Integrative Bioinformatics Analysis: Unraveling Variant Signatures and Single-Nucleotide Polymorphism Markers Associated with 5-FU-Based Chemotherapy Resistance in Colorectal Cancer Patients

Peters GJ. Drug resistance in colorectal cancer: general aspects. In: Drug resistance in colorectal cancer: molecular mechanisms and therapeutic strategies. Elsevier; 2020. p. 1–33.

Google Scholar 

Amerizadeh F, et al. The association of a genetic variant in multi-drug resistance gene and colorectal cancer susceptibility. Gene Rep. 2021;24:101252.

Article  CAS  Google Scholar 

Wu S, et al. Chemotherapeutic risk lncRNA-PVT1 SNP sensitizes metastatic colorectal cancer to FOLFOX regimen. Front Oncol. 2022;12:808889.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tutillo CA, Pinos MG, Castro MR. Genetic polymorphisms associated with toxicity in treatment with 5-fluorouracil in patients with colorectal cancer: a systematic review. Rev Oncol Ecuador. 2022;32:208–23.

Google Scholar 

Solier S, et al. DNA damage response pathways and cell cycle checkpoints in colorectal cancer: current concepts and future perspectives for targeted treatment. Curr Cancer Drug Targets. 2012;12:356–71.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jiang P, Sellers WR, Liu XS. Big data approaches for modeling response and resistance to cancer drugs. Annu Rev Biomed Data Sci. 2018;1:1–27.

Article  PubMed  PubMed Central  Google Scholar 

Tsuji S, et al. Potential responders to FOLFOX therapy for colorectal cancer by Random Forests analysis. Br J Cancer. 2012;106:126–32.

Article  CAS  PubMed  Google Scholar 

Estevez-Garcia P, et al. Gene expression profile predictive of response to chemotherapy in metastatic colorectal cancer. Oncotarget. 2015;6:6151–9.

Article  PubMed  PubMed Central  Google Scholar 

Del Rio M, et al. Gene expression signature in advanced colorectal cancer patients select drugs and response for the use of leucovorin, fluorouracil, and irinotecan. J Clin Oncol. 2007;25:773–80.

Article  PubMed  Google Scholar 

Li S, et al. Identification of HOXB8 and KLK11 expression levels as potential biomarkers to predict the effects of FOLFOX4 chemotherapy. Future Oncol. 2013;9:727–36.

Article  CAS  PubMed  Google Scholar 

Del Rio M, et al. Molecular subtypes of metastatic colorectal cancer are associated with patient response to irinotecan-based therapies. Eur J Cancer. 2017;76:68–75.

Article  PubMed  Google Scholar 

Davis Sean, Meltzer PS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics. 2007;23:1846–7.

Article  PubMed  Google Scholar 

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. 2012 The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 28(6):882-3

Ritchie ME, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.

Article  PubMed  PubMed Central  Google Scholar 

Ruhnau B. Eigenvector-centrality — a node-centrality? Soc Netw. 2000;22:357–65.

Article  Google Scholar 

Chen EY, et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14:128.

Article  PubMed  PubMed Central  Google Scholar 

Pires DE, Ascher DB, Blundell TL. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics. 2014;30:335–42.

Article  CAS  PubMed  Google Scholar 

Dehouck Y, et al. Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics. 2009;25:2537–43.

Article  CAS  PubMed  Google Scholar 

Zhou Y, Pan Q, Pires DE, Rodrigues CH, Ascher DB. 2023 DDMut: predicting effects of mutations on protein stability using deep learning. Nucleic Acids Res 51(W1):W122-8

Rodrigues CH, et al. mCSM-PPI2: predicting the effects of mutations on protein–protein interactions. Nucleic Acids Res. 2019;47:W338–44.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ashkenazy H, et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. 2016;44:W344–50.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang J, et al. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12(1):7–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993;2(9):1511–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laskowski RA, et al. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26(2):283–91.

Article  CAS  Google Scholar 

Brown NR, et al. CDK1 structures reveal conserved and unique features of the essential cell cycle CDK. Nat Commun. 2015;6:6769.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong Y, et al. Relationship between DNA repair gene XPD751 single-nucleotide polymorphisms and prognosis of colorectal cancer. Genet Mol Res. 2015;14:5390–8.

Article  CAS  PubMed  Google Scholar 

Stoehlmacher J, et al. A polymorphism of the XRCC1 gene predicts for response to platinum based treatment in advanced colorectal cancer. Anticancer Res. 2001;21:3075–9.

CAS  PubMed  Google Scholar 

Salimzadeh H, et al. Association of DNA repair gene variants with colorectal cancer: risk, toxicity, and survival. BMC Cancer. 2020;20:409.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Absenger G, et al. The cyclin D1 (CCND1) rs9344 G>A polymorphism predicts clinical outcome in colon cancer patients treated with adjuvant 5-FU-based chemotherapy. Pharmacogenomics J. 2014;14:130–4.

Article  CAS  PubMed  Google Scholar 

Azwar S, et al. Recent updates on mechanisms of resistance to 5-Fluorouracil and reversal strategies in colon cancer treatment. Biology (Basel). 2021;10:854.

CAS  PubMed  Google Scholar 

Cura Y, et al. Influence of single-nucleotide polymorphisms on clinical outcomes of capecitabine-based chemotherapy in colorectal cancer patients: a systematic review. Cancers. 2023;15:1821.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang WW, et al. Cantharidin induces G2/M phase arrest and apoptosis in human colorectal cancer colo 205 cells through inhibition of CDK1 activity and caspase-dependent signaling pathways. Int J Oncol. 2011;38:1067–73.

CAS  PubMed  Google Scholar 

Xi Q, et al. The expression of CDK1 is associated with proliferation and can be a prognostic factor in epithelial ovarian cancer. Tumor Biology. 2015;36:4939–48.

Article  CAS  PubMed  Google Scholar 

Zheng HP, et al. Integrated assessment of CDK1 upregulation in thyroid cancer. Am J Transl Res. 2019;11:7233–54.

CAS  PubMed  PubMed Central  Google Scholar 

Sung WW, et al. High nuclear/cytoplasmic ratio of Cdk1 expression predicts poor prognosis in colorectal cancer patients. BMC Cancer. 2014;14:951.

Article  PubMed 

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