Methods of predicting and monitoring tyrosine kinase inhibitor therapy

Abstract

The present invention provides methods for analyzing a combination of biomarkers to individualize tyrosine kinase inhibitor therapy in patients who have been diagnosed with cancer. In particular, the assay methods of the present invention are useful for predicting, identifying, or monitoring the response of a tumor, tumor cell, or patient to treatment with a tyrosine kinase inhibitor using an algorithm based upon biomarker profiling. The assay methods of the present invention are also useful for predicting whether a patient has a risk of developing toxicity or resistance to treatment with a tyrosine kinase inhibitor. In addition, the assay methods of the present invention are useful for monitoring tyrosine kinase inhibitor therapy in a patient receiving the drug to evaluate whether the patient will develop resistance to the drug. Furthermore, the assay methods of the present invention are useful for optimizing the dose of a tyrosine kinase inhibitor in a patient receiving the drug to achieve therapeutic efficacy and/or reduce toxic side-effects.

1 - 75 . (canceled) 
     
     
         76 . An assay method for predicting the response of a subject diagnosed with non-small cell lung cancer to treatment with gefitinib (Iressa®), said method comprising:
 (a) analyzing a sample obtained from said subject to determine the presence or absence of an activating mutation in the EGFR gene in said sample; 
 (b) analyzing said sample to determine the presence or absence of an activating mutation in the K-Ras gene when said activating mutation in the EGFR gene is absent; and 
 (c) predicting an increased likelihood that said subject will respond to treatment with gefitinib when said activating mutation in the EGFR gene is present, and predicting a decreased likelihood that said subject will respond to treatment with gefitinib when said activating mutation in the K-Ras gene is present. 
 
     
     
         77 . The method of  claim 76 , wherein said activating mutation in the EGFR gene comprises a deletion, an insertion, or a single nucleotide substitution in the tyrosine kinase domain of the EGFR gene. 
     
     
         78 . The method of  claim 76 , wherein said activating mutation in the K-Ras gene results in a substitution in the K-Ras amino acid sequence selected from the group consisting of a cysteine for glycine at position 12 (G12C), a cysteine for glycine at position 13 (G13C), an aspartic acid for glycine at position 12 (G12D), a serine for glycine at position 12 (G12S), and a valine for glycine at position 12 (G12V). 
     
     
         79 . The method of  claim 76 , wherein said sample is selected from the group consisting of whole blood, serum, plasma, urine, nipple aspirate, lymph, saliva, fine needle aspirate, tumor tissue, and combinations thereof. 
     
     
         80 . The method of  claim 79 , wherein said sample comprises circulating tumor cells, circulating endothelial cells, circulating endothelial progenitor cells, cancer stem cells, or combinations thereof. 
     
     
         81 . The method of  claim 76 , wherein said method further comprises sending the results from said prediction to a clinician. 
     
     
         82 . The method of  claim 76 , further comprising recommending the administration of gefitinib to said subject when said subject is predicted to have an increased likelihood of responding to treatment with gefitinib. 
     
     
         83 . The method of  claim 76 , further comprising recommending the administration of another tyrosine kinase inhibitor or an alternative cancer therapy to said subject when said subject is predicted to have a decreased likelihood of responding to treatment with gefitinib. 
     
     
         84 . The method of  claim 76 , further comprising analyzing said sample to determine the EGFR and HER2 copy number, the level of EGFR, TGF-α, and PTEN protein expression, and the presence or absence of Erk (MAPK) and Akt activation when said activating mutation in the K-Ras gene is absent. 
     
     
         85 . The method of  claim 84 , wherein the EGFR and HER2 copy number, the level of EGFR, TGF-α, and PTEN protein expression, and the presence or absence of Erk (MAPK) and Akt activation are each assigned an index value. 
     
     
         86 . The method of  claim 85 , wherein a cumulative index value (CIV) is calculated by summing said index values assigned to the EGFR and HER2 copy number, the level of EGFR, TGF-α, and PTEN protein expression, and the presence or absence of Erk (MAPK) and Akt activation, and wherein said index values assigned to the EGFR copy number and the level of EGFR protein expression are multiplied by a factor of 2. 
     
     
         87 . The method of  claim 86 , further comprising comparing said CIV to an index cutoff value. 
     
     
         88 . The method of  claim 87 , wherein said subject is predicted to have an increased likelihood of responding to treatment with gefitinib when said CIV is greater than or equal to said index cut-off value. 
     
     
         89 . The method of  claim 88 , further comprising recommending the administration of gefitinib to said subject. 
     
     
         90 . The method of  claim 87 , wherein said subject is predicted to have a decreased likelihood of responding to treatment with gefitinib when said CIV is less than said index cut-off value. 
     
     
         91 . The method of  claim 90 , further comprising recommending the administration of another tyrosine kinase inhibitor or an alternative cancer therapy to said subject. 
     
     
         92 . The method of  claim 76 , wherein the presence or absence of said activating mutation in the EGFR or K-Ras genes is determined by the polymerase chain reaction (PCR). 
     
     
         93 . The method of  claim 84 , wherein the EGFR and HER2 copy number is determined by fluorescence in situ hybridization (FISH) or PCR. 
     
     
         94 . The method of  claim 84 , wherein the level of EGFR, TGF-α, and PTEN protein expression is determined by immunohistochemistry (IHC) or an immunoassay. 
     
     
         95 . The method of  claim 84 , wherein the presence or absence of Erk (MAPK) and Akt activation is determined by IHC.