In silico Characterization of Esophageal Cancer Predominant Genes

Year 2023, , 1255 - 1264, 18.12.2023

Gizem Köprülülü Küçük

https://doi.org/10.16984/saufenbilder.1274006

Abstract

Cancer is an important health problem nowadays. One of these problems is esophageal cancer (EC). The 7th most common cancer is EC worldwide. Rhomboid-related biomarkers play an important role in EC. Analysis of such biomarkers can yield important insights into the role of rhomboid 5 Homolog 2 (RHBDF2) in cancer pathology. The characterization of genes was made in silico tools such as STRING, SWISS-MODEL, UCSF Chimera ver 1.15, ProtParam, and GeneCards. The protein interactions string of the rhomboid 5 homologs 2 (RHBDF2) gene was obtained from STRING. Epidermal growth factor (EGF), and ADAM Metallopeptidase Domain 17 (ADAM17) genes were detected as related genes. Amino acid sequences of these genes were obtained from NCBI. Homology models, and Ramachandran graphic of RHBDF2, ADAM17, and EGF genes were created by the SWISS-MODEL database and UCSF Chimera ver 1.15 program. Physicochemical properties of RHBDF2, ADAM17, and EGF genes were calculated by the ProtParam database. Subcellular localizations were detected by the GeneCards server. As a result of this study, genomic and subcellular localization of RHBDF2, ADAM17, and EGF genes were obtained. Amino acid sequences, 3D-protein structures, and physicochemical properties were detected.

Keywords

Eusopagheal cancer, homology model, rhomboid 5 homologs 2 (RHBDF2), epidermal growth factor (EGF), ADAM Metallopeptidase Domain 17 (ADAM17)

