ABSTRACT: We have previously shown that patients with systemic sclerosis (SSc) exhibit increased frequencies of autoreactive transitional B cells, including those with anti-topoisomerase I (ATA+) specificity, an autoantibody associated with progressive interstitial lung disease. This suggests that defective transitional B cell tolerance drives autoimmunity in SSc, however, the mechanism underpinning reduced censorship of these early B cells remains undefined. To investigate this, we applied single-cell transcriptomic and B cell receptor (BCR) sequencing to dissect the molecular and repertoire features of transitional B cells isolated from early-stage ATA+ treatment-naive SSc patients. This revealed four distinct transitional B cell clusters: T1, T2, CD27+ and marginal zone precursors (MZP). Novel marker genes were identified within these clusters, including the pro-apoptotic gene HRK which was specifically enriched in the MZP cluster. These findings were validated using a publicly available single-cell dataset. Among these transitional clusters, T1 B cells were significantly expanded in SSc patients, with a two-fold increase compared with matched healthy controls, suggesting elevated bone marrow output or increased exodus of transitional B cells in SSc. Additionally, pro-survival genes such as IL4R, TCL1A and S100A10 were significantly upregulated in SSc, whilst a key negative regulator of PI3K/AKT signalling, FOX01 was significantly reduced. Interferon responsive genes (IFITM1 and IFITM2) were also significantly increased in SSc transitional B cells, consistent with dysregulated interferon signalling in SSc. BCR analysis revealed significantly increased CDR3 hydrophobicity in SSc, notably in the T2 cluster, where a trend towards increased usage of the autoimmunity-associated gene IGHV4-39 was also observed. Furthermore, the κ/λ light chain ratio was elevated in the majority of SSc patients, perhaps implying incomplete receptor editing. Collectively, our findings support divergent transitional B cell development and activation in SSc, with an AKT-driven pathway likely promoting autoreactive transitional B cell survival.
