A genomic enhancer signature associates with hepatocellular carcinoma prognosis

Martínez-Jiménez, 2020, A compendium of mutational cancer driver genes, Nat Rev Cancer, 20, 555, 10.1038/s41568-020-0290-x Muntean, 2009, Epigenetic dysregulation in cancer, Am J Pathol, 175, 1353, 10.2353/ajpath.2009.081142 Gopi, 2021, Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains, Nat Commun, 12, 1419, 10.1038/s41467-021-21707-1 Sung, 2021, Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries, CA Cancer J Clin, 71, 209, 10.3322/caac.21660 London, 2006 Petrick, 2019, The changing epidemiology of primary liver cancer, Curr Epidemiol Rep, 6, 104, 10.1007/s40471-019-00188-3 Liu, 2020, Identification of key genes and important histone modifications in hepatocellular carcinoma, Comput Struct Biotechnol J, 18, 2657, 10.1016/j.csbj.2020.09.013 Hayashi, 2014, Concurrent activation of acetylation and tri-methylation of H3K27 in a subset of hepatocellular carcinoma with aggressive behavior, PLoS One, 9, 10.1371/journal.pone.0091330 Boix, 2021, Regulatory genomic circuitry of human disease loci by integrative epigenomics, Nature, 590, 300, 10.1038/s41586-020-03145-z Heinz, 2015, The selection and function of cell type-specific enhancers, Nat Rev Mol Cell Biol, 16, 144, 10.1038/nrm3949 Zhai, 2022, Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in hepatocellular carcinoma: the PLANET study, Natl Sci Rev, 9, nwab192, 10.1093/nsr/nwab192 Zhai, 2017, The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma, Nat Commun, 8, 4565, 10.1038/ncomms14565 Anene-Nzelu, 2020, Assigning distal genomic enhancers to cardiac disease–causing genes, Circulation, 142, 910, 10.1161/CIRCULATIONAHA.120.046040 Jeon, 2023, Multi-region sampling with paired sample sequencing analyses reveals sub-groups of patients with novel patient-specific dysregulation in hepatocellular carcinoma, BMC Cancer, 23, 118, 10.1186/s12885-022-10444-3 Bushnell, 2014 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat Methods, 9, 357, 10.1038/nmeth.1923 Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 Tarasov, 2015, Sambamba: fast processing of NGS alignment formats, Bioinformatics, 31, 2032, 10.1093/bioinformatics/btv098 Ramírez, 2014, deepTools: a flexible platform for exploring deep-sequencing data, Nucleic Acids Res, 42, W187, 10.1093/nar/gku365 Durand, 2016, Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments, Cell Syst, 3, 95, 10.1016/j.cels.2016.07.002 Cresswell, 2020, TADCompare: an R package for differential and temporal analysis of topologically associated domains, Front Genet, 11, 158, 10.3389/fgene.2020.00158 Ernst, 2012, ChromHMM: automating chromatin-state discovery and characterization, Nat Methods, 9, 215, 10.1038/nmeth.1906 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, 15, 550, 10.1186/s13059-014-0550-8 Karolchik, 2004, The UCSC Table Browser data retrieval tool, Nucleic Acids Res, 32, D493, 10.1093/nar/gkh103 Phanstiel, 2014, Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures, Bioinformatics, 30, 2808, 10.1093/bioinformatics/btu379 Yu, 2015, ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization, Bioinformatics, 31, 2382, 10.1093/bioinformatics/btv145 Sharma, 2020, Onco-fetal reprogramming of endothelial cells drives immunosuppressive macrophages in hepatocellular carcinoma, Cell, 183, 377, 10.1016/j.cell.2020.08.040 Jeon, 2020, Bivalent genes that undergo transcriptional switching identify networks of key regulators of embryonic stem cell differentiation, BMC Genomics, 21, 614, 10.1186/s12864-020-07009-8 Maechler M. Diptest: Hartigan’s dip test statistic for unimodality – corrected. 2021. https://github.com/mmaechler/diptest Young Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol Cell, 38, 576, 10.1016/j.molcel.2010.05.004 Zhang, 2020, hTFtarget: a comprehensive database for regulations of human transcription factors and their targets, Genomics Proteomics Bioinformatics, 18, 120, 10.1016/j.gpb.2019.09.006 Soltis, 2020, MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes, BMC Bioinformatics, 21, 338, 10.1186/s12859-020-03695-z Cerami, 2012, The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data, Cancer Discov, 2, 401, 10.1158/2159-8290.CD-12-0095 Kassambara Bernstein, 2010, The NIH roadmap epigenomics mapping consortium, Nat Biotechnol, 28, 1045, 10.1038/nbt1010-1045 Kundaje, 2015, Integrative analysis of 111 reference human epigenomes, Nature, 518, 317, 10.1038/nature14248 DeLaForest, 2019, HNF4A regulates the formation of hepatic progenitor cells from human iPSC-derived endoderm by facilitating efficient recruitment of RNA pol II, Genes, 10, 21, 10.3390/genes10010021 Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci, 102, 15545, 10.1073/pnas.0506580102 Domcke, 2020, A human cell atlas of fetal chromatin accessibility, Science, 370, 10.1126/science.aba7612 Hoshida, 2008, Gene expression in fixed tissues and outcome in hepatocellular carcinoma, N Engl J Med, 359, 1995, 10.1056/NEJMoa0804525 Boyault, 2007, Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets, Hepatology, 45, 42, 10.1002/hep.21467 Hoshida, 2009, Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma, Cancer Res, 69, 7385, 10.1158/0008-5472.CAN-09-1089 De Matteis, 2018, Aberrant metabolism in hepatocellular carcinoma provides diagnostic and therapeutic opportunities, Oxid Med Cell Longev, 2018, 10.1155/2018/7512159 Martínez-Reyes, 2018, Acetyl-CoA-directed gene transcription in cancer cells, Genes Dev, 32, 463, 10.1101/gad.315168.118 Suzuki, 2021, Metabolic alteration in hepatocellular carcinoma: mechanism of lipid accumulation in well-differentiated hepatocellular carcinoma, Can J Gastroenterol Hepatol, 2021, 10.1155/2021/8813410 Jühling, 2021, Targeting clinical epigenetic reprogramming for chemoprevention of metabolic and viral hepatocellular carcinoma, Gut, 70, 157, 10.1136/gutjnl-2019-318918 Liberzon, 2011, Molecular signatures database (MSigDB) 3.0, Bioinformatics, 27, 1739, 10.1093/bioinformatics/btr260