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Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene
Tikam Chand Dakal1, Deepak Kala2, Gourav Dhiman2
1Department of Biosciences, Manipal University Jaipur, Dehmi Kalan, Off Jaipur-Ajmer Expressway, Jaipur, 303007, Rajasthan, India. tikam260707@gmail.com.
Scientific Reports
|July 28, 2017
Summary
This study identifies damaging non-synonymous SNPs (nsSNPs) in the interleukin-8 (IL-8) gene using computational methods. These high-confidence nsSNPs impact IL-8 protein structure and function, potentially serving as biomarkers for gastric and lung cancer.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Interleukin-8 (IL-8) plays a role in inflammation and cancer.
- Non-synonymous single nucleotide polymorphisms (nsSNPs) can alter protein function.
- Understanding the impact of nsSNPs is crucial for disease association studies.
Purpose of the Study:
- To identify and characterize deleterious nsSNPs in the IL-8 gene using an in-silico approach.
- To analyze the structural and functional consequences of high-confidence nsSNPs.
- To investigate the potential of IL-8 deregulation as a prognostic marker in gastric and lung cancer.
Main Methods:
- Sequence homology analysis using SIFT and PROVEAN to predict damaging nsSNPs.
- Structure-homology analysis with PolyPhen-2 to identify high-confidence nsSNPs.
- Analysis of amino acid residue conservation, protein stability, structural superimposition, RSMD, and docking for functional impact assessment.
Main Results:
- 23 nsSNPs were predicted as putatively damaging by SIFT/PROVEAN.
- 9 nsSNPs (K4T, E31A, E31K, S41Y, I55N, P59L, P59S, L70P, V88D) were identified as high-confidence damaging.
- These nsSNPs were shown to affect IL-8 protein structure and function.
- IL-8 deregulation was associated with gastric and lung cancer detection.
Conclusions:
- The study provides a comprehensive in-silico analysis of nsSNPs in the IL-8 gene.
- Identified high-confidence nsSNPs have significant implications for IL-8 protein structure and function.
- IL-8 deregulation emerges as a potential prognostic marker for specific cancers.
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