Transcriptomic Analysis of Insulin-Sensitive Tissues from Anti-Diabetic Drug Treated ZDF Rats, a T2DM Animal Model

<div><p>Gene expression changes have been associated with type 2 diabetes mellitus (T2DM); however, the alterations are not fully understood. We investigated the effects of anti-diabetic drugs on gene expression in Zucker diabetic fatty (ZDF) rats using oligonucleotide microarray technology to identify gene expression changes occurring in T2DM. Global gene expression in the pancreas, adipose tissue, skeletal muscle, and liver was profiled from Zucker lean control (ZLC) and anti-diabetic drug treated ZDF rats compared with those in ZDF rats. We showed that anti-diabetic drugs regulate the expression of a large number of genes. We provided a more integrated view of the diabetic changes by examining the gene expression networks. The resulting sub-networks allowed us to identify several biological processes that were significantly enriched by the anti-diabetic drug treatment, including oxidative phosphorylation (OXPHOS), systemic lupus erythematous, and the chemokine signaling pathway. Among them, we found that white adipose tissue from ZDF rats showed decreased expression of a set of OXPHOS genes that were normalized by rosiglitazone treatment accompanied by rescued blood glucose levels. In conclusion, we suggest that alterations in OXPHOS gene expression in white adipose tissue may play a role in the pathogenesis and drug mediated recovery of T2DM through a comprehensive gene expression network study after multi-drug treatment of ZDF rats.</p></div

Selected enriched sub-networks.

<p>The color of the pie chart in the node illustrates the proportion of treatment condition and the angle size is the observed frequency of differentially expressed genes (DEGs) for specific drugs in the four tissues. Border color indicates expression patterns. Node shape is tissue type. Enriched pathway: (A) oxidative phosphorylation, (B) chemokine signaling pathway, (C) systemic lupus erythematosus.</p

Hierarchical clustering analysis.

<p>(A) Expression heat-map with 5,650 differentially expressed genes (DEGs) (excluding the common response DEGs) in all 48 samples. The first row of the color legend under the hierarchical clustering by column indicates sample's tissue type, and the second is the drug type. Another color legend on the side identifies the drug target information. (B) Expression heat-map with 857 genes in 12 muscle samples. (<i>p</i> value <0.05 and remove common DEGs and drug-response DEGs) G, Glimepiride; M, Metformin; R, Rosiglitazone; N, normal ZLC.</p

Effects of anti-diabetic drugs on the oral glucose tolerance test (OGTT) in ZDF rats.

<p>(A) OGTT in diabetic ZDF rat (▪, black squares), normal ZLC rats (□, white squares), rosiglitazone (○, white circles), metformin (◊, white diamonds) and glimepiride (Δ, white triangles)-treated diabetic ZDF rats. (B) The glucose area under the curve (AUC) during the course of the experiments was calculated. * <i>p</i><0.05, ** <i>p</i><0.01.</p

A Venn- diagram showing overlap of differentially expressed gene by multiple group comparison.

<p>(A) Comparison between drug conditions with each tissue condition (B) comparison between tissue conditions with each drug condition. Significant differentially expressed genes (<i>p</i> value <0.01) are given for each normal ZLC group and the rosiglitazone, glimepiride, and metformin- treated groups.</p

Evaluation of oxidative phosphorylation-related genes transcription.

<p>Quantitative polymerase chain reaction (PCR) mRNA expression for genes involved in oxidative phosphorylation in white adipose tissue of ZLC or ZDF rats treated with rosiglitazone. * <i>p</i><0.05, ** <i>p</i><0.01.</p

Gene-gene interaction network among the experimental groups.

<p>An integrated network was generated by the Human Net database. Edges represent interactions between significantly expressed genes.</p