{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T07:31:33Z","timestamp":1792222293929,"version":"4.4.0"},"reference-count":49,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T00:00:00Z","timestamp":1756425600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Diabetic nephropathy (DN), a major complication of type 2 diabetes mellitus (DM), is driven by complex mechanisms involving mitochondrial dysfunction, senescence, and chronic inflammation. Despite therapeutic advances, interventions specifically targeting mitochondrial dysfunction, senescence, and inflammation remain elusive.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>An integrative analysis was performed on bulk RNA-seq data from DN and normal kidney samples to identify differentially expressed genes (DEGs) associated with the disease. Weighted gene co-expression network analysis (WGCNA) was utilized to reveal gene modules linked to DN, mitochondrial dysfunction, and senescence. The key genes were determined using multiple machine learning approaches, and their diagnostic value was verified using external datasets. At single-cell resolution, the cellular landscape of DN was explored and the distinct expression patterns across different cell types were explored. Key genes and markers associated with mitochondrial dysfunction and senescence were validated through single-cell RNA sequencing (scRNA-seq) data and <jats:italic>in vitro<\/jats:italic> high-glucose-induced HK-2 cell models. Finally, functional studies were conducted using Small interfering RNA (siRNA)-mediated gene knockdown to predict the biological roles of selected targets.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We identified 2,176 DEGs between DN and normal kidney tissues, among which 259 mitochondrial-related genes (MRGs) and 273 senescence-related genes (SRGs) were significantly enriched in inflammatory and metabolic pathways. WGCNA revealed DN-associated gene modules strongly linked to mitochondrial dysfunction and senescence. Through integrated machine learning, five hub genes\u2014CLDN1, TYROBP, HDAC9, CASP3, and RCN1\u2014were selected, with the support vector machine (SVM) model achieving high diagnostic accuracy. ScRNA-seq revealed 13 distinct kidney cell types, with proximal tubule (PT) cells emerging as key contributors to the signaling pathway associated with mitochondrial dysfunction and senescence. These transcriptomic findings were corroborated by functional assays, in which HDAC9 upregulation in high-glucose-stimulated HK-2 cells was accompanied by mitochondrial impairment and increased levels of p53, p21, p16, and senescence associated secretory phenotype (SASP) factors. Conversely, HDAC9 knockdown mitigated these effects, underscoring its pathogenic role in DN.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Mitochondrial dysfunction and senescence-associated inflammation contribute to DN progression. The five identified hub genes demonstrate strong diagnostic potential, and HDAC9 is likely to be a potential therapeutic target for reducing mitochondrial injury, senescence, and inflammation in DN.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fimmu.2025.1627173","type":"journal-article","created":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T04:12:06Z","timestamp":1756440726000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Integrative transcriptomic and machine learning analyses identify HDAC9 as a key regulator of mitochondrial dysfunction and senescence-associated inflammation in diabetic nephropathy"],"prefix":"10.3389","volume":"16","author":[{"given":"Junming","family":"Huang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Pang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenglong","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guanglin","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinji","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaohua","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,8,29]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.diabres.2021.109119","article-title":"IDF Diabetes Atlas: Global, regional and country-level diabetes prevalence estimates for 2021 and projections for 2045","volume":"183","author":"Sun","year":"2022","journal-title":"Diabetes Res Clin Pract"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2023.1236837","article-title":"Editorial: A year in review: discussions in systems endocrinology","volume":"14","author":"Lorenzo","year":"2023","journal-title":"Front Endocrinol"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1016\/j.rceng.2019.10.012","article-title":"Diabetic cardiomyopathy","volume":"222","author":"Lorenzo-Almor\u00f3s","year":"2022","journal-title":"Rev Cl\u00ednica Espa\u00f1ola (English Edition)"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.5527\/wjn.v13.i2.95410","article-title":"Unleashing the pathological role of epithelial-to-mesenchymal transition in diabetic nephropathy: The intricate connection with multifaceted mechanism","volume":"13","author":"Balakumar","year":"2024","journal-title":"World J Nephrol"},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1097\/imna-d-23-00029","article-title":"Update on the pathogenesis, diagnosis, and treatment of diabetic tubulopathy","volume":"11","author":"Liu","year":"2024","journal-title":"Integr Med Nephrol Androl"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.5527\/wjn.v13.i4.98880","article-title":"Neutrophil gelatinase-associated lipocalin, kidney injury molecule-1, and periostin: Novel urinary biomarkers in diabetic nephropathy","volume":"13","author":"Varatharajan","year":"2024","journal-title":"World J Nephrol"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2024.1423784","article-title":"The role of intercellular communication in diabetic nephropathy","volume":"15","author":"Wang","year":"2024","journal-title":"Front