DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome

Crucial Roles of RSAD2/viperin in Immunomodulation, Mitochondrial Metabolism and Autoimmune Diseases

Autoimmune diseases are typically characterized by aberrant activation of immune system that leads to excessive inflammatory reactions and tissue damage. Nevertheless, precise targeted and efficient therapies are limited. Thus, studies into novel therapeutic targets for the management of autoimmune diseases are urgently needed. Radical S-adenosyl methionine domain-containing 2 (RSAD2) is an interferon-stimulated gene (ISG) renowned for the antiviral properties of the protein it encodes, named viperin. An increasing number of studies have underscored the new roles of RSAD2/viperin in immunomodulation and mitochondrial metabolism. Previous studies have shown that there is a complex interplay between RSAD2/vipeirn and mitochondria and that binding of the iron-sulfur (Fe-S) cluster is necessary for the involvement of viperin in mitochondrial metabolism. Viperin influences the proliferation and development of immune cells as well as inflammation via different signaling pathways. However, the function of RSAD2/viperin varies in different studies and a comprehensive overview of this emerging theme is lacking. This review will describe the characteristics of RSAD2/viperin, decipher its function in immunometabolic processes, and clarify the crosstalk between RSAD2/viperin and mitochondria. Furthermore, we emphasize the crucial roles of RSAD2 in autoimmune diseases and its potential application value.

Functional significance of DNA methylation: epigenetic insights into Sjögren's syndrome

Sjögren's syndrome (SjS) is a systemic, highly diverse, and chronic autoimmune disease with a significant global prevalence. It is a complex condition that requires careful management and monitoring. Recent research indicates that epigenetic mechanisms contribute to the pathophysiology of SjS by modulating gene expression and genome stability. DNA methylation, a form of epigenetic modification, is the fundamental mechanism that modifies the expression of various genes by modifying the transcriptional availability of regulatory regions within the genome. In general, adding a methyl group to DNA is linked with the inhibition of genes because it changes the chromatin structure. DNA methylation changes the fate of multiple immune cells, such as it leads to the transition of naïve lymphocytes to effector lymphocytes. A lack of central epigenetic enzymes frequently results in abnormal immune activation. Alterations in epigenetic modifications within immune cells or salivary gland epithelial cells are frequently detected during the pathogenesis of SjS, representing a robust association with autoimmune responses. The analysis of genome methylation is a beneficial tool for establishing connections between epigenetic changes within different cell types and their association with SjS. In various studies related to SjS, most differentially methylated regions are in the human leukocyte antigen (HLA) locus. Notably, the demethylation of various sites in the genome is often observed in SjS patients. The most strongly linked differentially methylated regions in SjS patients are found within genes regulated by type I interferon. This demethylation process is partly related to B-cell infiltration and disease progression. In addition, DNA demethylation of the runt-related transcription factor (RUNX1) gene, lymphotoxin-α (LTA), and myxovirus resistance protein A (MxA) is associated with SjS. It may assist the early diagnosis of SjS by serving as a potential biomarker. Therefore, this review offers a detailed insight into the function of DNA methylation in SjS and helps researchers to identify potential biomarkers in diagnosis, prognosis, and therapeutic targets.

Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren's Syndrome

OBJECTIVE

B cells are important in the pathogenesis of primary Sjögren's syndrome (pSS). Patients positive for Sjögren's syndrome antigen A/Sjögren syndrome antigen B (SSA/SSB) autoantibodies are more prone to systemic disease manifestations and adverse outcomes. We aimed to determine the role of B cell composition, gene expression, and B cell receptor usage in pSS subgroups stratified for SSA/SSB antibodies.

METHODS

Over 230,000 B cells were isolated from peripheral blood of patients with pSS (n = 6 SSA-, n = 8 SSA+ single positive and n = 10 SSA/SSB+ double positive) and four healthy controls and processed for single-cell RNA sequencing (scRNA-seq) and single-cell variable, diversity, and joining (VDJ) gene sequencing (scVDJ-seq).

RESULTS

We show that SSA/SSB+ patients present the highest and lowest proportion of naïve and memory B cells, respectively, and the highest up-regulation of interferon-induced genes across all B cell subtypes. Differential usage of IGHV showed that IGHV1-69 and IGHV4-30-4 were more often used in all pSS subgroups compared with controls. Memory B cells from SSA/SSB+ patients displayed a higher proportion of cells with unmutated VDJ transcripts compared with other pSS patient groups and controls, indicating altered somatic hypermutation processes. Comparison with previous studies revealed heterogeneous clonotype pools, with little overlap in CDR3 sequences. Joint analysis using scRNA-seq and scVDJ-seq data allowed unsupervised stratification of patients with pSS and identified novel parameters that correlated to disease manifestations and antibody status.

