OTHR-17. PHYLOGENETIC RESOLUTION OF TISSUE-SPECIFIC METASTOGENIC CLONES IN RENAL CELL CARCINOMA

Genomic factors predictive of organ-specific tropism have been established in several models of cancer. However, the evolutionary dynamics at work in metastatic carcinoma have yet to be characterized in detail. We identified a cohort of clear cell renal cell carcinoma (RCC) patients who also had multiple metastasectomies, and performed deep sequencing and statistical inference of subclonal populations to infer phylogeny and essential genetic features acquired prior to systemic dissemination and site-specific colonization. Exome capture and deep sequencing were performed on tissues from 3 patients with polymetastatic RCC (including 12 metastases, multiple regions of primary tumors, and paired germline tissue) to a mean depth of 250x. Somatic point mutations were called with Mutect, and insertions and deletions with Strelka and VarScan. Validation was performed with a custom NimbleGen panel hybridized to a custom sequence library and sequenced to a mean depth of >500x. Allele-specific copy number and clonal prevalence were established using ABSOLUTE, and analyzed with Pyclone across primary and metastatic lesions to determine clonal architecture. Phylogenetic reconstruction identified ancestral clones, with attendant driver mutations in RCC tumor suppressors (including VHL, SETD2, PBRM1, MTOR) and independent subclonal populations in the metastases of all 3 patients. In an index case with multiple metastases separated spatially and temporally, bone and soft tissue metastases demonstrate apparent independent ancestors. Convergent loss of known tumor suppressors was also noted in all cases, and in several cases found in conjunction with de novo mutations in known RCC driver genes acquired late in tumor development. In this demonstration of subclonal and evolutionary analysis of multiple paired multi-organ RCC metastases, we identified subclonal populations characterized by alteration of several tumor suppressors which subsequently exhibited organ-specific patterns of metastasis.