Single cell RNAseq on rheumatoid arthritis-related interstitial lung disease
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE307297 | GEO | 2026/02/06
REPOSITORIES: GEO
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Project description:Interstitial lung disease (ILD) poses a serious threat in patients with rheumatoid arthritis (RA). However, the impact of cornerstone drugs, including methotrexate (MTX) and TNF blockade, on RA-associated ILD (RA-ILD) remains controversial. Our study using an SKG mouse model and single-cell transcriptomics revealed that MTX exacerbates pulmonary inflammation by promoting immune cell infiltration, Th17 activation, and fibrosis. In contrast, TNF blockade ameliorates these features and inhibits ILD progression. Analysis of data from a human RA-ILD cohort revealed that patients with ILD progression had persistently higher systemic inflammation than those without progression, particularly among the subgroup undergoing MTX treatment. These findings highlight the need for personalized therapeutic approaches in RA-ILD, given the divergent outcomes of MTX and TNF blockade.
2024-10-02 | GSE271209 | GEO
Project description:Lung disease is the most overrepresented cause of death in rheumatoid arthritis (RA). Animal studies have demonstrated potentiated autoimmunity, arthritis, and profibrotic/inflammatory lung disease with a combination of airborne exposures and collagen-induced arthritis (CIA), a model that recapitulates features of RA-associated interstitial lung disease (RA-ILD). As patients with RA-ILD demonstrate unique circulating monocyte subpopulations, this study aims to characterize lung infiltrating monocytes/macrophages in a mouse model of RA-ILD and determine whether reducing these cells mitigates the development of lung disease. Autoimmune-prone DBA/1J mice received intranasal inhalation of lipopolysaccharide (LPS) daily for up to 5 weeks and CIA induction. Experimental groups included Sham (saline injection/saline inhalation), CIA (CIA/saline), LPS (saline/LPS), and CIA+LPS (CIA/LPS). Lung disease was assessed by longitudinal imaging, lung function measurements, bronchoalveolar lavage fluid, lung tissues, and lung histopathology. Cell subpopulations were analyzed by single cell RNA-sequencing. Unsupervised clustering revealed 16 discrete clusters among the experimental groups with 2 robust clusters characterized as infiltrating inflammatory monocytes/macrophages for both CIA+LPS and CIA. The interaction of inhalation-induced airway inflammation and autoimmune arthritis results in lung disease associated with uniquely activated infiltrating inflammatory monocytes-macrophages that mediate adverse lung consequences. Whereas the induced monocyte/Mɸ immunophenotype is more aligned to CIA than endotoxin exposure, co-exposure modeling renders unique features that potentially inform the pathogenesis and treatment of RA-ILD.
2025-04-30 | GSE284234 | GEO
Project description:MZB1 is an endoplasmic reticulum residential protein preferentially expressed in plasma cells, marginal zone and B1 B cells. Recent studies on murine B cells shows that it interacts with the tail piece of IgM and IgA heavy chain and promotes the secretion of these two classes of immunoglobulin. However, its role in primary human B cells has yet to be determined and how its function is regulated is still unknown. The conversion of peptidylarginine to peptidycitrulline, also known as citrullination, by peptidylarginine deiminases (PADs) can critically influence the function of proteins in immune cells, such as neutrophils and T cells; however, the role of PADs in B cells remains to be elucidated. In an unbiased analysis of the human citrullinomeic analysis, we found that MZB1 was preferentially enriched in the pool of citrullinated lung proteins obtained from patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) compared to those from idiopathic pulmonary fibrosis or chronic obstructive pulmonary diseases. The citrullination of MZB1 was confirmed with mass spectrometry, in vitro citrullination, and binding by phenylglyoxal in the absence or presence of a PAD2-specific inhibitor AFM-30a. Ablation or pharmacological inhibition of PAD2 in primary human B cells attenuated the secretion of IgM and IgA but not IgG or the differentiation of IgM or IgA-expressing plasmablasts, recapitulating the effect of ablating MZB1. In addition, the physical interaction between endogenous MZB1 and IgM/IgA was attenuated by AFM-30a. Taken together, our data confirm the function of MZB1 in primary human plasmablasts and suggest that PAD2 promotes IgM/IgA secretion by citrullinating MZB1, thereby contributing to the pathogenesis of rheumatoid arthritis and RA-ILD.
