Methods for assessing rna patterns

Abstract

Methods and compositions for the characterizing of cancers by assessing RNA levels, such as determining an RNA pattern, are provided herein. The diagnosis, prognosis, monitoring and treatment or a cancer can be determined by detecting one or more RNAs, such as microRNAs.

1 . A method of characterizing a biological sample from a subject comprising: (a) contacting a biological sample from a subject with one or more binding agent capable of binding EpCAM; (b) determining the level or presence of EpCAM bound in step a; and comparing the level or presence determined in step b to a reference, thereby characterizing said biological sample. 
     
     
         2 . The method of  claim 1 , wherein the characterizing comprises a characterization selected from the group consisting of diagnosis, prognosis, staging, grading, determination of drug efficacy, monitoring the status of the subject's response or resistance to a treatment, selection of a therapeutic, and a combination thereof. 
     
     
         3 . The method of  claim 2 , wherein the subject is non-responsive to a current therapeutic being administered to the subject. 
     
     
         4 . The method of  claim 3 , wherein the therapeutic is a cancer therapeutic. 
     
     
         5 . The method of  claim 1 , wherein the reference is derived from a subject without a cancer. 
     
     
         6 . The method of  claim 1 , wherein the reference is derived from the subject over a time course. 
     
     
         7 . The method of  claim 1 , wherein the biological sample comprises a bodily fluid. 
     
     
         8 . The method of  claim 1 , wherein the bodily fluid comprises a bodily fluid selected from the group consisting of peripheral blood, serum, plasma, urine, semen, prostatic fluid, cowper's fluid, pre-ejaculatory fluid, and a combination thereof. 
     
     
         9 . The method of  claim 1 , wherein the bodily fluid comprises plasma or serum. 
     
     
         10 . The method of  claim 1 , wherein said biological sample comprises one or more membrane vesicles. 
     
     
         11 . The method of  claim 1 , further comprising contacting said biological sample with one or more binding agent capable of binding one or more proteins selected from the group consisting of CD9, CD63, CD81, and a combination thereof. 
     
     
         12 . The method of  claim 1 , further comprising isolating RNA from said biological sample and determining the presence or level of miR-141 in said isolated RNA. 
     
     
         13 . The method of  claim 1 , wherein the one or more binding agent is selected from the group consisting of DNA molecule, RNA molecule, antibody, antibody fragment, aptamer, peptoid, zDNA, peptide nucleic acid (PNA), locked nucleic acids (LNA), lectin, peptide, dendrimer, chemical compound, and a combination thereof. 
     
     
         14 . The method of  claim 1 , further comprising contacting the biological sample with one or more binding agent selected from the group consisting of PSA, PSMA, mAB 5D4, XPSM-A9, XPSM-A10, Galectin-3, E-selectin, Galectin-1, E4 (IgG2a kappa), and a combination thereof. 
     
     
         15 . The method of  claim 10 , further comprising isolating said one or more membrane vesicles using a technique selected from the group consisting of size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfluidic separation, and a combination thereof. 
     
     
         16 . The method of  claim 10 , wherein the one or more membrane vesicles are isolated using affinity selection using a binding agent that is capable of binding a target selected from the group consisting of PSMA, CD9, CD63, CD81, EpCAM, fragments thereof, and a combination thereof. 
     
     
         17 . The method of  claim 10 , further comprising isolating RNA from said one or more membrane vesicles and determining the presence or level of miR-141 in the isolated RNA. 
     
     
         18 . The method of  claim 10 , wherein the one or more membrane vesicles are isolated from the biological sample using one or more binding agents capable of binding a target selected from the group consisting of PSA, TMPRSS2, FASLG, TNFSF10, PSMA, NGEP, I1-7RI, CSCR4, CysLT1R, TRPM8, Kv1.3, TRPV6, TRPM8, PSGR, MISIIR, galectin-3, PCA3, TMPRSS2:ERG, fragments thereof, and a combination thereof. 
     
     
         19 . The method of  claim 10 , wherein the one or more membrane vesicles comprise membrane vesicles with a diameter of about 30 nm to about 1000 nm. 
     
     
         20 . The method of  claim 10 , wherein the one or more membrane vesicles comprise membrane vesicles with a diameter of about 30 nm to about 300 nm.