Abstract 4094: Allosteric chromatin activity transition mechanisms drive epigenetic dosage compensation in essential genes triggered by oncogene activation in TRACERx
Authors: Francisco Gimeno-Valiente, Carla Castignani, Xiaohong Liu, Georgia Stavrou, Nana E. Mensah, Elizabeth Larose Cadieux, Özgen Deniz, Mariam Jamal-Hanjani, Stephan Beck, Jonas Demeulemeester, Miljana Tanic, Charles Swanton, Peter Van Loo, Nnennaya Kanu
Journal: Cancer Research (2025)

Lung TRACERx is a prominent study employing multi-region and longitudinal multi-omics sequencing to unravel the evolutionary trajectories of cancer. While aberrant DNA methylation is described in most cancers, its interplay with genomic alterations and chromatin remodeling in non-small cell lung cancer (NSCLC) is less understood. We propose Allosteric Chromatin Activity Transition (AllChAT) as a framework to elucidate epigenetic dosage compensation mechanisms, focusing on essential genes impacted by oncogene-driven DNA methylation changes. The study utilized multi-region sampling from 59 NSCLC patients, encompassing 217 tumor regions and 59 adjacent normal tissue samples. RRBS was performed to profile DNA methylation patterns, with tumor-specific methylation rates determined using the CAMDAC tool. WES was conducted to identify somatic mutations and copy number alterations via ASCAT. Additionally, ChIP-seq for H3K4me3 and H3K27me3 was carried out on TRACERx patient-derived cell lines (PDCs) to investigate chromatin state changes associated with epigenetic transitions.We identified oncogenes such as RAC1, EGFR, and CDK4, whose expression scales with amplification and exhibited lower methylation levels in tumour regions where amplified compared to non-amplified tumor regions. We also discovered oncogene-proximal genes under dosage compensation by DNA methylation associated with amplification of CCND1 in LUSC and LUAD, as well as CDK4, KRAS, and GNAS, specifically in LUAD. These dosage-compensated genes were enriched for essential genes. Using chromatin immunoprecipitation on TRACERx patient derived cell lines (PDCs) from 2 tumors and one normal sample, we observed that oncogenes such as CDKN1B, FGFR1, and JAK2 were co-amplified and associated with chromatin opening and hypomethylation at amplified loci compared to non-amplified loci. Additionally, we found essential passenger genes, including NOP2, DCTN6 and FOXD4, were associated with closed chromatin and increased DNA methylation at the respective loci when amplified compared to when not amplified in tumor PDCs compared to the normal PDC. As observed in TRACERx tumor tissues, we observed evidence for AllChAT around LRRC34 when co-amplified with the PI3KCA oncogene in both tumor PDCs. Conversely, as expected, no evidence of AllChAT was observed in non-amplified control regions such as for the essential passenger genes TOMM40 and RPS9 located proximal to the ERCC2 oncogene when not amplified nor for the essential gene ECT2 located proximal to PIK3CA. Taken together, these data suggest that copy number alterations around amplified oncogenes might trigger an allosteric chromatin transition and DNA hypermethylation of co-amplified passenger genes, which might be crucial to the regulation of essential genes during tumor evolution. Citation Format: Francisco Gimeno-Valiente, Carla Castignani, Xiaohong Liu, Georgia Stavrou, Nana E. Mensah, Elizabeth Larose Cadieux, Özgen Deniz, Mariam Jamal-Hanjani, Stephan Beck, Jonas Demeulemeester, Miljana Tanic, Charles Swanton, Peter Van Loo, Nnennaya Kanu. Allosteric chromatin activity transition mechanisms drive epigenetic dosage compensation in essential genes triggered by oncogene activation in TRACERx [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4094.