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Gene screening of colorectal cancers via network analysis

Vahid Mansouri, Mostafa Rezaei Tavirani, Sina Rezaei Tavirani
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Abstract

Aim: Identifying crucial genes related to colorectal cancers via protein-protein interaction (PPI) network analysis is the aim of this study.

Background: colorectal cancer as major reason of mortality is evaluated by genetic and proteomic approaches to find suitable biomarkers. Chromosomal instability plays crucial role in CRC. Expression change of large numbers of genes is reported.

Methods: Differentially expressed genes related to CRCs which obtained from different proteomic methods were extracted from a review article of Paula Álvarez-Chaver et al. The genes interacted by Cytoscape software via STRING database. The central nodes determined and were enriched for biological terms by ClueGO. Action map for central genes was illustrated by CluePedia. The critical genes in CRC were introduced.

Results: Among 123 query genes, 114 one recognized by software and were included in the network. SRC, EGFR, PCNA, IL8, CTNNB1, TIMP1, CDH1, and HSPD1 were determined as central genes. After gene ontology analysis SRC, EGFR, and CDH1 were identified as critical genes related to CRC.

Conclusion: It seems that SRC, EGFR, and CDH1 and the related pathways are possible biomarkers for CRC.

Keywords: Colorectal cancer, Biomarker, Gene.

(Please cite as: Mansouri V, Rezaei Tavirani M, Rezaei Tavirani S. Gene screening of colorectal cancers via network analysis. Gastroenterol Hepatol Bed Bench 2019;12(2):149-154).


Keywords

Colorectal cancer, Biomarker, Gene.

References

Haggar FA, Boushey RP. Colorectal cancer epidemiology: incidence, mortality, survival, and risk factors. Clin Colon Rectal Surg 2009;22:191-7

Winawer SJ, Fletcher RH, Miller L, Godlee F, Stolar M, Mulrow C, et al. Colorectal cancer screening: clinical guidelines and rationale. Gastroenterol 1997;112:594-642.

Bardelli A, Siena S. Molecular mechanisms of resistance to cetuximab and panitumumab in colorectal cancer. J Clin Oncol 2010;28:1254-61.

Markowitz SD, Bertagnolli MM. Molecular basis of colorectal cancer. New England J Med 2009;361:2449-60.

Khambata-Ford S, Garrett CR, Meropol NJ, Basik M, Harbison CT, Wu S, et al. Expression of epiregulin and amphiregulin and K-ras mutation status predict disease control in metastatic colorectal cancer patients treated with cetuximab. J Clin Oncol 2007;25:3230-7.

Kashfi SM, Behboudi Farahbakhsh F, Nazemalhosseini Mojarad E, Mashayekhi K, Azimzadeh P, Romani S, et al. Interleukin-16 polymorphisms as new promising biomarkers for risk of gastric cancer. Tumour Biol. 2016;37:2119-26.

Kim NH, Lee MY, Park JH, Park DI, Sohn CI, Choi K, et al. Serum CEA and CA 19-9 Levels are Associated with the Presence and Severity of Colorectal Neoplasia. Yonsei Med J 2017;58:918-24.

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol 2011;12:R60.

Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol 2006;24:971.

Network CGA. Comprehensive molecular characterization of human colon and rectal cancer. Nat 2012;487:330.

Safari-Alighiarloo N, Rezaei-Tavirani M, Taghizadeh M, Tabatabaei SM, Namaki S. Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis. Peer J 2016;4:e2775.

Rezaei-Tavirani M, Rezaei-Tavirani S, Ahmadi N, Naderi N, Abdi S. Pancreatic adenocarcinoma protein-protein interaction network analysis. Gastroenterol Hepatol Bed Bench 2017;10:S85.

Zamanian–Azodi M, Rezaei–Tavirani M, Hasanzadeh H, Rad SR, Dalilan S. Introducing biomarker panel in esophageal, gastric, and colon cancers; a proteomic approach. Gastroenterol Hepatol Bed Bench 2015;8:6.

Zamanian-Azodi M, Rezaei-Tavirani M, Rahmati-Rad S, Hasanzadeh H, Tavirani MR, Seyyedi SS. Protein-Protein Interaction Network could reveal the relationship between the breast and colon cancer. Gastroenterol Hepatol Bed Bench 2015;8:215.

Álvarez-Chaver P, Otero-Estévez O, De la Cadena MP, Rodríguez-Berrocal FJ, Martínez-Zorzano VS. Proteomics for discovery of candidate colorectal cancer biomarkers. World Journal of Gastroenterology: WJG 2014;20:3804.

Zhi J, Sun J, Wang Z, Ding W. Support vector machine classifier for prediction of the metastasis of colorectal cancer. Int J Mol Med 2018;41:1419-26.

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, et al. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res 2017;45:D362-8.

Bindea G, Galon J, Mlecnik B. CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics 2013;29:661-3.

Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009;25:1091-3.

Sen B, Johnson FM. Regulation of SRC family kinases in human cancers. J Signal Transduct 2011;2011:865819

Irby RB, Yeatman TJ. Role of Src expression and activation in human cancer. Oncogene 2000;19:5636.

Creedon H, Brunton VG. Src kinase inhibitors: promising cancer therapeutics? Crit Rev Oncog 2012;17:145-59.

Metzger B, Chambeau L, Begon DY, Faber C, Kayser J, Berchem G, et al. The human epidermal growth factor receptor (EGFR) gene in European patients with advanced colorectal cancer harbors infrequent mutations in its tyrosine kinase domain. BMC Med Genetics 2011;12:144.

Kohsaka S, Nagano M, Ueno T, Suehara Y, Hayashi T, Shimada N, et al. A method of high-throughput functional evaluation of EGFR gene variants of unknown significance in cancer. Sci Trans Med 2017;9:eaan6566.

Liu X, Chu KM. E-cadherin and gastric cancer: cause, consequence, and applications. Biomed Res Int 2014;2014:637308.

Wheeler J, Kim H, Efstathiou J, Ilyas M, Mortensen NM, Bodmer W. Hypermethylation of the promoter region of the E-cadherin gene (CDH1) in sporadic and ulcerative colitis associated colorectal cancer. Gut 2001;48:367-71.

Widschwendter A, Ivarsson L, Blassnig A, Müller HM, Fiegl H, Wiedemair A, et al. CDH1 and CDH13 methylation in serum is an independent prognostic marker in cervical cancer patients. Int J cancer 2004;109:163-6.




DOI: https://doi.org/10.22037/ghfbb.v12i2.1567