704
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

Molecular analysis to identify novel potential biomarkers as drug targets in colorectal cancer therapy: an integrated bioinformatics analysis

, , , , , , & show all
Article: 2326699 | Received 25 Oct 2023, Accepted 29 Feb 2024, Published online: 18 Mar 2024

References

  • Favoriti P, Carbone G, Greco M, Pirozzi F, Pirozzi RE, Corcione F. Worldwide burden of colorectal cancer: a review. Updates Surg. 2016 Mar;68(1):7–14. doi:10.1007/s13304-016-0359-y.
  • Rahib L, Smith BD, Aizenberg R, Rosenzweig AB, Fleshman JM, Matrisian LM. Projecting cancer incidence and deaths to 2030: the unexpected burden of thyroid, liver, and pancreas cancers in the United States. Cancer Res. 2014 Jun 1;74(11):2913–21. doi:10.1158/0008-5472.CAN-14-0155.
  • Hull R, Francies FZ, Oyomno M, Dlamini Z. Colorectal cancer genetics, incidence and risk factors: In search for targeted therapies. Cancer Manag Res. 2020 Oct 9;12:9869–9882. doi: 10.2147/CMAR.S251223.
  • Mohandas KM. Colorectal cancer in India: controversies, enigmas and primary prevention. Indian J Gastroenterol. 2011 Feb;30(1):3–6. doi:10.1007/s12664-010-0076-2.
  • Patil PS, Saklani A, Gambhire P, Mehta S, Engineer R, De’souza A, Chopra S, Bal M. Colorectal cancer in India: an audit from a tertiary center in a low prevalence area. Indian J Surg Oncol. 2017 Dec;8(4):484–490. doi:10.1007/s13193-017-0655-0.
  • Rawla P, Sunkara T, Barsouk A. Epidemiology of colorectal cancer: incidence, mortality, survival, and risk factors. Prz Gastroenterol. 2019;14(2):89–103. doi:10.5114/pg.2018.81072.
  • Tanaka T. Colorectal carcinogenesis: Review of human and experimental animal studies. J Carcinog. 2009;8(1):5. doi:10.4103/1477-3163.49014.
  • Fearon ER. Molecular genetics of colorectal cancer. Annu Rev Pathol. 2011;6:479–507. doi:10.1146/annurev-pathol-011110-130235.
  • Mundade R, Imperiale TF, Prabhu L, Loehrer PJ, Lu T. Genetic pathways, prevention, and treatment of sporadic colorectal cancer. Oncoscience. 2014 Jun 30;1(6):400–6. doi:10.18632/oncoscience.59.
  • Coppedè F, Lopomo A, Spisni R, Migliore L. Genetic and epigenetic biomarkers for diagnosis, prognosis and treatment of colorectal cancer. World J Gastroenterol. 2014 Jan 28;20(4):943–956. doi:10.3748/wjg.v20.i4.943.
  • Mudassar S, Khan MS, Khan NP, Andrabi KI. Possible role of proto-oncogenes in colorectal cancer—A population based study. Colorectal cancer-surgery, diagnostic and treatment. 2014.
  • Nakayama M, Oshima M. Mutant p53 in colon cancer. J Mol Cell Biol. 2019 Apr 1;11(4):267–276. doi:10.1093/jmcb/mjy075.
  • Banks RE, Dunn MJ, Hochstrasser DF, Sanchez JC, Blackstock W, Pappin DJ, Selby PJ. Proteomics: new perspectives, new biomedical opportunities. Lancet. 2000 Nov 18;356(9243):1749–56. doi:10.1016/S0140-6736(00)03214-1.
  • Clough E, Barrett T. The gene expression omnibus database. Methods Mol Biol. 2016;1418:93–110. doi:10.1007/978-1-4939-3578-9_5.
  • Tomczak K, Czerwińska P, Wiznerowicz M. The cancer genome atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn). 2015;19(1A):A68–77. doi:10.5114/wo.2014.47136.
  • Chandrashekar DS, Bashel B, Balasubramanya SAH, Creighton CJ, Ponce-Rodriguez I, Chakravarthi BVSK, Varambally S. UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia. 2017 Aug;19(8): 19. 8. 649–658. 10.1016/j.neo.2017.05.002. Epub 2017 Jul 18.
  • Guan L, Tang Y, Li G, Qin Z, Li S. Comprehensive analysis of role of cyclin-dependent kinases family members in colorectal cancer. Front Oncol. 2022 Jun 22;12:921710. doi:10.3389/fonc.2022.921710.
  • Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S. et al. Towards a knowledge-based human protein atlas. Nat Biotechnol. 2010 Dec;28(12):1248–50. doi:10.1038/nbt1210-1248.
  • von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003 Jan 1;31(1):258–261. doi:10.1093/nar/gkg034.
  • Kohl M, Wiese S, Warscheid B. Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol. 2011;696:291–303. doi:10.1007/978-1-60761-987-1_18.
  • Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A. et al. FunRich: an open access standalone functional enrichment and interaction network analysis tool. Proteomics. 2015 Aug;15(15):2597–2601. doi:10.1002/pmic.201400515.
  • Díez-Villanueva A, Mallona I, Peinado MA. Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer. Epigenetics & Chromatin. 2015 Jun 23;8(1):22. 10.1186/s13072-015-0014-8. PMID: 26113876; PMCID: PMC4480445.
  • Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks. Proc Int AAAI Conf Web Social Media. 2009 March;3(1):361–362. doi:10.1609/icwsm.v3i1.13937.
