Methods and systems of using exosomes for determining phenotypes

Abstract

Exosomes can be used for detecting biomarkers for diagnostic, therapy-related or prognostic methods to identify phenotypes, such as a condition or disease, for example, the stage or progression of a disease. Cell-of-origin exosomes can be used in profiling of physiological states or determining phenotypes. Biomarkers or markers from cell-of-origin specific exosomes can be used to determine treatment regimens for diseases, conditions, disease stages, and stages of a condition, and can also be used to determine treatment efficacy. Markers from cell-of-origin specific exosomes can also be used to identify conditions of diseases of unknown origin.

1 . A method of obtaining a protein profile of a microvesicle population, comprising:
 (a) contacting a microvesicle population with a binding agent that is specific to EpCAM to determine the level or presence of EpCAM on said microvesicle;   (b) comparing said level or presence to a reference sample to determine if the EpCAM protein profile of said microvesicle population is elevated or reduced compared to said reference sample, thereby obtaining a protein profile of a microvesicle.   
     
     
         2 . The method of  claim 1 , wherein the contacting comprises directly contacting a biological fluid with said binding agent. 
     
     
         3 . The method of  claim 1 , comprising isolating the microvesicle population from a biological fluid before said contacting. 
     
     
         4 . The method of  claim 2 , wherein said biological fluid comprises a bodily fluid. 
     
     
         5 . The method of  claim 4 , wherein said bodily fluid comprises peripheral blood, serum, plasma, ascites, urine, cerebrospinal fluid (CSF), sputum, saliva, bone marrow, synovial fluid, aqueous humor, amniotic fluid, cerumen, breast milk, broncheoalveolar lavage fluid, semen, prostatic fluid, cowper's fluid or pre-ejaculatory fluid, female ejaculate, sweat, fecal matter, hair, tears, cyst fluid, pleural and peritoneal fluid, pericardial fluid, lymph, chyme, chyle, bile, interstitial fluid, menses, pus, sebum, vomit, vaginal secretions, mucosal secretion, stool water, pancreatic juice, lavage fluids from sinus cavities, bronchopulmonary aspirates, blastocyl cavity fluid, or umbilical cord blood. 
     
     
         6 . The method of  claim 1 , wherein said microvesicle comprises microvesicles having a diameter of about 30 nm to about 1,500 nm. 
     
     
         7 . The method of  claim 3 , wherein said isolating comprises size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfluidic separation, or a combination thereof. 
     
     
         8 . The method of  claim 5 , wherein said bodily fluid is from a subject that has or is suspected to have cancer. 
     
     
         9 . The method of  claim 8 , wherein the cancer comprises prostate, lung, colon, breast, bladder, endometrial, liver, pancreatic, ovarian, esophageal or kidney cancer. 
     
     
         10 . The method of  claim 1 , further comprising contacting said microvesicle population with a second binding agent that is specific for EpCAM. 
     
     
         11 . The method of  claim 10 , wherein said second binding agent comprises an antigen, DNA molecule, RNA molecule, antibody, antibody fragment, aptamer, peptoid, zDNA, peptide nucleic acid (PNA), locked nucleic acids (LNA), lectin, peptide, dendrimer or chemical compound. 
     
     
         12 . The method of  claim 1 , wherein said binding agent comprises an antigen, DNA molecule, RNA molecule, antibody, antibody fragment, aptamer, peptoid, zDNA, peptide nucleic acid (PNA), locked nucleic acids (LNA), lectin, peptide, dendrimer or chemical compound. 
     
     
         13 . The method of  claim 1 , wherein said reference is derived from a subject over a time course. 
     
     
         14 . The method of  claim 1 , further comprising contacting said microvesicle population with an additional binding agent specific to CD9, CD63 or CD81. 
     
     
         15 . The method of  claim 1 , further comprising isolating one or more nucleic acid molecule from said microvesicle population to determine the presence or level of said one or more nucleic acid molecule. 
     
     
         16 . The method of  claim 15 , wherein said one or more nucleic acid molecule comprises TMPRSS2-ERG. 
     
     
         17 . The method of  claim 8 , wherein the cancer is prostate cancer.