title: Identification of core gene networks and hub genes associated with progression of non-alcoholic fatty liver disease by RNA sequencing.
abstract: OBJECTIVE
  Non-alcoholic fatty liver disease (NAFLD) progresses because of the interaction between numerous genes. Thus, we carried out a weighted gene coexpression network analysis to identify core gene networks and key genes associated with NAFLD progression.
  
  
  METHODS
  We enrolled 39 patients with mild NAFLD (fibrosis stages 0-2) and 21 with advanced NAFLD (fibrosis stages 3-4). Total RNA was extracted from frozen liver biopsies, and sequenced to capture a large dynamic range of expression levels.
  
  
  RESULTS
  A total of 1777 genes differentially expressed between mild and advanced NAFLD (q-value <0.05) clustered into four modules. One module was enriched for genes that encode cell surface or extracellular matrix proteins, and are involved in cell adhesion, proliferation, and signaling. This module formed a scale-free network containing four hub genes (PAPLN, LBH, DPYSL3, and JAG1) overexpressed in advanced NAFLD. PAPLN is a component of the extracellular matrix, LBH and DPYSL3 are reported to be tumor suppressors, and JAG1 is tumorigenic. Another module formed a random network, and was enriched for genes that accumulate in the mitochondria. These genes were downregulated in advanced NAFLD, reflecting impaired mitochondrial function. However, the other two modules did not form unambiguous networks. KEGG analysis indicated that 71 differentially expressed genes were involved in "pathways in cancer". Strikingly, expression of half of all differentially expressed genes was inversely correlated with methylation of CpG sites (q-value <0.05). Among clinical parameters, serum type IV collagen 7 s was most strongly associated with the epigenetic status in NAFLD.
  
  
  CONCLUSIONS
  Newly identified core gene networks suggest that the NAFLD liver undergoes mitochondrial dysfunction and fibrosis, and acquires tumorigenic potential epigenetically. Our data provide novel insights into the pathology and etiology of NAFLD progression, and identify potential targets for diagnosis and treatment.
authors.affiliation: Department of Medical Innovation, Osaka University Hospital, Suita, Japan.
authors.forename: Kikuko
authors.initials: K
authors.lastname: Hotta
authors.affiliation: Department of Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan.
authors.forename: Masataka
authors.initials: M
authors.lastname: Kikuchi
authors.affiliation: Pharmacogenomics, Kyoto University Graduate School of Medicine, Kyoto, Japan.|Laboratory of Radiation Safety, National Center for Geriatrics and Gerontology, Obu, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Kitamoto
authors.affiliation: Pharmacogenomics, Kyoto University Graduate School of Medicine, Kyoto, Japan.|Advanced Research Facilities and Services, Hamamatsu University School of Medicine, Hamamatsu, Japan.
authors.forename: Aya
authors.initials: A
authors.lastname: Kitamoto
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Ogawa
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Honda
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Takaomi
authors.initials: T
authors.lastname: Kessoku
authors.affiliation: Department of Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan.|Medical Solutions Division, NEC Corporation, Tokyo, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Kobayashi
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Masato
authors.initials: M
authors.lastname: Yoneda
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Kento
authors.initials: K
authors.lastname: Imajo
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Tomeno
authors.affiliation: Department of Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Nakaya
authors.affiliation: Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Saito
authors.affiliation: Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Nakajima
keywords: DNA methylation; fibrosis; next-generation RNA sequencing; non-alcoholic fatty liver disease; weighted gene coexpression network analysis