Methods for prediction of clinical outcome to epidermal growth factor receptor inhibitors by cancer patients

Abstract

Disclosed are biomarkers, methods and assay kits for the identification of cancer patients who are predicted to benefit, or not to benefit, from the therapeutic administration of an epidermal growth factor receptor (EGFR) inhibitor. The biomarkers of the present invention include detection of EGFR and HER 2 gene amplification and polysomy, EGFR protein expression, EGFR mutations, phosphorylated Akt protein expression, and various combinations of such biomarkers, as well as the combination of these biomarkers with mutations in the tyrosine kinase domain of the EGFR gene. Increased EGFR gene copy number, increased HER2 gene copy number, increased EGFR protein expression, activated AKT protein expression (phosphorylated AKT) and EGFR mutations are all associated with better outcome for cancer patients treated with EGFR inhibitors. The invention provides a diagnostic paradigm based on each of these tests and combinations of these tests to select cancer patients who will benefit from EGFR inhibitor therapy, as well as a diagnostic paradigm to select cancer patients who will not benefit from EGFR inhibitor therapy.

1 . A method to select a cancer patient who is predicted to benefit or not benefit from therapeutic administration of an EGFR inhibitor, comprising:
 a) detecting in a sample of tumor cells from a patient a level of a biomarker selected from the group consisting of:
 i) a level of amplification of the epidermal growth factor receptor (EGFR) gene; 
 ii) a level of polysomy of the EGFR gene; 
 iii) a level of amplification of the human tyrosine kinase receptor-type receptor (HER2) gene; and 
 iv) a level of polysomy of the HER2 gene; 
   b) comparing the level of the biomarker in the tumor cell sample to a control level of the biomarker selected from the group consisting of:
 i) a control level of the biomarker that has been correlated with sensitivity to the EGFR inhibitor; and 
 ii) a control level of the biomarker that has been correlated with resistance to the EGFR inhibitor; and 
   c) selecting the patient as being predicted to benefit from therapeutic administration of the EGFR inhibitor, if the level of the biomarker in the patient's tumor cells is statistically similar to or greater than the control level of the biomarker that has been correlated with sensitivity to the EGFR inhibitor, or if the level of the biomarker in the patient's tumor cells is statistically greater than the level of the biomarker that has been correlated with resistance to the EGFR inhibitor; or   d) selecting the patient as being predicted to not benefit from therapeutic administration of the EGFR inhibitor, if the level of the biomarker in the patient's tumor cells is statistically less than the control level of the biomarker that has been correlated with sensitivity to the EGFR inhibitor, or if the level of the biomarker in the patient's tumor cells is statistically similar to or less than the level of the biomarker that has been correlated with resistance to the EGFR inhibitor.   
     
     
         2 - 5 . (canceled) 
     
     
         6 . The method of  claim 1 , wherein the step of detecting comprises using a chimeric nucleotide probe that hybridizes to the EGFR gene and to chromosome 7 centromere sequences. 
     
     
         7 . The method of  claim 1 , wherein the step of detecting comprises using a chimeric nucleotide probe that hybridizes to the HER2 gene and to chromosome 17 centromere sequences. 
     
     
         8 - 20 . (canceled) 
     
     
         21 . The method of  claim 1 , wherein the step of detecting is performed by fluorescent in situ hybridization (FISH). 
     
     
         22 . The method of  claim 1 , wherein the step of comparing comprises comparing the biomarker level in the tumor cells to a control level of the biomarker in one or more control cells that are resistant to the EGFR inhibitor. 
     
     
         23 . The method of  claim 1 , wherein the step of comparing comprises comparing the biomarker level in the tumor cells to a control level of the biomarker in one or more control cells that are sensitive to the EGFR inhibitor. 
     
     
         24 . The method of  claim 1 , wherein the control level of the biomarker that has been correlated with sensitivity and/or resistance to the EGFR inhibitor has been predetermined. 
     
     
         25 . 
     
     
         26 . The method of  claim 1 , wherein a patient having a tumor sample with about 4 or more copies of the EGFR gene in greater than or equal to about 40% of cells is predicted to benefit from treatment with the EGFR inhibitor. 
     
     
         27 . The method of  claim 1 , wherein a patient is predicted to benefit from to treatment with the EGFR inhibitor, when the patient has a tumor sample with EGFR gene clusters or:
 a) a ratio of EGFR gene copies to chromosome 7 copies per cell of about 2 or more; or   b) an average of about 15 or more copies of the EGFR gene per cell in greater than or equal to about 10% of analyzed cells.   
     
     
         28 . The method of  claim 1 , wherein a patient having a tumor sample with 3 or more copies of the HER2 gene in less than about 40% of cells is predicted to be a poor- or non-responder from treatment with the EGFR inhibitor. 
     
