title: Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease.
abstract: OBJECTIVE
  Cirrhosis and liver cancer are potential outcomes of advanced nonalcoholic fatty liver disease (NAFLD). It is not clear what factors determine whether patients will develop advanced or mild NAFLD, limiting noninvasive diagnosis and treatment before clinical sequelae emerge. We investigated whether DNA methylation profiles can distinguish patients with mild disease from those with advanced NAFLD, and how these patterns are functionally related to hepatic gene expression.
  
  
  METHODS
  We collected frozen liver biopsies and clinical data from patients with biopsy-proven NAFLD (56 in the discovery cohort and 34 in the replication cohort). Samples were divided into groups based on histologic severity of fibrosis: F0-1 (mild) and F3-4 (advanced). DNA methylation profiles were determined and coupled with gene expression data from the same biopsies; differential methylation was validated in subsets of the discovery and replication cohorts. We then analyzed interactions between the methylome and transcriptome.
  
  
  RESULTS
  Clinical features did not differ between patients known to have mild or advanced fibrosis based on biopsy analysis. There were 69,247 differentially methylated CpG sites (76% hypomethylated, 24% hypermethylated) in patients with advanced vs mild NAFLD (P < .05). Methylation at fibroblast growth factor receptor 2, methionine adenosyl methyltransferase 1A, and caspase 1 was validated by bisulfite pyrosequencing and the findings were reproduced in the replication cohort. Methylation correlated with gene transcript levels for 7% of differentially methylated CpG sites, indicating that differential methylation contributes to differences in expression. In samples with advanced NAFLD, many tissue repair genes were hypomethylated and overexpressed, and genes in certain metabolic pathways, including 1-carbon metabolism, were hypermethylated and underexpressed.
  
  
  CONCLUSIONS
  Functionally relevant differences in methylation can distinguish patients with advanced vs mild NAFLD. Altered methylation of genes that regulate processes such as steatohepatitis, fibrosis, and carcinogenesis indicate the role of DNA methylation in progression of NAFLD.
authors.affiliation: Department of Obstetrics and Gynecology, Duke University, Durham, North Carolina.
authors.forename: Susan K
authors.initials: SK
authors.lastname: Murphy
authors.forename: Hyuna
authors.initials: H
authors.lastname: Yang
authors.forename: Cynthia A
authors.initials: CA
authors.lastname: Moylan
authors.forename: Herbert
authors.initials: H
authors.lastname: Pang
authors.forename: Andrew
authors.initials: A
authors.lastname: Dellinger
authors.forename: Manal F
authors.initials: MF
authors.lastname: Abdelmalek
authors.forename: Melanie E
authors.initials: ME
authors.lastname: Garrett
authors.forename: Allison
authors.initials: A
authors.lastname: Ashley-Koch
authors.forename: Ayako
authors.initials: A
authors.lastname: Suzuki
authors.forename: Hans L
authors.initials: HL
authors.lastname: Tillmann
authors.forename: Michael A
authors.initials: MA
authors.lastname: Hauser
authors.forename: Anna Mae
authors.initials: AM
authors.lastname: Diehl
mesh_terms: D000328:Adult; D001706:Biopsy; D020170:Caspase 1 / Q000235:genetics / Q000502:physiology; D015331:Cohort Studies; D018899:CpG Islands / Q000235:genetics / Q000502:physiology; D019175:DNA Methylation / Q000235:genetics / Q000502:physiology*; D003937:Diagnosis, Differential; D018450:Disease Progression; D005234:Fatty Liver / Q000175:diagnosis / Q000235:genetics / Q000503:physiopathology*; D005260:Female; D005786:Gene Expression Regulation / Q000502:physiology; D006801:Humans; D008099:Liver / Q000378:metabolism / Q000473:pathology; D008297:Male; D008716:Methionine Adenosyltransferase / Q000235:genetics / Q000502:physiology; D008875:Middle Aged; D065626:Non-alcoholic Fatty Liver Disease; D051497:Receptor, Fibroblast Growth Factor, Type 2 / Q000235:genetics / Q000502:physiology; D012720:Severity of Illness Index; D059467:Transcriptome / Q000235:genetics / Q000502:physiology*
chemical_list: C506577:MAT1A protein, human; D008716:Methionine Adenosyltransferase; C496353:FGFR2 protein, human; D051497:Receptor, Fibroblast Growth Factor, Type 2; D020170:Caspase 1
keywords: (GEx); AHCY; ALDH1L1; BMI; CASP1; CGI; CpG islands; DM; DNA Methylation; FGFR2; Gene Expression; MAT1A; MTHFD; Microarrays; NAFLD; NASH; TSS; UTR; adenosyl homocysteine; aldehyde dehydrogenase 1 family, member L1; body mass index; caspase 1; differentially methylated; fibroblast growth factor receptor 2; gene expression; methionine adenosyl methyltransferase 1A; methylenetetrahydrofolate dehydrogenase 2; nonalcoholic fatty liver disease; nonalcoholic steatohepatitis; transcription start site; untranslated region
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