Probing the Association of EPCAM Gene Single Nucleotide Polymorphisms with Genetic Disorders

Main Article Content

Fatima Razzaq
Rashida Naseem

Abstract

Background: Mutations in the EPCAM gene can lead to the absence of this protein from epithelial cell surfaces, resulting in various disorders such as Lynch syndrome, congenital tufting enteropathy, cholestatic liver disease, and a range of cancers. Therefore, analyzing mutations in this gene is significant from diagnostic and prognostic perspectives. This study examines the effect of various mutations in the EPCAM gene on different attributes of the encoded protein.


Objective: The objective of this study was to analyze the impact of single nucleotide polymorphisms (SNPs) in the EPCAM gene on the protein's structural and functional properties, aiming to identify potential predictive biomarkers for EPCAM-associated diseases.


Methods: The study focused on the EPCAM gene transcript EPCAM-201, with ENSEMBL transcript ID ENST00000263735.9 and NCBI Reference Sequence NM_002354.3. The gene sequence was retrieved from the NCBI database, and SNPs were selected from the ENSEMBL database. A total of 21 variants were selected to design twenty-one cases. These cases were analyzed using various bioinformatics tools, including EXPASY for nucleotide sequence translation, HOPE server for 3D structure analysis, CELLO2GO for sub-cellular localization, and PROTPARAM for physicochemical parameter prediction. Data collection adhered to the principles outlined in the Declaration of Helsinki. Statistical analyses were conducted using SPSS version 25, with descriptive statistics and appropriate tests to determine the significance of the observed variations.


Results: Analysis revealed that sixteen SNPs, namely rs994384264, rs1280024892, rs1294456118, rs149875996, rs767811939, rs750826481, rs754293486, rs748292053, rs1460762372, rs1294456118, rs149875996, rs754293486, rs748292053, rs771063031, rs776854951, and rs267606785, significantly altered the 3D structure of mutated proteins. Among these SNPs, rs994384264 and rs149875996 also affected the sub-cellular localization of proteins. Additionally, four mutations—rs1280024892, rs1460762372, rs987919056, and rs771029207—caused alterations in extinction coefficient, isoelectric point (pI), aliphatic index, and instability index.


Conclusion: These single nucleotide variants might serve as predictive biomarkers for EPCAM-associated diseases, aiding in diagnosis and prognosis. Variants predicted in this study require further experimental validation to confirm their clinical utility.

Article Details

How to Cite
Razzaq, F., & Rashida Naseem. (2024). Probing the Association of EPCAM Gene Single Nucleotide Polymorphisms with Genetic Disorders. Journal of Health and Rehabilitation Research, 4(2), 1138–1144. https://doi.org/10.61919/jhrr.v4i2.956
Section
Articles
Author Biographies

Fatima Razzaq, The University of Lahore Pakistan.

Institute of Molecular Biology and Biotechnology, The University of Lahore Pakistan.

Rashida Naseem, The University of Lahore Pakistan.

Institute of Molecular Biology and Biotechnology, The University of Lahore Pakistan.

References

Pathak SJ, Mueller JL, Okamoto K, Das B, Hertecant J, Greenhalgh L, et al. EPCAM mutation update: Variants associated with congenital tufting enteropathy and Lynch syndrome. Human mutation. 2019;40(2):142-61.

Farr A, Nelson A, Truex J, Hosier S. Epithelial heterogeneity in the murine thymus: a cell surface glycoprotein expressed by subcapsular and medullary epithelium. Journal of Histochemistry & Cytochemistry. 1991;39(5):645-53.

Went P, Vasei M, Bubendorf L, Terracciano L, Tornillo L, Riede U, et al. Frequent high-level expression of the immunotherapeutic target Ep-CAM in colon, stomach, prostate and lung cancers. British journal of cancer. 2006;94(1):128-35.

Abe H, Kuroki M, Imakiire T, Yamauchi Y, Yamada H, Arakawa F, et al. Preparation of recombinant MK-1/Ep-CAM and establishment of an ELISA system for determining soluble MK-1/Ep-CAM levels in sera of cancer patients. Journal of immunological methods. 2002;270(2):227-33.

Litvinov SV, Velders MP, Bakker HA, Fleuren GJ, Warnaar SO. Ep-CAM: a human epithelial antigen is a homophilic cell-cell adhesion molecule. The Journal of cell biology. 1994;125(2):437-46.

Litvinov SV, Bakker HAM, Gourevitch MM, Velders MP, Warnaar SO. Evidence for a role of the epithelial glycoprotein 40 (Ep-CAM) in epithelial cell-cell adhesion. Cell adhesion and communication. 1994;2(5):417-28.

