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RNA-seq Analysis of Sox9f/f and Sox9HKO Mouse Primary Hepatocyte Transcriptomes

ABSTRACT: Purpose: To identify the alterations of genes transcriptional profile of hepatocytes obtained from Sox9f/f mice and Sox9HKO mice treated with partial hepatectomy (PHx). Methods: Sox9HKO mice were generated by Sox9f/f mice injected with AAV-TBG-Cre via tail. Sox9f/f mice and Sox9HKO mice were treated with PHx to induce liver regeneration. Liver mRNA profiles of 12-week-old Sox9f/f and Sox9HKO mice treated with PHx were generated by deep sequencing, using Illumina Novaseq 6000. We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05. RT–PCR validation was performed using SYBR Green PCR Kit. Results: We identified the transcripts in the hepatocytes of Sox9f/f and Sox9HKO mice. 1379 transcripts showed differential expression between Sox9f/f and Sox9HKO mouse hepatocytes, with a |log2FC| > 1 and P value < 0.05. Altered expression of 4 genes was confirmed by qRT–PCR. Conclusion: Our study represents the first detailed analysis of liver transcriptomes of Sox9HKO mice during liver regeneration. RNA-seq based transcriptome analysis would provide us with a better understanding of the complex biologic functions of Sox9 in the hepatocyte during the pricess of hepatocyte proliferation in mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE278894 | GEO | 2025/11/25

REPOSITORIES: GEO

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Project description:The role of PPARα in gene regulation in mouse liver is well characterized. However, less is known about the effect of PPARα activation in human liver. The aim of the present study was to better characterize the impact of PPARα activation on gene regulation in human liver by combining transcriptomics with the use of hepatocyte humanized livers. To that end, chimeric mice containing hepatocyte humanized livers were given an oral dose of 300 mg/kg fenofibrate daily for 4 days. Livers were collected and analysed by hematoxilin and eosin staining, qPCR, and transcriptomics. Transcriptomics data were compared with existing datasets on fenofibrate treatment in normal mice. The human hepatocytes exhibited excessive lipid accumulation. Fenofibrate increased the size of the mouse but not human hepatocytes, and tended to reduce steatosis in the human hepatocytes. Quantitative PCR indicated that induction of PPARα targets by fenofibrate was less pronounced in the human hepatocytes than in the residual mouse hepatocytes. Transcriptomics analysis indicated that, after filtering, a total of 282 genes was significantly different between fenofibrate- and control-treated mice (P<0.01). 123 genes were significantly lower and 159 genes significantly higher in the fenofibrate-treated mice, including many established PPARα targets such as FABP1, HADHB, HADHA, VNN1, PLIN2, ACADVL and HMGCS2. According to gene set enrichment analysis, fenofibrate upregulated interferon/cytokine signaling-related pathways in hepatocyte humanized liver, but downregulated these pathways in normal mouse liver. Also, fenofibrate downregulated pathways related to DNA synthesis in hepatocyte humanized liver but not in normal mouse liver. The results support the major role of PPARα in regulating hepatic lipid metabolism, and underscore the more modest effect of PPARα activation on gene regulation in human liver compared to mouse liver. The data suggest that PPARα may have a suppressive effect on DNA synthesis in human liver, and a stimulatory effect on interferon/cytokine signalling.

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RNA-seq Analysis of Sox9f/f and Sox9HKO Mouse Primary Hepatocyte Transcriptomes

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