Abstract 2333: Methylation based phylogeny and timing in cancer

Abstract

Abstract Knowing the chronological sequence of genetic alterations during cancer development and progression is crucial for understanding the process of transformation of normal tissue into malignant tumors. This can offer insights into the etiology and intrinsic cellular mechanisms of the process, presenting opportunities for early detection and treatment of initial disease stages, as well as highlight key events as potential therapeutic. Current methods of establishing progression histories of cancers rely either on direct sequencing of premalignant lesions, which are seldom available for tumors or on computational inference timing methods capable of reconstructing the history from primary tumor data. These methods require genome or exome sequencing data from a relatively large cohort of tumors and provide limited resolution due to overall scarcity of somatic mutations. We utilize a different source of genetic information, genome methylation, that also “records” historic information about acquisition and development of mutations. Over 28 million methylated CpG sites exist in the genome with several percent of them differentially methylated (DMS) between tissue types and tumor vs adjacent normal tissue. The several orders of magnitude higher density of distinctly methylated sites provides unprecedented resolution, needs fewer tumors, can be merged with driver mutation data and co-analyzed with “methylation clock” information that allows to establish early development, phylogeny and progression at unprecedented resolution. We developed methods for whole genome bisulfite sequencing (WGBS), reduced representation bisulfite sequencing (RRBS) and Oxford Nanopore Technologies native methylation sequencing data. Somatic DMS sites have distinct properties from somatic point mutations, can appear and disappear in the process of tumor evolution and development allowing for unique configuration of methylated islands. Our tools perform single sample and cohort level “timing”, multi-sample phylogeny reconstruction and cancer population reconstruction by integrating methylation and mutation information from the same sample. These new methods will significantly contribute to our understanding of cancer initiation and progression at a resolution not available previously. Citation Format: Nataliya Guteneva, Eliezer Lichter, Ignaty Leshchiner. Methylation based phylogeny and timing in cancer [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 2333.