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The aptamer of claim 31, wherein the active agent comprises a therapeutic agent or a diagnostic agent. A pharmaceutical composition comprising a therapeutically effective amount of the aptamer of any of claims or a salt thereof, and a pharmaceutically acceptable carrier or diluent. A method of treating or ameliorating a disease or disorder, comprising administering the composition of claim 34 to a subject in need thereof. The method of claim 36, wherein the biological activity of microvesicles comprises immune suppression or transfer of genetic information.

The method of any of claims , wherein the disease or disorder comprises a neoplastic, proliferative, or inflammatory disease or disorder. A pharmaceutical composition comprising a therapeutically effective amount of the aptamer of claim 26 or a salt thereof, and a pharmaceutically acceptable carrier or diluent. A kit comprising an aptamer of any preceding claim, or a pharmaceutical composition thereof. A method comprising contacting the aptamer of any of claims with a biological sample and detecting the presence or absence of binding of the aptamer to a microvesicle in the biological sample.

The method of claim 41, wherein the biological sample comprises blood or a blood component. The method of claim 41, wherein the aptamer is conjugated to a substrate prior to the contacting with the biological sample. The method of claim 43, wherein the substrate comprises a bead. The method of claim 41, wherein the aptamer is conjugated to a detectable label.

A method of detecting a presence or level of a microvesicle population in a biological sample suspected of containing the microvesicle population, comprising contacting the biological sample with one or more binding agent specific to the microvesicle population and one or more aptamer of any of claims , and detecting microvesicles that are recognized by both the one or more binding agent and the one or more aptamer, thereby detecting the presence or level of the microvesicle population in the biological sample.

The method of claim 46, wherein the biological sample comprises a tissue sample, a cell culture, or a bodily fluid. The method of claim 47, wherein the bodily fluid comprises peripheral blood, sera, 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.

The method of claim 47, wherein the bodily fluid comprises blood, serum or plasma. The method of claim 46, wherein the one or more binding agent comprises an antibody or aptamer to a microvesicle surface antigen selected from Table 3, Table 4, and a combination thereof. The method of claim 46, wherein the one or more binding agent comprises an antibody or aptamer to a microvesicle surface antigen selected from a target in Table The method of claim 46, wherein the one or more binding agent is conjugated to a substrate prior to the contacting with the biological sample.

The method of claim 54, wherein the one or more aptamer is conjugated to a detectable label. The method of claim 46, wherein the one or more binding agent is conjugated to a detectable label. The method of claim 56, wherein the one or more aptamer is conjugated to a substrate prior to the contacting with the biological sample. The method of claim 46, wherein the one or more aptamer is conjugated to a substrate prior to the contacting with the biological sample.

The method of claim 46, wherein the one or more aptamer is conjugated to a detectable label. The method of any of claims , wherein detecting the presence or level of the microvesicle population in the biological sample provides a diagnosis, prognosis or theranosis of a disease. The method of claim 60, wherein the disease comprises a cancer. The method of claim 61, wherein the cancer comprises a prostate cancer. The method of claim 61, wherein the cancer comprises a breast cancer. A method of characterizing a disease or disorder, comprising: a contacting a biological test sample with one or more aptamer of any of claims ; b detecting a presence or level of a complex between the one or more aptamer and the target bound by the one or more aptamer in the biological test sample formed in step a ; and c comparing the presence or level detected in step b to a reference level from a biological control sample, thereby characterizing the disease or disorder.

The method of claim 65, wherein the biological test sample and biological control sample each comprise a tissue sample, a cell culture, or a biological fluid. The method of claim 66, wherein the biological fluid comprises a bodily fluid. The method of claim 67, wherein the bodily fluid comprises peripheral blood, sera, 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.

The method of claim 67, wherein the bodily fluid comprises blood, serum or plasma. The method of claim 66, wherein the biological fluid comprises microvesicles. The method of claim 65, wherein the one or more aptamer binds a polypeptide or fragment thereof. The method of claim 65, wherein the polypeptide or fragment thereof is soluble or membrane bound.

The method of claim 65, wherein the polypeptide or fragment thereof comprises a biomarker in Table 3 or Table 4. The method of claim 65 or 70, wherein the one or more aptamer binds a microvesicle surface antigen in the biological sample. The method of any of claims , wherein the characterizing comprises a diagnosis, prognosis or theranosis of the disease or disorder.

The method of claim 75, wherein the disease or disorder comprises a cancer. The method of claim 77, wherein the cancer comprises a prostate cancer. The method of claim 77, wherein the cancer comprises a breast cancer. A kit comprising a reagent for carrying out the method of any of claims Use of a reagent for carrying out the method of any of claims The kit of claim 81 or use of claim 82, wherein the reagent comprises an aptamer of any of claims The composition of claim 84 or 85, comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 60, 70, 80, 90, , , , , , , , , , , , , , , , , , , or all oligonucleotides listed in SEQ ID NOs.

A composition of matter comprising one or more oligonucleotides set forth in any of Tables capable of binding to a plurality of targets present in a biological sample. A composition of matter comprising one or more oligonucleotide listed in any of Tables The composition of claim 88 or 89, comprising 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 oligonucleotides listed in Table 23 or Table A method for characterizing a condition for a test sample comprising: contacting a microvesicle sample with a plurality of oligonucleotides capable of binding one or more target s present in said microvesicle sample, identifying a set of oligonucleotides that form a complex with the sample wherein the set is predetermined to characterize a condition for the sample, thereby characterizing a condition for a sample.

A method of diagnosing a sample as cancerous or predisposed to be cancerous, comprising contacting a microvesicle sample with a plurality of oligonucleotides that are predetermined to preferentially form a complex with microvesicles from a cancer sample as compared to microvesicles from a non-cancer sample. The method of claim 92 or 93, wherein the plurality of oligonucleotides are pre-selected through a one or more steps of positive or negative selection, wherein positive selection comprises selection of oligonucleotides against a sample having substantially similar characteristics compared to the test sample, and wherein negative selection comprises selection of oligonucleotides against a sample having substantially different characteristics compared to the test sample.

The method of claim 92, wherein step b comprises performing high- throughput sequencing, amplification, or hybridization to an array. The method of claim 92, wherein the sample is from a subject suspected of having or being predisposed to having a cancer.

A method of characterizing a disease or disorder, comprising: a contacting a biological test sample with a plurality of oligonucleotides; b detecting a presence or level of a complex formed in step a between each of the members of the plurality of oligonucleotides and the biological test sample; and c comparing the presence or level detected in step b to a reference level, thereby characterizing the disease or disorder. The method of claim 98, wherein the biological test sample and biological control sample each comprise a tissue sample, a cell culture, or a biological fluid.

The method of claim 99, wherein the biological fluid comprises a bodily fluid. The method of claim , wherein the bodily fluid comprises peripheral blood, sera, 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.

The method of claim , wherein the bodily fluid comprises blood, serum or plasma. The method of claim 99, wherein the biological fluid comprises microvesicles. The method of claim , wherein the biological test sample is contacted with a plurality of oligonucleotides before isolating microvesicles. The method of claim , wherein the biological test sample comprises isolated microvesicles. The method of claim 98, wherein the one or more aptamer binds a polypeptide or fragment thereof.