CONCLUSION

We describe heterogeneity and molecular characteristics in B cells from patients with pSS, providing clues to intrinsic differences in B cells that affect the phenotype and outcome and allowing stratification of patients with pSS at improved resolution.

CXCL9 may serve as a potential biomarker for primary Sjögren's syndrome with extra-glandular manifestations

BACKGROUND

Primary Sjögren's syndrome (pSS) is an autoimmune condition that causes harm to exocrine glands and also has extra-glandular manifestations (EGM). pSS patients with EGM have a worse prognosis than those with only sicca symptoms. Previous studies have shown that the minor salivary glands (MSG) of pSS patients exhibit a unique profile of cytokines and chemokines compared to healthy controls. However, there is a lack of research comparing pSS with EGM (pSS-EGM) and pSS without EGM (pSS-non-EGM). This study aims to explore potential biomarkers associated with pSS, particularly pSS with EGM.

METHODS

By utilizing RNA sequencing, we conducted an analysis on the gene expression profiles of MSG in 63 patients diagnosed with pSS, as well as 12 non-pSS individuals. Furthermore, we also investigated the MSG of pSS patients, both with and without EGM. Through bioinformatics analysis, we identified genes with differential expression (DEGs) and determined the core hub genes using PPI network. We then analyzed the top 20 DEGs and their correlation with the patients' clinical characteristics, and validated our findings using peripheral blood plasma.

RESULTS

A total of 725 differentially expressed genes (DEGs) were identified in the comparison between pSS and non-pSS groups, and 727 DEGs were observed between pSS-EGM and pSS-non-EGM. It is noteworthy that the expression levels of CXCL9 were higher in both pSS patients and pSS-EGM when compared to the control group. Taking into consideration the significance of the top 20 DEGs in relation to clinical parameters and the central hub genes, we ultimately chose CXCL9. In comparison to the non-pSS group, pSS patients exhibited notably greater expression of the CXCL9 gene in the MSG, as well as higher levels of CXCL9 protein in their plasma (p < 0.001). Furthermore, the expression of the CXCL9 gene and levels of CXCL9 protein were notably higher in pSS patients accompanied by EGM and those with SSA antibodies. Additionally, a correlation was found between the expression of the CXCL9 gene and the EULAR Sjogren's Syndrome Disease Activity Index (ESSDAI), as well as with immunoglobulin G (IgG) levels and erythrocyte sedimentation rate (ESR). Meanwhile, the protein levels of CXCL9 were found to be correlated with IgG levels and ESSDAI.

CONCLUSION

CXCL9 proves to be a valuable biomarker in pSS, specifically due to its strong ability to differentiate between pSS patients with EGM and those without EGM. There is a significant correlation between CXCL9 and various clinical parameters both at the gene and protein level. Therefore, CXCL9 could be a potential target for future treatment of pSS.

Uncovering potential new biomarkers and immune infiltration characteristics in primary Sjögren's syndrome by integrated bioinformatics analysis

Primary Sjögren's syndrome (pSS) is known as autoimmune disease characterized by damage to endocrine glands, such as the salivary and lacrimal glands. This study aimed to identify potential biomarkers for pSS using integrated bioinformatics analysis and explore the relationship between differentially expressed genes (DEGs) and immune infiltration. Three pSS datasets (GSE7451, GSE23117, and GSE40611) from the gene expression omnibus database were integrated. All the datasets were processed in R (version 4.0.3). A total of 16 immune cells and 13 immune functions were obtained. The top immune cell and immune function were "activated" dendritic cells and major histocompatibility complex class I. Correlation analysis showed the top correlation among 16 immune cells were B cells and tumor infiltrating lymphocytes, check-point and T cell co-stimulation, respectively. In comparisons of immune score, "activated" dendritic cells (.657 vs 594, P < .001), B cells (.492 vs 434, P = .004), macrophages (.631 vs 601, P = .010), inflammation-promoting (.545 vs 478, P < .001), Type I interferon Reponse (.728 vs 625, P < .001) and so on were higher in pSS than control group. In correlation analysis, the up-regulation of interferon induced protein with tetratricopeptide repeats 1 gene was strongly correlated with Type I interferon response with a correlation coefficient of .87. The receiver operating characteristic curve of 5 genes showed that the area under curve was.891. In the verification model, the area under curve was.881. In addition, disease ontology analysis supported the association between DEGs and pSS. In summary, pSS has a variety of DEGs in immune infiltration, which is worthy of the attention from clinicians.

