Reagents and methods for use in cancer diagnosis, classification and therapy

Abstract

Methods and reagents for classifying tumors and for identifying new tumor classes and subclasses. Methods for correlating tumor class or subclass with therapeutic regimen or outcome, for identifying appropriate (new or known) therapies for particular classes or subclasses, and for predicting outcomes based on class or subclass. New therapeutic agents and methods for the treatment of cancer.

1 . A method of identifying interaction partners whose binding to tumor markers correlates with patient prognosis, the method comprising steps of: 
 providing a set of potential interaction partners; and    contacting the set of potential interaction partners with a collection of tumor samples that includes samples of tumors from patients with different prognosis', so that interaction partners that bind differentially to the tumor samples are identified.    
     
     
         2 . The method of  claim 1 , further comprising a step of: 
 defining a panel of the differentially binding interaction partners whose collective binding correlates with a particular patient prognosis.    
     
     
         3 . A method of assessing prognosis of a patient having a particular tumor, the method comprising steps of: 
 obtaining a tumor sample from a patient with unknown prognosis;    contacting the sample with a panel of interaction partners whose binding has been correlated with a particular prognosis; and    assessing the patient's likely prognosis based upon binding of the panel to the tumor sample.    
     
     
         4 . A method of identifying interaction partners whose binding to tumor markers correlates with responsiveness to therapy, the method comprising steps of: 
 providing a set of potential interaction partners; and    contacting the set of potential interaction partners with a collection of tumor samples that includes samples of tumors that respond differently to therapy, so that interaction partners that bind differentially to the tumor samples are identified.    
     
     
         5 . The method of  claim 4 , further comprising a step of: 
 defining a panel of the differentially binding interaction partners whose collective binding correlates with a particular response to therapy.    
     
     
         6 . A method of predicting responsiveness of a particular tumor to therapy, the method comprising steps of: 
 providing a sample from a tumor of unknown responsiveness;    contacting the sample with a panel of interaction partners whose binding has been correlated with a particular response to therapy; and    assessing the tumor's likely responsiveness to therapy based on binding by the panel to the tumor sample.    
     
     
         7 . A method of identifying interaction partners whose binding to tumor markers correlates with tumor class or subclass, the method comprising steps of: 
 providing a set of potential interaction partners;    contacting the set of interaction partners with a collection of tumor samples that includes samples from different tumor classes or subclasses, so that interaction partners that bind differentially to the tumor samples are identified.    
     
     
         8 . The method of  claim 7 , further comprising: 
 defining a panel of the differentially binding interaction partners whose collective binding correlates with a particular tumor class or subclass.    
     
     
         9 . A method of classifying a tumor, the method comprising steps of: 
 providing a sample from the tumor; and    contacting the sample with a panel of interaction partners whose binding has been correlated with the identity of a particular class or subclass of tumors.    
     
     
         10 . The method of  claim 1 ,  4 , or  7 , wherein certain interaction partners exhibit differential binding due to specific binding to polypeptides that are expressed by tumor cells of a particular tumor class or subclass.  
     
     
         11 . The method of  claim 1 ,  4 , or  7 , wherein certain interaction partners exhibit differential binding due to lack of binding to polypeptides that are expressed by tumor cells of a particular tumor class or subclass.  
     
     
         12 . The method of  claim 1 ,  4 , or  7 , wherein at least one of the interaction partners is an antibody.  
     
     
         13 . The method of  claim 12 , wherein the antibody is selected from the group consisting of monoclonal antibodies, polyclonal antibodies, antibody fragments, chimeric antibodies, and combinations thereof.  
     
     
         14 . The method of  claim 1 ,  4 , or  7 , wherein the collection of tumor samples comprises tumor samples from solid tumors.  
     
     
         15 . The method of  claim 1 ,  4 , or  7 , wherein the collection of tumor samples comprises tumor samples from breast tumors.  
     
     
         16 . The method of  claim 1 ,  4 , or  7 , wherein the collection of tumor samples comprises tumor samples from lung tumors.  
     
     
         17 . The method of  claim 1 ,  4 , or  7 , wherein the collection of tumor samples comprises tumor samples from colon tumors.  
     
     
         18 . The method of  claim 1 ,  4 , or  7 , wherein the collection of tumor samples comprises tumor samples from ovarian tumors.  
     
     
         19 . The method of  claim 1 ,  4 , or  7 , wherein the collection of tumor samples comprises tumor samples having a common trait selected from the group consisting of tissue of origin, stage of tumor, microscopic characteristics, submicroscopic characteristics, and combinations thereof.  
     
     
         20 . The method of  claim 2 ,  5 , or  8 , wherein the binding correlates with a p-value of less than 0.05.  
     
     
         21 . The method of  claim 3 ,  6 , or  9 , wherein the interaction partners are antibodies.  
     
     
         22 . The method of  claim 21 , wherein the antibodies are selected from the group consisting of monoclonal antibodies, polyclonal antibodies, antibody fragments, chimeric antibodies, and combinations thereof.  
     
     
         23 . The method of  claim 3 ,  6 , or  9 , wherein the tumor sample is a sample of a solid tumor.  
     
     
         24 . The method of  claim 3 ,  6 , or  9 , wherein the tumor sample is a sample of a breast tumor.  
     
     
         25 . The method of  claim 3 ,  6 , or  9 , wherein the tumor sample is a sample of a lung tumor.  
     
     
         26 . The method of  claim 3 ,  6 , or  9 , wherein the tumor sample is a sample of a colon tumor.  
     
     
         27 . The method of  claim 3 ,  6 , or  9 , wherein the tumor sample is a sample of an ovarian tumor.  
     
     
         28 . A kit comprising: 
 a panel of interaction partners whose binding with tumor samples has been correlated with patient prognosis.    
     
     
         29 . A kit comprising: 
 a panel of interaction partners whose binding with tumor samples has been correlated with responsiveness to therapy.    
     
     
         30 . A kit comprising: 
 a panel of interaction partners whose binding with tumor samples has been correlated with the identity of a particular class or subclass of tumors.    
     
     
         31 . The kit of  claim 28 ,  29 , or  30 , wherein the interaction partners are antibodies.  
     
     
         32 . The kit of  claim 31 , wherein the antibodies are selected from the group consisting of monoclonal antibodies, polyclonal antibodies, antibody fragments, chimeric antibodies, and combinations thereof.  
     
     
         33 . A method of identifying an interaction partner that is useful as a therapeutic agent for the treatment of cancer, the method comprising steps of: 
 providing a set of interaction partners that bind specifically with polypeptides expressed by tumor cells;    contacting the set of interaction partners with a collection of tumor samples; and    identifying interaction partners whose binding inhibits tumor cell growth.    
     
     
         34 . A therapeutic agent for the treatment of cancer comprising: 
 at least one interaction partner that binds specifically with a polypeptide expressed by tumor cells so that tumor cell growth is inhibited.    
     
     
         35 . The therapeutic agent of  claim 34 , wherein the interaction partner is identified according to the method of  claim 33.