NAD modulates DNA methylation and cell differentiation

Ummarino, Simone; Bassal, Mahmoud; Zhang, Yanzhou; Seelam, Andy Joe; Kobayashi, I; Borchiellini, Marta; Ebralidze, Alexander K.; Trinh, Bon Q.; Kobayashi, Susumu; Ruscio, Annalisa Di

doi:10.1101/2020.07.31.231555

Cited by 1 publication

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References 47 publications

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“…N A D + h a s b e e n r e p o r t e d t o e n h a n c e D N A demethylation (57). NAD + is also a substrate for polyribose polymerase 1 (PARP1), a nuclear protein that plays a key role in DNA methylation (58). Tumor NAD metabolism mainly regulates DNA demethylation through Tet1mediated Dnmts, and NAD metabolism regulates and induces PD-L1 expression by controlling DNA demethylation (13).…”

Section: Discussionmentioning

confidence: 99%

Prognostic value of nicotinamide adenine dinucleotide (NAD+) metabolic genes in patients with stomach adenocarcinoma based on bioinformatics analysis

Cai

Lin

et al. 2022

J Gastrointest Oncol

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Background: Because stomach adenocarcinoma (STAD) has a poor prognosis, it is necessary to explore new prognostic genes to stratify patients to guide existing individualized treatments.Methods: Survival and clinical information, RNA-seq data and mutation data of STAD were acquired from The Cancer Genome Atlas (TCGA) database. Fifty-one nicotinamide adenine dinucleotide (NAD + ) metabolism-related genes (NMRGs) were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome databases. Differentially expressed NMRGs (DE-NMRGs) between STAD and normal samples were screened, and consistent clustering analysis of STAD patients was performed based on the DE-NMRGs. Survival analysis, Gene Set Enrichment Analysis (GSEA), mutation frequency analysis, immune microenvironment analysis and drug prediction were performed among different clusters.Additionally, the differentially expressed genes (DEGs) among different clusters were selected, and the intersections of DEGs and DE-NMRGs were selected as the prognostic genes. Finally, quantitative realtime polymerase chain reaction (qRT-PCR) was performed on a human gastric mucosa epithelial cell line and cancer cell line to verify the expression of the prognostic genes.Results: A total of 27 DE-NMRGs and two clusters were selected. There was a difference in survival between clusters 1 and 2. Furthermore, 18 DE-NMRGs were significantly different between clusters 1 and 2. The different Gene Ontology (GO) biological processes and KEGG pathways between clusters 1 and 2 were mainly enriched in cyclic nucleotide mediated signaling, synaptic signaling and hedgehog signaling pathway, etc. The somatic mutation frequencies were different between the two clusters, and TTN was the highest mutated gene in the patients of the clusters 1 and 2. Additionally, eight immune cells, immune score, stromal score, and estimate score were different between clusters 1 and 2. The patients in cluster 2 were sensitive to CTLA4 inhibitor treatment. Furthermore, the top five drugs (AP.24534, BX.795, Midostaurin, WO2009093927 and CCT007093) were significantly higher in cluster 1 than in cluster 2. Finally, three genes (AOX1, NNMT and PTGIS) were acquired as prognostic, and their expressions were consistent with the results of bioinformatics analysis.Conclusions: Three prognostic genes related to NAD + metabolism in STAD were screened out, which provides a theoretical basis and reference value for future treatment and prognosis of STAD.

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Section: Discussionmentioning

confidence: 99%