Unraveling Crucial Mitochondria-Related Genes in the Transition from Ulcerative Colitis to Colorectal Cancer

References

• Ekbom A, Helmick C, Zack M, et al. Ulcerative colitis and colorectal cancer. A population-based study. N Engl J Med. 1990;323(18):1228–1233. doi:10.1056/NEJM199011013231802
   PubMed Web of Science ®Google Scholar
• Sebastian S, Hernández V, Myrelid P, et al. Colorectal cancer in inflammatory bowel disease: results of the 3rd ECCO pathogenesis scientific workshop (I). J Crohns Colitis. 2014;8(1):5–18. doi:10.1016/j.crohns.2013.04.008
   PubMed Web of Science ®Google Scholar
• Roger AJ, Munoz-Gomez SA, Kamikawa R. The origin and diversification of mitochondria. Curr Biol. 2017;27(21):R1177–R1192. doi:10.1016/j.cub.2017.09.015
   PubMed Web of Science ®Google Scholar
• Pasquale V, Ducci G, Campioni G, et al. Profiling and targeting of energy and redox metabolism in grade 2 bladder cancer cells with different invasiveness properties. Cells. 2020;9(12):2669. doi:10.3390/cells9122669
   PubMed Web of Science ®Google Scholar
• Winter JM, Yadav T, Rutter J. Stressed to death: mitochondrial stress responses connect respiration and apoptosis in cancer. Mol Cell. 2022;82(18):3321–3332. doi:10.1016/j.molcel.2022.07.012
   PubMed Web of Science ®Google Scholar
• Sabatino ME, Grondona E, Sosa LDV, et al. Oxidative stress and mitochondrial adaptive shift during pituitary tumoral growth. Free Radic Biol Med. 2018;120:41–55. doi:10.1016/j.freeradbiomed.2018.03.019
   PubMed Web of Science ®Google Scholar
• Cha H, Lee S, Hwan Kim S, et al. Increased susceptibility of IDH2-deficient mice to dextran sodium sulfate-induced colitis. Redox Biol. 2017;13:32–38. doi:10.1016/j.redox.2017.05.009
   PubMed Web of Science ®Google Scholar
• Haberman Y, Karns R, Dexheimer PJ, et al. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nat Commun. 2019;10(1):38. doi:10.1038/s41467-018-07841-3
   PubMed Web of Science ®Google Scholar
• Verma A, Pittala S, Alhozeel B, et al. The role of the mitochondrial protein VDAC1 in inflammatory bowel disease: a potential therapeutic target. Mol Ther. 2022;30(2):726–744. doi:10.1016/j.ymthe.2021.06.024
   PubMed Web of Science ®Google Scholar
• Wu Z, Xiao C, Long J, et al. Mitochondrial dynamics and colorectal cancer biology: mechanisms and potential targets. Cell Commun Signaling. 2024;22(1):91. doi:10.1186/s12964-024-01490-4
   PubMed Web of Science ®Google Scholar
• Ussakli CH, Ebaee A, Binkley J, et al. Mitochondria and tumor progression in ulcerative colitis. J Natl Cancer Inst. 2013;105(16):1239–1248. doi:10.1093/jnci/djt167
   PubMedGoogle Scholar
• Tanaka T, Kobunai T, Yamamoto Y, et al. Assessment of the changes in mitochondrial gene polymorphism in ulcerative colitis and the etiology of ulcerative colitis-associated colorectal cancer. Anticancer Res. 2020;40(1):101–107. doi:10.21873/anticanres.13931
   PubMed Web of Science ®Google Scholar
• Hsu N-Y, Nayar S, Gettler K, et al. NOX1 is essential for TNFα-induced intestinal epithelial ROS secretion and inhibits M cell signatures. Gut. 2023;72(4):654–662. doi:10.1136/gutjnl-2021-326305
   PubMed Web of Science ®Google Scholar
• Chen R. Up-regulation of mitochondrial chaperone TRAP1 in ulcerative colitis associated colorectal cancer. World J Gastroenterol. 2014;20(45):17037–17048. doi:10.3748/wjg.v20.i45.17037
   PubMed Web of Science ®Google Scholar
• Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013;41(Database issue):D991–5. doi:10.1093/nar/gks1193
   PubMed Web of Science ®Google Scholar
• Parang B, Barrett CW, Williams CS. AOM/DSS Model of Colitis-Associated Cancer. Methods Mol Biol. 2016;1422:297–307.