The method of claim 98, wherein the polypeptide or fragment thereof is soluble or membrane bound. The method of claim 98, wherein the polypeptide or fragment thereof comprises a biomarker in Table 3 or Table 4. The method of claim 98 or , wherein the one or more aptamer binds a microvesicle surface antigen in the biological sample. The method of claim , wherein the disease or disorder comprises a cancer, a premalignant condition, an inflammatory disease, an immune disease, an autoimmune disease or disorder, a cardiovascular disease or disorder, neurological disease or disorder, infectious disease or pain.

The method of claim 91, wherein the condition is a disease or disorder. The method of claim 92, wherein the plurality of oligonucleotides is capable of preferentially binding a microvesicle that is shed from diseased cells versus normal cells.

The method of claim , wherein the diseased cells are associated with a cancer, a premalignant condition, an inflammatory disease, an immune disease, an autoimmune disease or disorder, a cardiovascular disease or disorder, neurological disease or disorder, infectious disease or pain. The method of claim , or , wherein the premalignant condition comprises Barrett's Esophagus. The method of claim , or , wherein the autoimmune disease comprises inflammatory bowel disease IBD , Crohn's disease CD , ulcerative colitis UC , pelvic inflammation, vasculitis, psoriasis, diabetes, autoimmune hepatitis, multiple sclerosis, myasthenia gravis, Type I diabetes, rheumatoid arthritis, psoriasis, systemic lupus erythematosis SLE , Hashimoto's Thyroiditis, Grave's disease, Ankylosing Spondylitis Sjogrens Disease, CREST syndrome, Scleroderma, Rheumatic Disease, organ rejection, Primary Sclerosing Cholangitis, or sepsis.

The method of claim , or , wherein the cardiovascular disease comprises atherosclerosis, congestive heart failure, vulnerable plaque, stroke, ischemia, high blood pressure, stenosis, vessel occlusion or a thrombotic event. The method of claim , or , wherein the neurological disease comprises Multiple Sclerosis MS , Parkinson's Disease PD , Alzheimer's Disease AD , schizophrenia, bipolar disorder, depression, autism, Prion Disease, Pick's disease, dementia, Huntington disease HD , Down's syndrome, cerebrovascular disease, Rasmussen's encephalitis, viral meningitis, neurospsychiatric systemic lupus erythematosus NPSLE , amyotrophic lateral sclerosis, Creutzfeldt-Jacob disease, Gerstmann-Straussler- Scheinker disease, transmissible spongiform encephalopathy, ischemic reperfusion damage e.

The method of claim , or , wherein the pain comprises fibromyalgia, chronic neuropathic pain, or peripheral neuropathic pain. The method of claim , or , wherein the infectious disease comprises a bacterial infection, viral infection, yeast infection, Whipple's Disease, Prion Disease, cirrhosis, methicillin-resistant staphylococcus aureus, HIV, HCV, hepatitis, syphilis, meningitis, malaria, tuberculosis, influenza. The method of any of claims , wherein the plurality of oliognucleotides comprises a composition of any of claims A method for identifying oligonucleotides specific for a test sample comprising: a enriching a plurality of oligonucleotides for a sample to provide a set of oligonucleotides predetermined to form a complex with a target sample; b contacting the plurality in a with a test sample to allow formation of complexes of oligonucleotides with test sample; c recovering oligonucleotides that formed complexes in b to provide a recovered subset of oligonucleotides; and d profiling the recovered subset of oligonucleotides by high-throughput sequencing, amplification or hybridization, thereby identifying oligonucleotides specific for a test sample.

The method of claim , wherein the test sample comprises a plurality of microvesicles. The kit of claim or use of claim , wherein the reagent comprises an aptamer of any of claims A method of identifying a target-specific aptamer profile for a biological sample, comprising contacting a biological test sample with a pool of aptamer molecules, contacting the pool to a control or reference biological sample, identifying one or more aptamers that bind to a component in said test sample but not to the control or reference sample, thereby identifying an aptamer profile for said biological test sample.

A method of selecting a pool of aptamers, comprising: a contacting a biological control sample with a pool of oligonucleotides; b isolating a first subset of the pool of oligonucleotides that do not bind the biological control sample; c contacting the biological test sample with the first subset of the pool of oligonucleotides; and d isolating a second subset of the pool of oligonucleotides that bind the biological test sample, thereby selecting the pool of aptamers.

The method of claim , wherein the pool of oligonucleotides comprises at least 10 2, 10 8, 9, 10 10, 10 11, 10 12, 10 13, 10 14, 10 15, 10 16, 10 12, or at least 10 18 oligonucleotides. The method of claim , wherein steps a - d are repeated at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or at least 20 times, wherein the pool of aptamers selected in step d is used as the pool of oligonucleotides in step a in each iteration.

The method of claim , wherein the biological test sample and biological control sample comprise microvesicles. The method of claim , wherein the biological test sample and optionally biological control sample comprise a bodily fluid. The method of claim , wherein the bodily fluid comprises peripheral blood, sera, 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, pre- ejaculatory fluid, female ejaculate, sweat, fecal matter, hair, tears, cyst fluid, pleural fluid, peritoneal fluid, malignant 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 or other lavage fluids.

The method of claim , wherein the biological test sample and optionally biological control sample comprise a cell culture medium. The method of claim , wherein the biological test sample comprises a diseased sample and the biological control sample comprises a non-diseased sample. A method of selecting a group of aptamers, comprising: a contacting a pool of aptamers to a population of microvesicles from a first sample; b enriching a subpool of aptamers that show affinity to the population of microvesicles from the first sample; c contacting the subpool to a second population of microvesicles from a second sample; and d depleting a second subpool of aptamers that show affinity to the second population of microvesicles from the second sample, thereby selecting the group of aptamers that have preferential affinity for the the population of microvesicles from the first sample.

The method of claim , wherein steps a - d are repeated at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 times, wherein the group of aptamers selected in step d is used as the pool of aptamers in step a in each iteration. The method of claim , further comprising identifying the members of the selected group of aptamers, optionally wherein the identifying is performed by high-throughput sequencing. The method of claim , wherein the first sample comprises a diseased sample and the second sample comprises a control sample, optionally wherein the control sample is a non-disease sample.

A method of selecting a group of aptamers, comprising: a contacting a pool of aptamer candidates to a sample comprising a target molecule; b removing unbound aptamer candidates; c contacting the sample with a ligand to the target molecule; and d isolating aptamer candidates that are disassociated from the target molecule by competition with the ligand, thereby selecting the group of aptamers that bind the same target as the ligand. The method of claim , wherein the target molecule comprises a protein.

The method of claim , wherein the protein is a microvesicle surface antigen. The method of claim , wherein the target molecule is tethered to a substrate. The method of claim , wherein the target molecule is a surface antigen of a microvesicle and the microvesicle is tethered to a substrate.

The method of claim , wherein the ligand comprises a small molecule or protein. The method of claim , wherein the ligand comprises an antibody. The method of claim , wherein steps a - d are repeated at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 times, wherein the aptamer candidates isolated in the step d are used the pool of aptamer candidates input into step a in each iteration.

