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Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry
Published on: June 26, 2018
Integrated transcriptomic and epigenomic profiling reveals conserved molecular subtypes across systemic autoimmune
Yu Fan1, Miaotong Su1, Lijun Yu1
1Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China.
Annals of the Rheumatic Diseases
|May 30, 2026
Summary
Two conserved molecular subtypes, megakaryocyte-enriched and B-cell-enriched, were identified across rheumatoid arthritis, lupus, and Sjögren's syndrome. These subtypes exhibit distinct cellular and regulatory programs, offering potential for targeted therapies in systemic autoimmune diseases.
Area of Science:
- Immunology
- Genomics
- Epigenetics
Background:
- Rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and primary Sjögren's syndrome (pSS) are systemic autoimmune diseases (SADs) with overlapping features but significant heterogeneity.
- Understanding shared molecular underpinnings can reveal new therapeutic targets.
Purpose of the Study:
- To define conserved molecular subtypes across RA, SLE, and pSS.
- To investigate the transcriptional and epigenetic basis of these subtypes.
Main Methods:
- Profiling of 262 treatment-naïve Chinese Han patients using bulk RNA sequencing, ATAC-seq, and single-cell RNA sequencing (scRNA-seq).
- Discovery and validation cohorts were used to ensure reproducibility.
- Integration of multiomics data to correlate molecular subtypes with clinical phenotypes and regulatory landscapes.
Main Results:
- Identification of two robust molecular subtypes: megakaryocyte-enriched and B-cell-enriched, consistent across all three SADs.
- The megakaryocyte-enriched subtype associated with higher platelet counts, disease activity, and organ involvement.
- Distinct epigenomic landscapes and regulatory programs identified for each subtype, with specific gene associations (e.g., ZFP36L1, RAD51B for megakaryocytes; MAF, PRDM1 for B-cells).
Conclusions:
- Multiomics profiling defines two conserved molecular subtypes across RA, SLE, and pSS.
- These subtypes possess distinct cellular and regulatory programs.
- This cross-disease classification may guide precision medicine and the development of targeted therapies for SADs.
