Identification and validation of NAD+ metabolism-related biomarkers in patients with diabetic peripheral neuropathy

• Published in: Frontiers in endocrinology (Lausanne) Vol. 15; p. 1309917
• Main Authors: Ye, Chenhao, Fu, Yuedong, Zhou, Xijie, Zhou, Feiya, Zhu, Xuwei, Chen, Yiheng
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 2024
• Subjects: bioinformatic analysis; Biomarkers; Diabetes Mellitus; Diabetic Neuropathies - diagnosis; Diabetic Neuropathies - genetics; diabetic peripheral neuropathy; gene expression; Humans; MicroRNAs; NAD; nicotinamide adenine dinucleotide metabolism; Nicotinamide-Nucleotide Adenylyltransferase; RNA, Messenger; nicotinamide adenine dinucleotide metabolism; diabetic peripheral neuropathy; bioinformatic analysis; biomarkers; gene expression
• ISSN: 1664-2392; 1664-2392
• DOI: 10.3389/fendo.2024.1309917

The mechanism of Nicotinamide Adenine Dinucleotide (NAD+) metabolism-related genes (NMRGs) in diabetic peripheral neuropathy (DPN) is unclear. This study aimed to find new NMRGs biomarkers in DPN. DPN related datasets GSE95849 and GSE185011 were acquired from the Gene Expression Omnibus (GEO) database. 51 NMRGs were collected from a previous article. To explore NMRGs expression in DPN and control samples, differential expression analysis was completed in GSE95849 to obtain differentially expressed genes (DEGs), and the intersection of DEGs and NMRGs was regarded as DE-NMRGs. Next, a protein-protein interaction (PPI) network based on DE-NMRGs was constructed and biomarkers were screened by eight algorithms. Additionally, Gene Set Enrichment Analysis (GSEA) enrichment analysis was completed, biomarker-based column line graphs were constructed, lncRNA-miRNA-mRNA and competing endogenouse (ce) RNA networks were constructed, and drug prediction was completed. Finally, biomarkers expression validation was completed in GSE95849 and GSE185011. 5217 DEGs were obtained from GSE95849 and 21 overlapping genes of DEGs and NMRGs were DE-NMRGs. Functional enrichment analysis revealed that DE-NMRGs were associated with glycosyl compound metabolic process. The PPI network contained 93 protein-interaction pairs and 21 nodes, with strong interactions between NMNAT1 and NAMPT, NADK and NMNAT3, ENPP3 and NUDT12 as biomarkers based on 8 algorithms. Expression validation suggested that ENPP3 and NUDT12 were upregulated in DPN samples (P < 0.05). Moreover, an alignment diagram with good diagnostic efficacy based on ENPP3 and NUDT12 were identified was constructed. GSEA suggested that ENPP3 was enriched in Toll like receptor (TLR) pathway, NUDT12 was enriched in maturity onset diabetes of the young and insulin pathway. Furthermore, 18 potential miRNAs and 36 Transcription factors (TFs) were predicted and the miRNA-mRNA-TF networks were constructed, suggesting that ENPP3 might regulate hsa-miR-34a-5p by affecting MYNN. The ceRNA network suggested that XLOC_013024 might regulate hsa-let-7b-5p by affecting NUDT12. 15 drugs were predicted, with 8 drugs affecting NUDT12 such as resveratrol, and 13 drugs affecting ENPP3 such as troglitazone. ENPP3 and NUDT12 might play key roles in DPN, which provides reference for further research on DPN.