2023-11-23 | PXD047044 | Pride
Project description:Objective: Peptidylarginine deiminases (PADs) modulate immune cell function and contribute to the development of rheumatoid arthritis (RA), which frequently co-occurs with interstitial lung disease (ILD). Fibroblasts exhibit organ-specific function and play pathogenic roles in RA and ILD. This study aims to examine the cell-autonomous role of PADs in regulating gene expression of fibroblasts from various organs. Methods: Fibroblasts of various organs and thioglycolate elicited peritoneal cells were harvested from wild type, PAD2-deficient, or PAD4-deficient mice. Primary human lung fibroblasts were subjected to CRISPR-mediated PAD2 ablation. Bulk RNA sequencing was performed to identify PAD2-regulated genes. Differential expression was subsequently confirmed, and basal and TNFα-induced gene expression were measured, using quantitative PCR, flow cytometry, and/or ELISA. Results: PAD2 transcript levels in lung fibroblasts increased with age, a trend not observed in fibroblasts from other organs. While PAD2 deficiency had a limited impact on the overall transcriptome of lung fibroblasts, it consistently reduced the expression of Podoplanin (PDPN) and TNFRSF1b across fibroblasts from all mouse organs and human lung fibroblasts. Lung fibroblasts exhibited the highest IL-6 expression among all sources of fibroblast. Notably, PAD2 deficiency, but not PAD4 deficiency, attenuated TNFα-induced IL-6 expression in fibroblasts from lung and synovium but not other organs. Conclusion: PAD2 is expressed in lung fibroblasts in an age-dependent manner and cell-autonomously regulates TNFα-induced gene expression of fibroblasts based on their organ origin, particularly lung and synovium. These findings suggest a novel pathogenic role for PAD2 in rheumatoid arthritis (RA) and offer a plausible explanation for the observed lung-synovium connection.
2026-03-25 | GSE307854 | GEO
Project description:Activated fibroblast-like synoviocytes (FLS) are drivers of synovitis and structural joint damage in rheumatoid arthritis (RA). Despite the use of disease-modifying drugs, only about 50% of RA patients reach remission in real-world settings. We used an unbiased approach to investigate the effects of standard-of-care methotrexate (MTX) and a Janus kinase inhibitor, tofacitinib (TOFA), on gene expression in RA-FLS, in order to identify untargeted disease mediators.
2024-10-04 | GSE266310 | GEO
Project description:Purpose: The goal of this study is to compare transcriptome profiling (RNA-seq) of lung tissue biopsies derived from patients with idiopathic pulmonary fibrosis (IPF or IPF-UIP), or rheumatoid arthritis-associated interstitial diseases (RA-ILD or RA-UIP), or non-usual interstitial pneumonia (non-UIP) controls. Methods: Total RNA was extracted using the RNeasy kit (Qiagen) from fresh frozen lung tissue obtained from the Lung Tissue Repository Consortium (LTRC). RNA samples were then sent to the Genome Analysis Core at Mayo Clinic for sequencing using conventional Illumina mRNA-Seq protocols. A total of 23,295 genes were probed using this platform. Results: RNA-seq data revealed considerable transcriptomic differences between the groups. A heat map generated with the most differentially expressed genes (P<0.05) revealed two distinct gene expression profiles among the three groups. The heat map for the 3 RA-UIP and 20 IPF patients showed a similar gene expression pattern, which contrasted significantly from the non-UIP control group. Conclusions: The RNA-Seq data analysis shows similarities and differences between gene expression profiles of RA-UIP and IPF, suggesting both shared and differential disease-causing mechanistic pathways. Transcriptomic data distinguishes the RA-UIP group from IPF via JAK2-related JAK/STAT signaling pathways.
