Abstract 6231: Multi-omic characterisation of clear cell renal carcinoma reveals endogenous and exogenous processes related to its aetiology
Authors: Ricardo Cortez Cardoso Penha, Alexandra Sexton Oates, Sergey Senkin, Han La Park, Nicolas Alcala, Matthieu Foll, Karl Smith-Byrne, Paul Brennan, James Mckay
Journal: Cancer Research (2024)

Abstract Endogenous and exogenous exposures are associated with distinctive molecular marks in somatic tissues, including human tumours. Integrative multi-omic approaches could help improving the resolution to detect the molecular marks associated with disease aetiology. Here, we leveraged the overlapping molecular information of clear cell renal cell carcinomas (ccRCC) tumours from Mutographs cohort by integrating DNA methylation, transcriptome, and whole-genome sequencing-based somatic mutation data to explore and gain new insights into exposures linked to ccRCC aetiology. Our novel framework identified important sources of biological variance across ccRCC tumours that were summarized as molecular components. We inferred these molecular ccRCC components into independent datasets to further explore their relationship with molecular and epidemiological features of ccRCC, normal adjacent kidney tissues, and other cancer types. Our results revealed a major ccRCC molecular component correlating with cellular mitotic age-related features, particularly the mitotic epigenetic clock (age-adjusted epiTOC2), clock-like DNA mutational signatures (SBS1/ID1), and telomere attrition. This molecular component was overrepresented in ccRCC tumours in comparison with normal paired kidney tissues, associating with PBRM1 and SETD2 somatic cancer driver mutations, genome stability, tumor stage, grade and ccRCC patient survival, independently to chronological age. Pan-cancer analysis supported the mitotic-age effect, represented by this molecular component, in other cancer types. Another ccRCC component was associated with tobacco usage, the presence of tobacco related DNA mutational and methylation signatures, increased total mutation burden, and sex. This component was also related to the epigenetic regulation of xenobiotic metabolism-related genes (e.g., GSTP1), further suggesting a relationship with genotoxic compounds. We further identified molecular components related to the ccRCC tumour microenvironment and cell proliferation, including one component related to BAP1 cancer driver mutations, pro-inflammatory immune cells, and ccRCC patient survival. In conclusion, our study reports a novel framework to molecular characterize ccRCC tumours using an integrative multi-omic approach, providing additional insights into the molecular footprints of endogenous and exogenous exposures in ccRCC tumours, including molecular components with prognostic value for patients. Citation Format: Ricardo Cortez Cardoso Penha, Alexandra Sexton Oates, Sergey Senkin, Han La Park, Nicolas Alcala, Matthieu Foll, Karl Smith-Byrne, Paul Brennan, James Mckay. Multi-omic characterisation of clear cell renal carcinoma reveals endogenous and exogenous processes related to its aetiology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6231.