Method for predicting and evaluating responsiveness to cancer treatment with dna-damaging chemotherapeutic agents

Abstract

Provided herein are methods directed to the prediction and early assessment of the efficacy of cancer treatment regimens, in particular in patients undergoing therapy with a DNA-damaging chemotherapeutic agent, by determining expression levels of certain proteins found to be useful as biomarkers in circulating tumor cells obtained from the patient both prior to and post-treatment.

1 . A method for predicting the efficacy of treatment with a DNA-damaging chemotherapeutic agent in a patient diagnosed with cancer, the method comprising:
 determining the baseline expression level of one or more proteins selected from the group consisting of topoisomerase I, RAD51, Ki-67, and ABCG2 in circulating tumor cells obtained from the patient prior to treatment with a chemotherapeutic agent to thereby predict the responsiveness of the tumor cells to treatment with the DNA-damaging chemotherapeutic agent,   wherein   for topoisomerase I, elevated baseline expression levels indicate a predisposition to responsiveness to treatment with the DNA-damaging therapeutic agent and suppressed baseline expression levels indicate a predisposition for unresponsiveness to treatment with the DNA-damaging therapeutic agent;   for RAD51, elevated baseline expression levels indicate a predisposition for unresponsiveness to treatment with the DNA-damaging agent and suppressed baseline expression levels indicate a predisposition to responsiveness to treatment;   for Ki-67, elevated baseline expression levels indicate a predisposition to responsiveness to treatment with the DNA-damaging therapeutic agent and suppressed baseline expression levels indicate a predisposition for unresponsiveness to treatment,   for ABCG2, elevated baseline expression levels indicate a predisposition for unresponsiveness to treatment with the DNA-damaging agent and suppressed baseline expression levels indicate a predisposition to responsiveness to treatment,   wherein (i) determining whether a baseline expression level of the protein is elevated or suppressed is based upon a comparison to the mean and/or median baseline expression level of the protein in circulating tumor cells of the overall study population, (ii) the treatment comprises administering a therapeutically effective amount of the DNA-damaging therapeutic agent to the patient, and (iii) the DNA-damaging chemotherapeutic agent is selected from camptothecin, irinotecan, topotecan, etoposide, SN-38 and poly(ethylene glycol)-modified versions thereof.   
     
     
         2 . A method for assessing the response of a patient diagnosed with cancer to treatment with a DNA-damaging chemotherapeutic agent, the method comprising:
 (i) determining the baseline expression level of one or more proteins selected from γ-H2Ax, RAD-51 and TUNEL in circulating tumor cells obtained from the patient prior to treatment with the chemotherapeutic agent,   (ii) treating the patient by administering a dosage amount of the DNA-damaging chemotherapeutic agent on a given dosing schedule,   (iii) determining the expression level of the one or more proteins in circulating tumor cells obtained from the patient following said treating step,   (iv) for the one or more proteins, comparing the expression level in step (iii) with the baseline expression level in step (i),   wherein an increase in expression level is predictive of overall responsiveness to treatment with the DNA-damaging therapeutic agent and a decrease or no change in expression level is predictive of unresponsiveness to treatment, and the DNA-damaging chemotherapeutic agent is selected from camptothecin, irinotecan, topotecan, etoposide, SN-38 and poly(ethylene glycol)-modified versions thereof.   
     
     
         3 . A method for optimizing the therapeutic treatment regimen of a patient diagnosed with cancer, wherein the treatment regimen comprises administration of a DNA-damaging chemotherapeutic agent selected from camptothecin, irinotecan, topotecan, etoposide, SN-38 and poly(ethylene glycol)-modified versions thereof, the method comprising:
 (i) determining the baseline expression level of one or more proteins selected from topoisomerase I, RAD51, ABCG2, and topoisomerase II in circulating tumor cells obtained from the patient prior to treatment with the chemotherapeutic agent,   (ii) treating the patient by administering a dosage amount of the DNA-damaging chemotherapeutic agent on a given dosing schedule,   (iii) determining the expression level of the one or more proteins in circulating tumor cells obtained from the patient following said treating step,   (iv) for the one or more proteins, comparing the expression level in step (iii) with the baseline expression level in step (i),   (v) determining the resistivity or responsiveness of the patient to the treatment regimen by a method other than that of step (iv),   (vi) in the event of resistivity of the patient to the treatment as determined in step (v), examining the change in expression level for said one or more proteins from step (iv), to thereby postulate a mechanism of action related to the resistivity of the patient to treatment, and   (vii) based upon the postulation, developing a revised treatment regimen to include administration of one or more different chemotherapeutic agents that act on the tumor cells by a mechanism other than that postulated in step (vi) as being related to the development of resistivity, to thereby arrive at an improved therapeutic treatment regimen for said patient.   
     
     
         4 . The method of  claim 1 , wherein the circulating tumor cells are obtained by dielectrophoresis field-flow fractionation. 
     
     
         5 . The method of  claim 2 , wherein the circulating tumor cells are obtained by dielectrophoresis field-flow fractionation. 
     
     
         6 . The method of  claim 3 , wherein the circulating tumor cells are obtained by dielectrophoresis field-flow fractionation. 
     
     
         7 . The method of  claim 1 , wherein the cancer is breast cancer. 
     
     
         8 . The method of  claim 2 , wherein the cancer is breast cancer. 
     
     
         9 . The method of  claim 3 , wherein the cancer is breast cancer. 
     
     
         10 . The method of  claim 1 , wherein the baseline expression levels of the one or more proteins and the expression levels of the one or more proteins following treatment are determined based upon the percentage of positive cells and/or mean fluorescent intensity of the circulating tumor cells stained for detection of the one or more proteins. 
     
     
         11 . The method of  claim 2 , wherein the baseline expression levels of the one or more proteins and the expression levels of the one or more proteins following treatment are determined based upon the percentage of positive cells and/or mean fluorescent intensity of the circulating tumor cells stained for detection of the one or more proteins. 
     
     
         12 . The method of  claim 3 , wherein the baseline expression levels of the one or more proteins and the expression levels of the one or more proteins following treatment are determined based upon the percentage of positive cells and/or mean fluorescent intensity of the circulating tumor cells stained for detection of the one or more proteins. 
     
     
         13 . The method of  claim 2 , wherein determining step (iii) is carried out before the second cycle of treatment. 
     
     
         14 . The method of  claim 3 , wherein determining step (iii) is carried out before the second cycle of treatment. 
     
     
         15 . The method of  claim 2 , wherein said steps (ii)-(iv) are optionally repeated for 2-4 additional cycles. 
     
     
         16 . The method of  claim 15 , wherein the cycle comprises administering the chemotherapeutic agent every 3 weeks. 
     
     
         17 . The method of  claim 2 , wherein upon observation of a decrease in expression level of the one or more proteins in step (iv), either the dosage amount or dosing schedule in step (ii) or both are altered. 
     
     
         18 . The method of  claim 2 , wherein upon observation of a decrease in expression level of the one or more proteins in step (iv), selection of the chemotherapeutic agent administered to the patient is altered.