Clinical significance of the mutational landscape and fragmentation of circulating-tumor DNA in renal cell carcinoma.

Reliable biomarkers for renal cell carcinoma (RCC) have yet to be found. Circulating-tumor DNA (ctDNA) is an emerging resource to detect and monitor molecular characteristics of various tumors. This study aims to clarify the clinical utility of ctDNA for RCC. Fifty-three patients histologically diagnosed as clear cell RCC were enrolled. Targeted sequencing was performed using plasma cell-free DNA (cfDNA) and tumor DNA. We applied droplet digital PCR to validate detected mutations. cfDNA fragment size was also evaluated using a microfluidics-based platform and sequencing. Proportion of cfDNA fragments was defined as the ratio of small (50-166 bp) to large (167-250 bp) cfDNA fragments. The association of mutant allele frequency of ctDNA with clinical course was analyzed. Prognostic potential was evaluated using log-rank test. A total of 38 mutations across 16 (30%) patients were identified from cfDNA, including mutations in TP53 (n=6) and VHL (n=5), and median mutant allele frequency of ctDNA was 10%. We designed specific droplet digital PCR probes for 11 mutations and detected the same mutations in both cfDNA and tumor DNA. Positive ctDNA was significantly associated with a higher proportion of cfDNA fragments (P=0.033), indicating RCC patients with ctDNA had shorter fragment sizes of cfDNA. Interestingly, the changes of mutant allele frequency in ctDNA concurrently correlated with clinical course. Positive ctDNA and fragmentation of cfDNA were significantly associated with poor cancer-specific survival (P<0.001, P=0.011). In conclusion, our study demonstrates the clinical utility of ctDNA status and cfDNA fragment size as biomarkers for prognosis and disease monitoring in RCC. This article is protected by copyright. All rights reserved.

Cancer science. 2018 Dec 10 [Epub ahead of print]

Yoshiyuki Yamamoto, Motohide Uemura, Masashi Fujita, Kazuhiro Maejima, Yoko Koh, Makoto Matsushita, Kosuke Nakano, Yujiro Hayashi, Cong Wang, Yu Ishizuya, Toshiro Kinouchi, Takuji Hayashi, Kyosuke Matsuzaki, Kentaro Jingushi, Taigo Kato, Atsunari Kawashima, Takeshi Ujike, Akira Nagahara, Kazutoshi Fujita, Ryoichi Imamura, Hidewaki Nakagawa, Norio Nonomura

Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan., Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan., Department of Therapeutic Urologic Oncology, Osaka University Graduate School of Medicine, Suita, Japan.