Microarray analysis of peripheral blood mononuclear cells isolated from patients with ANCA-associated vasculitis and healthy controls
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Paul Lyons
PROVIDER: E-MTAB-12008 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Autoimmune diseases are common and debilitating, but their severe manifestations could be reduced if biomarkers were available to allow individual tailoring of the potentially toxic immunosuppressive therapy required for their control. Clinically useful biomarkers have been identified using DNA microarrays in cancer but not autoimmunity. We show that transcriptional profiling of purified CD8 T cells, but not unseparated cells, identifies two distinct patient subgroups predicting long-term prognosis in two different autoimmune diseases, anti-neutrophil cytoplasmic antibody (ANCA) – associated vasculitis (AAV) and systemic lupus erythematosus (SLE). We show that genes defining the poor prognostic group are enriched for genes of the IL7R pathway, TCR signalling and those expressed by memory T cells. Furthermore, the poor prognostic group is associated with an expanded CD8 T cell memory population. These subgroups, which are also found in the normal population and can be identified by measuring expression of only three genes, raise the prospect of individualized therapy and suggest novel potential therapeutic targets in autoimmunity.
2010-06-02 | E-MTAB-157 | biostudies-arrayexpress
Project description:To study monocyte and macrophage activation in ANCA-associtated vasculitis (AAV), we performed bulk RNA sequencing of bead-selected monocytes and in vitro cultured monocyte-derived macrophages from AAV patients and healthy controls. Overview patients included for sequencing monocytes: - AAV active disease, n=4, MPO-AAV=4 - AAV remission, n=10, PR3-AAV=5, MPO-AAV=5 - Healthy controls, n=6 Overview patients included for sequencing monocyte-derived macrophages: - AAV active, n=1, PR3-AAV=1 - AAV remission, n=3, PR3-AAV=3 - Healthy controls, n=3
2024-06-20 | E-MTAB-13676 | biostudies-arrayexpress
Project description:The effect of anti-MPO and anti-PR3 IgG from patients with ANCA vasculitis on human monocytes.
| PRJNA911181 | ENA
Project description:Purpose: The goal of this study was to compare gene expression profiles from whole blood RNA-Seq data from pediatric ANCA-associated vasculitis patients to identify mechanistic endotypes. Methods: Whole blood mRNA profiles were generated from pediatric and adult vasculitis patients using Illumina GAIIx or Hi Seq 2500 RNA-Seq. Fastq files were alinged to human genome version GRC38.91 using STAR v2.6 and count data was generated with HTSEQ v0.61p1. Counts that passed quality and minimum expression filteres were anlayzed by hierarchical clustering based on Euclidean distance, and then for differential expression with DESeq2. Results: Our workflow identified 14,156 transcripts consistently expressed in vasculitis patients. Distance hierarchcial clustering identified three groups within these pediatric samples, and two groups plus one outlier in the adult samples. The two largest pediatric clusters were used as groups for differential expression analysis with the DESeq2 package for R. DE analysis identified 3,809 differentially expressed genes between clusters. Between the two adult groups, 1,682 genes were differentially expressed. DE genes were anlayzed for enrichment using ReatomePA as the reference database. This analysis revealed that genes involved in T-cell mediated immunity are more highly expressed in pediatric patients that fell into one endotype and those involved in neutrophil and Toll-like receptor mediated inflammation are more highly expressed in pediatric patients that fell into the other endotype group. Similar results were also seen in adults. Conclusions: This study utilizes RNA-Seq data to investigate the etiologies of ANCA-associated vasculitis. Using this approach we have identified T-cell mediated immunity and Toll-like receptor mediated inflammation as potentially differing inflammatory mechanisms in both pediatric and adult vasculitis patients that do not fall along normal diagnostic criteria.
2021-01-01 | GSE129752 | GEO
Project description:Copy number variation (CNV) has been shown to be common in regions of the genome coding for immune-related genes, and thus impacts upon polygenic autoimmunity. Low copy number of FCGR3B has recently been associated with systemic lupus erythematosus (SLE). FcγRIIIb is a glycosylphosphatidylinositol-linked, low affinity receptor for IgG found predominantly on human neutrophils. We present novel data demonstrating that both in a family with FcγRIIIb-deficiency, and in the normal population, FCGR3B CNV correlates with protein expression, with neutrophil uptake of and adherence to immune complexes, and with soluble serum FcγRIIIb. Reduced FcγRIIIb expression is thus likely to contribute to the impaired clearance of immune complexes which is a feature of SLE, explaining the association between low FCGR3B CNV and SLE that we have confirmed in a Caucasian population. In contrast, anti-neutrophil cytoplasmic antibody -associated vasculitis (AASV), a disease not associated with immune complex deposition, is associated with high FCGR3B CN. Thus we define a role for FCGR3B CNV in immune complex clearance, a function which may explain why low FCGR3B CNV is associated with SLE but not AASV. This is the first report of an association between disease-related gene CNV and variation in protein expression and function that may contribute to autoimmune disease susceptibility.
2008-10-02 | E-TABM-463 | biostudies-arrayexpress
Project description:These data are part of a body of work exploring the effect of IgG from patients with ANCA vasculitis on human monocytes in vitro. Please see the relevant publication for a full description.
