Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models
BackgroundUlcerative colitis (UC) is a chronic inflammatory disease of the colonic mucosa with increasing incidence worldwide. Growing evidence highlights the pivotal role of nicotinamide adenine dinucleotide (NAD+) metabolism in UC pathogenesis, prompting our investigation into the subtype-specific...
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Frontiers Media S.A.
2025-02-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1479421/full |
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| author | Linglin Tian Huiyang Gao Tian Yao Tian Yao Yuhao Chen Linna Gao Jingxiang Han Lanqi Zhu He Huang He Huang He Huang |
| author_facet | Linglin Tian Huiyang Gao Tian Yao Tian Yao Yuhao Chen Linna Gao Jingxiang Han Lanqi Zhu He Huang He Huang He Huang |
| author_sort | Linglin Tian |
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| description | BackgroundUlcerative colitis (UC) is a chronic inflammatory disease of the colonic mucosa with increasing incidence worldwide. Growing evidence highlights the pivotal role of nicotinamide adenine dinucleotide (NAD+) metabolism in UC pathogenesis, prompting our investigation into the subtype-specific molecular underpinnings and diagnostic potential of NAD+ metabolism-related genes (NMRGs).MethodsTranscriptome data from UC patients and healthy controls were downloaded from the GEO database, specifically GSE75214 and GSE87466. We performed unsupervised clustering based on differentially expressed NAD+ metabolism-related genes (DE-NMRGs) to classify UC cases into distinct subtypes. GSEA and GSVA identified potential biological pathways active within these subtypes, while the CIBERSORT algorithm assessed differential immune cell infiltration. Weighted gene co-expression network analysis (WGCNA) combined with differential gene expression analysis was used to pinpoint specific NMRGs in UC. Robust gene features for subtyping and diagnosis were selected using two machine learning algorithms. Nomograms were constructed and their effectiveness was evaluated using receiver operating characteristic (ROC) curves. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to verify gene expression in cell lines.ResultsIn our study, UC patients were classified into two subtypes based on DE-NMRGs expression levels, with Cluster A exhibiting enhanced self-repair capabilities during inflammatory responses and Cluster B showing greater inflammation and tissue damage. Through comprehensive bioinformatics analyses, we identified four key biomarkers (AOX1, NAMPT, NNMT, PTGS2) for UC subtyping, and two (NNMT, PARP9) for its diagnosis. These biomarkers are closely linked to various immune cells within the UC microenvironment, particularly NAMPT and PTGS2, which were strongly associated with neutrophil infiltration. Nomograms developed for subtyping and diagnosis demonstrated high predictive accuracy, achieving area under curve (AUC) values up to 0.989 and 0.997 in the training set and up to 0.998 and 0.988 in validation sets. RT-qPCR validation showed a significant upregulation of NNMT and PARP9 in inflamed versus normal colonic epithelia, underscoring their diagnostic relevance.ConclusionOur study reveals two NAD+ subtypes in UC, identifying four biomarkers for subtyping and two for diagnosis. These findings could suggest potential therapeutic targets and contribute to advancing personalized treatment strategies for UC, potentially improving patient outcomes. |
| format | Article |
| id | doaj-art-6bb9c87a28f944a2a414c71b23eb3887 |
| institution | Kabale University |
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| language | English |
| publishDate | 2025-02-01 |
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| series | Frontiers in Immunology |
| spelling | doaj-art-6bb9c87a28f944a2a414c71b23eb38872025-02-05T07:32:47ZengFrontiers Media S.A.Frontiers in Immunology1664-32242025-02-011610.3389/fimmu.2025.14794211479421Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic modelsLinglin Tian0Huiyang Gao1Tian Yao2Tian Yao3Yuhao Chen4Linna Gao5Jingxiang Han6Lanqi Zhu7He Huang8He Huang9He Huang10Department of Gastroenterology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, ChinaThe First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, ChinaDepartment of Gastrointestinal Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, ChinaCenter of Clinical Epidemiology and Evidence Based Medicine, Shanxi Medical University, Taiyuan, Shanxi, ChinaThe First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, ChinaThe First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, ChinaThe First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, ChinaThe First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, ChinaThe First Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, ChinaDepartment of Gastrointestinal Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, ChinaDepartment of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, ChinaBackgroundUlcerative colitis (UC) is a chronic inflammatory disease of the colonic mucosa with increasing incidence worldwide. Growing evidence highlights the pivotal role of nicotinamide adenine dinucleotide (NAD+) metabolism in UC pathogenesis, prompting our investigation into the subtype-specific molecular underpinnings and diagnostic potential of NAD+ metabolism-related genes (NMRGs).MethodsTranscriptome data from UC patients and healthy controls were downloaded from the GEO database, specifically GSE75214 and GSE87466. We performed unsupervised clustering based on differentially expressed NAD+ metabolism-related genes (DE-NMRGs) to classify UC cases into distinct subtypes. GSEA and GSVA identified potential biological pathways active within these subtypes, while the CIBERSORT algorithm assessed differential immune cell infiltration. Weighted gene co-expression network analysis (WGCNA) combined with differential gene expression analysis was used to pinpoint specific NMRGs in UC. Robust gene features for subtyping and diagnosis were selected using two machine learning algorithms. Nomograms were constructed and their effectiveness was evaluated using receiver operating characteristic (ROC) curves. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to verify gene expression in cell lines.ResultsIn our study, UC patients were classified into two subtypes based on DE-NMRGs expression levels, with Cluster A exhibiting enhanced self-repair capabilities during inflammatory responses and Cluster B showing greater inflammation and tissue damage. Through comprehensive bioinformatics analyses, we identified four key biomarkers (AOX1, NAMPT, NNMT, PTGS2) for UC subtyping, and two (NNMT, PARP9) for its diagnosis. These biomarkers are closely linked to various immune cells within the UC microenvironment, particularly NAMPT and PTGS2, which were strongly associated with neutrophil infiltration. Nomograms developed for subtyping and diagnosis demonstrated high predictive accuracy, achieving area under curve (AUC) values up to 0.989 and 0.997 in the training set and up to 0.998 and 0.988 in validation sets. RT-qPCR validation showed a significant upregulation of NNMT and PARP9 in inflamed versus normal colonic epithelia, underscoring their diagnostic relevance.ConclusionOur study reveals two NAD+ subtypes in UC, identifying four biomarkers for subtyping and two for diagnosis. These findings could suggest potential therapeutic targets and contribute to advancing personalized treatment strategies for UC, potentially improving patient outcomes.https://www.frontiersin.org/articles/10.3389/fimmu.2025.1479421/fullulcerative colitisNAD+ metabolismbioinformaticsmachine learningimmune cell infiltrationsubtype |
| spellingShingle | Linglin Tian Huiyang Gao Tian Yao Tian Yao Yuhao Chen Linna Gao Jingxiang Han Lanqi Zhu He Huang He Huang He Huang Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models Frontiers in Immunology ulcerative colitis NAD+ metabolism bioinformatics machine learning immune cell infiltration subtype |
| title | Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models |
| title_full | Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models |
| title_fullStr | Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models |
| title_full_unstemmed | Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models |
| title_short | Interactions between NAD+ metabolism and immune cell infiltration in ulcerative colitis: subtype identification and development of novel diagnostic models |
| title_sort | interactions between nad metabolism and immune cell infiltration in ulcerative colitis subtype identification and development of novel diagnostic models |
| topic | ulcerative colitis NAD+ metabolism bioinformatics machine learning immune cell infiltration subtype |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2025.1479421/full |
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