title: Roles of microRNAs in immunopathogenesis of non-alcoholic fatty liver disease revealed by integrated analysis of microRNA and mRNA expression profiles.
abstract: BACKGROUND
  The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoholic fatty liver disease (NAFLD).
  
  
  METHODS
  We analyzed differentially expressed microRNA and mRNA expression profiles of CD4+ T lymphocytes from the liver and mesenteric lymph nodes (MLNs) of mice with NAFLD using microarrays and RNA sequencing. Normal mice were used as controls. The target genes of microRNAs were predicted by TargetScan. Integrative analysis showed that the mRNAs were overlapped with microRNAs. Furthermore, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the key genes and pathways. Then, 16 microRNAs and 10 mRNAs were validated by qRT-PCR.
  
  
  RESULTS
  Microarray analysis suggested that 170 microRNAs were significantly de-regulated in CD4+ T lymphocytes from the liver between the two groups. Eighty mRNAs corresponded with microRNA targeted genes. KEGG analysis indicated that the MAPK pathway was consistently augmented in the liver of NAFLD mice. miR-23b, let-7e, miR-128 and miR-130b possibly played significant parts in the MAPK pathways. Furthermore, between the two groups, 237 microRNAs were significantly de-regulated in CD4+ T lymphocytes from MLNs. 38 mRNAs coincided with microRNA target genes. The metabolic pathway was consistently enriched in the MLNs of NAFLD mice. miR-206-3p, miR-181a-5p, miR-29c-3p and miR-30d-5p likely play important roles in the regulation of metabolic pathways.
  
  
  CONCLUSIONS
  The results of this study presented a new perspective on the application of integrative analysis to identify complex regulation means involved in the immunological pathogenesis of NAFLD.
authors.affiliation: Institute of Clinical Molecular Biology and Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China. liuyulan@pkuph.edu.cn.
authors.forename: Yu-Jun
authors.initials: YJ
authors.lastname: Zhang
authors.forename: Ying
authors.initials: Y
authors.lastname: Hu
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.forename: Yu-Jing
authors.initials: YJ
authors.lastname: Chi
authors.forename: Wei-Wei
authors.initials: WW
authors.lastname: Jiang
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.forename: Yu-Lan
authors.initials: YL
authors.lastname: Liu
mesh_terms: D000818:Animals; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology / Q000378:metabolism; D019295:Computational Biology; D004195:Disease Models, Animal; D004734:Energy Metabolism / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D005819:Genetic Markers; D006801:Humans; D008099:Liver / Q000276:immunology / Q000378:metabolism*; D008297:Male; D008810:Mice, Inbred C57BL; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D065626:Non-alcoholic Fatty Liver Disease / Q000175:diagnosis / Q000235:genetics* / Q000276:immunology / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome
chemical_list: D005819:Genetic Markers; D035683:MicroRNAs; D012333:RNA, Messenger