Bio-informatics analysis of a gene co-expression module in adipose tissue containing the diet-responsive gene Nnat

Abstract

Background: Obesity causes insulin resistance in target tissues - skeletal muscle, adipose tissue, liver and the brain. Insulin resistance predisposes to type-2 diabetes (T2D) and cardiovascular disease (CVD). Adipose tissue inflammation is an essential characteristic of obesity and insulin resistance. Neuronatin (Nnat) expression has been found to be altered in a number of conditions related to inflammatory or metabolic disturbance, but its physiological roles and regulatory mechanisms in adipose tissue, brain, pancreatic islets and other tissues are not understood.

Results: We identified transcription factor binding sites (TFBS) conserved in the Nnat promoter, and transcription factors (TF) abundantly expressed in adipose tissue. These include transcription factors concerned with the control of: adipogenesis (Pparγ, Klf15, Irf1, Creb1, Egr2, Gata3); lipogenesis (Mlxipl, Srebp1c); inflammation (Jun, Stat3); insulin signalling and diabetes susceptibility (Foxo1, Tcf7l2). We also identified NeuroD1 the only documented TF that controls Nnat expression. We identified KEGG pathways significantly associated with Nnat expression, including positive correlations with inflammation and negative correlations with metabolic pathways (most prominently oxidative phosphorylation, glycolysis and gluconeogenesis, pyruvate metabolism) and protein turnover. 27 genes, including; Gstt1 and Sod3, concerned with oxidative stress; Sncg and Cxcl9 concerned with inflammation; Ebf1, Lgals12 and Fzd4 involved in adipogenesis; whose expression co-varies with Nnat were identified, and conserved transcription factor binding sites identified on their promoters. Functional networks relating to each of these genes were identified.

Conclusions: Our analysis shows that Nnat is an acute diet-responsive gene in white adipose tissue and hypothalamus; it may play an important role in metabolism, adipogenesis, and resolution of oxidative stress and inflammation in response to dietary excess.

Figure 1

Transcription factor module in six Nnat promoter sequences. There are 20 significant five-element modules found in the six promoter sequences of Nnat for six species (Human, Mus, Can, Sus, Bos, Rat), sequence in 1200 bp upstream and 800 bp downstream, here shows TFBSs for V$EVI1 - V$EGRF - V$E2FF - V$NRF1 - V$LEFF, on the Nnat promoter closely and together in the similar region of the six species separately just upstream of the major TSP.

Figure 2

Mouse Nnat co-expression gene tissue-specific PPI network. All Nnat co-expression genes in Table 3 and their first neighbours in mouse PPI network showing expressed in WAT, hypothalamus and pancreas, generated a tissue-specific network with 151 nodes and 447 links. The eight genes in yellow are Nnat co-varying genes in Table 3. Two obesity relative genes App and Tcf7l2 and their direct associated genes linked by red edges.