دورية أكاديمية
أعرض في EDS

An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.

التفاصيل البيبلوغرافية
العنوان: An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.
المؤلفون: Liu X; Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America., Gillis N; Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, United States of America., Jiang C; Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America., McCofie A; Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America., Shaw TI; Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America., Tan AC; Department of Oncological Sciences, Huntsman Cancer Institute, The University of Utah, Salt Lake City, Utah, United States of America., Zhao B; Division of Infectious Disease, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America., Wan L; Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America., Duckett DR; Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, United States of America., Teng M; Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America.
المصدر: PLoS computational biology [PLoS Comput Biol] 2024 Feb 09; Vol. 20 (2), pp. e1011873. Date of Electronic Publication: 2024 Feb 09 (Print Publication: 2024).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: San Francisco, CA : Public Library of Science, [2005]-
مواضيع طبية MeSH: Super Enhancers* , Neoplasms*/genetics, Humans ; Epigenomics ; Enhancer Elements, Genetic/genetics ; Gene Expression Regulation
مستخلص: Super enhancers (SE), large genomic elements that activate transcription and drive cell identity, have been found with cancer-specific gene regulation in human cancers. Recent studies reported the importance of understanding the cooperation and function of SE internal components, i.e., the constituent enhancers (CE). However, there are no pan-cancer studies to identify cancer-specific SE signatures at the constituent level. Here, by revisiting pan-cancer SE activities with H3K27Ac ChIP-seq datasets, we report fingerprint SE signatures for 28 cancer types in the NCI-60 cell panel. We implement a mixture model to discriminate active CEs from inactive CEs by taking into consideration ChIP-seq variabilities between cancer samples and across CEs. We demonstrate that the model-based estimation of CE states provides improved functional interpretation of SE-associated regulation. We identify cancer-specific CEs by balancing their active prevalence with their capability of encoding cancer type identities. We further demonstrate that cancer-specific CEs have the strongest per-base enhancer activities in independent enhancer sequencing assays, suggesting their importance in understanding critical SE signatures. We summarize fingerprint SEs based on the cancer-specific statuses of their component CEs and build an easy-to-use R package to facilitate the query, exploration, and visualization of fingerprint SEs across cancers.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2024 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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معلومات مُعتمدة: R01 CA255398 United States CA NCI NIH HHS; R01 AI123420 United States AI NIAID NIH HHS; R01 CA262530 United States CA NCI NIH HHS; P30 CA076292 United States CA NCI NIH HHS; R03 DE030580 United States DE NIDCR NIH HHS
تواريخ الأحداث: Date Created: 20240209 Date Completed: 20240223 Latest Revision: 20240224
رمز التحديث: 20240224
مُعرف محوري في PubMed: PMC10883583
DOI: 10.1371/journal.pcbi.1011873
PMID: 38335222
قاعدة البيانات: MEDLINE
الوصف
تدمد:1553-7358
DOI:10.1371/journal.pcbi.1011873