The method of claim , further comprising identifying the members of the selected group of aptamers, optionally wherein the identifying is performed by high throughput sequencing. A method of selecting one or more aptamer that bind a target of interest, comprising: a separating the target from a first biological sample to form a target depleted biological sample; b tethering the separated target to a substrate; c mixing the tethered target with an interfering biological sample; d contacting the mixture from c with a starting aptamer library; and e recovering members of the aptamer library that preferentially bind the tethered target, thereby selecting the one or more aptamer that bind the target.

The method of claim , wherein the substrate comprises a bead or planar surface. The method of claim , wherein the interfering biological sample comprises the target depleted biological sample from a. The method of claim , wherein the target comprises a microvesicle. The method of claim , wherein the target comprises a microvesicle of interest and the interfering biological sample comprises a non-target microvesicle.

The method of claim , wherein the non-target microvesicle is tethered to a different substrate than the target microvesicle prior to step c. The method of claim , wherein the substrate comprises a magnetic bead and the different substrate comprises a non-magnetic bead, or wherein the substrate comprises a non-magnetic bead and the different substrate comprises a magnetic bead. The method of claim , wherein the first biological sample comprises a diseased sample and the interfering biological sample comprises a non-disease sample.

The method of claim , wherein the first biological sample comprises a non-disease sample and the interfering biological sample comprises a disease sample. A method for identifying a plurality of target ligands comprising, a contacting a reference microvesicle population with a plurality of ligands that are capable of binding one or more microvesicle surface markers; b isolating a plurality of reference ligands, wherein the plurality of reference ligands comprise a subset of the plurality of ligands that do not have an affinity for the reference microvesicle population; c contacting one or more test microvesicle with the plurality of reference ligands; and d identifying a subset of ligands from the the plurality of reference ligands that form complexes with a surface marker on the one or more test microvesicle, thereby identifying the plurality of target ligands.

The method of claim , further comprising identifying the surface marker of the target microvesicle. A method of identifying an aptamer specific to a target of interest, comprising a contacting a pool of candidate aptamers with one or more assay components, wherein the assay components do not comprise the target of interest; b recovering the members of the pool of candidate aptamers that do not bind to the one or more assay components in a ; c contacting the members of the pool of candidate aptamers recovered in b with the target of interest in the presence of one or more confounding target; and d recovering a candidate aptamer that binds to the target of interest in step c , thereby identifying the aptamer specific to the target of interest.

The method of claim , wherein steps a - b are repeated at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or at least 20 times before step c is performed. The method of claim , wherein steps c - d are repeated at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or at least 20 times before identifying the aptamer specific to the target of interest.

The method of claim , wherein the pool of candidate aptamers comprises at least 10 6, 10 7, 8, 10 9, 10 10, 10 11, 10 12, 10 13, 10 14, 10 15, 10 16, 10 17, or at least 10 18 nucleic acid sequences. The method of claim , wherein the one or more assay components comprise one or more of a substrate, a bead, a planar array, a column, a tube, a well, or a filter.

The method of claim , wherein the target of interest and the one or more confounding target comprises a protein. The method of claim , wherein the target of interest and the one or more confounding target comprises a microvesicle. The method of claim , wherein the target of interest and the one or more confounding target comprises one or more microvesicle surface antigen. The method of claim , wherein the one or more microvesicle surface antigen is selected from Tables 3, 4 and The method of claim , wherein the one or more microvesicle surface antigen is a biomarker of a disease or disorder.

The method of claim , , , , or , wherein the disease comprises a cancer, a premalignant condition, an inflammatory disease, an immune disease, an autoimmune disease or disorder, a cardiovascular disease or disorder, neurological disease or disorder, infectious disease or pain.

The method of claim , wherein the premalignant condition comprises Barrett's Esophagus. The method of claim , wherein the cardiovascular disease comprises atherosclerosis, congestive heart failure, vulnerable plaque, stroke, ischemia, high blood pressure, stenosis, vessel occlusion or a thrombotic event. The method of claim , wherein the neurological disease comprises Multiple Sclerosis MS , Parkinson's Disease PD , Alzheimer's Disease AD , schizophrenia, bipolar disorder, depression, autism, Prion Disease, Pick's disease, dementia, Huntington disease HD , Down's syndrome, cerebrovascular disease, Rasmussen's encephalitis, viral meningitis, neurospsychiatric systemic lupus erythematosus NPSLE , amyotrophic lateral sclerosis, Creutzfeldt-Jacob disease, Gerstmann-Straussler- Scheinker disease, transmissible spongiform encephalopathy, ischemic reperfusion damage e.

The method of claim , wherein the pain comprises fibromyalgia, chronic neuropathic pain, or peripheral neuropathic pain. The method of claim , wherein the infectious disease comprises a bacterial infection, viral infection, yeast infection, Whipple's Disease, Prion Disease, cirrhosis, methicillin-resistant staphylococcus aureus, HIV, HCV, hepatitis, syphilis, meningitis, malaria, tuberculosis, influenza.

A method for identifying binding agents comprising contacting a plurality of extracellular microvesicles with a randomly generated library of binding agents, identifying a subset of the library of binding agents that have an affinity to one or more components of the extracellular microvesicles. A method of characterizing a phenotype comprising contacting a test biological sample with the one or more aptamer that bind the target from any of claims as depends from claim The method of claim , wherein characterizing the phenotype comprises detecting a disease or disorder in any of claims The method of any of claims , further comprising identifying one or more target of the selected aptamers.

A method of identifying a target of a binding agent comprising: a contacting the binding agent with the target to bind the target with the binding agent, wherein the target comprises a surface antigen of a microvesicle; b disrupting the microvesicle under conditions which do not disrupt the binding of the target with the binding agent; c isolating the complex between the target and the binding agent; and d identifying the target bound by the binding agent.

The method of claim , wherein the binding agent comprises an aptamer identified by the method of any of claims The method of claim , wherein the binding agent is identified by the method of claim The method of claim , wherein the binding agent comprises a ligand identified by the method of any of claims The method of claim , wherein the target comprises a protein, nucleic acid, lipid or carbohydrate.

The method of claim , wherein the target is cross-linked to the binding agent prior to step b. The method of claim , wherein disrupting the microvesicle in step b comprises use of one or more of a detergent, a surfactant, a solvent, an enzyme, mechanical shear, bead milling, homogenation, microfluidization, sonication, French Press, impingement, a colloid mill, decompression, osmotic shock, thermolysis, freeze-thaw, and desiccation.

The method of claim , wherein the enzyme comprises one or more of lysozyme, lysostaphin, zymolase, cellulase, mutanolysin, a glycanase, a protease, and mannase. The method of claim , wherein the binding agent is tethered to a substrate. The method of claim , wherein the substrate comprises a microsphere. The method of claim , wherein the substrate comprises a planar substrate. The method of claim , wherein the binding agent is labeled.

The method of claim , wherein isolating the complex between the target and the binding agent comprises capturing the binding agent via the label. The method of claim , wherein the label comprises a biotin label. The method of claim , wherein the target comprises a protein and identifying the target comprises use of mass spectrometry MS , peptide mass fingerprinting PMF; protein fingerprinting , sequencing, N-terminal amino acid analysis, C-terminal amino acid analysis, Edman degradation, chromatography, electrophoresis, two-dimensional gel electrophoresis 2D gel , antibody array, and immunoassay.

