Endocrinology · Medical Literature
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.
Clinical relevance
Among rodent studies reporting significant modulation of NAD+ levels in adipose tissue alongside significant gene expression changes, which protein-coding genes, canonical pathways, protein-protein interaction networks, master regulators, and human disease associations can be identified through integrative functional bioinformatic analysis? __SNAPSHOT__ {"studyDesign":"Systematic literature search followed by integrative functional bioinformatic analysis (pathway enrichment, protein-protein interaction network analysis, master regulator identification, and human disease association mapping); not a primary experimental study","setting":"Faculty of Medical Sciences, Goce Delčev University, Štip, North Macedonia; Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA. Eligible source studies were rodent (mouse and/or rat) in vivo studies.","sampleSize":"17 eligible rodent studies identified; 113 unique NAD+-associated protein-coding genes extracted for downstream analysis","population":"Rodent models (species not individually specified in the abstract) in which NAD+ levels in adipose tissue were significantly modulated and contemporaneous adipose-depot-matched gene expression data were reported; human patient populations were not studied directly","intervention":"Integrative bioinformatic analysis of genes co-occurring with significant NAD+ alterations in adipose tissue across multiple rodent studies (no experimental intervention performed by the present authors)","comparator":"Not applicable (secondary bioinformatic analysis; no experimental comparator group)","primaryOutcome":"Identification of significantly enriched canonical pathways, protein-protein interaction networks, master regulators, and human disease associations among 113 NAD+-associated protein-coding genes extracted from eligible rodent transcriptomic studies","followUp":"Not applicable (cross-sectional bioinformatic synthesis of published data)","fundingSource":"Not reported in the abstract"}
Key findings
From a systematic search of the literature, 17 rodent studies were identified that reported both significant modulation of adipose-tissue NAD+ levels and significant changes in gene expression within the same adipose depot. From these studies, 113 unique NAD+-associated protein-coding genes were extracted. Pathway enrichment analysis demonstrated significant enrichment of multiple canonical pathways among these genes, with thermogenesis explicitly identified in the abstract as one enriched pathway; additional enriched pathways, protein-protein interaction network details, specific master regulators, and human disease associations were reported in the full publication but were not included in the supplied abstract and therefore cannot be summarized here without risk of fabrication. No primary quantitative effect sizes, p-values, confidence intervals, or network statistics were included in the provided abstract. No adverse event data are applicable to this study type. All numerical outputs beyond those stated in the abstract are not reported.
Practice implications
This study provides a hypothesis-generating, secondary bioinformatic synthesis—not a primary clinical trial—and its findings must be interpreted accordingly. It establishes that a defined set of 113 protein-coding genes is co-expressed with NAD+ alterations in rodent adipose tissue and that these genes are enriched in biologically plausible pathways (e.g., thermogenesis) consistent with the known roles of the NAD+/SIRT axis in metabolic regulation. What the study does NOT establish: (1) causality between NAD+ changes and any specific gene expression alteration; (2) whether these gene signatures translate to human adipose biology; (3) clinical relevance of any individual gene or pathway to patient outcomes; (4) whether therapeutic manipulation of NAD+ levels in humans would recapitulate the transcriptomic changes observed in rodents. The findings apply specifically to rodent models (species, sex distribution, and metabolic phenotypes of source studies not individually described in the abstract). Human patients—including those with obesity, type 2 diabetes, or insulin resistance—were not directly studied. The study addresses a recognized gap: prior literature focused on preselected gene subsets rather than an unbiased, integrated approach. The bioinformatic framework may help prioritize candidate pathways and master regulators for future experimental validation. Practice should not change based on this analysis alone; it is appropriately viewed as a foundation for hypothesis generation and future mechanistic or translational research. Only the abstract was available for this summary, which substantially limits the ability to appraise analytic methods, gene ontology database versions, statistical thresholds applied, or completeness of the systematic search. __LIMITATIONS__ Only an abstract was available for review; full methodological details, complete results, statistical thresholds, and sensitivity analyses cannot be assessed.,All source data are derived from rodent studies; interspecies differences in NAD+ metabolism, adipose depot biology, and gene regulation limit direct extrapolation to human physiology or pathology.,The systematic search identified only 17 eligible studies, yielding 113 genes—a relatively small gene set that may reflect stringent eligibility criteria or publication gaps, and which may not capture the full landscape of NAD+-responsive genes in adipose tissue.,Integrative bioinformatic analyses (pathway enrichment, protein-protein interaction, master regulator identification) are inherently dependent on the completeness and currency of the reference databases used; results may shift with database updates.,The approach aggregates genes across heterogeneous rodent models (varying species, sexes, metabolic phenotypes, adipose depots, and NAD+-modulating interventions), introducing biological heterogeneity that bioinformatic methods cannot fully resolve.,Protein-protein interaction and master regulator analyses infer regulatory relationships from existing literature and computational models and do not constitute experimental validation of any regulatory axis.,Publication bias in the source studies (favoring positive or statistically significant findings) may systematically distort the gene list.,Human disease associations are derived from computational mapping to existing disease databases and do not establish causal or mechanistic links in human patients.,Funding sources are not reported in the abstract, precluding assessment of potential conflicts of interest.,The distinction between statistical significance (enrichment p-values) and biological or clinical significance of the identified pathways cannot be assessed from the abstract alone. __BOTTOM_LINE_CATEGORY__ promising_but_preliminary __BOTTOM_LINE__ This integrative bioinformatic synthesis identifies 113 protein-coding genes co-occurring with NAD+ alterations in rodent adipose tissue and maps them to canonical pathways including thermogenesis, providing a structured, hypothesis-generating framework for understanding NAD+/SIRT-axis biology in adipose (dys)function. The findings are exploratory and rodent-derived, and do not establish causality, human translatability, or clinical actionability. This work is best used to prioritize candidate genes and pathways for targeted experimental validation rather than to inform current clinical practice.