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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 March 2026 | Viewed by 1746

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Special Issue Editor

Dr. Julian Ramírez-Bello

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Guest Editor

Subdirección de Investigación Clínica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City 14080, Mexico
Interests: autoimmune diseases; genetics; human variability; genomics

Special Issue Information

Dear Colleagues,

Autoimmune diseases (ADs) account for approximately 8% of human pathologies worldwide. ADs are generally multifactorial, influenced by genetic, environmental, hormonal, and immunological factors. In this group of pathologies, there is a loss of immune tolerance to self-antigens, leading to an impaired immune system. Consequently, immune cells remain constantly dysregulated and active, producing various types of autoantibodies and affecting different organs and/or systems.

Reporting genetic variations (such as SNVs and CNVs), mutations, mRNAs, microRNAs, lncRNAs, and other molecular factors associated with ADs can aid in identifying risk factors for these multifactorial diseases. In this Special Issue, “Genetics and Omics in Autoimmune Diseases”, we invite the submission of original research articles, short communications, and reviews on current and emerging concepts in ADs.

Topics of interest include genetics, genomics, transcriptomics, massive sequencing, etc., in ADs such as rheumatoid arthritis, systemic lupus erythematosus, Sjögren's syndrome, autoimmune thyroiditis, type 1 diabetes, multiple sclerosis, antiphospholipid syndrome, and IgG4-related disease, among others.

Dr. Julian Ramírez-Bello
Guest Editor

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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Keywords

autoimmune diseases
genetics
genomics
omics
single-nucleotide variants
copy number variants
variation
susceptibility
mRNAs
microRNAs
long non-coding RNAs
masive sequencing

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Published Papers (4 papers)

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14 pages, 371 KB

Open AccessArticle

Variants in IRF5 Increase the Risk of Primary Sjögren’s Syndrome in the Mexican Population

by Julian Ramírez-Bello, Isaac Alberto López-Briceño, Guillermo Valencia-Pacheco, Rosa Elda Barbosa-Cobos, Gabriela Hernández-Molina, Silvia Jiménez-Morales, Iván Sammir Aranda-Uribe, Isela Montúfar-Robles and Swapan K. Nath

Int. J. Mol. Sci. 2026, 27(2), 599; https://doi.org/10.3390/ijms27020599 - 7 Jan 2026

Viewed by 99

Abstract

Primary Sjögren’s syndrome (pSS) is an autoimmune disease characterized by inflammation and damage to salivary and lacrimal glands. Its etiology involves both genetic and environmental factors. Among susceptibility genes, IRF5 has been highlighted in European populations, but evidence in non-European groups remains limited. This study evaluated whether IRF5 variants rs2004640G/T, rs2070197T/C, rs10954213G/A, and rs59110799G/T are associated with pSS susceptibility, clinical manifestations, or the presence of autoantibodies in a Mexican population. The diagnosis was confirmed by rheumatologists using the 2016 ACR–EULAR classification criteria for pSS. Genotyping was performed using TaqMan probes in 231 controls and 132 pSS patients from central Mexico. Associations were analyzed through binary logistic regression under different genetic models, adjusting for age and geographic origin. Clinical correlations were examined with SNPStats, and haplotypes were constructed using Haploview. Results showed that all four IRF5 variants were significantly associated with pSS susceptibility. Moreover, rs2004640, rs2070197, and rs10954213 variants were associated with arthritis, a frequent clinical manifestation in pSS patients. This represents the first evidence in a Latin American population demonstrating that IRF5 variants contribute to increased risk of developing pSS. These findings suggest ethnicity-specific genetic influences and highlight the importance of expanding research beyond European cohorts. Replication in larger samples and functional analyses are needed to confirm these associations and clarify their biological relevance. Full article

(This article belongs to the Special Issue Genetics and Omics in Autoimmune Diseases)

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22 pages, 924 KB

Open AccessArticle

Identifying a Common Autoimmune Gene Core as a Tool for Verifying Biological Significance and Applicability of Polygenic Risk Scores

by Victoria Sergeevna Shchekina, Nikita Aleksandrovich Batashkov, Anna Arkadievna Maznina, Julia Aleksandrovna Krupinova, Viktor Pavlovich Bogdanov, Anna Vasilievna Korobeinikova, Dmitry Igorevich Tychinin, Olga Valentinovna Glushkova, Ekaterina Sergeevna Petriaikina, Dmitry Vladimirovich Svetlichnyy, Mary Woroncow, Vladimir Sergeevich Yudin, Anton Arturovich Keskinov, Sergey Mikhailovich Yudin, Veronika Igorevna Skvortsova, Dmitry Vyacheslavovich Tabakov, Andrei Andreevich Deviatkin and Pavel Yu. Volchkov

Int. J. Mol. Sci. 2026, 27(1), 543; https://doi.org/10.3390/ijms27010543 - 5 Jan 2026

Viewed by 179

Abstract

Polygenic autoimmune diseases (ADs) have several common features that are caused by a complex interplay of genetic and environmental factors. Common pathophysiological mechanisms include dysregulation of the immune system, chronic inflammation, and epigenetic changes influenced by external factors. For the prediction of the genetic predisposition of AD manifestation, polygenic risk scale (PRS), or polygenic scores (PGSs), are used. Use of PRSs faces several challenges such as applicability on a specific population, performance comparison, and estimation of biological relevance based on SNP number. We compared PRS with different numbers of SNPs and tried to find the common genetic core of ADs. Our analysis revealed a list of the most common altered genes, which we annotated and interpreted. Clustering of PRS based on used genes showed that clusters of ADs remained consistent across all chosen PRS sizes. We concluded that PRS size does not have an impact on biological relevance. Full article