The kit of claim , wherein the one or more reagent comprises an aptamer identified by the method of any of claims The nucleic acid of any of claims , wherein the nucleic acid is further modified to comprise at least one chemical modification. The nucleic acid of claim , wherein the modification is selected from the group consisting: a chemical substitution at a sugar position; a chemical substitution at a phosphate position; and a chemical substitution at a base position of the nucleic acid.

The nucleic acid of claim , wherein the modification is selected from the group consisting of: incorporation of a modified nucleotide, 3' capping, biotinylation, conjugation to an amine linker, conjugation to a high molecular weight, non-immunogenic compound, conjugation to a lipophilic compound. The nucleic acid of claim , wherein the non-immunogenic, high molecular weight compound is a polyalkylene glycol. The nucleic acid of claim , wherein the polyalkylene glycol is polyethylene glycol.

A method of treating or ameliorating a disease or disorder, comprising administering the composition of claim to a subject in need thereof. The method of claim , wherein the biological activity of microvesicles comprises immune suppression or transfer of genetic information. The method of any of claims , wherein the disease or disorder comprises a neoplastic, proliferative, or inflammatory disease or disorder.

A pharmaceutical composition comprising a therapeutically effective amount of the aptamer of claim or a salt thereof, and a pharmaceutically acceptable carrier or diluent. A kit comprising an aptamer of any of claims , or a pharmaceutical composition thereof. A method comprising contacting the aptamer of any of claims with a biological sample and detecting the presence or absence of binding of the aptamer to a microvesicle in the biological sample. The method of claim , wherein the biological sample comprises blood or a blood component.

The method of claim , wherein the aptamer is conjugated to a substrate prior to the contacting with the biological sample. The method of claim , wherein the substrate comprises a bead. The method of claim , wherein the aptamer is conjugated to a detectable label. A method of detecting a presence or level of a microvesicle population in a biological sample suspected of containing the microvesicle population, comprising contacting the biological sample with one or more binding agent specific to the microvesicle population and one or more aptamer of any of claims , and detecting microvesicles that are recognized by both the one or more binding agent and the one or more aptamer, thereby detecting the presence or level of the microvesicle population in the biological sample.

The method of claim , wherein the one or more binding agent comprises an antibody or aptamer to a microvesicle surface antigen selected from Table 3 and Table 4, and a combination thereof. The method of claim , wherein the one or more binding agent is conjugated to a substrate prior to the contacting with the biological sample. The method of claim , wherein the one or more binding agent is conjugated to a detectable label. The method of claim , wherein the one or more aptamer is conjugated to a substrate prior to the contacting with the biological sample.

The method of claim , wherein the one or more aptamer is conjugated to a detectable label. The method of any of claims , wherein detecting the presence or level of the microvesicle population in the biological sample provides a diagnosis, prognosis or theranosis of a disease.

The method of claim , wherein the disease comprises a cancer. The method of claim , wherein the cancer comprises a breast cancer. A method of characterizing a disease or disorder, comprising: a contacting a biological test sample with one or more aptamer of any of claims ; b detecting a presence or level of a complex between the one or more aptamer and the target bound by the one or more aptamer in the biological test sample formed in step a ; c contacting a biological control sample with the one or more aptamer; d detecting a presence or level of a complex between the one or more aptamer and the target bound by the one or more aptamer in the biological control sample formed in step c ; and e comparing the presence or level detected in steps b and d , thereby characterizing the disease or disorder.

The method of claim , wherein the biological test sample and biological control sample each comprise a tissue sample, a cell culture, or a biological fluid. The method of claim , wherein the biological fluid comprises a bodily fluid. The method of claim , wherein the bodily fluid comprises peripheral blood, sera, 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.

The method of claim , wherein the bodily fluid comprises blood, serum or plasma. The method of claim , wherein the biological fluid comprises microvesicles. The method of claim , wherein the one or more aptamer binds a polypeptide or fragment thereof.

The method of claim , wherein the polypeptide or fragment thereof is soluble or membrane bound. The method of claim , wherein the polypeptide or fragment thereof comprises a biomarker in Table 3 or Table 4. The method of claim or , wherein the one or more aptamer binds a microvesicle surface antigen in the biological sample. The method of any of claims , wherein the characterizing comprises a diagnosis, prognosis or theranosis of the disease or disorder. The method of claim , wherein the disease or disorder comprises a cancer.

A kit comprising a reagent for carrying out the method of any of claims Use of a reagent for carrying out the method of any of claims The kit of claim or use of claim , wherein the reagent comprises an aptamer of any of claims The kit or use of claim , wherein the reagent further comprises at least one of: a a reagent configured to isolate a microvesicle, optionally wherein the at least one reagent configured to isolate a microvesicle comprises a binding agent to a microvesicle antigen, a column, a substrate, a filtration unit, a polymer, polyethylene glycol, PEG, PEG, a particle or a bead; b at least one oligonucleotide configured to act as a primer or probe in order to amplify, sequence, hybridize or detect the oligonucleotide or plurality of oligonucleotides; and c a reagent configured to remove one or more abundant protein from a sample, wherein optionally the one or more abundant protein comprises at least one of albumin, immunoglobulin, fibrinogen and fibrin.

The composition of claim , wherein the at least two subset libraries are manufactured with amounts of nucleotides similar or equal to at least two rows in Table The composition of claim , wherein the nucleotides consist of naturally occurring nucleotides. The composition of claim , wherein the nucleotides comprise modified naturally occurring nucleotides. The composition of claim , wherein the nucleotides comprise non- naturally occurring nucleotides.

A method of generating an input library of any of claims , comprising contacting the at least two subset libraries to generate the input library. An oligonucleotide having a sequence that comprises a 5' transposon adapter region, an offset region comprising 0 or more nucleotides located 5' to the transposon adapter region, a variable region located 5' to the offset region, and a left primer region located 5' to the variable region. A plurality of oligonucleotides comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , 10 6, 10 7, 8, 10 9, 10 10, 10 11, 10 12, 10 13, 10 14, 10 15, 10 16, 10 17, or at least 10 18 different oligonucleotide sequences, wherein each of the oligonucleotide sequences comprises a 5' transposon adapter region, an offset region comprising 0 or more nucleotides located 5' to the transposon adapter region, a variable region located 5' to the offset region, and a left primer region located 5' to the variable region.

A method of identifying an aptamer, comprising performing a SELEX selection process using an oligonucleotide or plurality of oligonucleotides according to any of claims The method of claim , wherein the selection process comprises at least one round of positive selection against a target of interest and optionally at least one round of negative selection against a target other than the target of interest. A method comprising contacting an oligonucleotide or plurality of oligonucleotides with a sample and detecting the presence or level of binding of the oligonucleotide or plurality of oligonucleotides to a target in the sample, wherein optionally the oligonucleotide or plurality of oligonucleotides are according to any of claims The method of claim , wherein the sample comprises a biological sample, an organic sample, an inorganic sample, a tissue, a cell culture, a bodily fluid, blood, serum, a cell, a microvesicle, a protein complex, a lipid complex, a carbohydrate, or any combination, fraction or variation thereof.