   PubMedGoogle Scholar
• Singh K, Coburn LA, Asim M, et al. Ornithine decarboxylase in macrophages exacerbates colitis and promotes colitis-associated colon carcinogenesis by impairing m1 immune responses. Cancer Res. 2018;78(15):4303–4315. doi:10.1158/0008-5472.CAN-18-0116
   PubMed Web of Science ®Google Scholar
• Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:3. doi:10.2202/1544-6115.1027
   PubMedGoogle Scholar
• Ito K, Murphy D. Application of ggplot2 to pharmacometric graphics. CPT Pharmacometrics Syst Pharmacol. 2013;2(10):e79. doi:10.1038/psp.2013.56
   PubMedGoogle Scholar
• Yu G, Wang L-G, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Wu T, Hu E, Xu S, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation. 2021;2(3):100141. doi:10.1016/j.xinn.2021.100141
   Web of Science ®Google Scholar
• Ashburner M. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–29. doi:10.1038/75556
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30. doi:10.1093/nar/28.1.27
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Kirsch R, Koutrouli M, et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023;51(D1):D638–D646. doi:10.1093/nar/gkac1000
   PubMed Web of Science ®Google Scholar
• Barbie DA, Tamayo P, Boehm JS, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009;462(7269):108–112. doi:10.1038/nature08460
   PubMed Web of Science ®Google Scholar
• Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinf. 2013;14(1):7. doi:10.1186/1471-2105-14-7
   PubMed Web of Science ®Google Scholar
• Tibshirani R. The lasso method for variable selection in the cox model. Stat Med. 1997;16(4):385–395. doi:10.1002/(sici)1097-0258(19970228)16:4<385::aid-sim380>3.0.co;2-3
   PubMed Web of Science ®Google Scholar
• Simon N, Friedman J, Hastie T, et al. Regularization paths for cox’s proportional hazards model via coordinate descent. J Stat Softw. 2011;39(5):1–13. doi:10.18637/jss.v039.i05
   PubMed Web of Science ®Google Scholar
• Rigatti SJ. Random Forest. J Insur Med. 2017;47(1):31–39. doi:10.17849/insm-47-01-31-39.1
   PubMedGoogle Scholar
• Izmirlian G. Application of the random forest classification algorithm to a SELDI-TOF proteomics study in the setting of a cancer prevention trial. Ann N Y Acad Sci. 2004;1020(1):154–174. doi:10.1196/annals.1310.015
   PubMedGoogle Scholar
• 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(1):77. doi:10.1186/1471-2105-12-77
   PubMed Web of Science ®Google Scholar
• Shilova ON, Shilov ES, Lieber A, et al. Disassembling a cancer puzzle: cell junctions and plasma membrane as targets for anticancer therapy. J Control Release. 2018;286:125–136. doi:10.1016/j.jconrel.2018.07.030
   PubMed Web of Science ®Google Scholar
• Yamaguchi H, Condeelis J. Regulation of the actin cytoskeleton in cancer cell migration and invasion. Biochim Biophys Acta. 2007;1773(5):642–652. doi:10.1016/j.bbamcr.2006.07.001
   PubMed Web of Science ®Google Scholar
• Applegate CC, Lane MA. Role of retinoids in the prevention and treatment of colorectal cancer. World J Gastrointest Oncol. 2015;7(10):184–203. doi:10.4251/wjgo.v7.i10.184
   PubMed Web of Science ®Google Scholar
• Li J, Ji Y, Chen N, et al. Colitis-associated carcinogenesis: crosstalk between tumors, immune cells and gut microbiota. Cell Biosci. 2023;13(1):194. doi:10.1186/s13578-023-01139-8
   PubMed Web of Science ®Google Scholar
• Ng SC, Plamondon S, Al-Hassi HO, et al. A novel population of human CD56+ human leucocyte antigen D-related (HLA-DR+) colonic lamina propria cells is associated with inflammation in ulcerative colitis. Clin Exp Immunol. 2009;158(2):205–218. doi:10.1111/j.1365-2249.2009.04012.x
   PubMed Web of Science ®Google Scholar
• Nishikawa M, Oshitani N, Matsumoto T, et al. Accumulation of mitochondrial DNA mutation with colorectal carcinogenesis in ulcerative colitis. Br J Cancer. 2005;93(3):331–337. doi:10.1038/sj.bjc.6602664
