Abstract 28P
Background
Lung TRACERx is a prominent study employing multi-region and longitudinal multi-omics sequencing to unravel the evolutionary trajectories of cancer. Although aberrant DNA methylation patterns have been widely described in nearly all human cancers, their interplay with genomic alterations in lung cancer is poorly understood. Incorporating the contribution of epigenetic modifications to cancer evolution trajectories within TRACERx could improve our understanding of the intricate relationship between genetic and epigenetic modifications.
Methods
Multi-region sampling from 61 patients (212 tumor regions) and 60 normal adjacent tissue samples was performed. Reduced representation bisulphite sequencing was performed and the CAMDAC tool (Larose Cadieux, 2020) was applied to determine purified tumor methylation rates. Whole exome sequencing and somatic copy number alterations (SCNAs) were inferred using ASCAT (Van Loo, 2010) and Methsig (Pan, 2021) was performed to discover candidate DNA methylation driver genes.
Results
We describe a novel method to determine intra-tumor methylation heterogeneity based on the mean euclidean distance between all CpGs, which correlated with established ITH scores, including SNV-, SCNA- and transcriptomic -ITH metrics. Through the integration of DNA methylation and genomic alterations in our multi-region cohort, we identify parallel mechanisms contributing to ubiquitous silencing of 32 out of 63 classical TSGs such as NSD1, GATA3 and MGA. Copy number loss of these TSGs preceded DNA methylation in the majority of tumors e.g. for FAT1 and RB1. In contrast, for NOTCH1 and GATA3, DNA methylation generally preceded copy number loss. Histology specific DNA methylation drivers, which were enriched with differentiation factors e.g. HOX and TBX genes, were predominantly hypermethylated prior to copy number loss. Finally, we describe DNA methylation-dependent dosage-compensation of essential genes amplified by virtue of their location proximal to amplified oncogenes.
Conclusions
We determine methylation heterogeneity, both the extent and relative timing of convergent repression mechanisms in tumor evolution, and discover DNA methylation-based driver genes in NSCLC.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
TRACERx.
Funding
CRUK, Pfizer, AstraZeneca, Bristol Myers Squibb, Roche-Ventana, Boehringer Ingelheim.
Disclosure
C. Swanton: Financial Interests, Personal, Research Grant: Pfizer, AstraZeneca, Bristol Myers Squibb, Roche-Ventana, Boehringer Ingelheim, Archer Dx Inc., Ono Pharmaceutical; Financial Interests, Personal, Advisory Board: AstraZeneca; Financial Interests, Personal, Advisory Role: Amgen, Pfizer, Novartis, GlaxoSmithKline, MSD, Bristol Myers Squibb, Celgene, AstraZeneca, Illumina, Genentech, Roche-Ventana, GRAIL, Medicxi, Metabomed, Bicycle Therapeutics, Sarah Cannon Research Institute, Apogen Biotechnologies; Financial Interests, Personal, Principal Investigator: Achilles Therapeutics. All other authors have declared no conflicts of interest.