Pashaj A, Yi X, Xia M, Canny S, Riethoven JJM, Moreau R. Characterization of genome-wide transcriptional changes in liver and adipose tissues of ZDF (fa/fa) rats fed R-␣-lipoic acid by next-generation sequencing. Physiol Genomics 45: 1136 -1143. First published October 8, 2013 doi:10.1152/physiolgenomics.00138.2013.-We report on the characterization of lipogenic tissue transcriptional networks that support physiological responses of obese rats to a lipid-lowering bioactive food compound, R-␣-lipoic acid (LA). Nine-week-old male Zucker diabetic fatty (fa/fa) rats were fed a chow diet supplemented with 3 g LA per kg diet or pair fed for 2 wk. At the end of the trial, high-quality RNA was extracted from the liver and epididymal fat and subjected to transcriptome analysis by RNA-Seq technology. Results showed a substantially higher number of differentially expressed genes [DEG, false discovery rate adjusted P Յ 0.05 and absolute log 2 (fold change) Ն 1] in the liver (110 genes) vs. epididymal fat (10 genes). Most epididymal fat DEG were also differentially expressed in liver and shared directionality of change. Gene Ontology (GO) analysis of these transcripts revealed significant enrichment of GO categories related to immune response, stress response, lipid metabolism, and carboxylic acid metabolic processes. Of interest, interferonrelated genes involved in defense against microorganisms and innate immune response were induced by LA. Lipid metabolism-related transcript changes observed in LA-fed animals included downregulation of lipogenic genes (Pnpla3, Pnpla5, Elovl6, Acly, Gpam, and Aacs) and concomitant upregulation of short-, medium-, and longchain fatty acid metabolic processes (Acot1, Acot2, Acsf2, and Crat). Transcriptional changes were accompanied by the lowering of abdominal adiposity and blood triacylglycerol levels. We conclude that LA dietary supplementation induces prominent gene expression changes in liver in support of significant improvement of whole-body lipid status. dyslipidemia; nonalcoholic fatty liver disease; nutritional genomics OVERSTIMULATED LIPOGENESIS by a surplus of dietary fat and carbohydrate contributes to the early stages of numerous metabolic diseases, chief among them is nonalcoholic fatty liver disease (NAFLD). NAFLD, defined as the presence of macrovesicular steatosis in the liver of individuals ingesting Ͻ20 g of alcohol per day, is the most common liver disease in the US. Its prevalence is increasing worldwide in parallel with the increasing incidences of obesity and Type 2 diabetes. Several studies have documented a strong association between NAFLD and traditional and nontraditional risk factors for cardiovascular disease (CVD) (40, 41). Accordingly, patients with NAFLD have an increased prevalence and incidence of CVD (5, 26). It is believed that NAFLD and CVD share common risk factors, such as visceral obesity, insulin resistance, hyperglycemia, hypertension, and dyslipidemia. Consequently, the remediation of NAFLD is expected to positively impact the number and severity o...