DNA Methylation Profile of Liver Tissue in End-Stage Cholestatic Liver Disease

References

• Wilson AS , PowerBE , MolloyPL. DNA hypomethylation and human diseases. Biochim. Biophys. Acta1775(1), 138–162 (2007).
   PubMed Web of Science ®Google Scholar
• Jeffries MA , SawalhaAH. Autoimmune disease in the epigenetic era: how has epigenetics changed our understanding of disease and how can we expect the field to evolve?Expert Rev. Clin. Immunol.11(1), 45–58 (2015).
   PubMed Web of Science ®Google Scholar
• Zhong J , AghaG , BaccarelliAA. The role of DNA methylation in cardiovascular risk and disease: methodological aspects, study design, and data analysis for epidemiological studies. Circ. Res.118(1), 119–131 (2016).
   PubMed Web of Science ®Google Scholar
• Jones PA . Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet.13(7), 484–492 (2012).
   PubMed Web of Science ®Google Scholar
• Rivera CM , RenB. Mapping human epigenomes. Cell155(1), 39–55 (2013).
   PubMed Web of Science ®Google Scholar
• Jones MJ , GoodmanSJ , KoborMS. DNA methylation and healthy human aging. Aging Cell14(6), 924–932 (2015).
   PubMed Web of Science ®Google Scholar
• Cheung AC , LaRussoNF , GoresGJ , LazaridisKN. Epigenetics in the primary biliary cholangitis and primary sclerosing cholangitis. Semin. Liver Dis.37(2), 159–174 (2017).
   PubMed Web of Science ®Google Scholar
• Klump B , HsiehCJ , DetteSet al. Promoter methylation of INK4a/ARF as detected in bile – significance for the differential diagnosis in biliary disease. Clin. Cancer Res.9(5), 1773–1778 (2003).
   PubMed Web of Science ®Google Scholar
• Andresen K , BobergKM , VedeldHMet al. Four DNA methylation biomarkers in biliary brush samples accurately identify the presence of cholangiocarcinoma. Hepatology61(5), 1651–1659 (2015).
   PubMed Web of Science ®Google Scholar
• Trauner M , GindinY , JiangZet al. Methylation signatures in peripheral blood are associated with marked age acceleration and disease progression in patients with primary sclerosing cholangitis. JHEP Reports2(1), 100060 (2020).
   PubMedGoogle Scholar
• Mitchell MM , LleoA , ZammataroLet al. Epigenetic investigation of variably X chromosome inactivated genes in monozygotic female twins discordant for primary biliary cirrhosis. Epigenetics6(1), 95–102 (2011).
   PubMed Web of Science ®Google Scholar
• Lleo A , ZhangW , ZhaoMet al. DNA methylation profiling of the X chromosome reveals an aberrant demethylation on CXCR3 promoter in primary biliary cirrhosis. Clin. Epigenetics7(1), 61 (2015).
   PubMedGoogle Scholar
• Arenas F , HervíasI , SáezEet al. Promoter hypermethylation of the AE2/SLC4A2 gene in PBC. JHEP Reports1(3), 145–153 (2019).
   PubMedGoogle Scholar
• Darwish Murad S , FidlerJL , PoteruchaJJet al. Longterm clinical and radiological follow-up of living liver donors. Liver Transpl.22(7), 934–942 (2016).
   PubMed Web of Science ®Google Scholar
• Lazaridis KN , LaRussoNF. Primary sclerosing cholangitis. N. Engl. J. Med.375(12), 1161–1170 (2016).
   PubMed Web of Science ®Google Scholar
• Nguyen DL , JuranBD , LazaridisKN. Primary biliary cirrhosis. Best Pract. Res. Clin. Gastroenterol.24(5), 647–654 (2010).
   PubMed Web of Science ®Google Scholar
• O’Shea RS , DasarathyS , McCulloughAJet al. Alcoholic liver disease. Hepatology51(1), 307–328 (2010).
   PubMed Web of Science ®Google Scholar
• Chalasani N , WilsonL , KleinerDE , CummingsOW , BruntEM , ÜnalpA. Relationship of steatosis grade and zonal location to histological features of steatohepatitis in adult patients with non-alcoholic fatty liver disease. J. Hepatol.48(5), 829–834 (2008).
   PubMed Web of Science ®Google Scholar
• Brunt EM , TiniakosDG. Histopathology of nonalcoholic fatty liver disease. World J. Gastroenterol.16(42), 5286–5296 (2010).
   PubMed Web of Science ®Google Scholar
• Batts KP , LudwigJ. Chronic hepatitis: an update on terminology and reporting. Am. J. Surg. Pathol.19(12), 1409–1417 (1995).
   PubMed Web of Science ®Google Scholar
• Gu H , SmithZD , BockC , BoyleP , GnirkeA , MeissnerA. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc.6(4), 468–481 (2011).
