Biomarkers of therapeutic responsiveness

Abstract

The present invention relates to methods of diagnosing breast cancer in a patient, as well as methods of monitoring the progression of breast cancer and/or methods of monitoring a treatment protocol of a therapeutic agent or a therapeutic regimen. The invention also relates to assay methods used in connection with the diagnostic methods described herein.

1 . A method for evaluating the efficacy of a treatment regimen in a patient diagnosed with breast cancer, said method comprising
 (a) obtaining a test sample from a patient undergoing said treatment regimen for breast cancer;   (b) measuring a level of a biomarker in said test sample, wherein said biomarker comprises (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof;   (c) comparing said level to a normal control level of said biomarker; and   (d) evaluating from said comparing step (c) whether said patient is responsive to said treatment regimen.   
     
     
         2 . A method for evaluating the efficacy of a treatment regimen in a patient diagnosed with breast cancer, said method comprising
 (a) ordering a test comprising a measurement of a level of a biomarker in a test sample obtained from a patient undergoing said treatment regimen for breast cancer, wherein said biomarker comprises (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof;   (b) comparing said level to a normal control level of said biomarker; and   (c) evaluating from said comparing step (b) whether said patient is responsive to said treatment regimen.   
     
     
         3 . A method of administering a treatment regimen to a patient in need thereof for treating breast cancer, comprising:
 (a) obtaining a test sample from a patient undergoing said treatment regimen for breast cancer;   (b) measuring a level of a biomarker in said test sample, wherein said biomarker comprises (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof;   (c) comparing said level to a normal control level of said biomarker;   (d) evaluating from said comparing step (c) whether said patient is responsive to said treatment regimen; and   (e) adjusting said treatment regimen based on said evaluating step (d).   
     
     
         4 . A method of administering a treatment regimen to a patient in need thereof for treating breast cancer, comprising:
 (a) obtaining a test sample from a patient prior to the commencement of said treatment regimen for breast cancer;   (b) measuring a level of a biomarker in said test sample, wherein said biomarker comprises (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof;   (c) comparing said level to a normal control level of said biomarker;   (d) evaluating from said comparing step (c) whether said patient will be responsive to said treatment regimen; and   (e) administering said treatment regimen based on said evaluating step (d).   
     
     
         5 . A method of administering a treatment regimen to a patient in need thereof for treating breast cancer, comprising:
 (a) evaluating a level of a biomarker in a test sample obtained from a patient undergoing said treatment regimen for breast cancer relative to a normal control level of said biomarker, wherein said biomarker comprises (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof; and   (b) adjusting said treatment regimen based on said evaluating step (a).   
     
     
         6 . A method of administering a treatment regimen to a patient in need thereof for treating breast cancer, comprising:
 (a) evaluating a level of a biomarker in a test sample obtained from a patient prior to the commencement of said treatment regimen for breast cancer relative to a normal control level of said biomarker, wherein said biomarker comprises (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof; and   (b) administering said treatment regimen based on said evaluating step (a).   
     
     
         7 . A method of treating breast cancer, comprising administering a VEGF-inhibitor to a patient whose levels of a biomarker for RCC or metastatic melanoma were determined to be at least 1.5-fold greater/less than those values in a normal control, wherein said biomarker of breast cancer is selected from (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof. 
     
     
         8 . The method of  claim 1  wherein said measuring step comprises conducting a multiplexed assay measurement of a plurality of said biomarkers in said test sample, wherein said multiplexed assay measurement is conducted using one reaction volume comprising said test sample. 
     
     
         9 . The method of  claim 1  wherein said method comprises measuring levels of two or more biomarkers. 
     
     
         10 . The method of  claim 9  wherein said measuring step comprises measuring levels of a first biomarker and an additional biomarker, wherein said first biomarker is a total form of a biomarker and said additional biomarker is a phosphorylated form of said biomarker. 
     
     
         11 . The method of  claim 1 , wherein said treatment regimen comprises administration of a therapeutic agent comprising gefitinib. 
     
     
         12 . The method of  claim 1  further comprising one or more additional measuring steps including:
 (x) measuring a baseline level(s) of said biomarker before said treatment regimen is initiated, and said evaluating step further comprises comparing said level and said baseline level; and 
 (y) measuring an interim level of said biomarker during said treatment regimen and said evaluating step further comprises comparing said level, said interim level and said baseline level. 
 
     
     
         13 . The method of  claim 1 , wherein said evaluating step comprises comparing said level of said biomarker to a detection cut-off level, wherein said level above said detection cut-off level is indicative of breast cancer. 
     
     
         14 . The method of  claim 1 , wherein said evaluating step comprises comparing said level of said biomarker to a detection cut-off level, wherein said level below said detection cut-off level is indicative of breast cancer. 
     
     
         15 . The method of  claim 1  further comprising determining from said level of said biomarker the disease progression of breast cancer. 
     
     
         16 . A kit for the analysis of a breast cancer panel comprising
 (a) a multi-well assay plate comprising a plurality of wells, each well comprising at least four discrete binding domains to which capture antibodies to the following human analytes are bound: (i) total and phosphorylated isoforms of Akt, MEK, mTOR, GSK3beta, and combinations thereof, (ii) p70S6K, eIF4EBP1, PTEN, and (iii) combinations thereof;   (b) in one or more vials, containers, or compartments, a set of labeled detection antibodies specific for said human analytes; and   (c) in one or more vials, containers, or compartments, a set of calibrator proteins.   
     
     
         17 . The kit of  claim 16  wherein said kit further comprises one or more diluents. 
     
     
         18 . The kit of  claim 16  wherein said detection antibodies are labeled with an electrochemiluminescent (ECL) label. 
     
     
         19 . The kit of  claim 18  wherein said kit further comprises an ECL read buffer. 
     
     
         20 . The kit of  claim 16  wherein said discrete binding domains are positioned on an electrode within said well. 
     
     
         21 . The kit of  claim 16  wherein said set of calibrator proteins comprise a lyophilized blend of proteins. 
     
     
         22 . The kit of  claim 16  wherein said set of calibrator proteins comprise a liquid formulation of calibrator proteins.