Systems and methods for matching oncology signatures

Abstract

Techniques to profile a disease or a disorder (e.g., a tumor) based on a protein activity signature are disclosed herein. An example method can include measuring quantitatively protein activity of a plurality of master regulator proteins in a sample from a disease or disorder; and profiling the tumor from the quantitative protein activity of the master regulator proteins. Also disclosed are methods of identifying a compound or compounds that treats diseases or disorders (e.g., inhibit tumor cell growth).

1 - 14 . (canceled) 
     
     
         15 . A processing method using a processor for screening for a therapeutic compound or agent based on an individual subject's sample, comprising:
 identifying a cell or tissue sample from a subject having a disease or disorder;   identifying a library comprising a plurality of possible therapeutic compounds or agents;   quantifying a protein activity of each of a plurality of master regulator proteins (MRPs) in the subject's cell or tissue sample to provide a subject sample-specific MRP activity signature comprising a plurality of activated and/or deactivated MRPs characteristic of the disease or disorder, wherein quantifying the protein activity of each MRP comprises obtaining a measured expression level for each of a plurality of transcriptional targets (regulon) for each MRP, and computationally inferring, using an algorithm processing arrangement, each MRP activity based, at least in part, on the measured regulon expression levels in the context of a tissue-specific regulatory model;   comparing, for each of the plurality of possible therapeutic compounds or agents, the subject sample-specific MRP activity signature to each of a corresponding plurality of quantified compound-perturbed or agent-perturbed MRP activity signatures of a cell line or an in vitro model that reflects, prior to perturbation in each case, the subject sample-specific MRP activity signature;   computing, using the algorithm processing arrangement, for each of the plurality of possible therapeutic compounds or agents, a statistical enrichment of the activated MRPs among the MRPs most deactivated by the compound or agent, and/or a statistical enrichment of the inactivated MRPs among the MRPs most induced by the compound or agent;   determining, using the algorithm processing arrangement, a subject sample-specific ranking of the compounds or agents according to the degree of enrichment, wherein the compounds or agents inducing the greatest enrichment are deemed as having the highest therapeutic value for the subject; and   identifying, among the plurality of possible therapeutic compounds or agents, a therapeutic compound or agent for treating the subject's disease or disorder based on the subject sample and the subject sample-specific ranking.   
     
     
         16 . The method of  claim 15 , wherein, with respect to the sample-specific MRP activity signature, the compound or agent induces global inversion of the protein activities of the activated MRPs among the MRPs most inactivated by the compound or agent, and/or of the inactivated MRPs among the MRPs most induced by the compound or agent. 
     
     
         17 . The method of  claim 15 , wherein said compound or agent is selected from the group consisting of small molecule chemical compounds, peptides, nucleic acids, oligonucleotides, antibodies, aptamers, modifications thereof, and combinations thereof. 
     
     
         18 . The method of  claim 15 , wherein the disease or disorder is a tumor. 
     
     
         19 . The method of  claim 18 , wherein the tumor is selected from the group consisting of glioblastoma, meningioma, leukemia, lymphoma, sarcoma, carcinoid, neuroendocrine, paraganglioma, melanoma, prostate, pancreatic, bladder, stomach, colon, breast, head & neck, kidney, gastric, small intestine, ovarian, hepatocellular, uterine corpus, and lung carcinoma. 
     
     
         20 - 21 . (canceled) 
     
     
         22 . The method of  claim 15 , wherein computationally inferring the protein activity of each MRP, comparing the subject sample-specific MRP activity signature to each of a plurality of quantified compound-perturbed or agent-perturbed MRP activity signatures, and computing, for each compound or agent, a statistical enrichment of the activated MRPs, and/or the statistical enrichment of the inactivated MRPs, comprises use of virtual inference of protein activity by enriched regulon analysis (VIPER). 
     
     
         23 - 25 . (canceled) 
     
     
         26 . The method of  claim 15 , wherein said sample from said disease or disorder is derived from an in vivo source and/or derived from an in vitro source. 
     
     
         27 . The method of  claim 26 , wherein said in vitro source is an in vitro model of the disease or disorder that has a similar master regulator signature profile for said disease or disorder. 
     
     
         28 . The method of  claim 26 , wherein said sample is selected from the group consisting of tissue extracts, cells, tissues, organs, blood, blood serum, body fluids, and combinations thereof. 
     
     
         29 . The method of  claim 26 , wherein said sample from said disease or disorder is at least one selected from the group consisting of a cell line, cultured cells, cultured tissue, and cultured tumor. 
     
     
         30 . The method of  claim 15 , wherein said regulons are inferred by ARACNe. 
     
     
         31 . The method of  claim 15 , further comprising validating the efficacy of a ranked drug using an in vivo model. 
     
     
         32 . The method of  claim 31 , wherein the in vivo model comprises a xenograft model. 
     
     
         33 . A system, comprising a processor, for computationally inferring the protein activities of each of a plurality of MRP, comparing a subject sample-specific MRP activity signature to each of a plurality of quantified compound-perturbed or agent-perturbed MRP activity signatures, and computing, for each compound or agent, a statistical enrichment of the activated MRPs, and/or the statistical enrichment of the inactivated MRPs. 
     
     
         34 . The system of  claim 33 , comprising use of virtual inference of protein activity by enriched regulon analysis (VIPER) algorithm.