Abstract 1311: Inter- and intra-tumor heterogeneity of genetic and immune profiles in hereditary clear cell renal cell carcinoma
Authors: Mariko Tabata, Yusuke Sato, Yasunori Kogure, Marni B. McClure, Yuji Kumade, Yuki Saito, Sumito Shingaki, Kota Yoshifuji, Junji Koya, Kazushi Yoshida, Takashi Kohno, Kenichi Chiba, Ai Okada, Yuichi Shiraishi, Haruki Kume, Keisuke Kataoka
Journal: Cancer Research (2020)

Abstract [Background] Von Hippel-Lindau (VHL) disease is an autosomal dominant hereditary cancer syndrome attributed to germline VHL mutation. Patients with this disease are at risk of developing multiple independent clear cell renal carcinomas (ccRCCs), which offers a unique opportunity to analyze inter- and intra-tumor heterogeneity of genetic and immune profiles in the same patient. [Method] We selected seven patients with clinically diagnosed VHL disease who underwent one or two surgeries, in each of which two to five ccRCC tumors (total, n = 25) were removed. We harvested one to six regions from each tumor (total, n = 48), and performed whole-exome sequencing on them, together with normal blood (n = 7), cyst (n = 3), and adjacent normal renal tissue (n = 7) specimens from these patients. In addition, we carried out RNA-sequencing (for 20 tumors and 3 adjacent tissues) and digital multiplexed gene expression analysis using the NanoString nCounter system with Human Immunology V2 panel (for 36 tumors and 5 adjacent tissues) to clarify their immune profiles. [Result] Germline VHL mutations were confirmed in all seven patients. A total of 1,141 non-silent somatic mutations (8-44 mutations per patient) were detected, including 22 mutations affecting previously reported driver genes (such as BAP1, PBRM1, PTEN, PIK3CA, and SETD2). In consistent with previous reports, tumors arising in this context are clonally independent and harbor distinct secondary events, including mutations and copy number alterations (as exemplified by loss of heterozygosity of 3p). By contrast, multiple specimens from the same tumor showed almost the same genetic alterations, although several subclonal mutations were observed. Unsupervised hierarchical clustering of gene expression data discovered two robust subsets with distinct immune-related signatures. Particularly, the subset with high immune signature (n = 29) showed increased antigen presentation machinery genes (B2M, TAP1 and TAP2) and cytotoxic T lymphocyte genes (CD8, PRF1, and GZMA) than that with low immune signature (n = 19), suggesting a higher cytolytic activity in the former subset. Pathway analysis revealed the enrichment of cytokine interaction, JAK-STAT signaling and Toll-like receptor signaling. Interestingly, specimens from the same tumor invariably showed a similar immune signature, whereas different tumors frequently exhibit different immune signatures despite the identical immune background, suggesting a greater difference of immune status across tumors than within a tumor. [Conclusion] This study delineates inter- and intra-tumor heterogeneity of genetic and immune profiles in hereditary clear cell renal cell carcinoma. Our findings demonstrate more profound inter-tumor than intra-tumor heterogeneity in immune status, suggesting that tumor factors have a greater impact on immune microenvironment than host factors. Citation Format: Mariko Tabata, Yusuke Sato, Yasunori Kogure, Marni B. McClure, Yuji Kumade, Yuki Saito, Sumito Shingaki, Kota Yoshifuji, Junji Koya, Kazushi Yoshida, Takashi Kohno, Kenichi Chiba, Ai Okada, Yuichi Shiraishi, Haruki Kume, Keisuke Kataoka. Inter- and intra-tumor heterogeneity of genetic and immune profiles in hereditary clear cell renal cell carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1311.