Longitudinal single-cell modeling reveals monocyte reprogramming in juvenile systemic sclerosis following autologous stem cell transplantation

Juvenile systemic sclerosis (jSSc) is a rare autoimmune disease marked by skin fibrosis and multi-organ involvement. Autologous stem cell transplantation (ASCT) is an emerging therapy for severe, treatment-refractory jSSc, but its effects on immune cell dynamics remain poorly understood. PBMCs were collected from three patients with jSSc before ASCT and at 6, 12, and 24 months post-ASCT. Patient and healthy control samples were profiled using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). We focused on monocytes, given their role in fibrosis-promoting inflammation. To detect longitudinal trends, pseudobulked gene expression (log scale) was regressed against time since ASCT. This approach identified widespread changes in jSSc monocytes, including decreased expression of systemic sclerosis-linked genes, such as SERPINE1. On the pathway level, NF-{kappa}B-associated inflammatory signaling was elevated in jSSc monocytes at baseline relative to healthy controls and decreased progressively post-ASCT. Genes related to mitochondrial function and oxidative phosphorylation progressively increased in expression after ASCT, suggesting a shift in metabolic state. Compositional changes in monocyte subpopulations were also identified and may have contributed to longitudinal gene expression patterns. Together, these findings characterize the dynamic immune changes in jSSc following ASCT and highlight a widely applicable longitudinal modeling framework for single-cell data.