Global analysis of epigenetic heterogeneity identifies divergent drivers of esophageal squamous cell carcinoma
W. CAO, H. Lee, W. Wu, A. Zaman, S. McCorkle, M. Yan, J. Chen, Q. Xing, N. Sinnott-Armstrong, H. Xu, M. R. Sailani, W. Tang, Y. Cui, J. Liu, H. Guan, P. Lv, X. Sun, L. SuniD, P. Han, Y. Lou, J. Chang, J. Wang, Y. Gao, J. Guo, G. Schenk, , T. G. Bivona
Abstract
Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to characterize the oncogenic drivers of esophageal squamous cell carcinoma (ESCC). We found 98% of CpGs are hypomethylated across the ESCC genome and two-thirds occur in long non-coding (lnc)RNA regions. DNA methylation and epigenetic heterogeneity both coincide with chromosomal topological alterations. Gene body methylation, polycomb repressive complex occupancy, and CTCF binding sites associate with cancer-specific gene regulation. Epigenetically-mediated activation of non-canonical WNT signaling and the lncRNA ESCCAL-1 were validated as potential ESCC driver alterations. Gene-specific cancer driver roles of epigenetic alterations and heterogeneity are identified.
02 /Specification & Classification
Click any tag to browse matching papersReproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Characterization of epigenetic alterations in esophageal cancer by whole-genome bisulfite sequencing
- Genome-wide methylation profiling identify hypermethylated HOXL subclass genes as potential markers for esophageal squamous cell carcinoma detection
Qiuning Yu, Namei Xia, … Xianping Lv·BMC Medical GenomicsPeer-reviewed·Nov 29, 2022
- Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN
Howard John Womersley, Daniel Muliaditan, … Lih Feng Cheow·bioRxiv·Feb 14, 2024
- Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation
- TP63, SOX2 and KLF5 Establish Core Regulatory Circuitry and Construct Cancer Specific Epigenome in Esophageal Squamous Cell Carcinoma
Y. Jiang, Y. Jiang, … H. P. Koeffler·bioRxiv·Nov 6, 2019
- Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma.
D. Hervas-Marin, F. Higgins, … J. Sandoval·bioRxiv·Sep 20, 2019