Gene expression profile of metabolic dysfunction in the aorta of male Sprague-Dawley rats following a short-term high fat diet

Diet-induced metabolic dysfunction precedes multiple disease states, including diabetes, heart disease, and atherosclerosis. The critical role of the vasculature in disease progression is established, yet the details of how gene expression changes in early cardiovascular disease remain an enigma. The objective of the current project was to evaluate whether a quantitative assessment of gene expression within the aorta of six-week old healthy male Sprague-Dawley rats compared to those exhibiting metabolic dysfunction symptoms could reveal potential mediators of vascular dysfunction. RNA was extracted from the aorta of four rats; two animals fed high-fat diet (HFD) shown to stimulate symptoms of metabolic dysfunction (including hypertension, weight gain, glucose intolerance, and insulin insensitivity) and two healthy animals that were fed a standard chow diet (CHOW) served as age-matched controls. Sequencing libraries were constructed from polyA-selected transcripts and 36-basepair reads were obtained from an Illumina Genome Analyzer IIx run. Data quality was examined with FASTQC. Reads were mapped to ENSEMBL release 79 of the rat genome (Rnor_5.0; GCA_000001895.3) using two methods, the Genomic Mapping and Alignment Program (GMAP) and Tophat, which uses splice site junction mapping (SJM).The results for each mapping program was quantitated per gene using HTSeq count. A low count cutoff was determined by a Zipf graph, in which the log abundance per gene is graphed against the log rank. Statistical analysis with Empirical Analysis of Digital Gene Expression data in R (EdgeR). Transcripts with a p(adj) ≤ 0.05 in at least one of the mapping techniques were subjected to Gene Ontology (GO) biological process term enrichment and network analysis using Cytoscape (v3.7.1) and the App ClueGO/CluePedia (v2.5.5). The resulting network was reframed by taking into consideration the tissue type and the experimental protocol.