In silico analysis of single nucleotide polymorphisms in the regulatory and coding region of e-cadherin encoding gene.

Sogand Kalantari,1 Majid tafrihi,2,*

1. Molecular & Cell Biology Research Lab 2, Department of Molecular and Cell Biology, Faculty of Sciences, University of Mazandaran
2. Molecular & Cell Biology Research Lab 2, Department of Molecular and Cell Biology, Faculty of Sciences, University of Mazandaran, Babolsar, Mazandaran, Iran.

Abstract

Introduction

E-cadherin is known as a tumor suppressor protein and is a critical protein involved in cell adherens junctions and maintenance of epithelial tissue integrity. mutations in cdh1 gene may dysregulated e-cadherin function, leading to disturbed cell-cell adhesion of epithelial tissues and infiltrative metastatic ability of cancer cells. in this study, by using publicly available computational tools, we performed in silico analyses to examine the effects of three nssnps in the coding region of the e-cadherin protein and a single nucleotide polymorphism in the promoter region of the e-cadherin encoding gene.

Methods

Three nssnps rs876658932 (r74g), rs878854691 (m1i), rs786202785 (e758k) in the coding region and rs16260 snp in the promoter region of the e- cadherin encoding gene were selected for in silico analysis. we have used online servers such as sift and polyphen, further analyses were performed using provean, snps & go, phd-snp, panther, pmut, hope project, cfssp servers and also chimera software, alpha version 1.12 to analyze the effect of nssnps on the structure of e-cadherin protein. at first, we wanted to find out the effects on protein function and stability. then, we used prediction tools snpinspector and matinspector to examine possible effects of rs16260 snp on the regulatory region of the cdh1 gene and transcription factor binding sites.

Results

Our primary analyses performed by provean, snps & go, phd-snp, panther, pmut showed that m1i substitution is neutral, but r74g could be possibly damaging and e758r substitution was found to be highly damaging. structural analysis using cfssp, hope project and chimera software showed that m1i and r74g substitutions are neutral or may have minor effects on the protein structure but e758k substitution has somewhat noticeable effects on the protein structure (including hydrogen binding). our analysis on regulatory snp using snpinspector showed that rs16260 snp resulted in deletion of two and generation of one transcription factor binding site but matinspector did not confirm the primary results.

Conclusion

We surveyed and compared available databases such as ncbi and dbsnp along with in silico prediction programs to assess the effects of deleterious functional variants on the protein functions. analyzing deleterious nssnps by both sequence and structure level has the added advantage of being able to assess the reliability of the generated prediction results by cross-referencing the results from both approaches. these results indicate that our approach successfully allowed us in selecting the deleterious snps that are likely to have functional impact on the cdh1 gene and contribute to susceptibility to cancer.

Keywords

Cdh1, e-cadherin, snp, in silico, cancer