The Role of Next-Generation Sequencing in Understanding the Genetic Predispositions and Pathophysiology of Autoimmune Rheumatic Diseases

Authors

  • Edward Ochs Sr. Clinical Research Associate, Australia. Author

Keywords:

Next-Generation Sequencing, Autoimmune Rheumatic Diseases, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Genetic Predisposition, Whole-Exome Sequencing, Transcriptomics

Abstract

Next-generation sequencing (NGS) technologies have significantly advanced our understanding of the genetic underpinnings of autoimmune rheumatic diseases (ARDs), such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and systemic sclerosis (SSc). These diseases, characterized by aberrant immune responses, often display complex genetic architectures involving multiple loci. This paper explores the utility of NGS in identifying disease-associated variants, elucidating gene expression patterns, and discovering novel biomarkers. A literature-based review of original studies highlights NGS's contribution to unraveling pathogenic mechanisms and genetic predispositions. Additionally, we present data summarizing major gene associations and discuss limitations and future research directions. The findings underscore the transformative role of NGS in precision medicine for ARDs.

References

[1] Kiryluk, Krzysztof, et al. “Rare Complement Pathway Variants in Pediatric Lupus.” Nature Genetics, vol. 54, no. 3, 2022, pp. 290–299.

[2] Panousis, Nikos I., et al. “Integrated RNA-Seq Analysis Identifies Distinct Interferon Signatures in Systemic Lupus Erythematosus.” Annals of the Rheumatic Diseases, vol. 78, no. 4, 2019, pp. 589–595.

[3] Chen, Bo, et al. “Whole-Genome Sequencing in Rheumatoid Arthritis Reveals Novel Non-Coding Variants.” Nature Communications, vol. 11, no. 1, 2020, p. 3609.

[4] Zhang, Fan, et al. “Transcriptome Analysis of Rheumatoid Arthritis Synovium Reveals Inflammatory Gene Modules.” Arthritis & Rheumatology, vol. 70, no. 3, 2018, pp. 456–465.

[5] Assassi, Shervin, et al. “Fibrotic Gene Signature from RNA-Seq in Systemic Sclerosis Skin Biopsies.” Journal of Investigative Dermatology, vol. 141, no. 9, 2021, pp. 2257–2265.

[6] López-Isac, Elena, et al. “Whole-Exome Sequencing Implicates DNA Repair Genes in Systemic Sclerosis.” Rheumatology, vol. 59, no. 4, 2020, pp. 987–996.

[7] Rice, Gail, et al. “Mutations in TREX1 Associated with Lupus-like Phenotypes.” Nature Genetics, vol. 45, no. 5, 2013, pp. 526–529.

[8] Bentham, James, et al. “Genetic Association Analyses Implicate Aberrant Regulation of Innate and Adaptive Immunity Genes in the Pathogenesis of Systemic Lupus Erythematosus.” Nature Genetics, vol. 47, no. 12, 2015, pp. 1457–1464.

[9] Okada, Yukinori, et al. “Genetics of Rheumatoid Arthritis Contributes to Biology and Drug Discovery.” Nature, vol. 506, no. 7488, 2014, pp. 376–381.

[10] Li, Yichuan, et al. “Whole-Exome Sequencing Identifies Rare Damaging Variants in Genes Involved in the Type I Interferon Pathway in Patients with Early-Onset Systemic Lupus Erythematosus.” Annals of the Rheumatic Diseases, vol. 80, no. 1, 2021, pp. 112–120.

[11] Arvaniti, Pinelopi, et al. “Uncovering Immune Cell-Specific Gene Signatures in RA Synovial Tissue Using Single-Cell RNA Sequencing.” Frontiers in Immunology, vol. 13, 2022, article 829664.

[12] Saevarsdottir, Saedis, et al. “FLI1 Polymorphism as a Risk Factor for Systemic Sclerosis Revealed by Sequencing and Functional Genomics.” Nature Communications, vol. 7, 2016, article 12380.

[13] Odhams, Chris A., et al. “Mapping Genomic Interactions Implicates Candidate Genes for Autoimmune Diseases Including SLE.” Nature Communications, vol. 10, no. 1, 2019, article 3121.

Downloads

Published

2025-01-28