Background/Purpose: DNA methylation plays a critical role in the pathogenesis of lupus. Although most epigenetic studies have focused on autosomal regions, the X chromosome remains underexplored. In this study, we investigate X chromosome DNA methylation patterns in male patients with lupus. Studying male individuals allows us to circumvent the analytical complexities posed by random X-inactivation in female patients with two X chromosomes, enabling a clearer view of epigenetic changes that may contribute to disease mechanisms.

Methods: A total of 16 male patients with childhood-onset lupus and 14 healthy male controls were included. DNA from peripheral blood mononuclear cells (PBMCs) was isolated to assess DNA methylation patterns using the Infinium MethylationEPIC v2.0 array (Illumina). Data processing and statistical analyses were conducted using the minfi and limma R packages. Group differences in methylation patterns were tested via linear regression, adjusting for age and estimated cell-type proportions. Gene ontology enrichment analysis was performed with Metascape.

Results: A total of 23,364 DNA methylation sites (CpGs) on the X chromosome were analyzed. Differential methylation analysis between cases and controls identified 1,120 CpG sites with suggestive associations (p < 0.05), mapping to 593 genes. Approximately half of these sites were hypomethylated in patients compared to controls, with several CpGs located in immune-related genes. Notably, several hypomethylated CpGs were found in genes involved in the toll-like receptor (TLR) signaling pathway, including TLR7, TASL, and BTK, which are key components of innate immune signaling pathways that drive the expression of pro-inflammatory cytokines. Pathway enrichment analysis of the top 100 most significant differentially methylated CpGs revealed overrepresentation of immune and regulatory pathways, such as positive regulation of type I interferon production, response to interleukin-1, and regulation of cellular response to growth factor stimulus, suggesting epigenetic remodeling of critical processes in disease pathogenesis.

Conclusion: These findings highlight previously underrecognized X chromosome DNA methylation changes in lupus, particularly in immune-related genes and pathways. Our results suggest that epigenetic dysregulation on the X chromosome may contribute to immune activation and disease pathogenesis, underscoring the importance of including sex chromosomes in lupus epigenetic studies.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/x-chromosome-dna-methylation-changes-suggest-epigenetic-contributions-to-immune-dysregulation-in-male-lupus/