Comprehensive characterization of high-risk coding and non-coding single nucleotide polymorphisms of human CXCR4 gene

Area of Science:

• Genetics and Molecular Biology
• Computational Biology
• Biochemistry

Background:

• The CXCR4 receptor (Fusin/CD184) is crucial for HIV entry and cellular processes, with its dysregulation linked to various pathologies, including cancers.
• Genetic variations, specifically single nucleotide polymorphisms (SNPs), in the CXCR4 gene can alter its function and contribute to disease development.
• Understanding the molecular impact of these SNPs is vital for deciphering disease mechanisms and developing targeted therapies.

Purpose of the Study:

• To computationally investigate the molecular effects of disease-vulnerable germ-line missense and non-coding SNPs in the CXCR4 gene.
• To predict the pathogenicity of nsSNPs and their impact on protein stability and structure.
• To evaluate the regulatory potential of non-coding SNPs on gene expression and miRNA binding.

Main Methods:

• Utilized a suite of bioinformatics tools (SIFT, PROVEAN, PolyPhen-2, etc.) for nsSNP pathogenicity prediction.
• Assessed protein stability, conservation, and structural alterations using tools like I-mutant 3.0, MUpro, Consurf, TM-align, and PyMOL.
• Performed molecular docking and MD simulations to evaluate functional impacts on protein-ligand interactions.
• Analyzed non-coding SNPs in UTR regions for regulatory effects on miRNA binding and gene expression using PolymiRTS and RegulomeDB.

Main Results:

• Identified 23 deleterious and pathogenic nsSNPs in the CXCR4 gene, with five (G55V, H79P, L80P, H113P, P299L) showing significant structural alterations.
• The H113P variant demonstrated a substantial impact on protein-ligand binding affinity and protein stability, as evidenced by molecular docking and MD simulations.
• Discovered five non-coding SNPs in the 3'-UTR capable of disrupting or creating miRNA binding sites, alongside other regulatory variations in UTR and intronic regions.

Conclusions:

• Germ-line genetic variations in CXCR4 can lead to deleterious functional consequences, impacting protein stability, structure, and ligand binding.
• Specific nsSNPs, like H113P, and non-coding SNPs affecting regulatory elements, are strongly associated with altered CXCR4 function and potential disease susceptibility.
• This computational analysis provides valuable insights into the functional impact of CXCR4 genetic variations, potentially guiding future therapeutic strategies for CXCR4-related diseases.