Non-invasive diagnosis of primary Sjögren's syndrome using ultrasonography and transcriptome biomarkers

Diagnosing primary Sjögren's syndrome (pSS) is difficult due to clinical heterogeneity and the absence of non-invasive specific biomarkers. To develop non-invasive pSS diagnosis methods that integrate classic clinical indexes, major salivary gland ultrasonography (SGUS), and gene expression profiles shared by labial gland and peripheral blood, we conducted a study on a cohort of 358 subjects. We identified differentially expressed genes (DEGs) in glands and blood that were enriched in defense response to virus and type I interferon production pathways. Four upregulated DEGs common in glands and blood were identified as hub genes based on the protein-protein interaction networks. A random forest model was trained using features, including SGUS, anti-SSA/Ro60, keratoconjunctivitis sicca tests, and gene expression levels of MX1 and RSAD2. The model achieved comparable pSS diagnosis accuracy to the golden standard method based on labial gland biopsy. Our findings implicate this novel model as a promising diagnosis technique of pSS.

Shared biomarkers of multi-tissue origin for primary Sjogren's syndrome and their importance in immune microenvironment alterations

With the recent advancement in omics and molecular techniques, a wealth of new molecular biomarkers have become available for the diagnosis and classification of primary Sjögren's syndrome (pSS) patients. However, whether these biomarkers are universal is of great interest to us. In this study, we used various methods to obtain shared biomarkers derived from multiple tissue in pSS patients and to explore their relationship with immune microenvironment alterations. First we identified differentially expressed genes (DEGs) between pSS and healthy controls utilizing nine mRNA microarray datasets obtained from the Gene Expression Omnibus (GEO). Then, shared biomarkers were filtered out using robust rank aggregation (RRA), data integration analysis, weighted gene co-expression network analysis (WGCNA), and least absolute selection and shrinkage operator (LASSO) regression; their roles in pSS and association with changes in the immune microenvironment were also analyzed. In addition, these biomarkers were further confirmed with both the testing set and immunohistochemistry (IHC). As a result, ten biomarkers, i.e., EPSTI1, IFI44, IFIT1, IFIT2, IFIT3, MX1, OAS1, PARP9, SAMD9L and TRIM22, were identified. Receiver operating characteristic (ROC) curves showed that the ten genes could discriminate pSS from controls. Gene set enrichment analysis (GSEA) showed that the enrichment of immune-related gene sets was significant in pSS patients with high expression of either biomarker. Furthermore, the association between some immunocytes and these biomarkers was identified. In the two distinct molecular patterns of pSS patients based on the expressions of these biomarkers, the proportions of immunocytes were significantly different. Our study identified shared biomarkers of multi-tissue origin and revealed their relationship with altered immune microenvironment in pSS patients. These markers not only have diagnostic implications but also provide potential immunotherapeutic targets for the clinical treatment of pSS patients.

Genetics and epigenetics of primary Sjögren syndrome: implications for future therapies

In primary Sjögren syndrome (pSS), chronic inflammation of exocrine glands results in tissue destruction and sicca symptoms, primarily of the mouth and eyes. Fatigue, arthralgia and myalgia are also common symptoms, whereas extraglandular manifestations that involve the respiratory, nervous and vascular systems occur in a subset of patients. The disease predominantly affects women, with an estimated female to male ratio of 14 to 1. The aetiology of pSS, however, remains incompletely understood, and effective treatment is lacking. Large-scale genetic and epigenetic investigations have revealed associations between pSS and genes in both innate and adaptive immune pathways. The genetic variants mediate context-dependent effects, and both sex and environmental factors can influence the outcome. As such, genetic and epigenetic studies can provide insight into the dysregulated molecular mechanisms, which in turn might reveal new therapeutic possibilities. This Review discusses the genetic and epigenetic features that have been robustly connected with pSS, putting them into the context of cellular function, carrier sex and environmental challenges. In all, the observations point to several novel opportunities for early detection, treatment development and the pathway towards personalized medicine.

