Biomarkers of Cancer

Abstract

Methods for diagnosing cancer based on detecting the presence of increased levels of expression of satellite repeats and/or Line-1.

1 . An in vitro method of detecting the presence of cancer in a subject, the method comprising:
 determining a level of Long Interspersed Nucleotide Element-1 (LINE-1) in a sample from the subject to obtain a test value;   comparing the test value to a reference value, wherein the reference value represents a threshold level of LINE-1, and   identifying the subject as having cancer when the level of LINE-1 in the subject is above the reference value, or identifying the subject as unlikely to have cancer when the level of LINE-1 in the subject is below the reference value.   
     
     
         2 . (canceled) 
     
     
         3 . An in vitro method of detecting the presence of cancer in a subject, the method comprising:
 determining a level of satellite transcripts in a sample from the subject to obtain a test value; and   comparing the test value to a reference value,   wherein a test value compared to the reference value indicates whether the subject has cancer.   
     
     
         4 . The method of  claim 2 , wherein the satellite transcripts comprise one or more of ALR, HSATII, GSATII, TAR1, and SST1. 
     
     
         5 . The method of  claim 4 , wherein the satellite transcript is ALR and/or HSATII, and the presence of a level of ALR and/or HSATII satellite transcripts above the reference level indicates that the subject has a tumor. 
     
     
         6 . The method of  claim 4 , wherein the satellite transcript is GSATII, TAR1 and/or SST1, and the presence of a level of GSATII, TAR1 and/or SST1 satellite transcripts below the reference level indicates that subject has a tumor. 
     
     
         7 . The method of  claim 1 , wherein the sample is known or suspected to comprise tumor cells. 
     
     
         8 . The method of  claim 7 , wherein the sample is a blood sample known or suspected of comprising circulating tumor cells (CTCs), or a biopsy sample known or suspected of comprising tumor cells. 
     
     
         9 . The method of  claim 3 , wherein the sample comprises free RNA in serum or RNA within exosomes in blood. 
     
     
         10 . The method of  claim 1 , wherein the subject is a human. 
     
     
         11 . The method of  claim 1 , wherein the cancer is a solid tumor of epithelial origin. 
     
     
         12 . An in vitro method of evaluating the efficacy of a treatment for cancer in a subject, the method comprising:
 determining a level of LINE-1 in a first sample from the subject to obtain a first value;   administering a treatment for cancer to the subject;   determining a level of LINE-1 in a subsequent sample obtained from the subject at a later time, to obtain a treatment value; and   comparing the first value to the treatment value,   wherein a treatment value that is below the first value indicates that the treatment is effective.   
     
     
         13 . An in vitro method of evaluating the efficacy of a treatment for cancer in a subject, the method comprising:
 determining a level of satellite transcripts in a first sample from the subject to obtain a first value;   administering a treatment for cancer to the subject;   determining a level of satellite transcripts in a subsequent sample obtained from the subject at a later time, to obtain a treatment value; and   comparing the first value to the treatment value,   wherein a treatment value that is below the first value indicates that the treatment is effective.   
     
     
         14 . The method of  claim 13 , wherein the satellite transcripts comprise one or more of ALR, HSATII, GSATII, TAR1, and SST1. 
     
     
         15 . The method of  claim 12 , wherein the first and second samples are known or suspected to comprise tumor cells. 
     
     
         16 . The method of  claim 15 , wherein the samples are blood samples known or suspected of comprising circulating tumor cells (CTCs), or biopsy samples known or suspected of comprising tumor cells. 
     
     
         17 . The method of  claim 13 , wherein the sample comprises free RNA in serum or RNA within exosomes in blood. 
     
     
         18 . The method of  claim 12 , wherein the treatment includes administration of a surgical intervention, chemotherapy, radiation therapy, or a combination thereof. 
     
     
         19 . The method of  claim 12 , wherein the subject is a human. 
     
     
         20 . The method of  claim 12 , wherein the cancer is a solid tumor of epithelial origin. 
     
     
         21 . The method of  claim 1 , comprising measuring a level of LINE-1 transcript. 
     
     
         22 . The method of  claim 12 , wherein the level is determined using a branched DNA assay. 
     
     
         23 . The method of  claim 11 , wherein the solid tumor of epithelial origin is pancreatic, lung, breast, prostate, renal, ovarian or colon cancer.