp21, Ubiquitin-conjugating enzyme E2 N, and UDP-glucosyltransferase 1; and   administering to said patient a therapeutically effective amount of the EGFR kinase inhibitor erlotinib if the patient is identified as one who is predicted to respond effectively to treatment with the EGFR kinase inhibitor.   
     
     
         19 . A method for treating human non-small cell lung cancer tumors in a patient, comprising:
 administering to said patient a therapeutically effective amount of the EGFR kinase inhibitor erlotinib if the patient has been identified as one who is predicted to respond effectively to treatment with the EGFR kinase inhibitor by the steps of:   assessing the level of an epithelial biomarker expressed by cells of the tumor relative to the expression level of said biomarker in a control cell sample that is either an epithelial tumor cell or a mesenchymal-like tumor cell that has undergone an epithelial-to-mesenchymal transition; and   determining whether said level is more similar to the high level of the biomarker in a tumor epithelial cell, or low level in a tumor mesenchymal-like cell that has undergone an epithelial-to-mesenchymal transition; and   predicting if the tumor will respond effectively to treatment with the EGFR kinase inhibitor, wherein high expression levels of tumor cell epithelial biomarkers correlate with a tumor that will respond effectively to treatment with the EGFR kinase inhibitor,   wherein the epithelial biomarker is one of phospho-14-3-3 epsilon, 14-3-3 sigma (Stratifin), phospho-serine/threonine phosphatase 2A, 4F2hc(CD98 antigen), adenine nucleotide translocator 2, annexin A3, ATP synthase beta chain, phospho-insulin receptor substrate p53/p54, Basigin (CD 147 antigen), phospho-CRK-associated substrate (p130Cas), Bcl-X, phospho-P-cadherin, phospho-calmodulin (CAM), Calpain-2 catalytic subunit, Cathepsin D, Cofilin-1, Calpain small subunit 1, Catenin beta-1, Catenin delta-1 (p 120 catenin), Cystatin B, phospho-DAZ-associated protein 1, Carbonyl reductase [NADPH], Diaphanous-related formin 1 (DRF 1), Desmoglein-2, Elongation factor 1-delta, Ezrin (p81), phospho-focal adhesion kinase 1, phospho-GRB2-associated binding protein 1, phospho-GRB2, GRP 78, Glutathione S-transferase P, 3-hydroxyacyl-CoA dehydrogenase, HSP70-1, elF3 p 110, Leukocyte elastase inhibitor, Importin-4, Integrin alpha-6, Integrin beta-4, phospho-Cytokeratin 17, Cytokeratin 19, Casein kinase I alpha, Protein kinase C delta, phospho-Erbin, LIM and SH3 domain protein 1 (LASP-1), 4F21c (CD98 light chain), L-lactate dehydrogenase A chain, phospho-LIN-7 homolog C, MAP (APC-binding protein EB 1), phospho-Met tyrosine kinase (HGF receptor), Mixed-lineage leukemia protein 2, Monocarboxylate transporter 4, Myosin-9, Myosin light polypeptide 6, Nicotinamide phosphoribosyltransferase, Niban-like protein (Meg-3), Ornithine aminotransferase, phospho-Occludin, Ubiquitin thiolesterase, PAF acetylhydrolase IB beta subunit, phospho-partitioning-defective 3 (PAR-3), phospho-programmed cell death 6-interacting protein, phospho-Programmed cell death protein 6, phospho-plakophilin-2, phospho-plakophilin-3, Protein phosphatase 1, Peroxiredoxin 5, Proteasome activator complex subunit 1, RuvB-like 1, S-100P, S-100L, Calcyclin, S100C, phospho-Sec23A, phospho-Sec23B,  Lysosome  membrane protein II (LIMP II), phospho-Amplaxin (EMS 1), SLP-2, Tumor calcium signal transducer 1, Transgelin-2, Transaldolase, Translationally controlled (TCTP), Tissue transglutaminase, Transmembrane protein Tmp21, Ubiquitin-conjugating enzyme E2 N, UDP-glucosyltransferase 1, phospho-p61-Yes, or phospho-Tight junction protein ZO-1.   
     
     
         20 . A method for treating human non-small cell lung cancer tumors in a patient, comprising:
 administering to said patient a therapeutically effective amount of the EGFR kinase inhibitor erlotinib if the patient has been identified as one who is predicted to respond effectively to treatment with the EGFR kinase inhibitor by the steps of:   assessing the level of two or more epithelial biomarkers expressed by a sample of tumor cells relative to the expression level of said biomarkers in a control cell sample that is either an epithelial carcinoma cell or a mesenchymal-like carcinoma cell, to determine whether the epithelial biomarker expression is more similar to that of an epithelial carcinoma cell or a mesenchymal-like carcinoma cell; and   predicting the sensitivity of tumor cell growth to inhibition by the EGFR kinase inhibitor, wherein simultaneous high expression levels of the two or more tumor cell epithelial biomarkers, as observed in epithelial carcinoma cells, correlates with high sensitivity of tumor cell growth to inhibition by the EGFR kinase inhibitor,   wherein the two or more epithelial biomarkers are selected from the group consisting of 14-3-3 sigma (Stratifin), 4F2hc(CD98 antigen), adenine nucleotide translocator 2, annexin A3, ATP synthase beta chain, Basigin (CD 147 antigen), Bcl-X, Calpain-2 catalytic subunit, Cathepsin D, Cofilin-1, Calpain small subunit 1, Catenin beta-1, Catenin delta-1 (p 120 catenin), Cystatin B, Carbonyl reductase [NADPH], Diaphanous-related formin 1 (DRF 1), Desmoglein-2, Elongation factor 1-delta, Ezrin (p81), GRP 78, Glutathione S-transferase P, 3-hydroxyacyl-CoA dehydrogenase, HSP70-1, elF3 p 110, Leukocyte elastase inhibitor, Importin-4, Integrin alpha-6, Integrin beta-4, Cytokeratin 19, Casein kinase I alpha, Protein kinase C delta, LIM and SH3 domain protein 1 (LASP-1), 4F21c (CD98 light chain), L-lactate dehydrogenase A chain, MAP (APC-binding protein EB 1), Mixed-lineage leukemia protein 2, Monocarboxylate transporter 4, Myosin-9, Myosin light polypeptide 6, Nicotinamide phosphoribosyltransferase, Niban-like protein (Meg-3), Ornithine aminotransferase, Ubiquitin thiolesterase, PAF acetylhydrolase IB beta subunit, Protein phosphatase 1, Peroxiredoxin 5, Proteasome activator complex subunit 1, RuvB-like 1, S-100P, S-100L, Calcyclin, S100C,  Lysosome  membrane protein II (LIMP II), SLP-2, Tumor calcium signal transducer 1, Transgelin-2, Transaldolase, Translationally controlled (TCTP), Tissue transglutaminase, Transmembrane protein Tmp21, Ubiquitin-conjugating enzyme E2 N, and UDP-glucosyltransferase 1; and   administering to said patient a therapeutically effective amount of the EGFR kinase inhibitor erlotinib if the patient is identified as one who is predicted to respond effectively to treatment with the EGFR kinase inhibitor.