   PubMed Web of Science ®Google Scholar
• Sun Z , BahetiS , MiddhaSet al. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics28(16), 2180–2181 (2012).
   PubMed Web of Science ®Google Scholar
• Xi Y , LiW. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics10, 232 (2009).
   PubMed Web of Science ®Google Scholar
• Li H , HandsakerB , WysokerAet al. The sequence alignment/map format and SAMtools. Bioinformatics25(16), 2078–2079 (2009).
   PubMed Web of Science ®Google Scholar
• Kim WR , BigginsSW , KremersWKet al. Hyponatremia and mortality among patients on the liver-transplant waiting list. N. Engl. J. Med.359(10), 1018–1026 (2008).
   PubMed Web of Science ®Google Scholar
• Bedossa P , PoynardT. An algorithm for the grading of activity in chronic hepatitis C. Hepatology24(2), 289–293 (1996).
   PubMed Web of Science ®Google Scholar
• Wu H , WangC , WuZ. A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data. Biostatistics14(2), 232–243 (2013).
   PubMed Web of Science ®Google Scholar
• Lizio M , HarshbargerJ , ShimojiHet al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol.16, 22 (2015).
   PubMed Web of Science ®Google Scholar
• Kramer A , GreenJ , PollardJJr , TugendreichS. Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics30(4), 523–530 (2014).
   PubMed Web of Science ®Google Scholar
• Raudvere U , KolbergL , KuzminIet al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res.47(W1), W191–W198 (2019).
   PubMed Web of Science ®Google Scholar
• Buchkremer S , HendelJ , KruppMet al. Library of molecular associations: curating the complex molecular basis of liver diseases. BMC Genomics11(1), 189 (2010).
   PubMedGoogle Scholar
• Tacutu R , ThorntonD , JohnsonEet al. Human ageing genomic resources: new and updated databases. Nucleic Acids Res.46(D1), D1083–D1090 (2018).
   PubMed Web of Science ®Google Scholar
• Bhattacharya S , DunnP , ThomasCGet al. ImmPort, toward repurposing of open access immunological assay data for translational and clinical research. Sci. Data5, 180015 (2018).
   PubMed Web of Science ®Google Scholar
• Bamford S , DawsonE , ForbesSet al. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br. J. Cancer91(2), 355–358 (2004).
   PubMed Web of Science ®Google Scholar
• Mazzone R , ZwergelC , ArticoMet al. The emerging role of epigenetics in human autoimmune disorders. Clin. Epigenetics11(1), 1–15 (2019).
   PubMedGoogle Scholar
• De Smet C , LoriotA. DNA hypomethylation in cancer: epigenetic scars of a neoplastic journey.Epigenetics5(3), 206–213 (2010).
   Google Scholar
• Coit P , YalavarthiS , OgnenovskiMet al. Epigenome profiling reveals significant DNA demethylation of interferon signature genes in lupus neutrophils. J. Autoimmun.58, 59–66 (2015).
   PubMed Web of Science ®Google Scholar
• Richardson B , ScheinbartL , StrahlerJ , GrossL , HanashS , JohnsonM. Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis. Arthritis Rheum.33(11), 1665–1673 (1990).
   PubMed Web of Science ®Google Scholar
• Lei W , LuoY , YanKet al. Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythematosus, systemic sclerosis, and dermatomyositis. Scand. J. Rheumatol.38(5), 369–374 (2009).
   PubMed Web of Science ®Google Scholar
• de Smet C , LoriotA. DNA hypomethylation in cancer: epigenetic scars of a neoplastic journey. Epigenetics5(3), 206–213 (2010).
   PubMed Web of Science ®Google Scholar
• De Smet C , LoriotA. DNA hypomethylation and activation of germline-specific genes in cancer. Adv. Exp. Med. Biol.754, 149–166 (2013).
   PubMed Web of Science ®Google Scholar
• Ahrendt SA , EisenbergerCF , YipLet al. Chromosome 9p21 loss and p16 inactivation in primary sclerosing cholangitis-associated cholangiocarcinoma. J. Surg. Res.84(1), 88–93 (1999).
   PubMed Web of Science ®Google Scholar
• Page A , PaoliP , MoranSalvador E , WhiteS , FrenchJ , MannJ. Hepatic stellate cell transdifferentiation involves genome-wide remodeling of the DNA methylation landscape. J. Hepatol.64(3), 661–673 (2016).
   PubMed Web of Science ®Google Scholar
• Somineni HK , ZhangX , BiaginiMyers JMet al. Ten-eleven translocation 1 (TET1) methylation is associated with childhood asthma and traffic-related air pollution. J. Allergy Clin. Immunol.137(3), 797–805.e5 (2016).