     
         29 . The method of  claim 1 , wherein a patient having a tumor sample with about 4 or more copies of the HER2 gene in greater than or equal to about 40% of cells is predicted to benefit from treatment with the EGFR inhibitor. 
     
     
         30 . The method of  claim 1 , wherein a patient is predicted to benefit from treatment with the EGFR inhibitor, when the patient has a tumor sample with HER2 gene clusters or:
 a) a ratio of HER2 gene copies to chromosome 17 copies per cell of about 2 or more; or   b) an average of about 15 or more copies of the HER2 gene per cell in greater than or equal to about 10% of analyzed cells.   
     
     
         31 . The method of  claim 1 , wherein selection of the patient in step (d) based on EGFR gene amplification or polysomy is reversed if the patient is selected as being predicted to benefit from therapeutic administration of the EGFR inhibitor based on HER2 gene amplification or polysomy. 
     
     
         32 . The method of  claim 1 , wherein the selection of the patient in step (c) based on EGFR gene amplification or polysomy and the positive selection of the patient based on HER2 gene amplification or polysomy increases the likelihood that the patient will respond to treatment with the EGFR inhibitor as compared to selection of the patient in step (c) based on EGFR gene amplification or polysomy alone. 
     
     
         33 . (canceled) 
     
     
         34 . (canceled) 
     
     
         35 . The method of  claim 1 , further comprising:
 a) detecting a level of expression of phosphorylated Akt protein in the tumor cell sample;   b) comparing the level of phosphorylated Akt protein expression in the tumor cell sample to a control level of phosphorylated Akt protein expression selected from the group consisting of:
 i) a control level that has been correlated with sensitivity to the EGFR inhibitor; and 
 ii) a control level that has been correlated with resistance to the EGFR inhibitor; and 
   c) selecting the patient as being predicted to benefit from therapeutic administration of the EGFR inhibitor, if the level of phosphorylated Akt protein expression in the patient's tumor cells is statistically similar to or greater than the control level of phosphorylated Akt protein expression that has been correlated with sensitivity to the EGFR inhibitor, or if the level of phosphorylated Akt protein expression in the patient's tumor cells is statistically greater than the level of phosphorylated Akt protein expression that has been correlated with resistance to the EGFR inhibitor; or   d) selecting the patient as being predicted to not benefit from therapeutic administration of the EGFR inhibitor, if the level of phosphorylated Akt protein expression in the patient's tumor cells is statistically less than the control level of phosphorylated Akt protein expression that has been correlated with sensitivity to the EGFR inhibitor, or if the level of phosphorylated Akt protein expression in the patient's tumor cells is statistically similar to or less than the level of phosphorylated Akt protein expression that has been correlated with resistance to the EGFR inhibitor.   
     
     
         36 . (canceled) 
     
     
         37 . The method of  claim 35 , wherein the step of detecting comprises detecting EGFR polysomy and expression of phosphorylated AKT protein. 
     
     
         38 . The method of  claim 1 , further comprising a step of detecting mutations in the tyrosine kinase domain EGFR gene, wherein detection of one or more mutations in the EGFR gene is further predictive that the patient will benefit from treatment with the EGFR inhibitor 
     
     
         39 - 49 . (canceled) 
     
     
         50 . The method of  claim 1 , wherein the EGFR inhibitor is selected from gefitinib, erlotinib, and cetuximab. 
     
     
         51 . (canceled) 
     
     
         52 . (canceled) 
     
     
         53 . An assay kit for selecting a cancer patient who is predicted to benefit or not to benefit from therapeutic administration of an EGFR inhibitor, the assay kit comprising:
 a) a means for detecting in a sample of tumor cells a level of a biomarker or a combination of biomarkers selected from the group consisting of:
 i) a level of amplification of the epidermal growth factor receptor (EGFR) gene; 
 ii) a level of polysomy of the EGFR gene; 
 iii) a level of amplification of the human tyrosine kinase receptor-type receptor (HER2) gene; 
 iv) a level of polysomy of the HER2 gene; 
 v) a level of EGFR protein expression; and 
 vi) a level of phosphorylated Akt protein expression; and 
   b) a control selected from the group consisting of:
 i) a control sample for detecting sensitivity to the EGFR inhibitor; 
 ii) a control sample for detecting resistance to the EGFR inhibitor; 
 iii) information containing a predetermined control level of the biomarker that has been correlated with sensitivity to the EGFR inhibitor; and 
 iv) information containing a predetermined control level of the biomarker that has been correlated with resistance to the EGFR inhibitor. 
   
     
     
         54 . The assay kit of  claim 53 , further comprising at least one means for detecting at least one mutation in the EGFR gene. 
     
     
         55 - 62 . (canceled)