   PubMed Web of Science ®Google Scholar
• Schapira AH. Mitochondrial diseases. Lancet. 2012;379(9828):1825–1834. doi:10.1016/S0140-6736(11)61305-6
   PubMed Web of Science ®Google Scholar
• Shen Y, Ma J, Yan R, et al. Impaired self-renewal and increased colitis and dysplastic lesions in colonic mucosa of AKR1B8-deficient mice. Clin Cancer Res. 2015;21(6):1466–1476. doi:10.1158/1078-0432.CCR-14-2072
   PubMed Web of Science ®Google Scholar
• Li Y, Tang M, Zhang FJ, et al. Screening of ulcerative colitis biomarkers and potential pathways based on weighted gene co-expression network, machine learning and ceRNA hypothesis. Hereditas. 2022;159(1):42. doi:10.1186/s41065-022-00259-4
   PubMed Web of Science ®Google Scholar
• Wang W, Li X, Zheng D, et al. Dynamic changes and functions of macrophages and M1/M2 subpopulations during ulcerative colitis-associated carcinogenesis in an AOM/DSS mouse model. Mol Med Rep. 2015;11(4):2397–2406. doi:10.3892/mmr.2014.3018
   PubMed Web of Science ®Google Scholar
• Punkenburg E, Vogler T, Büttner M, et al. Batf-dependent Th17 cells critically regulate IL-23 driven colitis-associated colon cancer. Gut. 2016;65(7):1139–1150. doi:10.1136/gutjnl-2014-308227
   PubMed Web of Science ®Google Scholar
• Yoshioka K, Ueno Y, Tanaka S, et al. Role of natural killer T cells in the mouse colitis-associated colon cancer model. Scand J Immunol. 2012;75(1):16–26. doi:10.1111/j.1365-3083.2011.02607.x
   PubMed Web of Science ®Google Scholar
• Huang E, Liu R, Lu Z, et al. NKT cells mediate the recruitment of neutrophils by stimulating epithelial chemokine secretion during colitis. Biochem Biophys Res Commun. 2016;474(2):252–258. doi:10.1016/j.bbrc.2016.04.024
   PubMed Web of Science ®Google Scholar
• Cheng X, Xu X, Chen D, et al. Therapeutic potential of targeting the wnt/beta-catenin signaling pathway in colorectal cancer. Biomed Pharmacother. 2019;110:473–481. doi:10.1016/j.biopha.2018.11.082
   PubMed Web of Science ®Google Scholar
• Shenoy AK, Fisher RC, Butterworth EA, et al. Transition from colitis to cancer: high Wnt activity sustains the tumor-initiating potential of colon cancer stem cell precursors. Cancer Res. 2012;72(19):5091–5100. doi:10.1158/0008-5472.CAN-12-1806
   PubMed Web of Science ®Google Scholar
• van Dekken H, Wink JC, Vissers KJ, et al. Wnt pathway-related gene expression during malignant progression in ulcerative colitis. Acta Histochem. 2007;109(4):266–272. doi:10.1016/j.acthis.2007.02.007
   PubMed Web of Science ®Google Scholar
• Martinez-Reyes I, Chandel NS. Mitochondrial TCA cycle metabolites control physiology and disease. Nat Commun. 2020;11(1):102. doi:10.1038/s41467-019-13668-3
   PubMed Web of Science ®Google Scholar
• Sullivan LB, Gui DY, Vander Heiden MG. Altered metabolite levels in cancer: implications for tumour biology and cancer therapy. Nat Rev Cancer. 2016;16(11):680–693. doi:10.1038/nrc.2016.85
   PubMed Web of Science ®Google Scholar
• Aman J, Margadant C. Integrin-dependent cell-matrix adhesion in endothelial health and disease. Circ Res. 2023;132(3):355–378. doi:10.1161/CIRCRESAHA.122.322332
   PubMed Web of Science ®Google Scholar
• Trzeciak-Jedrzejczyk A, Makosiej R, Kolejwa M, et al. The role of adhesion molecules in inflammatory bowel disease in children. Assessment of the possible risk of cardiovascular complications. Prz Gastroenterol. 2017;12(3):181–185. doi:10.5114/pg.2017.70480
   PubMedGoogle Scholar
• Ramachandran A, Madesh M, Balasubramanian KA. Apoptosis in the intestinal epithelium: its relevance in normal and pathophysiological conditions. J Gastroenterol Hepatol. 2000;15(2):109–120. doi:10.1046/j.1440-1746.2000.02059.x
   PubMed Web of Science ®Google Scholar
• Araki Y. Increased apoptosis and decreased proliferation of colonic epithelium in dextran sulfate sodium-induced colitis in mice. Oncol Rep. 2010;24(4):869–874. doi:10.3892/or.2010.869
   PubMed Web of Science ®Google Scholar