Profiling the peripheral immune response to ex vivo TNF stimulation in untreated juvenile idiopathic arthritis using single cell RNA sequencing

Abstract

Background Juvenile Idiopathic Arthritis (JIA) is an autoimmune disease with a heterogenous clinical presentation and unpredictable response to available therapies. This personalized transcriptomics study sought proof-of-concept for single-cell RNA sequencing to characterize patient-specific immune profiles. Methods Whole blood samples from six untreated children, newly diagnosed with JIA, and two healthy controls were cultured for 24 h with or without ex vivo TNF stimulation and subjected to scRNAseq to examine cellular populations and transcript expression in PBMCs. A novel analytical pipeline, scPool, was developed wherein cells are first pooled into pseudocells prior to expression analysis, facilitating variance partitioning of the effects of TNF stimulus, JIA disease status, and individual donor. Results Seventeen robust immune cell-types were identified, the abundance of which was significantly affected by TNF stimulus, which resulted in notable elevation of memory CD8 + T-cells and NK56 cells, but down-regulation of naïve B-cell proportions. Memory CD8 + and CD4 + T-cells were also both reduced in the JIA cases relative to two controls. Significant differential expression responses to TNF stimulus were also characterized, with monocytes showing more transcriptional shifts than T-lymphocyte subsets, while the B-cell response was more limited. We also show that donor variability exceeds the small degree of possible intrinsic differentiation between JIA and control profiles. An incidental finding of interest was association of HLA-DQA2 and HLA-DRB5 expression with JIA status. Conclusions These results support the development of personalized immune-profiling combined with ex-vivo immune stimulation for evaluation of patient-specific modes of immune cell activity in autoimmune rheumatic disease.

Whole blood stimulation as a tool for studying the human immune system

“…[89, 90]). In a pilot study, the combination of whole blood stimulation with single‐cell transcriptomics as a cellular readout has been reported for patients with juvenile idiopathic arthritis [91]. Single‐cell transcriptomic analysis identified monocytes as the strongest responding cell type to TNF stimulation, as expected, though granulocytes had been excluded due to PBMC isolation after stimulation.…”

TNFR1 Absence Is Not Crucial for Different Types of Cell Reaction to TNF: A Study of the TNFR1-Knockout Cell Model

“…There are studies showing that TNF stimulation leads to changes in the transcriptome of mononuclear cells [ 29 ]. However, our study provides previously unexplored data showing the effect of different doses of TNF on receptor expression and changes in the proliferation, apoptosis, and transcriptome of tumor cell lines of various origins.…”

Single-Cell Meta-Analysis of Neutrophil Activation in Kawasaki Disease and Multisystem Inflammatory Syndrome in Children Reveals Potential Shared Immunological Drivers

“…All studies were approved by the National Yang Ming Chiao Tung University institutional review board under NCTU-REC-109-036F. All the scRNA-seq PBMC data used in this study are publicly available: GSE168732, 15 GSE167029, 17 GSE183716, 25 GSE152450, 16 GSE166489, 19 GSE184330, 20 GSE205095, 26 GSE154386, 27 Ramirez-Sanchez et al, 28 GSE200743, 29 GSE217370, 30 GSE198616, 31 and GSE198891 32 (Tables S1–S3). In brief, we integrated and harmonized 9 cohorts with healthy control (HC), KD, MIS-C, dengue virus infection (DNV), juvenile idiopathic arthritis (JIA), and pediatric celiac disease (PCD) pediatric data.…”