High-throughput sequencing reveals altered expression of hepatic microRNAs in nonalcoholic fatty liver disease–related fibrosis

F Leti, I Malenica, M Doshi, A Courtright… - Translational …, 2015 - Elsevier
F Leti, I Malenica, M Doshi, A Courtright, K Van Keuren-Jensen, C Legendre, CD Still
Translational Research, 2015Elsevier
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 …
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.
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