The method of claim , wherein the target comprises a cell, an organelle, a protein complex, a lipoprotein, a carbohydrate, a microvesicle, a membrane fragment, a small molecule, a heavy metal, a toxin, or a drug. A method comprising: a contacting a biological sample comprising microvesicles with an oligonucleotide probe library, wherein the oligonucleotide probe library comprises an oligonucleotide or plurality of oligonucleotides according to any of claims ; b identifying oligonucleotides bound to at least a portion of the microvesicles; and c characterizing the sample based on a profile of the identified oligonucleotides.

A method comprising: a contacting a sample with an oligonucleotide probe library comprising at least 10 6, 7, 10 8, 10 9, 10 10, 10 11, 10 12, 10 13, 10 14, 10 15, 10 16, 10 17, or at least 10 18 different oligonucleotide sequences oligonucleotides to form a mixture in solution, wherein the oligonucleotides are capable of binding a plurality of entities in the sample to form complexes, wherein the oligonucleotide probe library comprises an oligonucleotide or plurality of oligonucleotides according to any of claims ; b partitioning the complexes formed in step a from the mixture; and c detecting oligonucleotides present in the complexes partitioned in step b to identify an oligonucleotide profile for the sample.

The method of claim , wherein the sequencing comprises high- throughput sequencing. The method of claim , wherein the complexes are formed between the oligonucleotide or plurality of oligonucleotides and at least one of the microvesicles. The method of claim , wherein the biological test sample and biological control sample comprise isolated microvesicles, wherein optionally the microvesicles are isolated using at least one of chromatography, filtration, ultrafiltration, centrifugation, ultracentrifugation, flow cytometry, affinity capture e.

The method of claim , wherein the oligonucleotide or plurality of oligonucleotides binds a polypeptide or fragment thereof. The method of claim , wherein the polypeptide or fragment thereof is soluble or membrane bound, wherein optionally the membrane comprises a microvesicle membrane.

The method of claim , wherein the oligonucleotide or plurality of oligonucleotides binds a microvesicle surface antigen in the biological sample. The method of claim , wherein the disease or disorder comprises a cancer, a premalignant condition, an inflammatory disease, an immune disease, an autoimmune disease or disorder, a cardiovascular disease or disorder, neurological disease or disorder, infectious disease or pain.

The method of claim , wherein the premalignant condition comprises Barrett's Esophagus. The method of claim , wherein the cardiovascular disease comprises atherosclerosis, congestive heart failure, vulnerable plaque, stroke, ischemia, high blood pressure, stenosis, vessel occlusion or a thrombotic event. The method of claim , wherein the neurological disease comprises Multiple Sclerosis MS , Parkinson's Disease PD , Alzheimer's Disease AD , schizophrenia, bipolar disorder, depression, autism, Prion Disease, Pick's disease, dementia, Huntington disease HD , Down's syndrome, cerebrovascular disease, Rasmussen's encephalitis, viral meningitis, neurospsychiatric systemic lupus erythematosus NPSLE , amyotrophic lateral sclerosis, Creutzfeldt-Jacob disease, Gerstmann-Straussler- Scheinker disease, transmissible spongiform encephalopathy, ischemic reperfusion damage e.

The method of claim , wherein the pain comprises fibromyalgia, chronic neuropathic pain, or peripheral neuropathic pain. The method of claim , wherein the infectious disease comprises a bacterial infection, viral infection, yeast infection, Whipple's Disease, Prion Disease, cirrhosis, methicillin-resistant staphylococcus aureus, HIV, HCV, hepatitis, syphilis, meningitis, malaria, tuberculosis, influenza.

Use of a reagent for can-3ring out the method of any of claims The kit of claim or use of claim , wherein the reagent comprises an oligonucleotide or plurality of oligonucleotides. The kit or use of claim , wherein the oligonucleotide or plurality of oligonucleotides comprise at least one oligonucleotide according to or derived from a library according to any one of claims or Note: Descriptions are shown in the official language in which they were submitted.

Provisional Patent Application Nos. The sequence listing is within the electronically filed text file that is identified as follows: [] File Name: eqList. The invention further relates to materials and methods for the administration of aptamers capable of binding to microvesicles. The microvesicles may be derived from cells indicative of cancer, e. The terms aptamer, oligonucleotide, polynucleotide, or the like may be used interchangeably herein.

Created by an in vitro selection process from pools of random sequence oligonucleotides, aptamers have been generated for over proteins including growth factors, transcription factors, enzymes, immunoglobulins, and receptors. A typical aptamer is 15 kDa in size nucleotides , binds its target with sub-nanomolar affinity, and discriminates against closely related targets e.

A series of structural studies have shown that aptamers are capable of using the same types of binding interactions e. Aptamers are produced by an entirely in vitro process, allowing for the rapid generation of initial leads, including therapeutic leads. In vitro selection allows the specificity and affinity of the aptamer to be tightly controlled and allows the generation of leads, including leads against both toxic and non-immunogenic targets. Aptamers as a class have demonstrated little or no toxicity or immunogenicity.

Whereas the efficacy of many monoclonal antibodies can be severely limited by immune response to antibodies themselves, it is extremely difficult to elicit antibodies to aptamers most likely because aptamers cannot be presented by T-cells via the MHC and the immune response is generally trained not to recognize nucleic acid fragments.

Chromatography B. This difference is primarily due to the comparatively low solubility and thus large volumes necessary for most therapeutic mAbs. In addition, the small size of aptamers allows them to penetrate into areas of conformational constrictions that do not allow for antibodies or antibody fragments to penetrate, presenting yet another advantage of aptamer-based therapeutics or prophylaxis.

Aptamers are chemically synthesized and are readily scaled as needed to meet production demand for diagnostic or therapeutic applications. Aptamers are chemically robust. In various embodiments, aptamers of the invention are used in diagnostic, prognostic or theranostic processes to screen a biological sample for the presence or levels of microvesicle surface antigens determined to provide a diagnostic readout. The diagnosis may be related to a cancer, e. In other embodiments, aptamers of the invention are chemically modified or composed in a pharmaceutical composition for therapeutic applications.

In a related aspect, the invention provides a plurality of oligonucleotides comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , or at least different oligonucleotide sequences, wherein each of the oligonucleotide sequences or a portion thereof is at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or percent homologous to SEQ ID NO.

In a related aspect, the invention provides a plurality of oligonucleotides comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 different oligonucleotide sequences, wherein each of the oligonucleotide sequences or a portion thereof is at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or percent homologous to SEQ ID NOs. In a related aspect, the invention provides a plurality of oligonucleotides comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 different oligonucleotide sequences, wherein each of the oligonucleotide Docket No.

In a related aspect, the invention provides a plurality of oligonucleotides comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, , , , , , , , or different oligonucleotide sequences, wherein each of the oligonucleotide sequences or a portion thereof is at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or percent homologous to SEQ ID NOs.

In still another related aspect, the invention provides a plurality of oligonucleotides comprising at least 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, , , , , , , , or different oligonucleotide sequences, wherein each of the oligonucleotide sequences or a portion thereof is at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99 or percent homologous to the SEQ ID NOs.

