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In this study, cytogenetic karyotyping was combined with transcriptomic profiling (RNA-seq) to elucidate resistance mechanisms by comparing two CRC cell lines: oxaliplatin-sensitive HCT116 and its resistant derivative HCT116 oxpl-R. Karyotyping unveiled tetraploidization and extensive genomic rearrangements in resistant cells, accompanied by prominent transcriptomic changes: 1807 differentially expressed genes (1216 upregulated and 519 downregulated). Pathway enrichment highlighted altered redox homeostasis and metabolic adaptation. Specifically, HCT116 oxpl-R cells exhibited elevated reactive oxygen species (ROS) production and enhanced energy metabolism. These findings establish a direct association between structural genomic alterations, transcriptional rewiring, and functional phenotypes in platinum resistance, providing a framework for targeting metabolic vulnerabilities in refractory CRC.<\/jats:p>","DOI":"10.3390\/ijms26188869","type":"journal-article","created":{"date-parts":[[2025,9,11]],"date-time":"2025-09-11T15:10:46Z","timestamp":1757603446000},"page":"8869","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Transcriptomic and Cytogenetic Analysis of Oxaliplatin-Resistant Colorectal Adenocarcinoma HCT116 Cells to Identify Markers Associated with Platinum Resistance"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8545-6052","authenticated-orcid":false,"given":"Alisa","family":"Morshneva","sequence":"first","affiliation":[{"name":"Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2650-4568","authenticated-orcid":false,"given":"Olga","family":"Gnedina","sequence":"additional","affiliation":[{"name":"Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ksenia","family":"Fedotova","sequence":"additional","affiliation":[{"name":"Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalija","family":"Yartseva","sequence":"additional","affiliation":[{"name":"Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nikolay","family":"Aksenov","sequence":"additional","affiliation":[{"name":"Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-5195","authenticated-orcid":false,"given":"Maria","family":"Igotti","sequence":"additional","affiliation":[{"name":"Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,11]]},"reference":[{"key":"ref_1","first-page":"12","article-title":"Cancer Statistics, 2024","volume":"74","author":"Siegel","year":"2024","journal-title":"CA Cancer J. Clin."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Roshandel, G., Ghasemi-Kebria, F., and Malekzadeh, R. (2024). Colorectal Cancer: Epidemiology, Risk Factors, and Prevention. Cancers, 16.","DOI":"10.3390\/cancers16081530"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Cree, I.A., and Charlton, P. (2017). Molecular Chess? Hallmarks of Anti-Cancer Drug Resistance. BMC Cancer, 17.","DOI":"10.1186\/s12885-016-2999-1"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.drup.2007.02.003","article-title":"Cancer Drug Resistance: The Central Role of the Karyotype","volume":"10","author":"Duesberg","year":"2007","journal-title":"Drug Resist. Updat."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/s41568-020-00321-1","article-title":"Aneuploidy as a Promoter and Suppressor of Malignant Growth","volume":"21","author":"Vasudevan","year":"2021","journal-title":"Nat. Rev. Cancer"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1021\/jm050916m","article-title":"Syntheses and Biological Activities of 3\u2019-Azido Disaccharide Analogues of Daunorubicin Against Drug-Resistant Leukemia","volume":"49","author":"Zhang","year":"2006","journal-title":"J. Med. Chem."},{"key":"ref_7","first-page":"4542","article-title":"Multidrug Resistance in Mitoxantrone-Selected HL-60 Leukemia Cells in the Absence of P-Glycoprotein Overexpression","volume":"49","author":"Harker","year":"1989","journal-title":"Cancer Res."