Immunol"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2024.1342837","article-title":"New insights into the role of immunity and inflammation in diabetic kidney disease in the omics era","volume":"15","author":"Hu","year":"2024","journal-title":"Front Immunol"},{"key":"B9","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/s00018-023-05078-y","article-title":"Mitochondrial oxidative damage reprograms lipid metabolism of renal tubular epithelial cells in the diabetic kidney","volume":"81","author":"Hou","year":"2024","journal-title":"Cell Mol Life Sci"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1038\/s41401-024-01298-5","article-title":"Mitochondrial calcium uniporter promotes kidney aging in mice through inducing mitochondrial calcium-mediated renal tubular cell senescence","volume":"45","author":"Xiong","year":"2024","journal-title":"Acta Pharmacol Sin"},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2017.00211","article-title":"Mitochondrial reactive oxygen species and kidney hypoxia in the development of diabetic nephropathy","volume":"8","author":"Schiffer","year":"2017","journal-title":"Front Physiol"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1038\/s41401-023-01064-z","article-title":"Astragalin ameliorates renal injury in diabetic mice by modulating mitochondrial quality control via AMPK-dependent PGC1\u03b1 pathway","volume":"44","author":"Sun","year":"2023","journal-title":"Acta Pharmacol Sin"},{"key":"B13","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1007\/s00018-023-05000-6","article-title":"Tubular TMEM16A promotes tubulointerstitial fibrosis by suppressing PGC-1\u03b1-mediated mitochondrial homeostasis in diabetic kidney disease","volume":"80","author":"Ji","year":"2023","journal-title":"Cell Mol Life Sci"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-022-00760-x","article-title":"Mitochondrial control of inflammation","volume":"23","author":"Marchi","year":"2023","journal-title":"Nat Rev Immunol"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.01.022","article-title":"Pattern recognition receptors and inflammation","volume":"140","author":"Takeuchi","year":"2010","journal-title":"Cell"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.835879","article-title":"Excessive activation of notch signaling in macrophages promote kidney inflammation, fibrosis, and necroptosis","volume":"13","author":"Ma","year":"2022","journal-title":"Front Immunol"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/ijms25052853","article-title":"Lymphatic system and the kidney: from lymphangiogenesis to renal inflammation and fibrosis development","volume":"25","author":"Stasi","year":"2024","journal-title":"IJMS"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2024.1450064","article-title":"Multi-omics insights implicate the remodeling of the intestinal structure and microbiome in aging","volume":"15","author":"Chen","year":"2024","journal-title":"Front Genet"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/s41574-018-0059-4","article-title":"Inflammaging: a new immune\u2013metabolic viewpoint for age-related diseases","volume":"14","author":"Franceschi","year":"2018","journal-title":"Nat Rev Endocrinol"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1038\/s41573-020-0067-7","article-title":"The quest to slow ageing through drug discovery","volume":"19","author":"Partridge","year":"2020","journal-title":"Nat Rev Drug Discov"},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2023.1193228","article-title":"Identification and analysis of cellular senescence-associated signatures in diabetic kidney disease by integrated bioinformatics analysis and machine learning","volume":"14","author":"Luo","year":"2023","journal-title":"Front Endocrinol"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1328757","article-title":"Integrative analysis of potential diagnostic markers and therapeutic targets for glomerulus-associated diabetic nephropathy based on cellular senescence","volume":"14","author":"Sun","year":"2024","journal-title":"Front Immunol"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3390\/ijms232315435","article-title":"Structural and functional changes in aging kidneys","volume":"23","author":"Dybiec","year":"2022","journal-title":"IJMS"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fendo.2022.924299","article-title":"Cellular senescence and regulated cell death of tubular epithelial cells in diabetic kidney disease","volume":"13","author":"Shen","year":"2022","journal-title":"Front Endocrinol"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.2337\/db20-er04b","article-title":"Erratum. Comparison of kidney transcriptomic profiles of early and advanced diabetic nephropathy reveals potential new mechanisms for disease progression","volume":"68","author":"Fan","year":"2019","journal-title":"Diabetes"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2020.110684","article-title":"Marein ameliorates diabetic nephropathy by inhibiting renal sodium glucose transporter 2 and activating the AMPK signaling pathway in db\/db mice and high glucose\u2013treated HK-2 cells","volume":"131","author":"Guo","year":"2020","journal-title":"Biomedicine Pharmacotherapy"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1111\/acel.13752","article-title":"Depletion of growth differentiation factor 15 (GDF15) leads to mitochondrial dysfunction and premature senescence in human dermal fibroblasts","volume":"22","author":"Wedel","year":"2023","journal-title":"Aging Cell"},{"key":"B28","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/s41419-024-06826-z","article-title":"Macrophage migration inhibitory factor (MIF) suppresses mitophagy through disturbing the protein interaction of PINK1-Parkin in sepsis-associated acute kidney injury","volume":"15","author":"Li","year":"2024","journal-title":"Cell Death Dis"},{"key":"B29","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/s41580-020-00314-w","article-title":"Cellular