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Clinical Rheumatology

Erschienen in:

13.05.2022 | Original Article

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

verfasst von: Yu Du, Jie Li, Jianhong Wu, Fanxin Zeng, Chengsong He

Erschienen in: Clinical Rheumatology | Ausgabe 9/2022

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Abstract

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.

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Titel: Exploration of the pathogenesis of Sjögren’s syndrome via DNA methylation and transcriptome analyses
verfasst von: Yu Du
Jie Li
Jianhong Wu
Fanxin Zeng
Chengsong He
Publikationsdatum: 13.05.2022
Verlag: Springer International Publishing
Erschienen in: Clinical Rheumatology / Ausgabe 9/2022
Print ISSN: 0770-3198
Elektronische ISSN: 1434-9949
DOI: https://doi.org/10.1007/s10067-022-06200-4

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