title: High-throughput sequencing reveals altered expression of hepatic microRNAs in nonalcoholic fatty liver disease-related fibrosis.
abstract: Recent evidence suggests that microRNAs (miRNAs), small, noncoding RNA molecules that regulate gene expression, may play a role in the regulation of metabolic disorders, including nonalcoholic fatty liver disease (NAFLD). To identify miRNAs that mediate NAFLD-related fibrosis, we used high-throughput sequencing to assess miRNAs obtained from liver biopsies of 15 individuals without NAFLD fibrosis (F0) and 15 individuals with severe NAFLD fibrosis or cirrhosis (F3-F4), matched for age, sex, body mass index, type 2 diabetes status, hemoglobin A1c, and use of diabetes medications. We used DESeq2 and Kruskal-Wallis test to identify miRNAs that were differentially expressed between NAFLD patients with or without fibrosis, adjusting for multiple testing using Bonferroni correction. We identified a total of 75 miRNAs showing statistically significant evidence (adjusted P value <0.05) for differential expression between the 2 groups, including 30 upregulated and 45 downregulated miRNAs. Quantitative reverse-transcription polymerase chain reaction analysis of selected miRNAs identified by sequencing validated 9 of 11 of the top differentially expressed miRNAs. We performed functional enrichment analysis of dysregulated miRNAs and identified several potential gene targets related to NAFLD-related fibrosis including hepatic fibrosis, hepatic stellate cell activation, transforming growth factor beta signaling, and apoptosis signaling. We identified forkhead box O3 and F-box WD repeat domain containing 7, E3 ubiquitin protein ligase (FBXW7) as potential targets of miR-182, and found that levels of forkhead box O3, but not FBXW7, were significantly decreased in fibrotic samples. These findings support a role for hepatic miRNAs in the pathogenesis of NAFLD-related fibrosis and yield possible new insight into the molecular mechanisms underlying the initiation and progression of liver fibrosis and cirrhosis.
authors.affiliation: Division of Diabetes, Cardiovascular and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Ariz.
authors.forename: Fatjon
authors.initials: F
authors.lastname: Leti
authors.affiliation: Division of Diabetes, Cardiovascular and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Ariz.
authors.forename: Ivana
authors.initials: I
authors.lastname: Malenica
authors.affiliation: Division of Diabetes, Cardiovascular and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Ariz.
authors.forename: Meera
authors.initials: M
authors.lastname: Doshi
authors.affiliation: Division of Diabetes, Cardiovascular and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Ariz.
authors.forename: Amanda
authors.initials: A
authors.lastname: Courtright
authors.affiliation: Division of Diabetes, Cardiovascular and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Ariz.
authors.forename: Kendall
authors.initials: K
authors.lastname: Van Keuren-Jensen
authors.affiliation: Division of Diabetes, Cardiovascular and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Ariz.
authors.forename: Christophe
authors.initials: C
authors.lastname: Legendre
authors.affiliation: Department of Gastroenterology and Nutrition, Geisinger Obesity Institute, Danville, PA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Still
authors.affiliation: Department of Biochemistry and Molecular Biology, Temple University School of Medicine, Philadelphia, PA.
authors.forename: Glenn S
authors.initials: GS
authors.lastname: Gerhard
authors.affiliation: Division of Diabetes, Cardiovascular and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Ariz. Electronic address: jdistefano@tgen.org.
authors.forename: Johanna K
authors.initials: JK
authors.lastname: DiStefano
mesh_terms: D003710:Demography; D015536:Down-Regulation / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008099:Liver / Q000378:metabolism / Q000473:pathology; D008103:Liver Cirrhosis / Q000150:complications* / Q000235:genetics* / Q000473:pathology; D008297:Male; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008875:Middle Aged; D065626:Non-alcoholic Fatty Liver Disease / Q000150:complications* / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D015854:Up-Regulation / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger