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ORIGINAL RESEARCH

Exploring the Relevance of Disulfidptosis to the Pathophysiology of Ulcerative Colitis by Bioinformatics Analysis

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Pages 2757-2774 | Received 10 Jan 2024, Accepted 25 Apr 2024, Published online: 06 May 2024

References

  • Ordás I, Eckmann L, Talamini M, Baumgart DC, Sandborn WJ. Ulcerative colitis. Lancet. 2012;380(9853):1606–1619. doi:10.1016/s0140-6736(12)60150-0
  • Ng SC, Shi HY, Hamidi N, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet. 2017;390(10114):2769–2778. doi:10.1016/s0140-6736(17)32448-0
  • Sun Y, Zhang Z, Zheng CQ, Sang LX. Mucosal lesions of the upper gastrointestinal tract in patients with ulcerative colitis: a review. World J Gastroenterol. 2021;27(22):2963–2978. doi:10.3748/wjg.v27.i22.2963
  • Shah SC, Itzkowitz SH. Colorectal Cancer in Inflammatory Bowel Disease: mechanisms and Management. Gastroenterology. 2022;162(3):715–730.e3. doi:10.1053/j.gastro.2021.10.035
  • de Souza HS, Fiocchi C. Immunopathogenesis of IBD: current state of the art. Nat Rev Gastroenterol Hepatol. 2016;13(1):13–27. doi:10.1038/nrgastro.2015.186
  • Oshi MA, Naeem M, Bae J, et al. Colon-targeted dexamethasone microcrystals with pH-sensitive chitosan/alginate/Eudragit S multilayers for the treatment of inflammatory bowel disease. Carbohydr Polym. 2018;198:434–442. doi:10.1016/j.carbpol.2018.06.107
  • Liu X, Nie L, Zhang Y, et al. Actin cytoskeleton vulnerability to disulfide stress mediates disulfidptosis. Nat Cell Biol. 2023;25(3):404–414. doi:10.1038/s41556-023-01091-2
  • Zheng P, Zhou C, Ding Y, Duan S. Disulfidptosis: a new target for metabolic cancer therapy. J Exp Clin Cancer Res. 2023;42(1):103. doi:10.1186/s13046-023-02675-4
  • Vancamelbeke M, Vanuytsel T, Farré R, et al. Genetic and transcriptomic bases of intestinal epithelial barrier dysfunction in inflammatory bowel disease. Inflamm Bowel Dis. 2017;23(10):1718–1729. doi:10.1097/mib.0000000000001246
  • Li K, Strauss R, Ouahed J, et al. Molecular comparison of adult and pediatric ulcerative colitis indicates broad similarity of molecular pathways in disease tissue. J Pediatr Gastroenterol Nutr. 2018;67(1):45–52. doi:10.1097/mpg.0000000000001898
  • Montero-Meléndez T, Llor X, García-Planella E, Perretti M, Suárez A. Identification of novel predictor classifiers for inflammatory bowel disease by gene expression profiling. PLoS One. 2013;8(10):e76235. doi:10.1371/journal.pone.0076235
  • Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457. doi:10.1038/nmeth.3337
  • Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26(12):1572–1573. doi:10.1093/bioinformatics/btq170
  • Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
  • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 2008;9:559. doi:10.1186/1471-2105-9-559
  • Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinf. 2011;12:77. doi:10.1186/1471-2105-12-77
  • Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinf. 2013;14:7. doi:10.1186/1471-2105-14-7
  • Garrido-Trigo A, Corraliza AM, Veny M, et al. Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease. Nat Commun. 2023;14(1):4506. doi:10.1038/s41467-023-40156-6
  • Olén O, Erichsen R, Sachs MC, et al. Colorectal cancer in ulcerative colitis: a Scandinavian population-based cohort study. Lancet. 2020;395(10218):123–131. doi:10.1016/s0140-6736(19)32545-0
  • Conrad K, Roggenbuck D, Laass MW. Diagnosis and classification of ulcerative colitis. Autoimmun Rev. 2014;13(4–5):463–466. doi:10.1016/j.autrev.2014.01.028
  • Tyler CJ, Guzman M, Lundborg LR, et al. Antibody secreting cells are critically dependent on integrin α4β7/MAdCAM-1 for intestinal recruitment and control of the microbiota during chronic colitis. Mucosal Immunol. 2022;15(1):109–119. doi:10.1038/s41385-021-00445-z
  • Kang S, Kim J, Park A, et al. TRIM40 is a pathogenic driver of inflammatory bowel disease subverting intestinal barrier integrity. Nat Commun. 2023;14(1):700. doi:10.1038/s41467-023-36424-0
  • Kalluri R. Basement membranes: structure, assembly and role in tumour angiogenesis. Nat Rev Cancer. 2003;3(6):422–433. doi:10.1038/nrc1094
  • Kuo DS, Labelle-Dumais C, Gould DB. COL4A1 and COL4A2 mutations and disease: insights into pathogenic mechanisms and potential therapeutic targets. Hum Mol Genet. 2012;21(R1):R97–110. doi:10.1093/hmg/dds346
  • Chen S, Puthanveetil P, Feng B, Matkovich SJ, Dorn GW, Chakrabarti S. Chakrabarti S. Cardiac miR-133a overexpression prevents early cardiac fibrosis in diabetes. J Cell Mol Med. 2014;18(3):415–421. doi:10.1111/jcmm.12218
  • Solé C, Moliné T, Vidal M, Ordi-Ros J, Cortés-Hernández J. An Exosomal Urinary miRNA Signature for Early Diagnosis of Renal Fibrosis in Lupus Nephritis. Cells. 2019;8(8):773. doi:10.3390/cells8080773
  • Savin IA, Markov AV, Zenkova MA, Sen’kova AV. Asthma and post-asthmatic fibrosis: a search for new promising molecular markers of transition from acute inflammation to pulmonary fibrosis. Biomedicines. 2022;10(5):1017. doi:10.3390/biomedicines10051017
  • Eshelman MA, Harris L, Deiling S, Koltun WA, Jeganathan NA, Yochum GS. Transcriptomic analysis of ileal tissue from Crohn’s disease patients identifies extracellular matrix genes that distinguish individuals by age at diagnosis. Physiol Genomics. 2020;52(10):478–484. doi:10.1152/physiolgenomics.00062.2020
  • Yang R, Liu Y, Wang Y, et al. Low PRRX1 expression and high ZEB1 expression are significantly correlated with epithelial-mesenchymal transition and tumor angiogenesis in non-small cell lung cancer. Medicine. 2021;100(4):e24472. doi:10.1097/md.0000000000024472
  • Kern MJ, Argao EA, Birkenmeier EH, Rowe LB, Potter SS. Genomic organization and chromosome localization of the murine homeobox gene Pmx. Genomics. 1994;19(2):334–340. doi:10.1006/geno.1994.1066
  • Dankel SN, Grytten E, Bjune JI, et al. COL6A3 expression in adipose tissue cells is associated with levels of the homeobox transcription factor PRRX1. Sci Rep. 2020;10(1):20164. doi:10.1038/s41598-020-77406-2
  • Zhang X, Ma L, Shen Y, Zhang C, Hou B, Zhou Y. Transcription factor paired related homeobox 1 (PRRX1) activates matrix metalloproteinases (MMP)13, which promotes the dextran sulfate sodium-induced inflammation and barrier dysfunction of NCM460 cells. Bioengineered. 2022;13(1):645–654. doi:10.1080/21655979.2021.2012549
  • Gao Y, Martin NI, van Haren MJ. Nicotinamide N-methyl transferase (NNMT): an emerging therapeutic target. Drug Discov Today. 2021;26(11):2699–2706. doi:10.1016/j.drudis.2021.05.011
  • Ulanovskaya OA, Zuhl AM, Cravatt BF. NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink. Nat Chem Biol. 2013;9(5):300–306. doi:10.1038/nchembio.1204
  • Liu M, Li L, Chu J, et al. Serum N(1)-methylnicotinamide is associated with obesity and diabetes in Chinese. J Clin Endocrinol Metab. 2015;100(8):3112–3117. doi:10.1210/jc.2015-1732
  • Schmeisser K, Parker JA. Nicotinamide-N-methyltransferase controls behavior, neurodegeneration and lifespan by regulating neuronal autophagy. PLoS Genet. 2018;14(9):e1007561. doi:10.1371/journal.pgen.1007561
  • Fedorowicz A, Mateuszuk Ł, Kopec G, et al. Activation of the nicotinamide N-methyltransferase (NNMT)-1-methylnicotinamide (MNA) pathway in pulmonary hypertension. Respir Res. 2016;17(1):108. doi:10.1186/s12931-016-0423-7
  • Wnorowski A, Wnorowska S, Kurzepa J, Parada-Turska J. Alterations in Kynurenine and NAD(+) salvage pathways during the successful treatment of inflammatory bowel disease suggest HCAR3 and NNMT as potential drug targets. Int J Mol Sci. 2021;22:24.
  • Woodfin A, Voisin MB, Nourshargh S. PECAM-1: a multi-functional molecule in inflammation and vascular biology. Arterioscler Thromb Vasc Biol. 2007;27(12):2514–2523. doi:10.1161/atvbaha.107.151456
  • Govender D, Harilal P, Dada M, Chetty R. CD31 (JC70) expression in plasma cells: an immunohistochemical analysis of reactive and neoplastic plasma cells. J Clin Pathol. 1997;50(6):490–493. doi:10.1136/jcp.50.6.490
  • Baumann CI, Bailey AS, Li W, Ferkowicz MJ, Yoder MC, Fleming WH. PECAM-1 is expressed on hematopoietic stem cells throughout ontogeny and identifies a population of erythroid progenitors. Blood. 2004;104(4):1010–1016. doi:10.1182/blood-2004-03-0989
  • Arijs I, De Hertogh G, Machiels K, et al. Mucosal gene expression of cell adhesion molecules, chemokines, and chemokine receptors in patients with inflammatory bowel disease before and after infliximab treatment. Am J Gastroenterol. 2011;106(4):748–761. doi:10.1038/ajg.2011.27
  • Bonafiglia QA, Lourenssen SR, Hurlbut DJ, Blennerhassett MG. Epigenetic modification of intestinal smooth muscle cell phenotype during proliferation. Am J Physiol Cell Physiol. 2018;315(5):C722–c733. doi:10.1152/ajpcell.00216.2018
  • Szczepanski HE, Flannigan KL, Mainoli B, et al. NR4A1 modulates intestinal smooth muscle cell phenotype and dampens inflammation-associated intestinal remodeling. FASEB j. 2022;36(11):e22609. doi:10.1096/fj.202101817RR
  • Cromer WE, Mathis JM, Granger DN, Chaitanya GV, Alexander JS. Role of the endothelium in inflammatory bowel diseases. World J Gastroenterol. 2011;17(5):578–593. doi:10.3748/wjg.v17.i5.578
  • Danese S, Dejana E, Fiocchi C. Immune regulation by microvascular endothelial cells: directing innate and adaptive immunity, coagulation, and inflammation. J Immunol. 2007;178(10):6017–6022. doi:10.4049/jimmunol.178.10.6017
  • Danese S, Panés J. Development of drugs to target interactions between leukocytes and endothelial cells and treatment algorithms for inflammatory bowel diseases. Gastroenterology. 2014;147(5):981–989. doi:10.1053/j.gastro.2014.08.044
  • Slack RJ, Macdonald SJF, Roper JA, Jenkins RG, Hatley RJD. Emerging therapeutic opportunities for integrin inhibitors. Nat Rev Drug Discov. 2022;21(1):60–78. doi:10.1038/s41573-021-00284-4