(This article belongs to the Special Issue Genetics and Omics in Autoimmune Diseases)

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22 pages, 2868 KB

Open AccessArticle

Genetic and Functional Characterization of STAT4 in Rheumatoid Arthritis Patients with Distinct Disease Activity

by Karla Mayela Bravo-Villagra, Rocio Guadalupe Hernández-Ruíz, Alejandra Landeros-Sáenz, Christian Johana Baños-Hernández, Sergio Cerpa-Cruz, Samuel García-Arellano, José Francisco Muñoz-Valle and Andres López-Quintero

Int. J. Mol. Sci. 2025, 26(20), 10011; https://doi.org/10.3390/ijms262010011 - 15 Oct 2025

Viewed by 1006

Abstract

Rheumatoid arthritis (RA) is characterized by chronic inflammation mediated by the JAK/STAT pathway. Variants in STAT4 have been associated with autoimmune susceptibility, but their functional role in RA remains unclear. The aim of this study was to genetically and functionally characterize STAT4 in RA patients with varying disease activity by analyzing two variants, mRNA expression, phosphorylated STAT4 (pSTAT4), and inflammatory cytokines (IL-12, IL-23, and IFN-γ). Sixty-three Mexican patients with RA were stratified into remission/low and moderate/high activity groups. Genotyping, STAT4 mRNA expression, pSTAT4 quantification, cytokine profiling, and treatment analyses were conducted. Patients receiving methotrexate, hydroxychloroquine, and sulfasalazine had higher IL-12 concentrations compared with those on other regimens. In remission/low activity patients, GC/GC carriers exhibited increased IL-12, PBMC levels, and anti-CCP antibodies, while GC/TT carriers in the moderate/high activity group showed distinct ESR values. Secondary analyses revealed that TT/TT carriers with STAT4 overexpression exhibited higher IFN-γ and IL-23 levels. IL-12 differences persisted among GC/GC carriers regardless of STAT4 expression status. In conclusion, these exploratory findings suggest potential interactions among STAT4 haplotypes, expression status, and treatment regimens influencing cytokine and inflammatory profiles in RA. However, due to the small subgroup sizes, the observed associations should be interpreted with caution and considered hypothesis-generating until validated in larger cohorts. Full article

(This article belongs to the Special Issue Genetics and Omics in Autoimmune Diseases)

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10 pages, 236 KB

Open AccessBrief Report

The H159Y Variant of the BAFF-R Gene (TNFRSF13C) Is Unrelated to the Risk of Developing Systemic Lupus Erythematosus and Sjögren’s Disease in a Mexican Population

by Itzel María Borunda-Calderón, Jazz Alan Corona-Angeles, Noemí Espinoza-García, Miguel Marín-Rosales, Diana Celeste Salazar-Camarena, Edith Oregon-Romero, Ramsés Alejandro Morales-Zambrano and Claudia Azucena Palafox-Sánchez

Int. J. Mol. Sci. 2026, 27(2), 726; https://doi.org/10.3390/ijms27020726 - 10 Jan 2026

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Abstract

Systemic Lupus Erythematosus (SLE) and primary Sjögren’s Disease (SjD) are autoimmune diseases characterized by the presence of autoantibodies that lead to damage in healthy tissues. The production of autoantibodies requires the activation and differentiation of B-lymphocytes into plasma cells. To achieve this effect, BAFF (B-lymphocyte activating factor), APRIL (A proliferation-inducing ligand), and their receptors are key factors. BAFF is a cytokine recognized by BAFF-R (BAFF receptor), which is increased and related to disease activity in both SLE and SjD patients. The H159Y mutation (rs61756766) in the gene encoding the BAFF-R, TNFRSF13C (Tumor Necrosis Factor Receptor Superfamily) has been shown in vitro to cause receptor hyperactivation via the NF-κB2 pathway. This study evaluated the frequency of this variant in a western Mexican population and its association with the risk of developing SLE and SjD. Genotypes of the TNFRSF13C H159Y (rs61756766) variant were determined by PCR-RFLP assay. sBAFF levels were measured by ELISA. The study included 300 SLE patients, 110 SjD patients, and 300 healthy subjects (HS). HS were in Hardy–Weinberg equilibrium. The data distribution was assessed using the Kolmogorov–Smirnov test. Group comparisons were conducted using the Chi-square test, Fisher’s exact test, or the Mann–Whitney U test, as appropriate. A p-value of <0.05 was considered statistically significant. In the Mexican population, allelic and genotypic distribution frequencies of the H159Y variant (rs61756766) were similar between SLE patients and HSs, while the variant was not found in SjD patients. SLE patients carrying the heterozygous CT genotype showed a trend toward higher soluble BAFF (sBAFF) levels than wild-type genotype patients. This variant does not confer risk to SLE or SjD in the Mexican population. However, the heterozygous genotype may be associated with high levels of sBAFF in SLE patients. Full article

(This article belongs to the Special Issue Genetics and Omics in Autoimmune Diseases)

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