Methods of diagnosing and treating cancer targeting extrachromosomal dna

Abstract

Provided herein are, inter alia, methods and compositions to detect, monitor and treat cancer, wherein the cancer includes amplified extrachromosomal oncogenes. The methods are useful for personalized treatment and exploit differential expression of amplified extrachromosomal oncogenes in cancer cells versus healthy cells.

1 . A method of detecting heterogeneity in a first cancer sample, said method comprising:
 (i) measuring a first level of a first amplified extrachromosomal cancer-specific nucleic acid in the cancer sample;   (ii) measuring an ecDNA level in the cancer sample;   (iii) assessing ecDNA heterogeneity in the cancer sample based on a comparison of the first level and the ecDNA level.   
     
     
         2 . The method of  claim 1  wherein the first cancer sample is selected from the group consisting of a blood-derived biological sample, a urine-derived biological sample, a tumor sample, or a tumor fluid sample. 
     
     
         3 . The method of  claim 1 , wherein the first extrachromosomal cancer-specific nucleic acid comprises an amplified oncogene. 
     
     
         4 . The method of  claim 1 , wherein measuring the first level comprises sequencing DNA from the first cancer sample. 
     
     
         5 . The method of  claim 4 , wherein the sequencing comprises whole genome sequencing. 
     
     
         6 . The method of  claim 1 , wherein measuring the ecDNA level comprises intracellular detection of the amplified extrachromosomal cancer-specific nucleic acid from the cancer sample. 
     
     
         7 . The method of  claim 6 , wherein measuring the ecDNA level comprises imaging a portion of the cancer sample. 
     
     
         8 . The method of  claim 6 , wherein intracellular detection comprises imaging metaphases from the cancer sample. 
     
     
         9 . The method of  claim 1 , further comprising the steps of:
 (iv) measuring a second level of a second amplified extrachromosomal cancer-specific nucleic acid in a second sample;   (v) measuring an ecDNA level in the second sample;   (vi) assessing ecDNA heterogeneity in the second sample based on a comparison of the second level and the ecDNA level in the second sample; and   (vii) comparing ecDNA heterogeneity in the first cancer sample and the second sample.   
     
     
         10 . The method of  claim 9 , wherein the first cancer sample and the second sample are from the same subject and wherein the second cancer sample is from a later time point. 
     
     
         11 . The method of  claim 9 , wherein the first cancer sample is from a subject and the second sample is a standard control. 
     
     
         12 . The method of  claim 11 , wherein the standard control is a healthy cell, a cancer cell, or an average value from a set of samples. 
     
     
         13 . The method of  claim 9 , wherein the amplified extrachromosomal cancer-specific nucleic acid and the second amplified extrachromosomal cancer-specific nucleic acid comprise the same amplicon. 
     
     
         14 . The method of  claim 9 , wherein the first amplified extrachromosomal cancer-specific nucleic acid and the second amplified extrachromosomal cancer- 
     
     
         15 . The method of  claim 9 , further comprising identifying an increase in ecDNA heterogeneity as a candidate for drug resistance development. 
     
     
         16 . The method of  claim 9 , wherein the second cancer sample is derived from a subject treated with an anti-cancer agent. 
     
     
         17 . The method of  claim 1 , wherein the comparison is further compared to a standard control. 
     
     
         18 . The method of  claim 17 , wherein the standard control is a healthy cell, a cancer cell, or an average value from a set of samples. 
     
     
         19 . The method of  claim 1 , further comprising determining an amplicon structure of one or more amplicons present on the ecDNA. 
     
     
         20 . The method of  claim 19 , wherein the determining step is performed by Amplicon Architect analysis, and wherein the Amplicon Architect analysis comprises:
 (a) identifying boundaries of one or more segments in a reference genome that are part of one of the one or more amplicons;   (b) building a breakpoint graph with nodes corresponding to segment-endpoints, and edges connecting pairs of nodes;   (c) estimating copy number of edges of the one or more segments;   (d) extracting one or more paths and cycles in the graph that correlate with the copy number; and   (e) constructing the amplicon structure from the paths and cycles.   
     
     
         21 . The method of  claim 20 , wherein an input to Amplicon Architect comprises whole genome sequencing from the first cancer sample. 
     
     
         22 . A method of detecting heterogeneity in a cancer sample, said method comprising the steps of:
 (i) measuring a first level of a first amplified extrachromosomal cancer-specific nucleic acid in the cancer sample;   (ii) identifying an ecDNA amplicon in the cancer sample;   (iii) measuring a second level of a second amplified extrachromosomal cancer-specific nucleic acid in the cancer sample, wherein the first amplified extrachromosomal cancer-specific nucleic acid and the second amplified extrachromosomal cancer-specific nucleic acid are comprised in the ecDNA amplicon;   (iv) assessing ecDNA heterogeneity in the cancer sample based on a comparison of the first level and the second level.   
     
     
         23 . The method of  claim 22 , further comprising the steps of:
 (a) performing steps (i), (ii) and (iii) on a second cancer sample; and   (b) comparing ecDNA heterogeneity in the first cancer sample and the second sample, wherein the second cancer sample is from the same subject as the first cancer sample and wherein the second cancer sample is from a later time point.