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RNA-seq analysis of livers of C57BL/6 mice upon antagomiR-122 and CL316243 treatment

ABSTRACT: Purpose: miR-122 plays a role in lipid metabolism in the liver. The goal of this study is to search for additional metabolic pathways in which miR-122 is involved. Methods: mice were administered with antagomiR-122 (to inhibit miR-122) or antagomiR-control together with CL316243 (β 3-adrenergic receptor agonist, which causes TG hydrolysis to FFAs). Liver mRNAS were generated from 4 mice in each group by deep sequencing using Illumina Nextseq 500 System. The sequence reads that passed quality filters were analyzed with TopHat followed by Cufflinks. The Ingenuity IPA and GeneAnalytics analysis were performed to untangle the biological processes involving the differentially expressed genes. Results: Cufflink algorithm revealed that 182 genes were differentially expressed in the mice livers. According to IPA analysis, the circadian rhythm pathway and adipogenesis were significantly disrupted. Conclutions: Inhibition of miR-122 Activates Several Metabolic Pathways Which Regulate Hepatic Triglycerides Synthesis and Storage

ORGANISM(S): Mus musculus

PROVIDER: GSE87848 | GEO | 2018/10/10

REPOSITORIES: GEO

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Project description:Hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths worldwide, reflecting the need for a better understanding of hepatocarcinogenesis. In this study, we examined the genome-wide expression profiles of both miRNAs and mRNAs from paired tumor and adjacent non-tumor tissues from a cohort of 96 HCC patients in Hong Kong where hepatitis B virus (HBV) is endemic. The comprehensive analysis of the coordinate expression of miRNAs and mRNAs reveals that miR-122 is under-expressed in HCC and that it is an important regulator for normal mitochondrial metabolism. A decreased level of miR-122 leads to an increase in expression of miR-122 seed-matched genes, a loss of mitochondrial metabolic function, and a decrease in the expression of many miR-122 secondary targets. These secondary targets are prognostic markers for HCC patients. Transcriptome profiling data from an additional 180 HCC and 40 liver cirrhotic patients in the same cohort were used to confirm the anti-correlation of miR-122 primary and secondary target gene sets. To test the HCC findings in normal mouse liver, we used an antagomir against miR-122 and identified altered gene expression profiling by microarray analysis in mouse in vivo experiments. The mouse data recapitulated the human HCC findings. Our anti-miR122 data further provided a direct link between increases in the mRNA levels of miR-122 controlled genes and impairments of mitochondrial metabolism. In summary, we find miR-122 loss may be detrimental to mitochondrial-related metabolisms in sustaining critical liver function and contribute to the morbidity and mortality of liver cancer patients. Mouse liver profiling: In one treatment regimen, four animals were given four doses of 100mg ASO/kg body weight, administered every other day, and sacrificed one day after the last dose. Four animals treated for four weeks were treated twice weekly with 50mg ASO/kg body weight, and sacrificed two days after the last dose. Mice were sacrificed in the morning, and liver was removed for further analysis. Samples from oligonucleotide-treated mice were referenced against samples from saline-treated mice in fluor-reversed pairs. Human liver profiling: For human HCC patient samples, 192 samples -- 96 resected tumor and 96 adjacent non-tumor liver tissues -- were collected from 96 patients who had undergone hepatectomy for curative treatment of HCC at Queen Mary Hospital, Pokfulam, Hong Kong between 1990 and 2007. Informed consents were obtained from patients regarding the use of the liver specimens for research. Samples were hybridized to Affymetrix arrays for mRNA profiling and were analyzed by quantitative PCR for microRNA profiling.

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RNA-seq analysis of livers of C57BL/6 mice upon antagomiR-122 and CL316243 treatment

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