Such a modification may be referred to as a "functional modification" herein. A functional modification may enhance or have minimal or no effect on functional aspects of an oligonucleotide. For example, the oligonucleotides may comprise DNA or RNA, incorporate various non- natural nucleotides, incorporate other chemical modifications, or comprise various deletions or insertions. Such modifications may facilitate synthesis, stability, delivery, labeling, etc, or may have little to no effect in practice.

In some cases, some nucleotides in an oligonucleotide may be substituted while maintaining functional aspects of the oligonucleotide. Similarly, 5' and 3' flanking regions may be substituted. In still other cases, only a portion of an oligonucleotide may be determined to direct its functionality such that other portions can be deleted or substituted.

Numerous techniques to synthesize and modify nucleotides and polynucleotides, including various chemical modifications, are disclosed herein or are known in the art. The sample may comprise a biological sample, an organic sample, an inorganic sample, a tissue, a cell culture, a bodily fluid, blood, serum, a cell, a microvesicle, a protein complex, a lipid complex, a carbohydrate, or any combination, fraction or variation thereof.

The target may comprise a cell, an organelle, a protein complex, a lipoprotein, a carbohydrate, a microvesicle, a membrane fragment, a small molecule, a heavy metal, a toxin, or a drug. The array can be any useful array, such as a planar or particle-based array. In a related aspect, the invention provides a plurality of oligonucleotides comprising at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , or different oligonucleotide sequences, wherein the plurality results from the method in this paragraph, wherein the library is capable of distinguishing a first phenotype from a second phenotype.

In some embodiments, the first phenotype comprises a disease or disorder and the second phenotype comprises a healthy state; or wherein the first phenotype comprises a disease or disorder and the second phenotype comprises a different disease or disorder; or wherein the first phenotype comprises a stage or progression of a disease or disorder and the second phenotype comprises a different stage or progression of the same disease or disorder; or wherein the first phenotype comprises a positive response to a therapy and the second phenotype comprises a negative response to the same therapy.

The sequencing may be high- throughput or next generation sequencing. In some embodiments, the biological fluid comprises a bodily fluid. Useful bodily fluids within the method of the invention comprise peripheral blood, sera, 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.

In some preferred embodiments, the bodily fluid comprises blood, serum or plasma. The biological fluid may comprise microvesicles. In such case, the complexes may be formed between the oligonucleotide or plurality of oligonucleotides and at least one of the microvesicles. The vesicles can also be isolated after contact with the oligonucleotide or plurality of oligonucleotides.

The polypeptide or fragment thereof can be soluble or membrane bound, wherein optionally the membrane comprises a microvesicle membrane. The membrane could also be from a cell or a fragment of a cell of vesicle. In some embodiments, the polypeptide or fragment thereof comprises a biomarker in Table 3 or Table 4. For example, the polypeptide or fragment thereof could be a general vesicle marker such as in Table 3 or a tissue-related or disease-related marker such as in Table 4.

The oligonucleotide or plurality of oligonucleotides may bind a microvesicle surface antigen in the biological sample. The premalignant condition can include without limitation Barrett's Esophagus. The cardiovascular disease can include without limitation one of atherosclerosis, congestive heart failure, vulnerable plaque, stroke, ischemia, high blood pressure, stenosis, vessel occlusion or a thrombotic event.

The neurological disease can include without limitation one of Multiple Sclerosis MS , Parkinson's Disease PD , Alzheimer's Disease AD , schizophrenia, bipolar disorder, depression, autism, Prion Disease, Pick's disease, dementia, Huntington disease HD , Down's syndrome, cerebrovascular disease, Rasmussen's encephalitis, viral meningitis, neurospsychiatric systemic lupus erythematosus NPSLE , amyotrophic lateral sclerosis, Creutzfeldt-Jacob disease, Gerstmann-Straussler- Scheinker disease, transmissible spongiform encephalopathy, ischemic reperfusion damage e.

The pain can include without limitation one of fibromyalgia, chronic neuropathic pain, or peripheral neuropathic pain. The infectious disease can include without limitation one of a bacterial infection, viral infection, yeast infection, Whipple's Disease, Prion Disease, cirrhosis, methicillin-resistant staphylococcus aureus, HIV, HCV, hepatitis, syphilis, meningitis, malaria, tuberculosis, or influenza.

One of skill will appreciate that the oligonucleotide or plurality of oligonucleotides or methods of the invention can be used to assess any number of these or other related diseases and disorders. As desired, a pool of oligonucleotides useful for characterizing various diseases is assembled to create a master pool that can be used to probe useful for characterizing the various diseases.

One of skill will also appreciate that pools of oligonucleotides useful for characterizing specific diseases or disorders can be created as well. The oligonucleotides and pools thereof can be modified as described herein. The oligonucleotides may incorporate various chemical modifications, additions, deletions, insertions, substitutions or other modifications so long as functional aspects of the oligonucleotides are enhanced or maintained in whole or in part. Ina related embodiment, the disease or disorder comprises Alzheimer's disease and the oligonucleotide or plurality of oligonucleotides useful for characterization thereof comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50 or all of SEQ ID NOs.

The disease or disorder may also comprise bronchial asthma and the oligonucleotide or plurality of oligonucleotides useful for characterization thereof comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50 or all of SEQ ID NOs. The oligonucleotides may incorporate various chemical modifications, Docket No.

In a related embodiment, the disease or disorder comprises a chronic obstructive pulmonary disease COPD and the oligonucleotide or plurality of oligonucleotides useful for characterization thereof comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50 or all of SEQ ID NOs. In a related embodiment, the disease or disorder comprises an acute myocardial infarction AMI or acute heart failure and the oligonucleotide or plurality of oligonucleotides useful for characterization thereof comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50 or all of SEQ ID NOs.

In a related embodiment, the disease or disorder comprises Chron's Disease and the oligonucleotide or plurality of oligonucleotides useful for characterization thereof comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50 or all of SEQ ID NOs. Relatedly, the disease or disorder may comprise diabetes mellitus type II and the oligonucleotide or plurality of oligonucleotides useful for characterization thereof comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50 or all of SEQ ID NOs.

Relatedly, the disease or disorder may comprise multiple sclerosis and the oligonucleotide or plurality of oligonucleotides useful for characterization thereof comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50 or all of SEQ ID NOs. In a related embodiment, the disease or disorder comprises Parkinson disease and the oligonucleotide or plurality of oligonucleotides Docket No.

The oligonucleotides may incorporate various chemical modifications, additions, deletions, insertions, Docket No. In a related embodiment, the disease or Docket No. In a similar aspect, the invention contemplates use of a reagent for carrying out the methods of the invention provided herein.

In embodiments, the reagent comprises an oligonucleotide or plurality of oligonucleotides. The oligonucleotide or plurality of oligonucleotides can be those provided herein. The reagent may comprise various other useful components including without limitation one or more of: a a reagent configured to isolate a microvesicle, optionally wherein the at least one reagent configured to isolate a microvesicle comprises a binding agent to a microvesicle antigen, a column, a substrate, a filtration unit, a polymer, polyethylene glycol, PEG, PEG, a particle or a bead; b at least one oligonucleotide configured to act as a primer or probe in order to amplify, sequence, hybridize or detect the oligonucleotide or plurality of oligonucleotides; and c a reagent configured to remove one or more abundant protein from a sample, wherein optionally the one or more abundant protein comprises at least one of albumin, immunoglobulin, fibrinogen and fibrin.