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Michalak, M., Lach, M.S., Antoszczak, M., Huczy\u0144ski, A., and Suchorska, W.M. (2020). Overcoming Resistance to Platinum-Based Drugs in Ovarian Cancer by Salinomycin and Its Derivatives\u2014An In Vitro Study. Molecules, 25.","DOI":"10.3390\/molecules25030537"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1007\/BF00210782","article-title":"Active vs. Passive Resistance, Dose-Response Relationships, High Dose Chemotherapy, and Resistance Modulation: A Hypothesis","volume":"14","author":"Stewart","year":"1996","journal-title":"Investig. New Drugs"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2810","DOI":"10.1080\/15384101.2015.1068482","article-title":"Chromosomal Instability, Tolerance of Mitotic Errors and Multidrug Resistance Are Promoted by Tetraploidization in Human Cells","volume":"14","author":"Kuznetsova","year":"2015","journal-title":"Cell Cycle"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1158\/0008-5472.CAN-10-3604","article-title":"Chromosomal Instability Confers Intrinsic Multi-Drug Resistance","volume":"71","author":"Lee","year":"2011","journal-title":"Cancer Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1768","DOI":"10.1093\/molbev\/msz104","article-title":"Aneuploidy Enables Cross-Adaptation to Unrelated Drugs","volume":"36","author":"Yang","year":"2019","journal-title":"Mol. Biol. Evol."},{"key":"ref_13","first-page":"359","article-title":"Structural Chromosomal Aberrations in the Colon Cancer Cell Line HCT 116\u2014Results of Inves-tigations Based on Spectral Karyotyping. Cytogenet","volume":"108","author":"Mohr","year":"2005","journal-title":"Genome Res."},{"key":"ref_14","unstructured":"(2025, September 03). ISCN 2020: An International System for Human Cytogenomic Nomenclature (2020) Reprint of \u201cCytogenetic and Genome Research 2020, Vol. 160, No. 7\u20138\u201d|Books Gateway|Karger Publishers. Available online: https:\/\/karger.com\/books\/book\/358\/ISCN-2020An-International-System-for-Human."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Aggarwal, V., Tuli, H.S., Varol, A., Thakral, F., Yerer, M.B., Sak, K., Varol, M., Jain, A., Khan, M.A., and Sethi, G. (2019). Role of Reactive Oxygen Species in Cancer Progression: Molecular Mechanisms and Recent Advancements. Biomolecules, 9.","DOI":"10.3390\/biom9110735"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Li, K., Deng, Z., Lei, C., Ding, X., Li, J., and Wang, C. (2024). The Role of Oxidative Stress in Tumorigenesis and Progression. Cells, 13.","DOI":"10.3390\/cells13050441"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s10549-022-06633-0","article-title":"Abundance of Reactive Oxygen Species (ROS) Is Associated with Tumor Aggressiveness, Immune Response and Worse Survival in Breast Cancer","volume":"194","author":"Oshi","year":"2022","journal-title":"Breast Cancer Res. Treat."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Banouh, M., Armisen, D., Bouguennec, A., Huneau, C., Sow, M.D., Pont, C., Salse, J., and Civ\u00e1\u0148, P. (2023). Low Impact of Polyploidization on the Transcriptome of Synthetic Allohexaploid Wheat. BMC Genom., 24.","DOI":"10.1186\/s12864-023-09324-2"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"9100","DOI":"10.1002\/ece3.5455","article-title":"Effects of Polyploidy on the Coordination of Gene Expression Between Organellar and Nuclear Genomes in Leucanthemum Mill. (Compositae, Anthemideae)","volume":"9","author":"Oberprieler","year":"2019","journal-title":"Ecol. Evol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.cancergencyto.2006.09.014","article-title":"Cytogenetic Characterization and Gene Expression Profiling of the Trastuzumab-Resistant Breast Cancer Cell Line JIMT-1","volume":"172","author":"Rennstam","year":"2007","journal-title":"Cancer Genet. Cytogenet."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"140","DOI":"10.3393\/jksc.2011.27.3.140","article-title":"Adjuvant Chemotherapy Using the FOLFOX Regimen in Colon Cancer","volume":"27","author":"Jeon","year":"2011","journal-title":"J. Korean Soc. Coloproctology"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Lin, Q., Luo, L., and Wang, H. (2021). A New Oxaliplatin Resistance-Related Gene Signature With Strong Predicting Ability in Colon Cancer Identified by Comprehensive Profiling. Front. Oncol., 11.","DOI":"10.3389\/fonc.2021.644956"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Yin, Y., Li, S., Liang, X., Li, K., Xie, M., and Hu, B. (2022). Construction and Validation of an Oxaliplatin-Resistant Gene Signature in Colorectal Cancer Patients Who Underwent Chemotherapy. Pharmaceuticals, 15.","DOI":"10.3390\/ph15091139"},{"key":"ref_24","first-page":"6011","article-title":"Induction of Resistance to Oxaliplatin in Cancer by a microRNA\/Fem1B\/Gli1 Pathway","volume":"13","author":"Su","year":"2023","journal-title":"Am. J. Cancer Res."