GEMIN4 Variants: Risk Profiling, Bioinformatics, and Dynamic Simulations Uncover Susceptibility to Bladder Carcinoma

Abdallah S Mohamed; Afrah F Salama; Magdy A Sabaa; Eman Toraih; Rami M Elshazli

doi:10.1016/j.arcmed.2024.102970

GEMIN4 Variants: Risk Profiling, Bioinformatics, and Dynamic Simulations Uncover Susceptibility to Bladder Carcinoma

Arch Med Res. 2024 Apr;55(3):102970. doi: 10.1016/j.arcmed.2024.102970. Epub 2024 Feb 23.

Authors

Abdallah S Mohamed¹, Afrah F Salama¹, Magdy A Sabaa², Eman Toraih³, Rami M Elshazli⁴

Affiliations

¹ Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt.
² Department of Urology, Faculty of Medicine, Tanta University, Tanta, Egypt.
³ Endocrine and Oncology Division, Department of Surgery, Tulane University School of Medicine, New Orleans, LA, USA; Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt. Electronic address: etoraih@tulane.edu.
⁴ Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, Egypt. Electronic address: relshazly@horus.edu.eg.

PMID: 38401326
DOI: 10.1016/j.arcmed.2024.102970

Abstract

Background: The relationship between GEMIN4 genetic variants and cancer, especially bladder carcinoma (BLCA), has been explored without conclusive results. This study aims to elucidate the link between GEMIN4 polymorphisms and BLCA susceptibility through genetic analyses, bioinformatics, and molecular dynamics (MD) simulations.

Methods: A cohort of 249 participants (121 BLCA patients and 128 unrelated controls) was enrolled. PCR was employed for allelic discrimination of GEMIN4 variants, followed by subgroup stratification, haplotype analyses, structural prediction using the AlphaFold2 prediction tool, subsequent MD simulations, structural analysis, and residue interaction mapping using Desmond, UCSF ChimeraX, and Cytoscape softwares.

Results: The rs.2740348*G variant demonstrated a protective role against BLCA in allelic (OR = 0.55, p = 0.002) and recessive (OR = 0.54, p = 0.017) models, whereas the rs.7813*T variant increased BLCA risk under the recessive model (OR = 1.90, p = 0.019). Haplotype analysis revealed a significant association between GEMIN4 haplotype (rs.2740348*C/rs.7813*T) with increased BLCA risk (OR = 2.01, p = 0.004). Univariate analysis revealed associations of the variants with albumin levels and absolute neutrophil count in BLCA patients. Pathogenicity evaluation categorized p.Gln450Glu as neutral and p.Arg1033Cys as deleterious. MD simulations revealed structural alterations and conformational shifts in the GEMIN4 protein induced by the Glu450 and Cys1033 mutations.

Conclusions: The study highlights the dual role of GEMIN4 variants in BLCA susceptibility, with rs.2740348 conferring protection and rs.7813 increasing risk. The Glu450 residue positively impacted protein stability, while Cys1033 had a detrimental effect on protein function. These findings underscore the significance of GEMIN4 variants in BLCA susceptibility and pave the way for future diagnostic and therapeutic initiatives.

Keywords: GEMIN4* rs.2740348; GEMIN4* rs.7813; Genetic variants and bladder carcinoma.

MeSH terms

Alleles
Carcinoma*
Computational Biology
Humans
Minor Histocompatibility Antigens
Ribonucleoproteins, Small Nuclear
Urinary Bladder
Urinary Bladder Neoplasms* / genetics

Substances

GEMIN4 protein, human
Minor Histocompatibility Antigens
Ribonucleoproteins, Small Nuclear