Genome-wide DNA Methylation Patterns in Monocytes Derived from Patients with Primary Sjögren Syndrome
Primary Sjögren syndrome (pSS) is a chronic autoimmune disorder characterized by lymphocytic infiltration of exocrine glands, leading to mucosal dryness and systemic manifestations affecting organs such as the kidneys, liver, and lungs. Emerging evidence highlights the role of epigenetic dysregulation, particularly DNA methylation, in the pathogenesis of pSS. This study investigates genome-wide DNA methylation patterns in peripheral blood monocytes from pSS patients, aiming to elucidate epigenetic contributions to disease mechanisms.
Patient Characteristics and Study Design
The study included 11 untreated pSS patients (10 female, 1 male; mean age 45.3 ± 13.7 years) and 5 age- and sex-matched healthy controls (HCs). All patients met the 2016 American College of Rheumatology/European League Against Rheumatism classification criteria for pSS. Clinical features included oral dryness (11/11), ocular dryness (8/11), joint pain (6/11), parotid gland swelling (3/11), and interstitial lung disease (4/11). Serological profiling revealed elevated IgG levels (median 23.05 g/L), anti-SSA positivity (11/11), anti-SSB positivity (9/11), and a mean EULAR Sjögren Syndrome Disease Activity Index (ESSDAI) score of 2.64 ± 1.15. Monocytes were isolated from peripheral blood mononuclear cells (PBMCs) using CD14 magnetic microbeads, achieving >95% purity. Genome-wide methylation profiling was performed using the Illumina Infinium Human Methylation 850K BeadChip.
Differential Methylation Profiles in pSS Monocytes
Comparative analysis identified 2,819 differentially methylated positions (DMPs) between pSS patients and HCs, with hypomethylation predominating (1,977 hypomethylated vs. 842 hypermethylated DMPs). These DMPs corresponded to 1,313 unique genes, including 460 located in gene promoter regions (299 hypomethylated, 129 hypermethylated, 32 mixed). Hypomethylated genes were enriched in interferon (IFN)-related pathways, such as IFI44L, MX1, PARP9, and IFITM1, which are critical for type I IFN signaling. Notably, IFI44L exhibited the most pronounced hypomethylation, with a β-value difference >0.6, suggesting robust dysregulation of IFN pathways in pSS monocytes.
Functional Enrichment of Methylated Genes
Gene ontology (GO) analysis revealed that hypomethylated genes were associated with antigen binding, transcriptional regulation (e.g., RNA polymerase II activity), and cell adhesion. Biological processes included IFN-γ signaling, antigen presentation, and metabolic pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted enrichment in Epstein-Barr virus infection, human T-lymphotropic virus type 1 infection, autoimmune thyroid disease, and allograft rejection. Metabolic pathways, such as type 1 diabetes and AMP-activated protein kinase (AMPK) signaling, were also implicated. These findings underscore the interplay between immune dysregulation, viral mimicry, and metabolic alterations in pSS.
Overlap with Salivary Gland Epithelial Cells
Comparative analysis with publicly available data from salivary gland epithelial cells (SGECs) of pSS patients revealed 20 overlapping DMPs corresponding to 12 genes (PTPRN2, TNK1, WDR8, TSPAN9, VIPR2, OBSCN, KCNT1, ZNF703, NEURL3, LMX1B, LOC146336, FTSJD2). Shared pathways included cell cycle regulation, cellular senescence, and interleukin-17 (IL-17) signaling. This overlap suggests convergent epigenetic mechanisms in immune cells and target tissues, potentially driving glandular dysfunction and systemic inflammation.
Clinical Correlations and Serological Associations
Subgroup analyses explored associations between methylation patterns and clinical features. Patients with high serum IgG levels (≥18 g/L) exhibited enrichment in Notch signaling, pyruvate metabolism, and tyrosine metabolism pathways, linking metabolic reprogramming to B-cell hyperactivity. Anti-SSA/SSB double-positive (DP) patients displayed 1,230 DMPs (984 genes), compared to only 54 DMPs (27 genes) in anti-SSA single-positive (SP) patients. DP-specific DMPs were enriched in Ras signaling, ribosome biogenesis, and AMPK pathways, while SP patients showed limited enrichment in Notch signaling. These findings suggest that autoantibody status influences epigenetic landscapes, with DP patients exhibiting broader pathway dysregulation.
Mechanistic Insights and Pathogenic Implications
The predominance of hypomethylation in pSS monocytes aligns with prior studies in CD4+ T cells, B cells, and SGECs, indicating a systemic epigenetic shift toward immune activation. Hypomethylation of IFN-inducible genes (IFI44L, MX1) may perpetuate IFN signature activation, a hallmark of pSS. Defective antigen presentation pathways, evidenced by hypomethylation of HLA genes, could impair immune tolerance, fostering autoantibody production. Metabolic pathway alterations, particularly in AMPK and pyruvate metabolism, may reflect adaptive responses to inflammatory stress, influencing monocyte differentiation and cytokine secretion.
The overlap between monocyte and SGEC methylation patterns highlights shared epigenetic drivers of glandular pathology. For example, IL-17 pathway enrichment may promote glandular inflammation, while cell cycle dysregulation could exacerbate tissue damage. Notch signaling, implicated in both high-IgG patients and autoimmune models, may enhance macrophage differentiation and cytokine production, contributing to chronic inflammation.
Limitations and Future Directions
While this study provides comprehensive methylation profiles, functional validation of candidate genes and pathways is needed. Longitudinal studies could clarify whether methylation changes precede disease onset or result from inflammation. Larger cohorts are required to validate associations with clinical subsets (e.g., anti-SSB positivity, interstitial lung disease). Mechanistic studies exploring DNMT3A and TET2 activity in pSS monocytes may reveal therapeutic targets to modulate epigenetic dysregulation.
Conclusion
This genome-wide analysis identifies significant DNA methylation alterations in pSS monocytes, emphasizing hypomethylation of IFN-related and immune regulatory genes. The convergence of epigenetic changes in monocytes and SGECs underscores their synergistic role in disease pathogenesis. These findings enhance understanding of pSS mechanisms and highlight potential biomarkers for diagnosis and targeted therapy.
doi.org/10.1097/CM9.0000000000001451
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