Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort

• Published in: Nature communications 2023-12, Vol.14 (1), p.8383-8383, Article 8383
• Main Authors: Fukagawa, Akihiko, Hama, Natsuko, Totoki, Yasushi, Nakamura, Hiromi, Arai, Yasuhito, Saito-Adachi, Mihoko, Maeshima, Akiko, Matsui, Yoshiyuki, Yachida, Shinichi, Ushiku, Tetsuo, Shibata, Tatsuhiro
• Format: Article
• Language: English
• Subjects: 38/39; 45/23; 631/208/69; 631/67/2329; 631/67/68/2486; 692/4028/67/589/1588/1351; Carcinogens; Chromatin; Chromosome 14; Gene sequencing; Genomic analysis; Genomics; Histology; Humanities and Social Sciences; Immune checkpoint; Kidney cancer; multidisciplinary; Mutagenesis; Pathogenesis; Renal cell carcinoma; Science; Science (multidisciplinary); Transcription factors; Transcriptomics; Transposase; Whole genome sequencing
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-44159-1

Renal cell carcinoma (RCC) comprises several histological types characterised by different genomic and epigenomic aberrations; however, the molecular pathogenesis of each type still requires further exploration. We perform whole-genome sequencing of 128 Japanese RCC cases of different histology to elucidate the significant somatic alterations and mutagenesis processes. We also perform transcriptomic and epigenomic sequencing to identify distinguishing features, including assay for transposase-accessible chromatin sequencing (ATAC-seq) and methyl sequencing. Genomic analysis reveals that the mutational signature differs among the histological types, suggesting that different carcinogenic factors drive each histology. From the ATAC-seq results, master transcription factors are identified for each histology. Furthermore, clear cell RCC is classified into three epi-subtypes, one of which expresses highly immune checkpoint molecules with frequent loss of chromosome 14q. These genomic and epigenomic features may lead to the development of effective therapeutic strategies for RCC. Renal cell carcinoma (RCC) subtypes are associated with different molecular alterations and clinical outcomes, but they need to be characterised in diverse cohorts. Here, the authors perform genomic, transcriptomic, and epigenomic profiling in a large cohort of Japanese RCC cases, and identify epi-subtypes associated with a particular immune environment.