Role of liquid sugar in regulating the hepatic transcriptome in a high fat Western diet model of NAFLD. Mus musculus

Purpose: The goals of this study are to use hepatic transcriptome profiling (RNA-seq) to examine the role of liquid sugar consumption in the progression of NAFLD. Methods: Hepatic mRNA profiles of 12-week chow (n=4), high fat Western diet (n=5), and high fat Western diet + fructose/sucore in the drinking water (n=5) fed mice were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We mapped about 100 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the livers of mice. RNA-seq data confirmed stable expression of X known liver specific genes. Approximately 10% of the transcripts showed differential expression between the XXX, with a fold change ≥1.5 and p value <0.05. Altered expression of XX genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several pathways that may contribute to NAFLD progression. RNA-seq data had a linear relationship with qRT–PCR: a goodness of fit (R2) of xxxx. Conclusions: Overall design: Hepatic mRNA profiles of chow, HFWD, and HFWD+F/S fed mice were generated by deep sequencing.