Genome-wide maps of liver in high-fat fed mice treated with kaempferol

Purpose: The goals of this study were to compare the liver transcriptome (RNA-seq) of mice induced by high fat diet and treated with kaempferol, and to reveal the effective treatment and biomarkers of kaempferol. Methods: mRNA profiles of six-week-old C57/BL6 which were fed with a control diet, high fat diet and treated with kaempferol were generated by sequencing, using Illumina HiSeq 4000 sequencer. The sequence reads that passed quality filters were controlled by Q30, using cutadapt software (v1.9.3). The high quality clean reads were aligned to the reference genome (UCSC MM10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs. Result: RNA-seq data confirmed stable expression of 277 common regulated differential genes among three groups with p-value <0.05, |Fold change| >1.5 and FPKM>1 in at least one group and the most five obvious differentially expressed genes were Cyp2b9, Cyp4a12b, Mup7, Mup17 and Mup16 while the metabolic pathways were involved in fatty acid degradation, ribosome, glyoxylic acid and dicarboxylic acid metabolism. Conclusion: Our study represents the first detailed analysis of hepatic transcriptomes, with high-fed diet induced treated with kaempferol, generated by RNA-seq technology. Our results show that kaempferol improved high fat diet induced NASH through change the expression of specific genes and RNA-seq based transcriptome may be a promising tool in exploring the anti-NASH effects of kaempferol and provided a better understanding of the mechanisms. Overall design: mRNA profiles of six-week-old C57/BL6 which were fed with a control diet, high fat diet and treated with kaempferol were generated by sequencing, using Illumina HiSeq 4000 sequencer.