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Yan, D., Tu, L., Yuan, H., Fang, J., Cheng, L., Zheng, X., and Wang, X. (2017). WBSCR22 Confers Oxaliplatin Resistance in Human Colorectal Cancer. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-15749-z"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"11283","DOI":"10.1073\/pnas.201398998","article-title":"Origin of Multidrug Resistance in Cells with and without Multidrug Resistance Genes: Chromosome Reassortments Catalyzed by Aneuploidy","volume":"98","author":"Duesberg","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"581","DOI":"10.37349\/etat.2024.00237","article-title":"Comparison of Primary and Passaged Tumor Cell Cultures and Their Application in Personalized Medicine","volume":"5","author":"Pipiya","year":"2024","journal-title":"Explor. Target. Anti-Tumor Ther."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1016\/j.cell.2018.08.027","article-title":"The Multifaceted Role of Chromosomal Instability in Cancer and Its Microenvironment","volume":"174","author":"Bakhoum","year":"2018","journal-title":"Cell"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.cell.2018.03.043","article-title":"Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal","volume":"173","author":"Turajlic","year":"2018","journal-title":"Cell"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1038\/nature08822","article-title":"The Landscape of Somatic Copy-Number Alteration across Human Cancers","volume":"463","author":"Beroukhim","year":"2010","journal-title":"Nature"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Ognibene, M., De Marco, P., Amoroso, L., Cangelosi, D., Zara, F., Parodi, S., and Pezzolo, A. (2023). Multiple Genes with Potential Tumor Suppressive Activity Are Present on Chromosome 10q Loss in Neuroblastoma and Are Associated with Poor Prognosis. Cancers, 15.","DOI":"10.3390\/cancers15072035"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2427","DOI":"10.1016\/j.devcel.2021.07.009","article-title":"Chromosomal Instability Accelerates the Evolution of Resistance to Anti-Cancer Therapies","volume":"56","author":"Lukow","year":"2021","journal-title":"Dev. Cell"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Galofr\u00e9, C., G\u00f6n\u00fcl Geyik, \u00d6., Asensio, E., Wangsa, D., Hirsch, D., Parra, C., Saez, J., Moll\u00e0, M., Y\u00fcce, Z., and Castells, A. (2020). Tetraploidy-Associated Genetic Heterogeneity Confers Chemo-Radiotherapy Resistance to Colorectal Cancer Cells. Cancers, 12.","DOI":"10.3390\/cancers12051118"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1196\/annals.1378.004","article-title":"Selective Resistance of Tetraploid Cancer Cells against DNA Damage-Induced Apoptosis","volume":"1090","author":"Castedo","year":"2006","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1101\/gad.1897010","article-title":"Chronic Cisplatin Treatment Promotes Enhanced Damage Repair and Tumor Progression in a Mouse Model of Lung Cancer","volume":"24","author":"Oliver","year":"2010","journal-title":"Genes Dev."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Rutledge, S.D., Douglas, T.A., Nicholson, J.M., Vila-Casades\u00fas, M., Kantzler, C.L., Wangsa, D., Barroso-Vilares, M., Kale, S.D., Logarinho, E., and Cimini, D. (2016). Selective Advantage of Trisomic Human Cells Cultured in Non-Standard Conditions. Sci. Rep., 6.","DOI":"10.1038\/srep22828"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2214","DOI":"10.1128\/MCB.16.5.2214","article-title":"Human Chromosome 3 Mediates Growth Arrest and Suppression of Apoptosis in Microcell Hybrids","volume":"16","author":"Speevak","year":"1996","journal-title":"Mol. Cell. Biol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Hank, N.C., Shapiro, J.R., and Scheck, A.C. (2006). Over-Representation