0118: Single-cell RNA sequencing of skin reveals vascular dysregulation in antiphospholipid syndrome

Background/Purpose: Antiphospholipid syndrome (APS) is a systemic autoimmune thromboinflammatory disorder defined by persistent antiphospholipid antibodies (aPL) and characterized clinically by macrovascular thrombosis, microvascular disease, and pregnancy morbidity. While aPL-mediated activation of endothelial cells and immune pathways has been established, the molecular drivers of tissue-level vascular dysfunction remain elusive. We performed single-cell RNA sequencing (scRNA-seq) of skin biopsies from patients with APS to identify local cellular and molecular drivers of disease pathogenesis.

Methods: Non-lesional skin biopsies were obtained from the upper thigh of patients with APS (n=6) and healthy controls (n=5). Single-cell suspensions were prepared via enzymatic and mechanical dissociation (Miltenyi Biotec), followed by SYTOX-Green-based FACS for live cell enrichment. Libraries were generated using Chromium Single Cell 5′ HT chemistry (10x Genomics), targeting ~20,000 cells/sample.
Sequencing data were processed with Cell Ranger v8.0.1 and analyzed using Seurat v5 in R for QC, integration, clustering, and annotation. Endothelial cells (ECs) were identified by canonical markers (VWF, CDH5, PECAM1); non-ECs (keratinocytes, immune cells, fibroblasts, pericytes, SMCs) were excluded. Differential gene expression and pathway enrichment analyses were performed comparing APS vs. control ECs.

Results: Four patients with APS had a triple-positive aPL profile; phenotypes included microvascular disease (n=2), macrovascular thrombosis (n=1), and one exhibited both. One APS patient was lupus anticoagulant-positive and had macrovascular disease with cardiac valve involvement; and one patient was positive for LA and anti-cardiolipin IgG with a history of macrovascular thrombosis. None of the patients had skin lesions at the time of biopsy.

Transcriptomic profiling of skin endothelial cells in APS revealed upregulation of genes involved in glycolysis, response to cytokine stimulus, NF-κB signal transduction, mitochondrial metabolism, cAMP signaling, and VEGF response (ALDOA, PLCG2, NDUFB1, SDF4, PRKAR1A, METAP2, EIF3J). Concurrently, genes related to RAS signaling, endosomal trafficking, chromatin organization, cell migration, endothelial cell development, tube formation, and barrier establishment were downregulated (RASGEF1B, RAPGEF6, RBFOX1, BCOR, ZNF366, RNF7, CTS, THSD7A). These gene expression changes were observed consistently across all six patients with APS compared to healthy controls.


Conclusion: Our single-cell transcriptomic analysis of non-lesional APS skin reveals a metabolically reprogrammed, pro-inflammatory, and stress-responsive endothelial phenotype.

Endothelial cells in APS skin demonstrated upregulation of genes associated with activation and inflammatory signaling, alongside downregulation of pathways involved in vascular homeostasis, signaling regulation, and barrier integrity. Together, these findings reveal a consistent transcriptional signature of endothelial dysfunction in APS skin and highlight opportunities to identify tissue-based biomarkers and potential therapeutic strategies targeting endothelial dysfunction in APS.