The aptamer may recognize a microvesicle surface antigen. Unless otherwise specified, one of skill in the art will appreciate that an aptamer may generally be synthesized in various forms of nucleic acid. The aptamers may also carry various chemical modifications and remain within the scope of the invention.

The modification may include without limitation a chemical substitution at a sugar position; a chemical substitution at a phosphate position; and a chemical substitution at a base position of the nucleic acid. In some embodiments, the modification is selected from the group consisting of: biotinylation, incorporation of a fluorescent label, incorporation of a modified nucleotide, a 2'-modified pyrimidine, 3' capping, conjugation to an amine linker, conjugation to a high molecular weight, non- immunogenic compound, conjugation to a lipophilic compound, conjugation to a drug, conjugation to a cytotoxic moiety, and labeling with a radioisotope, or other modification as disclosed herein.

The position of the modification can be varied as desired. For example, the biotinylation, fluorescent label, or cytotoxic moiety can be conjugated to the 5' end of the aptamer. The biotinylation, fluorescent label, or cytotoxic moiety can also be conjugated to the 3' end of the aptamer.

The nanoparticle can be selected from the group consisting of: liposomes, dendrimers, and comb polymers. In other embodiments, the cytotoxic moiety comprises a small molecule cytotoxic moiety. The small molecule cytotoxic moiety can include without limtation vinblastine hydrazide, calicheamicin, vinca alkaloid, a cryptophycin, a tubulysin, dolastatin, dolastatin, auristatin E, rhizoxin, epothilone B, epithilone D, taxoids, maytansinoids and any variants and derivatives thereof.

In still other embodiments, the cytotoxic moiety comprises a protein toxin. For example, the protein toxin can be selected from the group consisting of diphtheria toxin, ricin, abrin, gelonin, and Pseudomonas exotoxin A. Non- immunogenic, high molecular weight compounds for use with the invention include polyalkylene glycols, e.

Appropriate radioisotopes include yttrium, indium, iodine, lutetium, copper, rhenium, rhenium, bismuth, bismuth, astatine, and actinium- The aptamer may be labeled with a gamma-emitting radioisotope. For example, the active agent may be a therapeutic agent or a diagnostic agent. The invention also provides a pharmaceutical composition comprising a therapeutically effective amount of the aptamer or a salt thereof, and a pharmaceutically acceptable carrier or diluent.

Relatedly, the invention provides a method of treating or ameliorating a disease or disorder, comprising administering the pharmaceutical composition to a subject in need thereof. In an embodiment, the biological activity of microvesicles comprises immune suppression or transfer of genetic information. The disease or disorder can include without limitation those disclosed herein. For example, the disease or disorder may comprise a neoplastic, proliferative, or inflammatory, metabolic, cardiovascular, or neurological disease or disorder.

See above and further section "Phenotypes. As disclosed herein, the biological sample can be a tissue, fluid or cell culture sample. For example, the biological sample may comprise blood or a blood component. In some embodiments, the aptamer is conjugated to a substrate prior to the contacting with the biological sample. For example, the substrate may comprise a bead or a plate well. The aptamer may also be conjugated to a detectable label. Various configurations of the method are provided herein.

See, e. The bodily fluid can be any useful fluid, including without limitation one or more of peripheral blood, sera, 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 Docket No.

In some embodiments, the bodily fluid comprises blood, serum or plasma. In some embodiments, the one or more binding agent comprises an antibody or aptamer to a microvesicle surface antigen selected from Table 3, Table 4, and a combination thereof. For example, a "sandwich" format can be used. In some embodiments of the method, the one or more binding agent is conjugated to a substrate prior to the contacting with the biological sample.

In this configuration, the one or more aptamer may be conjugated to a detectable label to serve as a detector agent. In other embodiments, the one or more binding agent is conjugated to a detectable label. In this configuration, the one or more aptamer may be conjugated to a substrate prior to the contacting with the biological sample to serve as a capture agent.

In such cases, the one or more aptamer can act as either or both of a capture agent and a detection agent. The reference level may be derived from a level of the target in a healthy sample individual, e. The reference level may also be derived from an individual or sample having a treated, controlled, or alternate disease.

The bodily fluid can be any useful fluid, including without limitation one or more of peripheral blood, sera, 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.

In some Docket No. The biological fluid may comprise or be suspected to comprise microvesicles. The binding may be promiscuous or selective as desired. The polypeptide or fragment thereof can be soluble or membrane bound, e. The polypeptide or fragment thereof comprises a biomarker in Table 3 or Table 4. The one or more aptamer can bind a microvesicle surface antigen in the biological sample. For example, the reagent may comprise an aptamer disclosed herein.

The reagent may further comprise other useful components disclosed herein including without limitation at least one of: a a reagent configured to isolate a microvesicle, optionally wherein the at least one reagent configured to isolate a microvesicle comprises a binding agent to a microvesicle antigen, a column, a substrate, a filtration unit, a polymer, polyethylene glycol, PEG, PEG, a particle or a bead; b at least one oligonucleotide configured to act as a primer or probe in order to amplify, sequence, hybridize or detect the oligonucleotide or plurality of oligonucleotides; and c a reagent configured to remove one or more abundant protein from a sample, wherein optionally the one or more abundant protein comprises at least one of albumin, immunoglobulin, fibrinogen and fibrin.

The at least two subset libraries can be manufactured with amounts of nucleotides similar or equal to at least two rows in Table The nucleotides can consist of naturally occurring nucleotides or modified naturally occurring nucleotides as desired. The nucleotides can also comprise non-naturally occurring nucleotides. Such input oligonucleotide libraries may be referred to as "GC" libraries herein. The input oligonucleotide library can be screened or enriched to provide various aptamers or oligonucleotide probe libraries using the methods described herein.

In a related aspect, the invention provides a plurality of oligonucleotides comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , 10", , , , , , , or at least different oligonucleotide sequences, wherein each of the oligonucleotide sequences comprises a 5' transposon adapter region, an offset region comprising 0 or more nucleotides located 5' to the transposon adapter region, a variable region located 5' to the offset region, and a left primer region located 5' to the variable region.

Such oligonucleotides may be referred to herein as "balanced" oligonucleotides. The variable region may comprise "GC" library sequences as provided herein. Such selection or enrichment processes are described or provided herein, including without limitation SELEX and variations thereof. In an embodiment, the selection process comprises at least one round of positive selection against a target of interest and optionally at least one round of negative selection against a target other than the target of interest.

The sample may comprise a biological sample, such as an organic sample, an inorganic sample, a tissue, a cell culture, a bodily fluid, blood, serum, a cell, a microvesicle, a protein complex, a lipid complex, a carbohydrate, or any combination, fraction or variation thereof. The target can be any useful target, including without limitation a cell, an organelle, a protein complex, a lipoprotein, a carbohydrate, a microvesicle, a membrane fragment, a small molecule, a heavy metal, a toxin, or a drug.

In a related aspect, the invention provides a method of characterizing a disease or disorder, comprising: a contacting a biological test sample with a balanced oligonucleotide or plurality of balanced oligonucleotides; b detecting a presence or level of complexes formed in step a between the balanced oligonucleotide or plurality of balanced oligonucleotides and a target in the biological test sample; and c comparing the presence or level detected in step b to a reference level from a biological control sample, thereby characterizing the disease or disorder.

