Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database

Mohammad Uzzal Hossain; Ishtiaque Ahammad; Md Moniruzzaman; Mahbuba Akter Lubna; Arittra Bhattacharjee; Zeshan Mahmud Chowdhury; Istiak Ahmed; Md Billal Hosen; Shourov Biswas; Keshob Chandra Das; Chaman Ara Keya; Md Salimullah

doi:10.1002/cnr2.1906

Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database

Cancer Rep (Hoboken). 2023 Dec;6(12):e1906. doi: 10.1002/cnr2.1906. Epub 2023 Oct 22.

Affiliations

¹ Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh.
² Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh.
³ Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh.
⁴ Department of Clinical Oncology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh.
⁵ Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh.

Abstract

Background: Gastric cancer, which is also known as stomach cancer, can be influenced by both germline and somatic mutations. Non-synonymous Single Nucleotide Polymorphisms (nsSNPs) in germline have long been reported to play a pivotal role in cancer progression.

Aim: The aim of this study is to examine the nsSNP in GC-associated genes. The study also aims to develop a database with extensive information regarding the nsSNPs in the GC-associated genes and their impacts.

Methods and results: A total of 34,588 nsSNPs from 1,493,460 SNPs of the 40 genes were extracted from the available SNP database. Drug binding and energy minimization were examined by molecular docking and YASARA. To validate the existence of the germline CDH1 gene mutation (rs34466743) in the isolated blood DNA of gastric cancer (GC) patients, polymerase chain reaction (PCR) and DNA sequencing were performed. According to the results of the gene network analysis, 17 genes may interact with other types of cancer. A total of 11,363 nsSNPs were detected within the 40 GC genes. Among these, 474 nsSNPs were predicted to be damaging and 40 to be the most damaging. The SNPs in domain regions were thought to be strong candidates that alter protein functions. Our findings proposed that most of the selected nsSNPs were within the domains or motif regions. Free Energy Deviation calculation of protein structure pointed toward noteworthy changes in the structure of each protein that can demolish its natural function. Subsequently, drug binding confirmed the structural variation and the ineffectiveness of the drug against the mutant model in individuals with these germline variants. Furthermore, in vitro analysis of the rs34466743 germline variant from the CDH1 gene confirmed the strength and robustness of the pipeline that could expand the somatic alteration for causing cancer. In addition, a comprehensive gastric cancer polymorphism database named "GasCanBase" was developed to make data available to researchers.

Conclusion: The findings of this study and the "GasCanBase" database may greatly contribute to our understanding of molecular epidemiology and the development of precise therapeutics for gastric cancer. GasCanBase is available at: https://www.gascanbase.com/.

Keywords: GasCanBase; SNP; bioinformatics; database; gastric cancer; polymorphism.

MeSH terms

Germ Cells
Germ-Line Mutation
Humans
Molecular Docking Simulation
Polymerase Chain Reaction
Stomach Neoplasms* / genetics