Association of IL-17F rs2397084 (E126G), rs11465553 (V155I) and rs763780 (H161R) variants with rheumatoid arthritis and their effects on the stability of protein

Interleukin-17F (IL-17F), considered a pro-inflammatory cytokine, has been shown to contribute to skeletal tissue degradation and hence chronic inflammation in rheumatoid arthritis (RA). In this study we utilized bioinformatics tools to analyze the effect of three exonic SNPs (rs2397084, rs11465553,...

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Published in:PloS one 2023-09, Vol.18 (9), p.e0285874-e0285874
Main Authors: Ali, Yasir, Kausar, Masood, Farooq, Mazhar, Farooqi, Nadia, Ul Islam, Zia, Khan, Suleman, Aman, Aisha, Khan, Naveed, Kamil, Atif, Jalil, Fazal
Format: Article
Language:English
Subjects:
Arthritis
Autoimmune diseases
Bioinformatics
Biology and Life Sciences
Chi-square test
Chromosomes
Cytokines
Damage detection
Disease
DNA methylation
F protein
Gene expression
Genetic diversity
Genetic testing
Genetic variance
Genomes
Inflammation
Medicine and Health Sciences
Mutants
Mutation
Nucleotides
Pathogenesis
Phenotypes
Proteins
Research and Analysis Methods
Rheumatoid arthritis
Rheumatology
Single-nucleotide polymorphism
Stability
Statistical analysis
Structure-function relationships
Three dimensional models
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Summary:Interleukin-17F (IL-17F), considered a pro-inflammatory cytokine, has been shown to contribute to skeletal tissue degradation and hence chronic inflammation in rheumatoid arthritis (RA). In this study we utilized bioinformatics tools to analyze the effect of three exonic SNPs (rs2397084, rs11465553, and rs763780) on the structure and function of the IL-17F gene, and evaluated their association with RA in Pakistani patients. The predicted deleterious and damaging effects of identified genetic variants were assessed through the utilization of multiple bioinformatics tools including PROVEAN, SNP&GO, SIFT, and PolyPhen2. Structural and functional effects of these variants on protein structures were evaluated through the use of additional tools such as I-Mutant, MutPred, and ConSurf. Three-dimensional (3D) models of both the wild-type and mutant proteins were constructed through the utilization of I-TASSER software, with subsequent structural comparisons between the models conducted through the use of the TM-align score. A total of 500 individuals, 250 cases and 250 controls, were genotyped through Tri-ARMS-PCR method and the resultant data was statistically analyzed using various inheritance models. Our bioinformatics analysis showed significant structural differences for wild type and mutant protein (TM-scores and RMSD values were 0.85934 and 2.34 for rs2397084 (E126G), 0.87388 and 2.49 for rs11465553 (V155I), and 0.86572 and 0.86572 for rs763780 (H161R) with decrease stability for the later. Overall, these tools enabled us to predict that these variants are crucial in causing disease phenotypes. We further tested each of these single nucleotide variants for their association with RA. Our analysis revealed a strong positive association between the genetic variant rs763780 and the risk of developing rheumatoid arthritis (RA) at both the genotypic and allelic levels. The genotypic association was statistically significant[ χ 2 = 111.8; P value
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0285874