Immunological, Clinical, and Epidemiological Features of Guillain-Barré Syndrome Associated with SARS-CoV-2 Infection

Objectives. There is a growing interest in understanding the association between Guillain-Barré syndrome (GBS) and SARS-CoV-2 infection. The aim of this study was to analyse various characteristics of GBS before and after the pandemic outbreak and thus identify possible distinctive features of GBS associated with SARS-CoV-2 (GBS-S). Material and Methods. In our centre, we retrospectively reviewed the records of patients diagnosed with GBS between January 2018 and March 2022. Epidemiological, clinical, and immunological data were analysed and compared between patients with GBS according to the time of diagnosis and antecedent events. Results. Thirty-nine patients with GBS were included: nine (23.1%) were diagnosed with GBS-S. GBS-S was most frequent in 2020 (6/13, 46.1%). Most of these patients developed a postinfectious classic demyelinating variant (4/9, 44.4%) with frequent bilateral facial paralysis (4/9, 44.4%). Serum antiganglioside antibodies (AGAs) were found in 1/9 patients with GBS-S. Serum anti-SSA/Ro60 antibodies were highly prevalent in GBS-S (7/9 (77.8%) vs. 3/11 (27.3%), $p=0.019$ ). Three cases associated with SARS-CoV-2 vaccination (GBS-V) were detected. Of note, two had bilateral facial paralysis and anti-SSA/Ro60 antibodies. Conclusion. Our findings suggest that SARS-CoV-2 has become an important antecedent event associated with GBS in our setting. GBS-S shows a postinfectious demyelinating immune-mediated profile with negative serological testing for AGAs. Serum anti-SSA/Ro60 antibodies were found frequently in these patients. Bilateral facial paralysis stands out as a possible characteristic clinical feature both in GBS-S and GBS-V. Larger, prospective studies are needed for a better understanding of its immunopathogenesis.

Differential CpG DNA methylation of peripheral B cells, CD4+ T cells, and salivary gland tissues in IgG4-related disease

OBJECTIVES

Immunoglobulin-G4-related disease (IgG4-RD) is a distinct systemic autoimmune-mediated disease manifesting as chronic inflammation and tissue fibrosis. Since the role of DNA methylation in the pathogenesis of IgG4-RD is still unclear, we conduct this study to investigate epigenetic modifications in IgG4-RD.

METHODS

A genome-wide DNA methylation study was conducted with B cells, CD4⁺ T cells, and salivary gland tissues from IgG4-RD patients and matched controls by using the Illumina HumanMethylation 850K BeadChip. We further performed pyrosequencing and immunohistochemistry assays to validate the methylation status of some targets of interest.

RESULTS

We identified differentially methylated CpG sites including 44 hypomethylated and 166 hypermethylated differentially methylated probes (DMPs) in B cells and 260 hypomethylated and 112 hypermethylated DMPs in CD4⁺ T cells from 10 IgG4-RD patients compared with 10 healthy controls. We also identified 36945 hypomethylated and 78380 hypermethylated DMPs in salivary gland tissues of 4 IgG4-RD patients compared with 4 controls. DPM2 (cg21181453), IQCK (cg10266221), and ABCC13 (cg05699681, cg04985582) were hypermethylated and MBP (cg18455083) was hypomethylated in B cells, CD4⁺ T cells, and salivary gland tissues of IgG4-RD patients. We also observed the hypomethylated HLA-DQB2 in CD4⁺ T cells from IgG4-RD patients. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DMPs in salivary gland tissues of IgG4-RD patients revealed enrichment of pathways involved in the regulation of immune cell responses and fibrosis.

CONCLUSION

This is the first DNA methylation study in peripheral B cells, CD4⁺ T cells, and salivary gland tissues from IgG4-RD patients. Our findings highlighted the role of epigenetic modification of DNA methylation and identified several genes and pathways possibly involved in IgG4-RD pathogenesis.

Sjögren's syndrome: shedding light on emerging and key drug targets

INTRODUCTION

Sjögren's syndrome (SS) is an immune-mediated inflammatory condition characterized by sicca syndrome, musculoskeletal pain, and fatigue. Extra-glandular manifestations are common and there is a markedly increased risk of lymphoma development. SS is associated with high health-economic burden driven largely by the symptom burden on patients. Currently, there is no approved disease-modifying treatment and management is based on empirical evidence. Progress in the understanding of SS pathogenesis has led to an expanding portfolio of more targeted therapies under development.

AREAS COVERED

This review summarizes the key development in targeted biological therapies in SS including emerging targets. It also highlights the challenges in therapeutic development in SS such as disease heterogeneity and defining appropriate disease assessment tools to evaluate therapeutic efficacy.

EXPERT OPINION

Early trials in SS failed to meet their primary outcomes which may in part due to the use of inappropriate or insensitive study endpoints. Recent trials targeting B-cells, B-T cell co-stimulation and IFN signaling have shown promising results. Development of composite endpoints including patient reported outcomes and objective disease measure may provide a more holistic approach to disease assessment. The impact of these new tools on therapeutic development that benefit patients remains to be fully evaluated.