   PubMed Web of Science ®Google Scholar
• Tryndyak V , KindratI , DrevalK , ChurchwellMI , BelandFA , PogribnyIP. Effect of aflatoxin B1, benzo[a]pyrene, and methapyrilene on transcriptomic and epigenetic alterations in human liver HepaRG cells. Food Chem. Toxicol.121, 214–223 (2018).
   PubMed Web of Science ®Google Scholar
• Baptissart M , SèdesL , HolotaHet al. Multigenerational impacts of bile exposure are mediated by TGR5 signaling pathways. Sci. Rep.8(1), 1–12 (2018).
   PubMedGoogle Scholar
• Guicciardi ME , KrishnanA , BronkSF , HirsovaP , GriffithTS , GoresGJ. Biliary tract instillation of a SMAC mimetic induces TRAIL-dependent acute sclerosing cholangitis-like injury in mice. Cell Death Dis.8(1), e2535–e2535 (2017).
   PubMedGoogle Scholar
• Masyuk TV , MasyukAI , LarussoNF. TGR5 in the cholangiociliopathies. Dig. Dis. S.KargerAG ( Ed.). 420–425 (2015).
   Google Scholar
• Neuman M , AnguloP , MalkiewiczIet al. Tumor necrosis factor-α and transforming growth factor-β reflect severity of liver damage in primary biliary cirrhosis. J. Gastroenterol. Hepatol.17(2), 196–202 (2002).
   PubMed Web of Science ®Google Scholar
• Afford SC , Ahmed-ChoudhuryJ , RandhawaSet al. CD40 activation-induced, Fas-dependent apoptosis and NF-κB/AP-1 signaling in human intrahepatic biliary epithelial cells. FASEB J.15(13), 2345–2354 (2001).
   PubMed Web of Science ®Google Scholar
• Shackel NA , McGuinnessPH , AbbottCA , GorrellMD , McCaughanGW. Identification of novel molecules and pathogenic pathways in primary biliary cirrhosis: cDNA array analysis of intrahepatic differential gene expression. Gut49(4), 565–576 (2001).
   PubMed Web of Science ®Google Scholar
• Srivastava B , MellsGF , CordellHJet al. Fine mapping and replication of genetic risk loci in primary sclerosing cholangitis. Scand. J. Gastroenterol.47(7), 820–826 (2012).
   PubMed Web of Science ®Google Scholar
• Sebode M , PeiselerM , FrankeBet al. Reduced FOXP3+ regulatory T cells in patients with primary sclerosing cholangitis are associated with IL2RA gene polymorphisms. J. Hepatol.60(5), 1010–1016 (2014).
   PubMed Web of Science ®Google Scholar
• Wakabayashi K , LianZX , MoritokiYet al. IL-2 receptor α-/- mice and the development of primary biliary cirrhosis. Hepatology44(5), 1240–1249 (2006).
   PubMed Web of Science ®Google Scholar
• Terada R , YamamotoK , HakodaTet al. Stromal cell-derived factor-1 from biliary epithelial cells recruits CXCR4-positive cells: implications for inflammatory liver diseases. Lab. Investig.83(5), 665–672 (2003).
   PubMed Web of Science ®Google Scholar
• Adam L , ZoldanK , HofmannMet al. Follicular T helper cell signatures in primary biliary cholangitis and primary sclerosing cholangitis. Hepatol. Commun.2(9), 1051–1063 (2018).
   PubMed Web of Science ®Google Scholar
• Zimmer CL , von SethE , BuggertMet al. A biliary immune landscape map of primary sclerosing cholangitis reveals a dominant network of neutrophils and tissue-resident T cells. Sci. Transl. Med.13(599), eabb3107 (2021).
   PubMed Web of Science ®Google Scholar
• Li L , GaoY , WuQ , ChengASL , YipKY. New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation. Genome Res.29(4), 543–553 (2019).
   PubMed Web of Science ®Google Scholar
• Smith AK , KilaruV , KocakMet al. Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type. BMC Genomics15, 145 (2014).
   PubMed Web of Science ®Google Scholar
• Quddus J , JohnsonKJ , GavalchinJet al. Treating activated CD4+ T cells with either of two distinct DNA methyltransferase inhibitors, 5-azacytidine or procainamide, is sufficient to cause a lupus-like disease in syngeneic mice. J. Clin. Invest.92(1), 38–53 (1993).
   PubMed Web of Science ®Google Scholar
• Yung RL , QuddusJ , ChrispCE , JohnsonKJ , RichardsonBC. Mechanism of drug-induced lupus. I. Cloned Th2 cells modified with DNA methylation inhibitors in vitro cause autoimmunity in vivo. J. Immunol.154(6), 3025–3035 (1995).
   PubMed Web of Science ®Google Scholar
• de Andres MC , Perez-PampinE , CalazaMet al. Assessment of global DNA methylation in peripheral blood cell subpopulations of early rheumatoid arthritis before and after methotrexate. Arthritis Res. Ther.17(1), 233 (2015).
   PubMedGoogle Scholar