Integrative functional bioinformatic analysis of NAD+-associated protein coding genes in adipose tissue (dys)function – evidence from targeted rodent transcriptomic studies

Abstract

One of the key regulatory mechanisms in adipose biology is the NAD+/SIRT axis, which is disrupted in conditions such as obesity and insulin resistance. In recent years, increasing attention has been directed toward understanding the role of NAD+ in adipose biology, including through gene expression analyses. However, most published studies have focused on a limited set of preselected genes, and an integrated analysis of genes associated with NAD+ alterations in adipose tissue is lacking. The aim of this study was to conduct a systematic literature search to identify rodent studies reporting significant modulation of NAD+ levels in adipose tissue, along with significant changes in gene expression within the same adipose depot. The extracted genes were then subjected to integrative functional bioinformatic analyses to identify significantly enriched canonical pathways, protein-protein interactions, master regulators, and associations with human diseases. We identified 17 studies, from which 113 unique NAD+-associated protein coding genes were extracted. Pathway enrichment analysis revealed multiple canonical pathways significantly associated with these genes, including thermogenesis, the PPAR signaling pathway, the AMPK signaling pathway, and adipogenesis. In addition, several cellular pathways were identified for which direct experimental evidence of NAD+ involvement is currently lacking, such as the apelin signaling pathway and the relaxin signaling pathway. Protein-protein interaction analysis revealed three distinct protein clusters related to positive regulation of cold-induced thermogenesis, inflammation, and cellular respiration. Master regulator analysis identified several well-established regulators, such as leptin, PRDM16, PPARGC1A, AMP, glucose, fructose, and rosiglitazone, as well as regulators that have not yet been directly investigated in the context of NAD+ function in adipose biology. Finally, analysis of disease associations of NAD+-associated protein coding genes revealed links to nutritional and cardiometabolic diseases. In conclusion, this study highlights both well-established and previously unexplored canonical pathways and regulators of biological processes associated with the role of NAD+ in adipose biology, thereby identifying potential targets for future experimental investigation. Additionally, our systematic literature search revealed a notable lack of studies employing global transcriptomic approaches, as well as multi-omics studies with coupled bioinformatic analyses, which are essential for obtaining an in-depth and comprehensive understanding of the role of NAD+ in adipose biology.