Longitudinal CITE-seq analysis in juvenile-onset systemic sclerosis monocytes following autologous stem cell transplant

Juvenile systemic sclerosis (jSSc) is a rare and severe autoimmune disease marked by skin fibrosis and damage to multiple organ systems. This study implements autologous stem cell transplantation (ASCT), a newly available treatment protocol which aims to restore immune homeostasis, in this case amongst jSSc patients. Here, we analyze peripheral blood mononuclear cells (PBMCs) from 3 jSSc patients prior to ASCT and 6, 12, and 24 months post treatment. These samples were then sequenced and tagged with antibodies using cellular indexing of transcriptomes and epitopes (CITE-seq). To analyze these samples and how they change over time, this study implements a newly designed generalized linear model. It was adopted from an established method with a coefficient for time since ASCT to identify numerous genes and pathways with downward longitudinal trends, many of which have previously been implicated in SSc development, and may help further understand disease pathogenesis. Our longitudinal differential gene expression analysis focused mainly on monocytes, which demonstrated strong downwards trends in multiple pathogenic genes/pathways. Specifically, nuclear factor-B (NFB)-driven inflammatory signaling was increased in jSSc monocytes at baseline compared to healthy controls, but decreased to match healthy monocyte levels over time following ASCT. We also note a sharp longitudinal reduction in jSSc monocyte expression of SERPINE1, a gene which has previously been implicated in SSc pathogenesis.This workflow describes immune reprogramming in three jSSc patients who underwent ASCT and introduces a statistically-justified framework for longitudinal single-cell modeling.