of Specific Regions of Chromosome 22 in Cells from Human Glioma Correlate with Resistance to 1,3-Bis(2-Chloroethyl)-1-Nitrosourea. BMC Cancer, 6.","DOI":"10.1186\/1471-2407-6-2"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1038\/s41586-025-09071-2","article-title":"Concurrent Loss of the Y Chromosome in Cancer and T Cells Impacts Outcome","volume":"642","author":"Chen","year":"2025","journal-title":"Nature"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1038\/ng.2966","article-title":"Mosaic Loss of Chromosome Y in Peripheral Blood Is Associated with Shorter Survival and Higher Risk of Cancer","volume":"46","author":"Forsberg","year":"2014","journal-title":"Nat. Genet."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Srinivas, U.S., Tan, B.W.Q., Vellayappan, B.A., and Jeyasekharan, A.D. (2018). ROS and the DNA Damage Response in Cancer. Redox Biol., 25.","DOI":"10.1016\/j.redox.2018.101084"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Kumari, S., Badana, A.K., G, M.M., G, S., and Malla, R. (2018). Reactive Oxygen Species: A Key Constituent in Cancer Survival. Biomark. Insights, 13.","DOI":"10.1177\/1177271918755391"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.drup.2018.11.001","article-title":"Modulating ROS to Overcome Multidrug Resistance in Cancer","volume":"41","author":"Cui","year":"2018","journal-title":"Drug Resist. Updat."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1053\/j.seminoncol.2021.05.002","article-title":"Implications of Reactive Oxygen Species on Cancer Formation and Its Treatment","volume":"48","author":"Shah","year":"2021","journal-title":"Semin. Oncol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Bahman, F., Choudhry, K., Al-Rashed, F., Al-Mulla, F., Sindhu, S., and Ahmad, R. (2024). Aryl Hydrocarbon Receptor: Current Perspectives on Key Signaling Partners and Immunoregulatory Role in Inflammatory Diseases. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1421346"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/toxsci\/kft128","article-title":"Role of the Aryl Hydrocarbon Receptor in Carcinogenesis and Potential as a Drug Target","volume":"135","author":"Safe","year":"2013","journal-title":"Toxicol. Sci."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Vogel, C.F.A., Van Winkle, L.S., Esser, C., and Haarmann-Stemmann, T. (2020). The Aryl Hydrocarbon Receptor as a Target of Environmental Stressors\u2014Implications for Pollution Mediated Stress and Inflammatory Responses. Redox Biol., 34.","DOI":"10.1016\/j.redox.2020.101530"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4775","DOI":"10.1038\/s41467-018-06951-2","article-title":"Sustained Activation of the Aryl Hydrocarbon Receptor Transcription Factor Promotes Resistance to BRAF-Inhibitors in Melanoma","volume":"9","author":"Corre","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1158\/1078-0432.CCR-17-0396","article-title":"Activation of the Aryl Hydrocarbon Receptor Leads to Resistance to EGFR TKIs in Non-Small Cell Lung Cancer by Activating Src-Mediated Bypass Signaling","volume":"24","author":"Ye","year":"2018","journal-title":"Clin. Cancer Res."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Zhou, C., Wang, Z., Li, J., Wu, X., Fan, N., Li, D., Liu, F., Plum, P.S., Hoppe, S., and Hillmer, A.M. (2021). Aldo-Keto Reductase 1C3 Mediates Chemotherapy Resistance in Esophageal Adenocarcinoma via ROS Detoxification. Cancers, 13.","DOI":"10.3390\/cancers13102403"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1124\/pharmrev.120.000122","article-title":"Aldo-Keto Reductases and Cancer Drug Resistance","volume":"73","author":"Penning","year":"2021","journal-title":"Pharmacol. Rev."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"117413","DOI":"10.1016\/j.ejmech.2025.117413","article-title":"Discovery of Highly Potent AKR1Cs Pan-Inhibitors as Chemotherapeutic Potentiators to Restore Breast Cancer Drug Resistance","volume":"289","author":"Xing","year":"2025","journal-title":"Eur. J. Med. Chem."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1002\/cbin.11789","article-title":"ARID3A Promotes the Chemosensitivity of Colon Cancer by Inhibiting AKR1C3","volume":"46","author":"Li","year":"2022","journal-title":"Cell Biol. Int."