Cancer-related biological materials in microvesicles

Abstract

Disclosed herein are methods for assaying a biological sample from a subject by analyzing components of microvesicle fractions in aid of risk, diagnosis, prognosis or monitoring of or directing treatment of the subject for, a disease or other medical condition in the subject. Also disclosed are methods of treatment and identifying biomarkers using a microvesicle fraction of a subject. Kits, pharmaceutical compositions, and profiles related to the methods are also disclosed.

1 . A method for assaying a biological sample from a subject in aid of diagnosis, prognosis or monitoring of a disease or other medical condition in the subject, comprising the steps of:
 a. isolating a microvesicle fraction from a biological sample from a subject by filtering the sample followed by ultrafiltration concentration to produce a microvesicle fraction;   b. extracting nucleic acid from the fraction; and   c. detecting the presence or absence of a biomarker in the extracted nucleic acid;   wherein the biomarker is (i) a genetic aberration associated with diagnosis, prognosis, status or stage of a disease or other medical condition, (ii) a genetic aberration associated with a disease or other medical condition or with responsiveness to a specific therapy for the disease or other medical condition, or (iii) a genetic aberration associated with a determination of the subject's risk of developing a disease or other medical condition, and wherein the genetic aberration is in or corresponds to:
 i. a c-myc gene; 
 ii. a transposable element; 
 iii. a retrotransposon element; 
 iv. a satellite correlated gene; 
 v. a repeated DNA element; 
 vi. non-coding RNA other than miRNA; or 
 vii. a fragment of any of the foregoing. 
   
     
     
         2 . The method of  claim 1 , wherein the genetic aberration is in or corresponds to an element selected from the group consisting of: a transposable element listed in Table 4 or Table 5, or a fragment thereof; a retrotransposon element that is LINE, SINE or HERV, or a fragment thereof, a retrotransposon element that is Line1 (L1), ALU, HERV-H, HERV-K, HERV-K6, HERV-W or HERV-C, or a fragment thereof, a satellite correlated gene listed in Table 6, or a fragment thereof, a repeated DNA element listed in Table 8, or a fragment thereof; and a non-coding RNA listed in Table 9 (or a fragment thereof), other than miRNA. 
     
     
         3 - 27 . (canceled) 
     
     
         28 . A method for assaying a biological sample from a subject in aid of diagnosis, prognosis or monitoring of a disease or other medical condition in the subject, comprising the steps of:
 a. isolating a microvesicle fraction from a biological sample from a subject by filtering the sample followed by ultrafiltration concentration to produce a microvesicle fraction;   b. measuring a polypeptide activity in the fraction; and   c. determining whether the polypeptide activity is higher or lower than a normal or average activity for the polypeptide;   wherein an elevated or lowered activity is associated with diagnosis, prognosis, status or stage of a disease or other medical condition.   
     
     
         29 . The method of  claim 28 , wherein the polypeptide is an enzyme. 
     
     
         30 . The method of  claim 29 , wherein the enzyme is reverse transcriptase. 
     
     
         31 . The method of  claim 30 , wherein step (c) involves determining whether the reverse transcriptase activity is higher than a normal or average activity for reverse transcriptase. 
     
     
         32 - 39 . (canceled) 
     
     
         40 . The method of  claim 1 , wherein the genetic aberration is:
 a. a species of nucleic acid;   b. the level of expression of a nucleic acid;   c. a nucleic acid variant; or   d. a combination of any of the foregoing.   
     
     
         41 . The method of  claim 1 , wherein the nucleic acid is RNA and the genetic aberration is an expression profile. 
     
     
         42 . The method of  claim 1 , wherein the fragment contains more than 10 nucleotides. 
     
     
         43 . The method of  claim 1 , wherein the biological sample is a bodily fluid. 
     
     
         44 . The method of  claim 43 , wherein the bodily fluid is blood, serum, plasma, or urine. 
     
     
         45 . The method of  claim 1 , wherein the subject is a human subject. 
     
     
         46 . The method of  claim 1 , wherein the disease or other medical condition is brain cancer. 
     
     
         47 . The method of  claim 46 , wherein the brain cancer is medulloblastoma or glioblastoma. 
     
     
         48 . The method of  claim 1 , wherein the disease or other medical condition is melanoma. 
     
     
         49 . The method of  claim 1 , wherein the step of detecting the presence or absence of a biomarker in the extracted nucleic acid comprises microarray analysis, PCR, quantitative PCR, Digital Gene Expression, or direct sequencing. 
     
     
         50 . The method of  claim 1 , further comprising the step of enriching the microvesicle fraction for microvesicles originating from a specific cell type. 
     
     
         51 - 62 . (canceled) 
     
     
         63 . A method of treating a subject having a form of cancer in which cancer cells secrete microvesicles, the method comprising administering to the subject a therapeutically effective amount of a composition comprising:
 a. an inhibitor of microvesicle secretion;   b. an inhibitor of a reverse transcriptase;   c. a microvesicle neutralizer that neutralizes the pro-tumor progression activity of tumor microvesicles; or   d. any combination of the forgoing.   
     
     
         64 . The method of  claim 63 , wherein the inhibitor of microvesicle secretion is an inhibitor of RAB GTPase. 
     
     
         65 . The method of  claim 64 , where in the Rab GTPase is Rab 27a, Rab 27b or Rab 35. 
     
     
         66 . The method of  claim 63 , wherein the inhibitor of a reverse transcriptase is a nucleoside analog selected from the group comprising 3′-azido2′,3′-dideoxythymidine (AZT), 2′,3′-dideoxyinosine (ddI), 2′,3′-didehyro-3′-deoxythymidine (d4T), nevirapine and efavirenz. 
     
     
         67 . The method of  claim 63 , wherein the inhibitor of a reverse transcriptase is RNAi targeting the reverse transcriptase gene. 
     
     
         68 . The method of  claim 63 , wherein the microvesicle neutralizer is a biological agent that binds microvesicles and destroys the integrity of the microvesicles. 
     
     
         69 . (canceled) 
     
     
         70 . The method of  claim 28 , wherein the biological sample is a bodily fluid. 
     
     
         71 . The method of  claim 70 , wherein the bodily fluid is blood, serum, plasma, or urine. 
     
     
         72 . The method of  claim 28 , wherein the subject is a human subject. 
     
     
         73 . The method of  claim 28 , wherein the disease or other medical condition is brain cancer. 
     
     
         74 . The method of  claim 28 , wherein the brain cancer is medulloblastoma or glioblastoma. 
     
     
         75 . The method of  claim 28 , wherein the disease or other medical condition is melanoma. 
     
     
         76 . The method of  claim 28 , further comprising the step of enriching the microvesicle fraction for microvesicles originating from a specific cell type.