senescence in ageing: from mechanisms to therapeutic opportunities","volume":"22","author":"Di Micco","year":"2021","journal-title":"Nat Rev Mol Cell Biol"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1681\/ASN.2018121251","article-title":"Cellular senescence in the kidney","volume":"30","author":"Docherty","year":"2019","journal-title":"JASN"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.06.016","article-title":"A mitochondrial protein compendium elucidates complex I disease biology","volume":"134","author":"Pagliarini","year":"2008","journal-title":"Cell"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.182087","article-title":"Disruption of mitochondrial electron transport impairs urinary concentration via AMPK-dependent suppression of aquaporin 2","volume":"9","author":"Carty","year":"2024","journal-title":"JCI Insight"},{"key":"B33","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1038\/s41419-024-06833-0","article-title":"Mitochondrial metabolic reprogramming in diabetic kidney disease","volume":"15","author":"Fan","year":"2024","journal-title":"Cell Death Dis"},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2025.1624077","article-title":"The role of natural products in improving lipid metabolism disorder-induced mitochondrial dysfunction of diabetic kidney disease","volume":"16","author":"Deng","year":"2025","journal-title":"Front Physiol"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.7150\/ijbs.83906","article-title":"PTEN-induced kinase 1 exerts protective effects in diabetic kidney disease by attenuating mitochondrial dysfunction and necroptosis","volume":"19","author":"Sung","year":"2023","journal-title":"Int J Biol Sci"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.7150\/ijbs.89291","article-title":"MAPK1 mediates MAM disruption and mitochondrial dysfunction in diabetic kidney disease via the PACS-2-dependent mechanism","volume":"20","author":"Liu","year":"2024","journal-title":"Int J Biol Sci"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2021.751529","article-title":"Lipotoxic proximal tubular injury: A primary event in diabetic kidney disease","volume":"8","author":"Wang","year":"2021","journal-title":"Front Med"},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.1038\/s41574-020-0335-y","article-title":"The role of cellular senescence in ageing and endocrine disease","volume":"16","author":"Khosla","year":"2020","journal-title":"Nat Rev Endocrinol"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2020\/1234059","article-title":"Accelerated kidney aging in diabetes mellitus","volume":"2020","author":"Guo","year":"2020","journal-title":"Oxid Med Cell Longevity"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1038\/s41581-020-0256-y","article-title":"The tubular hypothesis of nephron filtration and diabetic kidney disease","volume":"16","author":"Vallon","year":"2020","journal-title":"Nat Rev Nephrol"},{"key":"B41","doi-asserted-by":"publisher","DOI":"10.1038\/s41569-018-0064-2","article-title":"Inflammageing: chronic inflammation in ageing, cardiovascular disease, and frailty","volume":"15","author":"Ferrucci","year":"2018","journal-title":"Nat Rev Cardiol"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1097\/imna-d-22-00027","article-title":"Research progress on the potential mechanisms of acute kidney injury and chronic kidney disease induced by proton pump inhibitors","volume":"10","author":"Song","year":"2023","journal-title":"Integr Med Nephrol Androl"},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.1161\/CIRCRESAHA.120.317723","article-title":"HDAC9: an inflammatory link in atherosclerosis","volume":"127","author":"Das","year":"2020","journal-title":"Circ Res"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.1080\/21691401.2020.1773487","article-title":"LINC00162 participates in the pathogenesis of diabetic nephropathy via modulating the miR-383\/HDAC9 signalling pathway","volume":"48","author":"Fan","year":"2020","journal-title":"Artif Cells Nanomedicine Biotechnol"},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.7150\/ijbs.115359","article-title":"Tryptophan metabolism as a target in gut microbiota, ageing and kidney disease","volume":"21","author":"Miao","year":"2025","journal-title":"Int J Biol Sci"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1016\/j.bcp.2024.116313","article-title":"Bile acid metabolism in health and ageing-related diseases","volume":"225","author":"Li","year":"2024","journal-title":"Biochem Pharmacol"},{"key":"B47","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.14336\/ad.2023.0222","article-title":"TGF-\u03b2 as A master regulator of aging-associated tissue fibrosis","volume":"14","author":"Ren","year":"2023","journal-title":"Aging Dis"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2023.1158166","article-title":"Identification and validation of aging-related gene signatures and their immune landscape in diabetic nephropathy","volume":"10","author":"Liang","year":"2023","journal-title":"Front Med"},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2024.1424644","article-title":"Integrating serum pharmacochemistry and network pharmacology to explore potential compounds and mechanisms of Alpiniae oxyphyllae fructus in the treatment of cellular senescence in diabetic kidney disease","volume":"11","author":"Yan","year":"2024","journal-title":"Front Med"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1627173\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T04:12:08Z","timestamp":1756440728000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1627173\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,29]]},"references-count":49,"alternative-id":["10.3389\/fimmu.2025.1627173"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2025.1627173","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,29]]},"article-number":"1627173"}}