2022-05-31 | GSE199152 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE21369: Gene expression profiles of interstitial lung disease (ILD) patients GSE21394: MicroRNA expression profiles of interstitial lung disease (ILD) patients Refer to individual Series
2011-04-19 | E-GEOD-21411 | biostudies-arrayexpress
Project description:Macrophage polarization and synovitis play significant roles in rheumatoid arthritis (RA). Chemokines are involved almost throughout the entire pathology of synovitis. However, the interaction between chemokines and macrophage polarization in RA has been seldom reported. This study found that chemokine C-C motif ligand 7 (CCL7) secreted by polarized M1 macrophages enhances M1 polarization, creating a positive feedback loop and revealing the role of CCL7 in the progression of rheumatoid arthritis. In this research, RNA sequencing indicated that M1 polarized macrophages secrete a large amount of CCL7, which further enhances M1 polarization. Through immunohistochemistry and enzyme-linked immunosorbent assay, it was found that the expression of CCL7 in the synovial tissue and serum of RA patients and mice was upregulated. Intra-articular injection of CCL7 recombinant protein exacerbated M1 polarization of macrophages, inflammation, fibrosis in the synovial tissue, and worsened arthritis pain in mice, which was improved after the injection of CCL7 neutralizing antibody. In addition, CCL7 promoted M1 polarization of macrophages and reversed the M2 polarization induced by IL-4, and it also promoted macrophage proliferation and migration. Although it had an inhibitory effect on chondrocyte activity, it did not show a significant impact on chondrocyte metabolism. Mechanistically, CCL7 targets CCR1 to promote M1 polarization of macrophages, a process partly mediated through the activation of the JAK2/STAT1 pathway. When stimulated by CCL7, macrophages secreted a vast amount of pro-inflammatory factors, exacerbating synovitis and cartilage damage, leading to the aggravation of RA disease. Our research established a positive feedback loop between M1 polarization of macrophages and CCL7, indicating that blocking CCL7 could improve the progression of RA, suggesting CCL7 as a potential target for RA treatment.
2025-01-08 | GSE285977 | GEO
Project description:Macrophage polarization and synovitis play significant roles in rheumatoid arthritis (RA). Chemokines are involved almost throughout the entire pathology of synovitis. However, the interaction between chemokines and macrophage polarization in RA has been seldom reported. This study found that chemokine C-C motif ligand 7 (CCL7) secreted by polarized M1 macrophages enhances M1 polarization, creating a positive feedback loop and revealing the role of CCL7 in the progression of rheumatoid arthritis. In this research, RNA sequencing indicated that M1 polarized macrophages secrete a large amount of CCL7, which further enhances M1 polarization. Through immunohistochemistry and enzyme-linked immunosorbent assay, it was found that the expression of CCL7 in the synovial tissue and serum of RA patients and mice was upregulated. Intra-articular injection of CCL7 recombinant protein exacerbated M1 polarization of macrophages, inflammation, fibrosis in the synovial tissue, and worsened arthritis pain in mice, which was improved after the injection of CCL7 neutralizing antibody. In addition, CCL7 promoted M1 polarization of macrophages and reversed the M2 polarization induced by IL-4, and it also promoted macrophage proliferation and migration. Although it had an inhibitory effect on chondrocyte activity, it did not show a significant impact on chondrocyte metabolism. Mechanistically, CCL7 targets CCR1 to promote M1 polarization of macrophages, a process partly mediated through the activation of the JAK2/STAT1 pathway. When stimulated by CCL7, macrophages secreted a vast amount of pro-inflammatory factors, exacerbating synovitis and cartilage damage, leading to the aggravation of RA disease. Our research established a positive feedback loop between M1 polarization of macrophages and CCL7, indicating that blocking CCL7 could improve the progression of RA, suggesting CCL7 as a potential target for RA treatment.
2025-01-08 | GSE267151 | GEO
Project description:Primary Sjögren’s syndrome (pSS) is a chronic systemic autoimmune disease characterized by typical autoantibody production and lymphocytic-mediated exocrine gland damage. Interstitial lung disease (ILD) is a common complication of pSS and can be associated with a poor prognosis. However, the pathogenesis of ILD in pSS is still unclear. In this study, we used RNA sequencing to investigate the gene-expression profile of the minor salivary glands (MSGs) from 36 patients with ILD-pSS and 128 patients with non-ILD-pSS. In the remarkably enriched chemokine-mediated signaling pathway, CXCR2 was found to be significantly elevated in both MSG and plasma from pSS patients with versus without ILD (p < 0.001). Furthermore, the CXCR2 expression level in MSG and plasma was significantly associated with the diffusing capacity of the lungs for carbon monoxide, erythrocyte sedimentation rate, and EULAR Sjögren’s Syndrome Disease Activity Index in ILD-pSS. Therefore, with its potential role in ILD progression in patients with pSS and its strong association with clinical manifestations of the disease, CXCR2 may serve as a useful index for disease activity in ILD associated with pSS.
2021-06-02 | GSE171896 | GEO