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Heibein, A.D., Guo, B., Sprowl, J.A., Maclean, D.A., and Parissenti, A.M. (2012). Role of Aldo-Keto Reductases and Other Doxorubicin Pharmacokinetic Genes in Doxorubicin Resistance, DNA Binding, and Subcellular Localization. BMC Cancer, 12.","DOI":"10.1186\/1471-2407-12-381"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"11305","DOI":"10.1021\/acs.jmedchem.9b02138","article-title":"Overview of AKR1C3: Inhibitor Achievements and Disease Insights","volume":"63","author":"Liu","year":"2020","journal-title":"J. Med. Chem."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1093\/jb\/mvac098","article-title":"Availability of Aldo-Keto Reductase 1C3 and ATP-Binding Cassette B1 as Therapeutic Targets for Alleviating Paclitaxel Resistance in Breast Cancer MCF7 Cells","volume":"173","author":"Matsunaga","year":"2023","journal-title":"J. Biochem."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.cbi.2010.12.017","article-title":"Roles of Rat and Human Aldo-Keto Reductases in Metabolism of Farnesol and Geranylgeraniol","volume":"191","author":"Endo","year":"2011","journal-title":"Chem. Biol. Interact."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"eaan2507","DOI":"10.1126\/science.aan2507","article-title":"A Pathology Atlas of the Human Cancer Transcriptome","volume":"357","author":"Uhlen","year":"2017","journal-title":"Science"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Tissue-Based Map of the Human Proteome","volume":"347","author":"Fagerberg","year":"2015","journal-title":"Science"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Moss, D.Y., Brown, C., Shaw, A., McCann, C., Lewis, N., Phillips, A., Gallagher, S., McDaid, W.J., Roe, A., and Coughlan, A.Y. (2024). Mitochondrial Metabolism Is a Key Determinant of Chemotherapy Sensitivity in Colorectal Cancer. bioRxiv.","DOI":"10.1101\/2024.09.12.611189"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"E251","DOI":"10.1111\/ans.13617","article-title":"Overexpression of NDUFA4L2 Is Associated with Poor Prognosis in Patients with Colorectal Cancer","volume":"87","author":"Lv","year":"2017","journal-title":"ANZ J. Surg."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"e70300","DOI":"10.1096\/fj.202402165RR","article-title":"A Multidimensional Pan-Cancer Analysis of NDUFA4L2 and Verification of the Oncogenic Value in Colon Cancer","volume":"39","author":"Yi","year":"2025","journal-title":"FASEB J."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.2","article-title":"Differential Analyses for RNA-Seq: Transcript-Level Estimates Improve Gene-Level Inferences","volume":"4","author":"Soneson","year":"2016","journal-title":"F1000Research"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Love, M.I., Huber, W., and Anders, S. (2014). Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2. Genome Biol., 15.","DOI":"10.1186\/s13059-014-0550-8"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"3088","DOI":"10.1093\/bioinformatics\/btx346","article-title":"karyoploteR: An R\/Bioconductor Package to Plot Customizable Genomes Displaying Arbitrary Data","volume":"33","author":"Gel","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R Package for Comparing Biological Themes Among Gene Clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS J. Integr. Biol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_70","unstructured":"Yu, G. (2025, September 08). Enrichplot: Visualization of Functional Enrichment Result. Available online: https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/enrichplot.html."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2(-Delta Delta C(T)) Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/18\/8869\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:44:13Z","timestamp":1760035453000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/18\/8869"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,11]]},"references-count":71,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["ijms26188869"],"URL":"https:\/\/doi.org\/10.3390\/ijms26188869","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,11]]}}}