  • Reimand J, Kull M, Peterson H, Hansen J, Vilo J. G: profiler–a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193–200. doi:10.1093/nar/gkm226.
  • Ogata H, Goto S, Fujibuchi W, Kanehisa M. Computation with the KEGG pathway database. Biosystems. 1998 Jun-Jul;47(1–2):119–28. doi:10.1016/s0303-2647(98)00017-3.
  • Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B. et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2018 Jan 4;46(D1):D649–D655. doi:10.1093/nar/gkx1132.
  • Tang Z, Li C, Kang B, Gao G, Li C, Zhang Z. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017 Jul 3;45(W1):W98–W102. doi:10.1093/nar/gkx247.
  • Porichi O, Nikolaidou ME, Apostolaki A, Tserkezoglou A, Arnogiannaki N, Kassanos D, Margaritis L, Panotopoulou E. BCL-2, BAX and P53 expression profiles in endometrial carcinoma as studied by real-time PCR and immunohistochemistry. Anticancer Res. 2009 Oct;29(10):3977–3982.
  • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545–50. doi:10.1073/pnas.0506580102.
  • Skrzypczak M, Goryca K, Rubel T, Paziewska A, Mikula M, Jarosz D, Pachlewski J, Oledzki J, Ostrowski J, Khanin R. Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability. PloS One. 2010 Oct 1;5(10):e13091. doi:10.1371/journal.pone.0013091.
  • Khamas A, Ishikawa T, Shimokawa K, Mogushi K, Iida S, Ishiguro M, Mizushima H, Tanaka H, Uetake H, Sugihara K. Screening for epigenetically masked genes in colorectal cancer using 5-aza-2’-deoxycytidine, microarray and gene expression profile. Cancer Genomics Proteomics. 2012 Mar-Apr;9(2):67–75.
  • Del Rio M, Mollevi C, Vezzio-Vie N, Bibeau F, Ychou M, Martineau P, Guan X-Y. Specific extracellular matrix remodeling signature of colon hepatic metastases. PLoS One. 2013 Sep 4;8(9):e74599. 10.1371/journal.pone.0074599. PMID: 24023955; PMCID: PMC3762755.
  • Kemper K, Versloot M, Cameron K, Colak S, de Sousa e Melo F, de Jong JH, Bleackley J, Vermeulen L, Versteeg R, Koster J. et al. Mutations in the Ras-Raf Axis underlie the prognostic value of CD133 in colorectal cancer. Clin Cancer Res. 2012 Jun 1;18(11):3132–3141. doi:10.1158/1078-0432.CCR-11-3066.
  • Wan Y, Zhang X, Leng H, Yin W, Zeng W, Zhang C. Identifying hub genes of papillary thyroid carcinoma in the TCGA and GEO database using bioinformatics analysis. PeerJ. 2020 Jul 9;8:e9120. doi:10.7717/peerj.9120.
  • Sawicki T, Ruszkowska M, Danielewicz A, Niedźwiedzka E, Arłukowicz T, Przybyłowicz KE. A review of colorectal cancer in terms of epidemiology, risk factors, development, symptoms and diagnosis. Cancers Basel. 2021 Apr 22;13(9):2025. doi:10.3390/cancers13092025.
  • Ansorge WJ. Next-generation DNA sequencing techniques. N Biotechnol. 2009 Apr;25(4):195–203. doi:10.1016/j.nbt.2008.12.009.
  • Sharma A, Yadav D, Rao P, Sinha S, Goswami D, Rawal RM, Shrivastava N. Identification of potential therapeutic targets associated with diagnosis and prognosis of colorectal cancer patients based on integrated bioinformatics analysis. Comput Biol Med. 2022 Jul;146:105688. doi:10.1016/j.compbiomed.2022.105688.
  • Miralaei N, Majd A, Ghaedi K, Peymani M, Safaei M. Integrated pan-cancer of AURKA expression and drug sensitivity analysis reveals increased expression of AURKA is responsible for drug resistance. Cancer Med. 2021 Sep;10(18):6428–6441. doi:10.1002/cam4.4161.
  • Tian Y, Tian X, Han X, Chen Y, Song CY, Jiang WJ, Tian DL. ABCE1 plays an essential role in lung cancer progression and metastasis. Tumour Biol. 2016 Jun;37(6):8375–82. doi:10.1007/s13277-015-4713-3.
  • Kim SK, Kim K, Ryu JW, Ryu TY, Lim JH, Oh JH, Min JK, Jung CR, Hamamoto R, Son MY. et al. The novel prognostic marker, EHMT2, is involved in cell proliferation via HSPD1 regulation in breast cancer. Int J Oncol. 2019 Jan;54(1):65–76. doi:10.3892/ijo.2018.4608.
  • Jiang Y, Chen F, Ren X, Yang Y, Luo J, Yuan J, Yuan J, Tong Q. RNA-Binding protein COL14A1, TNS1, NUSAP1 and YWHAE are valid biomarkers to predict peritoneal metastasis in gastric cancer. Front Oncol. 2022 Apr 19;12:830688. doi:10.3389/fonc.2022.830688.
  • Li D, Pan Z, Zhang K, Yu M, Yu D, Lu Y, Wang J, Zhang J, Zhang K, Du W. Identification of the differentially expressed genes of muscle growth and intramuscular fat metabolism in the development stage of yellow broilers. Genes. 2020 Feb 26;11(3):244. doi:10.3390/genes11030244.
  • Zhao P, Hu YC, Talbot IC. Expressing patterns of p16 and CDK4 correlated to prognosis in colorectal carcinoma. World J Gastroenterol. 2003 Oct;9(10):2202–2206. doi:10.3748/wjg.v9.i10.2202.