Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Peripheral Mononuclear Cells in Patients With Ankylosing Spondylitis

Abstract

ObjectiveGenetic studies on ankylosing spondylitis (AS) have identified more than 100 pathogenic genes. Building a bridge between these genes and biologically targeted therapies is the current research hotspot.MethodsWe integrated single-cell assaying transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) to explore the key genes and related mechanisms associated with AS pathogenesis.ResultsWe identified 18 cell types in peripheral mononuclear cells from patients with AS and normal controls and summarized the cell-type-specific abnormal genes by scRNA-seq. Interestingly, we found that the pathogenic gene NFKB involved in AS progression originated from CD8+ T cells. Moreover, we observed an abnormal tumor TNF pathway mediated by abnormal expression of TNF, NFKB, FOS, JUN, and JUNB, and scATAC-seq results confirmed the abnormal accessible binding sites of transcriptional factors FOS, JUN, and JUNB. The final magnetic bead sorting and quantitative real-time PCR(RT-qPCR) confirmed that NFKB, FOS, JUN, and JUNB in CD8+ T cells differed in the AS group.ConclusionsOur results revealed a possible mechanism by which NFKB abnormally regulates FOS, JUN, and JUNB and drives AS progression, providing a novel perspective from a single cell point of view in AS.

CD_99 G1 neutrophils modulate osteogenic differentiation of mesenchymal stem cells in the pathological process of ankylosing spondylitis

“…ClueGO analysis suggested that PTGS2, FOS, CXCL2 and CXCL8 in monocytic cells were highly correlated with AS-related inflammatory processes involved in MDP-ADIPOR2. Coincidentally, FOS is not only involved in the inflammatory response of AS peripheral blood mononuclear cells but also in the osteogenic differentiation of MSCs 11. Prostaglandin-endoperoxide synthase, also known as cyclooxygenase, is the key enzyme in prostaglandin biosynthesis and plays a critical role in regulating inflammatory responses 68.…”

“…This method has delivered revolutionary insights into cellular dynamics and heterogeneity and has the potential to investigate cell-to-cell variations, identify possible subpopulations and discover possible rare cell types 9. Although scRNA-seq is increasingly being applied, its application in AS has been limited to peripheral blood mononuclear cells and synovium of knee joint,10–13 leaving the transcriptomic heterogeneity within the pathological tissue of spine largely unknown.…”

Single-Cell Genomics for Investigating Pathogenesis of Inflammatory Diseases

“…AS is a chronic inflammatory disease featuring inflammation at the spine and sacroiliac joints with bone remodeling and ankylosis (Mauro et al, 2021). Applying single-cell RNA-seq and ATAC-seq on PBMCs from AS patients, NFKB expression and TNF signaling pathways have been shown to be upregulated in CD8 + T cells with abnormal accessibility of FOS, JUN, and JUNB (Xu et al, 2021). This finding suggests the role of effector CD8 + T cells in inflammatory cytokine secretion, including TNF-α.…”

Single Cell Transcriptome and Surface Epitope Analysis of Ankylosing Spondylitis Facilitates Disease Classification by Machine Learning

“…Several inflammatory pathways were observed to be significant in AS at a nominal level, including the signaling of inflammatory pathways such as IL-4/IL-13 signaling (Supplementary Table 5). Many of these pathways involved the upregulation of FOS and JUNB, which are also linked to the abnormal expression of NFKB in AS CD8 + T cells (32). Future studies are needed to follow up on these important inflammatory pathways.…”