De Leij L, Helrich W, Stein R, Mattes MJ. SCLC‐cluster‐2 antibodies detect the pancarcinoma/epithelial glycoprotein EGP‐2. International Journal of cancer. 1994;57(S8):60-3.

Linnenbach AJ, Seng BA, Wu S, Robbins S, Scollon M, Pyrc JJ, et al. Retroposition in a family of carcinoma-associated antigen genes. Molecular and cellular biology. 1993;13(3):1507-15.

Klein CE, Hartmann B, Schön MP, Weber L, Alberti S. Expression of 38-kD cell-surface glycoprotein in transformed keratinocyte cell lines, basal cell carcinomas, and epithelial germs. Journal of investigative dermatology. 1990;95(1):74-82.

Strnad J, Hamilton AE, Beavers LS, Gamboa GC, Apelgren LD, Taber LD, et al. Molecular cloning and characterization of a human adenocarcinoma/epithelial cell surface antigen complementary DNA. Cancer research. 1989;49(2):314-7.

Thampoe IJ, Ng JSC, Lloyd KO. Biochemical analysis of a human epithelial surface antigen: differential cell expression and processing. Archives of biochemistry and biophysics. 1988;267(1):342-52.

Moldenhauer G, Momburg F, Möller P, Schwartz R, Hämmerling GJ. Epithelium-specific surface glycoprotein of Mr 34,000 is a widely distributed human carcinoma marker. British journal of cancer. 1987;56(6):714-21.

Varki NM, Reisfeld RA, Walker LE. Antigens associated with a human lung adenocarcinoma defined by monoclonal antibodies. Cancer research. 1984;44(2):681-7.

Lipinski M, Parks DR, Rouse RV, Herzenberg LA. Human trophoblast cell-surface antigens defined by monoclonal antibodies. Proceedings of the National Academy of Sciences. 1981;78(8):5147-50.

Herlyn M, Steplewski Z, Herlyn D, Koprowski H. Colorectal carcinoma-specific antigen: detection by means of monoclonal antibodies. Proceedings of the National Academy of Sciences. 1979;76(3):1438-42.

Gaber A, Lenarčič B, Pavšič M. Current view on EpCAM structural biology. Cells. 2020;9(6):1361.

Winter MJ, Nagelkerken B, Mertens AEE, Rees-Bakker HAM, Briaire-de Bruijn IH, Litvinov SV. Expression of Ep-CAM shifts the state of cadherin-mediated adhesions from strong to weak. Experimental cell research. 2003;285(1):50-8.

Dollé L, Theise ND, Schmelzer E, Boulter L, Gires O, van Grunsven LA. EpCAM and the biology of hepatic stem/progenitor cells. American Journal of Physiology-Gastrointestinal and Liver Physiology. 2015.

Ladwein M, Pape UF, Schmidt DS, Schnölzer M, Fiedler S, Langbein L, et al. The cell–cell adhesion molecule EpCAM interacts directly with the tight junction protein claudin-7. Experimental cell research. 2005;309(2):345-57.

Jiang L, Shen Y, Guo D, Yang D, Liu J, Fei X, et al. EpCAM-dependent extracellular vesicles from intestinal epithelial cells maintain intestinal tract immune balance. Nature Communications. 2016;7(1):1-16.

Van Campenhout CA, Eitelhuber A, Gloeckner CJ, Giallonardo P, Gegg M, Oller H, et al. Dlg3 trafficking and apical tight junction formation is regulated by nedd4 and nedd4-2 e3 ubiquitin ligases. Developmental cell. 2011;21(3):479-91.

Maetzel D, Denzel S, Mack B, Canis M, Went P, Benk M, et al. Nuclear signalling by tumour-associated antigen EpCAM. Nature cell biology. 2009;11(2):162-71.

Münz M, Kieu C, Mack B, Schmitt B, Zeidler R, Gires O. The carcinoma-associated antigen EpCAM upregulates c-myc and induces cell proliferation. Oncogene. 2004;23(34):5748-58.

Osta WA, Chen Y, Mikhitarian K, Mitas M, Salem M, Hannun YA, et al. EpCAM is overexpressed in breast cancer and is a potential target for breast cancer gene therapy. Cancer research. 2004;64(16):5818-24.

Lei Z, Maeda T, Tamura A, Nakamura T, Yamazaki Y, Shiratori H, et al. EpCAM contributes to formation of functional tight junction in the intestinal epithelium by recruiting claudin proteins. Developmental biology. 2012;371(2):136-45.

