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 .- 190 . (canceled) 
     
     
         191 . A method of identifying at least one binding agent to an exosome, comprising:
 a) contacting a library of nucleic acids with a target exosome;   b) partitioning members of the library of nucleic acids that bound to the target exosome from the members of the library of nucleic acids which do not bind the target exosome; and   c) amplifying the partitioned members of the library of nucleic acids that bound to the target exosome; thereby identifying at least one binding agent to the exosome.   
     
     
         192 . The method of  claim 191 , further comprising repeating steps a)-c) at least one time, wherein the amplified nucleic acids from step c) are used as the input library of nucleic acids in the following repetition of step a). 
     
     
         193 . The method of  claim 191 , wherein the library of nucleic acids is pre-enriched against a target peptide prior to step a). 
     
     
         194 . The method of  claim 193 , wherein the target peptide is an exosome surface protein. 
     
     
         195 . The method of  claim 193 , wherein the target peptide is a cancer marker, a general exosome marker, or a tissue specific marker. 
     
     
         196 . The method of  claim 191 , wherein the at least one binding agent comprises DNA, RNA, or both. 
     
     
         197 . The method of  claim 191 , further comprising isolating at least one member of the library of nucleic acids that bound to the target exosome. 
     
     
         198 . The method of  claim 191 , further comprising isolating the target exosome prior to step a). 
     
     
         199 . The method of  claim 198 , wherein the target exosome is isolated using size exclusion chromatography, density gradient centrifugation, differential centrifugation, filtration, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfluidic separation, or combinations thereof. 
     
     
         200 . The method of  claim 191 , wherein the target exosome is isolated from a bodily fluid. 
     
     
         201 . The method of  claim 200 , wherein the bodily fluid comprises blood, plasma, serum, cerebrospinal fluid (CSF), urine, sputum, ascites fluid, synovial fluid, semen, nipple aspirates, saliva, bronchoalveolar lavage fluid, tears, oropharyngeal washes, feces, peritoneal fluids, pleural effusion, sweat, tears, aqueous humor, pericardial fluid, lymph, chyme, chyle, bile, stool water, amniotic fluid, breast milk, pancreatic juice, cerumen, Cowper's fluid, pre-ejaculatory fluid, female ejaculate, interstitial fluid, menses, mucus, pus, sebum, vaginal lubrication, vomit, or any combination thereof. 
     
     
         202 . The method of  claim 191 , wherein the target exosome is shed from a cell having a disease. 
     
     
         203 . The method of  claim 202 , wherein the disease comprises a cancer, an inflammatory disease, an immune disease, an autoimmune disease, a cardiovascular disease, a neurological disease, an infectious disease, or a pregnancy related condition. 
     
     
         204 . A method of capturing a target exosome, comprising:
 (i) providing at least one binding agent to an exosome, wherein the at least one binding agent was previously identified by the method of  claim 191 ;   (ii) contacting the at least one binding agent with a biological sample suspected of comprising the target exosome; and   (iii) capturing the target exosome bound by the at least one binding agent in step ii).   
     
     
         205 . The method of  claim 204 , wherein the at least one binding agent is bound to a substrate. 
     
     
         206 . The method of  claim 205 , wherein the substrate comprises a planar array, a well, or a particle. 
     
     
         207 . A method of detecting a target exosome, comprising:
 (i) providing at least one binding agent to an exosome identified by the method of  claim 191 ;   (ii) contacting the at least one binding agent with a biological sample suspected of comprising the target exosome; and   (iii) detecting the target exosome bound by the at least one binding agent in step ii).   
     
     
         208 . The method of  claim 207 , wherein the at least one binding agent is labeled. 
     
     
         209 . The method of  claim 208 , wherein the label comprises at least one fluorophore, quantum dot, enzyme, radioactive label, or a combination thereof.