References

• [1] M. Matejcic, M. I. Parker, “Gene-environment interactions in esophageal cancer,” Critical Reviews in Clinical Laboratory Sciences, vol 52, no. 5, pp. 211-31, 2015.
• [2] D. E. Lin, M. R. Wang, H. P. Koeffler, “Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients,” Gastroenterology, vol. 154, no. 2, pp. 374-89, 2018.
• [3] K. V. V. Kumar, R. Sagar, J. Mathew, “Squamous Cell Carcinoma: Esophagus,” IntechOpen, London: Daaboul H, 2020.
• [4] K. E. Li, “Mortality and incidence trends from esophagus cancer in selected geographic areas of China Cira 1970-90,” International Journal of Cancer, vol. 102, no. 3, pp. 271-274, 2002.
• [5] L. F. R. Pinto, A. M. T. Rossini, R. M. Albano, I. Felzenszwalb, C. V. M. Gallo, R. A. Nunes, “Mechanisms of esophageal cancer development in Brazilians,” Mutation Research, vol. 544, pp. 365-373, 2003.
• [6] H. Z. Zhang, G. F. Jin, H. B. Shen, “Epidemiologic differences in esophageal cancer between Asian and Western populations,” Chinese Journal of Cancer, vol. 31, no. 6, pp. 281-286, 2012.
• [7] X. Yang, X. Chen, M. Zhuang, Z. Yuan, S. Nie, M. Lu, W. Ye, “Smoking and alcohol drinking in relation to the risk of esophageal squamous cell carcinoma: A population-based case-control study in China,” Scientific Reports, vol. 7, no. 1, 2017.
• [8] J. Lagergren, “Etiology and risk factors for oesophageal adenocarcinoma: possibilities for chemoprophylaxis? Best Practice,” Practice & Research Clinical Gastroenterology, vol. 20, no. 5, pp. 803-812, 2006.
• [9] G. Nabi, H. Muhammad, S. N. Khan, A. A. Khan, “Etiological Factors of Esophageal Cancer,” The Journal of Toxicological Sciences, vol. 7, no. 3, pp. 188-197, 2015.
• [10] T. Hiyama, M. Yoshihara, S. Tanaka, K. Chayama, “Genetic polymorphisms and esophageal cancer risk,” International Journal of Cancer, vol. 121, no. 8, pp. 1643-1658, 2007.
• [11] M. Freeman, B. E. Kimmel, G. M. Rubin, “Identifying targets of the rough homeobox gene of Drosophila: evidence that rhomboid functions in eye development,” Development, vol. 116, pp. 335-346, 1992.
• [12] G. A. McQuibban, S. Saurya, M. Freeman, “Mitochondrial membrane remodeling regulated by a conserved rhomboid protease,” Nature, vol. 423, pp. 537-541, 2003.
• [13] T. Nakagawa, A. Guichard, C. P. Castro, Y. Xiao, M. Rizen, H. Z. Zhang, D. Hu, A. Bang, J. Helms, E. Bier, R. Derynck, “Characterization of a human rhomboid homolog, p100hRho/ RHBDF1, which interacts with TGF-α family ligands,” Developmental Dynamics, vol. 233, pp.1315–1331, 2005.
• [14] H. Zou, S. M. Thomas, Z. W. Yan, J. R. Grandis, A. Vogt, L. Y. Li, “Human rhomboid family-1 gene RHBDF1 participates in GPCR-mediated transactivation of EGFR growth signals in head and neck squamous cancer cells,” FASEB Journal, vol 23, pp. 425- 432, 2009.
• [15] R. A. Black, C. T. Rauch, C. J. Kozlosky, J. J. Peschon, J. L. Slack, M. F. Wolfson, B. J. Castner, K. L. Stocking, P. Reddy, S. Srinivasan, N. Nelson, N. Boiani, K. A. Schooley, M. Gerhart, R. Davis, J. N. Fitzner, R S. Johnson, R. J. Paxton,C. J. March, D. P. Cerretti, “A metalloproteinase disintegrin that releases tumour necrosis factor-alpha from cells,” Nature, vol. 385, pp. 729-733, 1997.
• [16] D. C. Blaydon, S. L. Etheridge, J. M. Risk, H. C. Hennies, L. J. Gay, R. Carroll, V. Plagnol, F. E. McDonald, H. P. Stevens, N. K. Spurr, D. T. Bishop, A. Ellis, J. Jankowski, J. K. Field, I. M. Leigh, A. P. South, D. P. Kelsall, “RHBDF2 mutations are associated with tylosis, a familial esophageal cancer syndrome,” The American Journal of Human Genetics, vol. 90, pp. 340-346, 2012.
• [17] Zunke, F., & Rose-John, S. (2017, November 1). The shedding protease ADAM17: Physiology and pathophysiology. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier B.V.
• [18] M. R. Schneider, E. Wolf, “The epidermal growth factor receptor ligands at a glance,” Journal of Cellular Physiology, vol. 218, no. 3, pp. 460- 466, 2009
• [19] G. Carpenter, S. Cohen, “Epidermal Growth Factor,” Annual Review of Biochemistry, vol 68, pp. 194-216, 1979
• [20] F. Gómez-Pinilla, D. J. Knauer, M. Nieto-Sampedro, “Epidermal growth factor receptor immunoreactivity in rat brain. Development and cellular localization,” Brain Research, vol. 438, no. 1, pp. 385-390, 1988
• [21] J. F. Thompson, “Specific receptors for epidermal growth factor in rat intestinal microvillus membranes,” American Physiological Society Journal, vol. 254, no. 3, pp. 429-435, 1988
• [22] D. Szklarczyk, A. L. Gable, K. C. Nastou, D. Lyon, R. Kirsch, S. Pyysalo, C. von Mering, “The STRING database in 2021: Customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets,” Nucleic Acids Research, vol. 49, pp. 605-612, 2021
• [23] National Center for Biotechnology InformationMar. 27, 2023. [Online]. Available: https://www.ncbi.nlm.nih.gov/protein/ Accessed
• [24] A. Bairoch, R. Apweiler, “The SWISS-PROT protein sequence database: Its relevance to human molecular medical research,” Journal of Molecular Medicine, 1997.
• [25] A. Waterhouse, M. Bertoni, S. Bienert, G. Studer, G. Tauriello, R. Gumienny, T.A. Schwede, “SWISS-MODEL: homology modeling of protein structures and complexes,” Nucleic Acids Research, pp. 296-303, 2018
• [26] E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, T. E. Ferrin, “UCSF Chimera—A Visualization System for Exploratory Research and Analysis,” Journal of Computational Chemistry, vol. 25, no. 13, pp. 1605-1612, 2004.
• [27] E. Gasteiger, C. Hoogland, A. Gattiker, S. Duvaud, M. R.Wilkins, R. D. Appel, A. Bairoch, The Proteomics Protocols Handbook, Humana Press, John M. Walker, 2005, pp. 571-607.
• [28] G. Stelzer, N. Rosen, I. Plaschkes, S. Zimmerman, M. Twik, S. Fishilevich, S. D. Lancet, “The GeneCards suite: From gene data mining to disease genome sequence analyses,” Current Protocols in Bioinformatics, 2016.
• [29] A. Kumar, S. Agarwal, J. A. Heyman, S. Matson, M. Heidtman, S. Piccirillo, M. Snyder, “Subcellular localization of the yeast proteome,” Genes & Development, vol. 16, pp.707-719, 2002.
• [30] W. K. Huh, J. V. Falvo, L. C. Gerke, A. S. Carroll, R. W. Howson, J. S. Weissman, E. K. O’Shea, “Global analysis of protein localization in budding yeast,” Nature, vol. 425, pp. 686-691, 2003
• [31] M. S. Scott, S. J. Calafell, D. Y. Thomas, M. T. Hallett, “Refining protein subcellular localization,” PLoS Computational Biology, vol 1, no 6 pp. 518-528, 2005
• [32] M. Zhang, B. Liao, X. Zhou, Y. He, H. Hong, H. Lin, J. Chen, “Effects of hydrophilicity/hydrophobicity of membrane on membrane fouling in a submerged membrane bioreactor, ”Bioresource Technology, vol. 175, pp. 59–67, 2015.