Introduction: Systemic sclerosis (SSc) is a heterogeneous systemic disease characterized by autoimmunity, fibrosis and vasculopathy. Antinuclear antibodies (ANA) are present in most of SSc patients and are strong diagnostic and prognostic biomarkers. Yet, their pathophysiological role remains unclear and they might be implicated in vasculopathy, in which endothelial cells (EC) are key players.

Methodology: To study the effect of ANA from SSc patients on EC, HUVEC were cultured in presence of purified IgG from: 10 SSc anti-topoisomerase-I positive patients (ATA), 10 SSc anticentromere positive patients (ACA), 10 anti-RNA polymerase III positive patients (RNAP), 10 healthy controls (HC) and 5 patients with systemic lupus erythematosus (SLE). After 24h, the proteome was analysed using LC-MS/MS and the transcriptome by RNA sequencing.

Results: Proteomics identified and quantified 2,141 proteins. Principal component analysis (PCA) showed 3 groups: a first including mostly ATA, a second with mostly ACA and a third group more heterogeneous including RNAP, SLE and HC. The proteomes comparison of EC in the presence of IgG from ATA vs HC and ACA vs HC revealed 614 and 288 differentially expressed (DE) proteins respectively. Proteins overexpressed in ATA group were enriched in macromolecule localization and protein binding. Overexpressed proteins in ACA group were enriched in RNA and mRNA proteins binding. Transcriptomics identified 16,802 genes. PCA revealed 2 groups: one homogeneous group composed by 5 ATA (“ATA2” group) and a second heterogeneous (5 ATA (“ATA1” group), ACA, RNAP, LES patients and HC). The transcriptomes comparison of EC in the presence of IgG from “ATA2” group vs HC revealed 7,639 DE genes, which were enriched in cell cycle process and regulation and DNA replication.

Conclusion: IgG from SSc patients influenced EC proteome and transcriptome profiles according to ANA status. This unabiased approach provided new insights regarding the role of ANA in SSc.