Song Y, Liu C, Liu X, Trottier J, Beaudoin M, Zhang L, et al. H19 promotes cholestatic liver fibrosis by preventing ZEB1‐mediated inhibition of epithelial cell adhesion molecule. Hepatology. 2017;66(4):1183-96.

Zheng X, Fan X, Fu B, Zheng M, Zhang A, Zhong K, et al. EpCAM inhibition sensitizes chemoresistant leukemia to immune surveillance. Cancer Research. 2017;77(2):482-93.

Maloy KJ, Powrie F. Intestinal homeostasis and its breakdown in inflammatory bowel disease. Nature. 2011;474(7351):298-306.

Tutlewska K, Lubinski J, Kurzawski G. Germline deletions in the EPCAM gene as a cause of Lynch syndrome–literature review. Hereditary cancer in clinical practice. 2013;11(1):1-9.

Yu X, Ge N, Guo X, Shen S, Liang J, Huang X, et al. Genetic variants in the EPCAM gene is associated with the prognosis of transarterial chemoembolization treated hepatocellular carcinoma with portal vein tumor thrombus. PloS one. 2014;9(4):e93416.

Warneke VS, Behrens HM, Haag J, Krüger S, Simon E, Mathiak M, et al. Members of the EpCAM signalling pathway are expressed in gastric cancer tissue and are correlated with patient prognosis. British journal of cancer. 2013;109(8):2217-27.

Gebauer F, Struck L, Tachezy M, Vashist Y, Wicklein D, Schumacher U, et al. Serum EpCAM expression in pancreatic cancer. Anticancer Research. 2014;34(9):4741-6.

Yang Y, Fei F, Song Y, Li X, Zhang Z, Fei Z, et al. Polymorphisms of Ep CAM gene and prognosis for non‐small‐cell lung cancer in Han C hinese. Cancer science. 2014;105(1):89-96.

Vorobyeva A, Konovalova E, Xu T, Schulga A, Altai M, Garousi J, et al. Feasibility of imaging EpCAM expression in ovarian cancer using radiolabeled DARPin Ec1. International Journal of Molecular Sciences. 2020;21(9):3310.

Gostner JM, Fong D, Wrulich OA, Lehne F, Zitt M, Hermann M, et al. Effects of EpCAM overexpression on human breast cancer cell lines. BMC cancer. 2011;11(1):1-14.

Seeber A, Untergasser G, Spizzo G, Terracciano L, Lugli A, Kasal A, et al. Predominant expression of truncated EpCAM is associated with a more aggressive phenotype and predicts poor overall survival in colorectal cancer. International journal of cancer. 2016;139(3):657-63.

Torres A, Pac-Sosińska M, Wiktor K, Paszkowski T, Maciejewski R, Torres K. CD44, TGM2 and EpCAM as novel plasma markers in endometrial cancer diagnosis. BMC cancer. 2019;19(1):1-11.

Pêgas KL, Cambruzzi E, Ferrelli RS, Silva CS, Guedes RR, Adami M, et al. Tufting enteropathy with EpCAM mutation: case report. Jornal Brasileiro de Patologia e Medicina Laboratorial. 2014;50:234-7.

Ozler O, Brunner-Véber A, Fatih P, Müller T, Janecke AR, Arikan C. Long-Term Follow-Up of Tufting Enteropathy Caused by EPCAM Mutation p. Asp253Asn and Absent EPCAM Expression. JPGN Reports. 2021;2(1):e029.

Yahyazadeh Mashhadi SM, Kazemimanesh M, Arashkia A, Azadmanesh K, Meshkat Z, Golichenari B, et al. Shedding light on the EpCAM: an overview. Journal of cellular physiology. 2019;234(8):12569-80.

Spizzo G, Fong D, Wurm M, Ensinger C, Obrist P, Hofer C, et al. EpCAM expression in primary tumour tissues and metastases: an immunohistochemical analysis. Journal of clinical pathology. 2011;64(5):415-20.

Jiang Y, Wang D, Wang W, Xu D. Computational methods for protein localization prediction. Computational and Structural Biotechnology Journal. 2021;19:5834-44.

Hubbard RE, Haider MK. Hydrogen bonds in proteins: role and strength. Encyclopedia of Life Sciences. 2010.

Pylaeva S, Brehm M, Sebastiani D. Salt bridge in aqueous solution: Strong structural motifs but weak enthalpic effect. Scientific reports. 2018;8(1):1-7.

Panja AS, Maiti S, Bandyopadhyay B. Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges. Scientific reports. 2020;10(1):1-9.

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