In some embodiments, the sequencing comprises high-throughput sequencing. Useful bodily fluids within the method of the invention comprise peripheral blood, sera, 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, Docket No.

The biological test sample and biological control sample may further comprise isolated microvesicles, wherein optionally the microvesicles are isolated using at least one of chromatography, filtration, ultrafiltration, centrifugation, ultracentrifugation, flow cytometry, affinity capture e. For example, the reagent may comprise one or more oligonucleotide having a sequence Docket No.

After washing and elution from the target, the eluted aptamers are again added to the target and allowed to bind. The antibody is then added to the reaction, competing with the aptamers at the epitope of the antibody. The aptamers displaced by the antibody are then collected.

The capture agent may bind a protein expressed on the surface of vesicles shed from diseased cells "disease vesicle". The detection agent, which may also be an aptamer or antibody, carries a detectable label, here a fluorescent signal. The detection agent binds to the captured vesicle and provides a detectable signal via its fluorescent label.

The detection agent can detect an antigen that is generally associated with vesicles, or is associated with a cell- of-origin or a disease, e. The detection agent can detect an antigen that is generally associated with vesicles, or is associated with a cell-of-origin or a disease, e.

The biomarker combinations can be detected using assays as shown in FIGs. In the figure, the sequence is shown with 6 thymine nucleotides added to the end, which can act as a spacer to attach a biotin molecule. This aptamer is also shown with a 6- thymine tail. In Step 1, a random pool of oligonucleotides is contacted with a biological sample from a normal patient.

In Step 2, the oligos that did not bind in Step 1 are added to a biological sample isolated from diseased patients. The bound oligos from this step are then eluted, captured via their biotin linkage and then combined again with normal biological sample. The unbound oligos are then added again to disease-derived biological sample and isolated. This process can be repeated iteratively.

The final eluted aptamers are tested against patient samples to measure the sensitivity and specificity of the set. Biological samples can include blood, including plasma or serum, or other components of the circulatory system, such as microvesicles. The aptamer to be tested is fixed to a substrate using a biotin tail and is incubated with various concentrations of target , and nM.

The test is performed on a surface plasmon resonance machine SPR. The SPR machine detects association and disassociation of the aptamer and the target. Target is applied until the association and disassociation events are equal, resulting in a plateau of the curve. The equations describing the curve at each concentration can then be used to calculate the KD of the aptamer see Table 5.

Fluorescently labeled Aptamer 4 was used as a detector in the microbead assay. The figure comprises an FPLC chromatogram with all product and fractions assigned in pools after checking quality on gel. The pools correspond to those indicated in FIG. The gel was blocked 0. The figure shows a binding agent , here an aptamer for purposes of illustration, tethered to a substrate The binding agent can be covalently attached to substrate The binding agent may also be non-covalently attached.

The binding agent binds to a surface antigen of microvesicle In the step signified by arrow i , the microvesicle is disrupted while leaving the complex between the binding agent and surface antigen intact.

Disrupted microvesicle is removed, e. In the step signified by arrow iii , the surface antigen is released from the binding agent The surface antigen can be analyzed to determine its identity. The aptamers were selected from an aptamer library as binding to microbeads conjugated to breast cancer-derived microvesicles.

Experimental details are in the Examples herein. Each plot shows a different aptamer. The Y-axis indicates level of binding. In each group of samples, binding of 9 purified aptamer candidates is shown. The input sample is indicated on the X axis from left to right as follows: 1 Cancer Exosome: aptamer binding to microbeads conjugated to microvesicles isolated from plasma samples from breast cancer patients; 2 Cancer Non-exosome: aptamer binding to microbeads conjugated to plasma samples from breast cancer patients after removal of microvesicles by ultracentrifugation; 3 Non-Cancer Exosome: aptamer binding to microbeads conjugated to microvesicles isolated from plasma samples from normal i.

In FIG. Cal refers to round 1 Docket No. Aptamers selected against cancer vesicles "Ca" and non- cancer microvesicles "nCa" are shown. Labeled aptamers after the indicated round of selection were incubated with bead-captured microvesicles. The number of aptamers binding to the bead- captured microvesicles was determined.

The Y-axis indicates the percentage of bound aptamers compared to total input. The fall off from rounds 7 to 13 may indicate removal of non- specific binders. The library in this figure comprised of randomly generated sequences 30 nucleotides in length flanked by primer annealing sequences. In the figure, capture aptamer is attached to substrate Target of interest is bound by capture aptamer Detection aptamer is also bound to target of interest Detection aptamer carries label which can be detected to identify target captured to substrate via capture aptamer A pool of aptamers to a target of interest is provided The pool is contacted with a test sample to be characterized The mixture is washed to remove unbound aptamers.

The remaining aptamers are disassociated and collected The collected aptamers are identified and the identity of the retained aptamers is used to characterize the phenotype A pool of aptamers identified as binding a microvesicle population is provided The input sample comprises microvesicles that are isolated Docket No.

The pool is contacted with the isolated microvesicles to be characterized The mixture is washed to remove unbound aptamers and the remaining aptamers are disassociated and collected Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. Other features, objects, and advantages of the invention will be apparent from the description. In the specification, the singular forms also include the plural unless the context clearly dictates otherwise.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In the case of conflict, the present Specification will control. The compositions and methods of the invention comprise the use of aptamers that bind microvesicle surface antigens or a functional fragment thereof.

The methods disclosed comprise diagnostic processes and techniques using one or more aptamer of the invention, to determine level or presence of relevant microvesicle surface antigens or a functional fragment thereof. Alternatively, an aptamer of the invention can also be used as a binding agent to capture, isolate, or enrich, a cell, cell fragment, vesicle or any other fragment or complex that comprises the surface antigens or functional fragments thereof.

The invention further discloses compositions and methods of oligonucleotide pools that can be used to detect a biomarker profile in a given sample. Unless otherwise specified, one of skill in the art will appreciate that an aptamer may generally be synthesized as either form of nucleic acid and carry various chemical modifications and remain within the scope of the invention. The term aptamer may be used in the art to refer to a single oligonucleotide that binds specifically to a target of interest through mechanisms other than Watson crick base pairing, similar to binding of a monoclonal antibody to a particular antigen.

Within the scope of this disclosure and unless stated explicitly or otherwise implicit in context, the terms aptamer and oligonucleotide can be used interchangeably to refer to an oligonucleotide capable of Docket No. The SELEX process is based on the unique insight that nucleic acids have sufficient capacity for forming a variety of two- and three-dimensional structures and sufficient chemical versatility available within their monomers to act as ligands i.

Molecules of any size or composition can serve as targets. Conserved sequences are sequences, other than the previously described fixed sequences, shared by a number of aptamers that bind to the same target. Typically the oligonucleotides of the starting pool contain fixed 5' and 3' terminal sequences which flank an internal region of random nucleotides.

The randomized nucleotides can be produced in a number of ways including chemical synthesis and size selection from randomly cleaved cellular nucleic acids. Random oligonucleotides can be synthesized from phosphodiester- linked nucleotides using solid phase oligonucleotide synthesis techniques well known in the art. Acid Res.

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