Identification of Gene Variations and Gene Expression in Allergic Diseases Using a Bioinformatics Approach

Naila Ismatun Hasanah; Ilham Alifiar; Rahmawati

doi:10.35451/0y6eqw75

Authors

Naila Ismatun Hasanah Universitas Bakti Tunas Husada
Ilham Alifiar Universitas Bakti Tunas Husada
Rahmawati Universitas Bakti Tunas Husada

DOI:

https://doi.org/10.35451/0y6eqw75

Keywords:

Penyakit Alergi, Single-Nucleotide Polymorphisms (SNP), Ekspresi Gen, Bioinformatika

Abstract

Background: Allergy is an abnormal or excessive immune response to allergens involving complex interactions between genetic and environmental factors. Identification of genetic variations contributing to allergy susceptibility is important to understand molecular mechanisms and support the development of personalized biomarkers and therapies. Objective: This study aimed to identify genetic variations and gene expression profiles associated with allergic diseases using a bioinformatics approach. Research Methods: The study was conducted using a bioinformatics approach by analyzing data from GWAS Catalog, HaploReg v4.2, SNPnexus, GTEx Portal, and Ensembl Genome Browser. Results: A total of 18 missense single-nucleotide polymorphism variants are associated with allergic diseases. Three variants, namely rs1805009 (MC1R), rs183884396 (TESPA1), and rs59039403 (NLRP10), show the highest prediction score (1.000), indicating the most significant biological impact. Gene expression analysis shows dominant expression in whole blood, EBV-transformed lymphocytes, and skin (sun-exposed). Conclusion: The identified missense variants potentially contribute to the pathogenesis of allergic diseases and may serve as a basis for the development of genetic biomarkers and personalized therapeutic approaches.

Downloads

Download data is not yet available.

References

[1] Jutel M, Agache I, Wiacek MZ, Akdis M, Chivato T, Giacco S del, et al. Nomenclature of allergic diseases and hypersensitivity reactions : Adapted to modern needs : An EAACI position paper. Allergy. 2023;78(11):2851–74.

[2] Vitte J, Vibhushan S, Bratti M, Blank U. Allergy , Anaphylaxis , and Nonallergic Hypersensitivity : IgE , Mast Cells , and Beyond. Medical Principles and Practice. 2022;31(6):501–15.

[3] Aldakheel FM. Allergic Diseases : A Comprehensive Review on Risk Factors , Immunological Mechanisms , Link with COVID-19 , Potential Treatments , and Role of Allergen Bioinformatics. International Journal of Environmental Research and Public Health. 2021;18(22):12105.

[4] Uffelmann E, Huang QQ, Munung NS, Vries J de, Okada Y, Martin AR, et al. Genome-wide association studies. Nature Reviews Methods Primers [Internet]. 2021;1(59):1–21. Available from: http://dx.doi.org/10.1038/s43586-021-00056-9

[5] Azzahra F, Wicaksono A, Nugraheni TP. Identifikasi Variasi Gen dan Ekspresi Gen yang Berhubungan dengan Kanker Ovarium dengan Pendekatan Bioinformatika. CERATA Jurnal Ilmu Farmasi. 2024;15(2):77–83.

[6] Fadista J, Manning AK, Florez JC, Groop L. The ( in ) famous GWAS P -value threshold revisited and updated for low-frequency variants. European Journal of Human Genetics. 2016;24(8):1202–5.

[7] Sankar J, Briget B, Hamad A, Shing L, Muthusamy K. Computational and molecular insights on non-synonymous SNPs associated with human RAAS genes : Consequences for Hypertension vulnerability. Journal of Genetic Engineering and Biotechnology [Internet]. 2025;23(1):100476. Available from: https://doi.org/10.1016/j.jgeb.2025.100476

[8] Chen Z, Boehnke M, Wen X, Mukherjee B. Revisiting the genome-wide significance threshold for common variant GWAS. G3 Genes|Genomes|Genetics. 2021;11(2):jkaa056.

[9] Kar SP, Quiros PM, Gu M, Jiang T, Mitchell J, Langdon R, et al. Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis. Nat Genet. 2022;54:1155–66.

[10] Yudhani RD, Pakha DN, Suyatmi S, Irham LM. Identifying pathogenic variants related to systemic lupus erythematosus by integrating genomic databases and a bioinformatic approach. Genomic and Informatics. 2023;21(3):1–11.

[11] Capritasari R, Irham LM, Azzahra F, Nugraha D. Identifikasi Varian Genetik Terkait Kejadian Infark Miokard Melalui Pendekatan Bioinformatik. Jurnal Kesehatan Bakti Tunas Husada : Jurnal Ilmu Ilmu Keperawatan, Analis Kesehatan dan Farmasi. 2023;23(1):29–37.

[12] Puspitaningrum AN, Perwitasari DA, Adikusuma W, Noor G, Dania H, Maliza R, et al. Integration of genomic databases and bioinformatic approach to identify genomic variants for s jogren ’ s syndrome on multiple continents. Media Farmasi: Jurnal Ilmu Farmasi (Journal of Pharmaceutical Science). 2022;19(2):71–81.

[13] Dybska E, Adams AT, Loras RD, Walkowiak J, Nowak JK. Waiting in the wings : RUNX3 reveals hidden depths of immune regulation with potential implications for inflammatory bowel disease. Scandinavian Journal of Immunology. 2021;93(5):e13025.

[14] Solingen C Van, Cyr Y, Scacalossi KR, Vries M De, Barrett TJ, Jong A De, et al. Long noncoding RNA CHROMR regulates antiviral immunity in humans. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(37):e2210321119.

[15] Wang L, Cai J, Zhao X, Ma L, Zeng P, Zhou L, et al. Palmitoylation prevents sustained inflammation by limiting NLRP3 inflammasome activation through chaperone-mediated autophagy. Molecular Cell [Internet]. 2023;83(2):281-297.e10. Available from: https://doi.org/10.1016/j.molcel.2022.12.002

[16] Schuler CF, Tsoi LC, Billi AC, Harms PW, Weidinger S, Gudjonsson JE. Genetic and Immunological Pathogenesis of Atopic Dermatitis. Journal Investigative Dermatology [Internet]. 2024;144(5):954–68. Available from: https://doi.org/10.1016/j.jid.2023.10.019

[17] Zhou Y. Targeting NLRP10 in Atopic Dermatitis : An Emerging Strategy to Modulate Epidermal Cell Death and Barrier Function. International Journal of Molecular Sciences. 2025;26(19):9623.

[18] Le L, Escobar IE, Ho T, Lefkovith AJ, Latteri E, Dennis MK, et al. SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation. Molecular Biology of the Cell. 2020;31(24):2687–702.

[19] Mun Y, Kim W, Shin D. Melanocortin 1 Receptor ( MC1R ): Pharmacological and Therapeutic Aspects. International Journal of Molecular Sciences. 2023;24(15):12152.

[20] Zhang W, Huang F, Ding X, Qin J, Wang W, Luo L. Identifying ALOX15-initiated lipid peroxidation increases susceptibility to ferroptosis in asthma epithelial cells. Biochimica et Biophysica Acta- Molecular Basis of Disease [Internet]. 2024;1870(5):167176. Available from: https://doi.org/10.1016/j.bbadis.2024.167176

[21] Chou V, Ii RVP, Aylward AJ, Ashour N, Taga M, Terzioglu G, et al. INPP5D regulates inflammasome activation in human microglia. Nature Communications. 2023;14(1):7552.