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Project description:In patients with GN or vasculitis, ANCAs are directed against proteinase 3 (PR3) or myeloperoxidase (MPO). The differences between PR3-ANCA-associated vasculitis (AAV) and MPO-AAV described in the past have been supplemented during the last decade. In this review, we discuss the differences between these two small-vessel vasculitides, focusing especially on possible etiologic and pathophysiologic differences. PR3-AAV is more common in northern parts of the world, whereas MPO-AAV is more common in southern regions of Europe, Asia, and the Pacific, with the exception of New Zealand and Australia. A genetic contribution has been extensively studied, and there is a high prevalence of the HLA-DPB1*04:01 allele in patients with PR3-AAV as opposed to patients with MPO-AAV and/or healthy controls. Histologically, MPO-AAV and PR3-AAV are similar but show qualitative differences when analyzed carefully. Clinically, both serotypes are difficult to distinguish, but quantitative differences are present. More organs are affected in PR3-AAV, whereas renal limited vasculitis occurs more often in patients with MPO-AAV. For future clinical trials, we advocate classifying patients by ANCA serotype as opposed to the traditional disease type classification.
| S-EPMC4587702 | biostudies-literature
Project description:The etiopathogenesis underlying myeloperoxidase anti-neutrophil cytoplasmic antibody associated glomerulonephritis (MPO-AAGN) remains incompletely understood. Furthermore, there are only limited treatment options and treatment resistance of MPO-AAGN is still a common problem. To identify new targeted treatment options, intrarenal single-cell RNA sequencing (scRNA-seq) was applied to kidney biopsies from MPO-AAGN patients and control health kidney tissues to define the transcriptomic landscape at single-cell resolution. Intrarenal scRNAseq was also applied to a pre-clinical mouse model of MPO-AAGN to show that this model of disease can be used to trial new targeted treatments. NF-κB pathway activation was confirmed in a variety of kidney cells in MPO-AAGN patients. Kidney infiltrating immune cells of MPO-AAGN patients were mainly enriched in inflammatory pathways including TNF signaling, IL-17 signaling and NOD-like receptor signaling. These findings were similar in our pre-clinical mouse model of MPO-AAGN. Furthermore, there was an overexpression of inflammasome related genes (AIM2, IFI16) in MPO-AAGN patients. A dynamic gene expression in glomerular resident cells was observed in MPO-AAGN, including increased expression of several genes, including CD9 and SPARC, which were closely related to parietal epithelial hyperplasia and crescent formation and lesion progression. Importantly, overexpression of HSP90AA1 in non-focal mesangial cells and endothelial cells was found and the expression of several chemokines (CCL20, CXCL3, CXCL8, CXCL1, CCL2) were upregulated in non-focal proximal tubule cells. Moreover, MPO-AAGN patients with treatment resistance had higher proportions of kidney infiltrating classical monocytes and CD8+ T cells. Elevated expression of SPARC and LAMA4 in mesangial cells, IL33 in endothelial cells, and CFL1 in several cell clusters (proximal tubule cells, loop of Helen, macrophages) were observed in MPO-AAGN patients with treatment resistance when compared with patients who achieved remission after induction therapy. These results offer new insight into the pathogenesis of the progression and treatment resistance MPO-AAGN. We have identified new therapeutic targets for MPO-AAGN that can be tested in a pre-clinical model of disease.
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Project description:To investigate proteins interacting with STING mutants, HEK 293T cells were co-transfected with three STING mutant expression plasmids (human STING WT, STING delCTT (aa343-379 deletion), STING del6 (aa325-379 deletion) in a pcDNA3.1+ backbone) and either pcDNA-cGAS expression plasmid or control empty pcDNA plasmid. Lysed cells were then immunoprecipitated using sheep anti-STING or control sheep anti-IgG antibodies and protein G magnetic Dynabeads.
2024-02-19 | PXD038063 | Pride
Project description:The cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthetase (cGAS) has emerged as a fundamental component fueling the anti-pathogen immunity. Because of its pivotal role in initiating innate immune response, the activity of cGAS must be tightly fine-tuned to maintain immune homeostasis in antiviral response. Here, we reported that neddylation modification was indispensable for appropriate cGAS-STING signaling activation. Blocking neddylation pathway using neddylation inhibitor MLN4924 substantially impaired the induction of type I interferon and proinflammatory cytokines, which was selectively dependent on Nedd8 E2 enzyme Ube2m. We further found that deficiency of the Nedd8 E3 ligase Rnf111 greatly attenuated DNA-triggered cGAS activation while not affecting cGAMP induced activation of STING, demonstrating that Rnf111 was the Nedd8 E3 ligase of cGAS. We further identified Lys231 and Lys421 as the key neddylation sites in human cGAS. Mechanistically, Rnf111 interacted with and polyneddylated cGAS, which in turn promoted its dimerization and enhanced the DNA-binding ability, leading to proper cGAS-STING pathway activation. In the same line, the Ube2m or Rnf111 deficiency mice exhibited severe defects in innate immune response and were susceptible to HSV-1 infection. Collectively, our study uncovered a vital role of the Ube2m-Rnf111 neddylation axis in promoting the activity of the cGAS-STING pathway and highlighted the importance of neddylation modification in antiviral defense.
2021-02-22 | PXD024088 | Pride