Exploration of the pathogenesis of Sjögren's syndrome via DNA methylation and transcriptome analyses

OBJECTIVES

Sjögren's syndrome (SS), a systemic autoimmune disorder, is characterized by dry mouth and eyes. However, SS pathogenesis is poorly understood. We performed bioinformatics analysis to investigate the potential targets and molecular pathogenesis of SS.

METHODS

Gene expression profiles (GSE157159) and methylation data (GSE110007) associated with SS patients were obtained from the Gene Expression Omnibus (GEO) database. Differentially methylated positions (DMPs) and differentially expressed genes (DEGs) were identified by the R package limma. The potential biological functions of DEGs were determined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Key DMPs were selected by overlap and the shrunken centroid algorithm, and corresponding genes were identified as hub genes, with their diagnostic value assessed by receiver operating characteristic (ROC) curves. The potential molecular mechanisms of hub genes were analyzed by protein-protein interaction (PPI) networks and single-gene gene set enrichment analysis (GSEA). Peripheral blood mononuclear cells (PBMCs) were collected from control and SS patients at The Affiliated Hospital of Southwest Medical University and Dazhou Central Hospital. The mRNA levels of hub genes were verified by quantitative real-time polymerase chain reaction (qRT-PCR).

RESULTS

We identified 788 DMPs and 2457 DEGs between the two groups. Functional enrichment analysis suggested that the DEGs were significantly enriched in T cell activation, leukocyte cell-cell adhesion, and cytokine-cytokine receptor interaction. TSS200, TSS1500, and 1stExon were identified as highly enriched areas of differentially methylated promoter CpG islands (DMCIs). In total, 61 differentially methylated genes (DMGs) were identified by the overlap of 2457 DEGs and 507 genes related to DMPs (DMPGs), of which 21 genes located near TSS200, TSS1500, and 1stExon were selected. Then, three key DMPs and the corresponding hub genes (RUNX3, HLA-DPA1, and CD6) were screened by the shrunken centroid algorithm and calculated to have areas under the ROC curve of 1.000, 0.931, and 0.986, respectively, indicating good diagnostic value. The GSEA results suggested that all three hub genes were highly associated with the immune response. Finally, positive mRNA expression of the three hub genes in clinical SS samples was verified by qRT-PCR, consistent with the GSE157159 data.

CONCLUSIONS

The identification of three hub genes provides novel insight into molecular mechanisms and therapeutic targets for SS. Key Points • Hub genes were screened by DNA methylation and transcriptome analyses. • The relative expression of hub genes in peripheral blood samples was verified by qRT-PCR. • HLA-DPA1 was correlated with the pathogenic mechanism of SS.

Disease mechanisms in Sjögren's syndrome: what do we know?

Why should we explore and study disease mechanisms? This is particularly important when we are dealing with complex pathogenesis without a direct causal agent e.g. syndromes with multiple organ involvements. Sjögren's syndrome is definitely such an entity. Also, there are a number of reasons for such studies such as disclosing the aetiology, to identify biomarkers for diagnosis and assessment of the disease process and monitor response to treatment, to determine targets for treatment, to define critical items in classification criteria, among others. Samples available for the study of disease mechanisms in Sjögren's syndrome have included serum (autoantibodies, cytokines), DNA (gene profiling, GWAS), cells (phenotypes/flow cytometry, proportion of cells/CyTOF), tissue (focal inflammation, germinal centres, mass cytometry), saliva (proteomics, biochemistry, mucosal immunity). An original explanatory concept for the pathogenesis of Sjögren's syndrome proposed a specific and self-perpetuating immune mediated loss of exocrine tissue as the principal cause of glandular hypofunction. This hypothesis however falls short of accommodating several Sjögren's syndrome-related phenomena and experimental findings. Today, the emergence of advanced bio-analytical platforms has further enabled the identification of central pathogenic processes and potential biomarkers. The purpose of this minor review is to highlight a selection of previous but also recent and novel aspects on the disease mechanisms in Sjögren's syndrome.

Integrative epigenomics in Sjögren´s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature

Primary Sjögren's syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study, we confirmed a vast coordinated hypomethylation and overexpression effects in IFN-related genes, what is known as the IFN signature. Stratified and conditional analyses suggest a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature and determining SS. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified potential new genetic variants associated with SS that might mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, autoantibody profiles, DNA methylation and gene expression in SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population.