MRNA profile in CD4+ T cell in healthy control and Primay biliary cholangitis (PBC) [mRNA]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE93170 | GEO | 2017/01/06
SECONDARY ACCESSION(S): PRJNA360235
REPOSITORIES: GEO
Similar Datasets
Project description:Primary biliary cholangitis (PBC), formally known as primary biliary cirrhosis, is an autoimmune liver disease of unknown pathogenesis. Consequently, therapeutic targets for PBC have yet to be identified. As CD4+ T cells play a pivotal role in immunological dysfunction observed in PBC, we analyzed microRNA(miRNA) and mRNA expression in CD4+ T cells to investigate PBC pathogenesis and identify novel therapeutic targets.
2017-01-06 | GSE93171 | GEO
Project description:microRNA-mRNA integral analysis in CD4+ T cell in primay biliary cholangitis (PBC)
| PRJNA360230 | ENA
Project description:Primary biliary cholangitis (PBC) is an autoimmune liver disease of unknown pathogenesis. We find a decreased number and immunosupressive function of double nagative T (DNT) cells in PBC patients. To further unveil the mechanism by which suppressive function and quantity of DNT cells in PBC patients was impaired, we performed a whole-transcriptome analysis on DNT cells isolated from 13 PBC patients and 6 HCs. Total RNA of DNT cells from HCs and PBC patients were isolated and assessed. Transcriptome sequencing libraries were then generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Differentially expressed genes with a fold change of >=2.0 and p < 0.05 between HC and PBC patients were submitted to GO and KEGG enrichment analysis. Thie biologic processes of GO enrichment analysis showed that cell co-stimulations, cell migration, apoptotic process, cell activation and cell cytotoxicity were enriched, which helped to explain the alterations in number and suppressive function of DNT cells between HCs and patients from a mRNA level. Meanwhile, we observed that T cell receptor signaling pathway was enriched in DEGS and all identified genes with GSEA. Additionally the leading-edge genes of this pathway exhibited downregulation in PBC patients, subsequently supported by real-time PCR. PIK3R1 and MAP3K8 exhibited more significant reduction in DNT cells from PBC patients.
2024-11-30 | GSE138888 | GEO
Project description:Background & Aims: Late-stage primary biliary cholangitis (PBC) is defined by bile duct loss, ductular reaction, peribiliary inflammation and fibrosis. Loss of anion exchanger 2 (AE2), the ‘bicarbonate umbrella’ and ductulo-canalicular junctions (DCJ) are hypothesized to promote PBC progression. The secretin (Sct)/secretin receptor (SR) axis controls cystic fibrosis transmembrane receptor (CFTR) activation and AE2 opening, and controls choleresis. We aimed to define the impact of Sct/SR signaling on biliary secretory processes and subsequent injury in late-stage PBC mouse model and human samples. Methods: Female and male wild-type (WT) and dominant-negative transforming growth factor beta receptor II (dnTGFβRII, late-stage PBC model) at 32 wks of age were treated with Sct for 1 wk or 8 wks. Pathways mediated by Sct were identified by RNA-seq in isolated cholangiocytes. Sct/SR/CFTR/AE2 expression and MUC1 levels were evaluated in human control and late-stage PBC. Results: Biliary Sct, SR, CFTR and AE2 expression is reduced in late-stage PBC mouse models and human samples. Sct treatment decreased bile duct loss, ductular reaction, inflammation and fibrosis in late-stage PBC models, as well as hepatic bile acid release and DCJ formation. RNA-seq identified that Sct promoted mature epithelial cell marker expression, specifically anterior grade 2 (Agr2, expressed only in cholangiocytes). Late-stage PBC models and human samples had reduced biliary MUC1, which was enhanced with Sct treatment. Conclusion: Loss of the Sct/SR pathway in late-stage PBC results in a faulty ‘bicarbonate umbrella’ and reduced Agr2 and mucin production. Sct restores cholangiocyte secretory processes and DCJ formation through enhanced mature cholangiocyte phenotypes and healthy bile duct growth. The Sct/SR axis may be a therapeutic target for late-stage PBC patients.
2022-06-17 | GSE202676 | GEO
Project description:Autoimmune Hepatitis (AIH) and Primary Biliary Cholangitis (PBC) are autoimmune diseases that target the liver in which the immune system produces an inappropriate response to self-antigens resulting in inflammation, damage, and dysfunction of hepatic tissues. Despite progress in the understanding of the etiopathogenesis and in the diagnostic and therapeutic approach of these diseases, critical issues remain concerning the early diagnosis of affected individuals. The present study aims to detect and characterize by a gel-based bottom-up proteomic approach the acid-insoluble fraction of salivary proteome from patients affected by AIH and PBC with respect to healthy controls (HCs). The study was performed on the salivary acid-insoluble proteins after in-gel digestion starting from: i) the entire SDS-PAGE lane; ii) a portion of the SDS-PAGE at lowest molecular weight (MW </= 25 kDa).
2023-10-24 | PXD039847 | Pride
Project description:Primary sclerosing cholangitis (PSC) is characterized by chronic inflammation and progressive fibrosis of the biliary tree. The bile acid receptor TGR5 is found on biliary epithelial cells (BECs), where it promotes secretion, proliferation and tight junction integrity. Thus, we speculated that changes in TGR5 expression in BECs may contribute to PSC pathogenesis.
2021-03-12 | GSE168758 | GEO
Project description:Primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC), and inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are heterogeneous chronic autoimmune diseases that may share underlying pathogenic mechanisms. Herein, we compared simultaneously analyzed blood transcriptomes from patients with PBC, PSC, and IBD.
2019-05-01 | GSE119600 | GEO
Project description:Characterization of liver immune cell subsets of primary biliary cholangitis (PBC) mouse models using single-cell RNA sequencing
| PRJNA773416 | ENA
Project description:We report in this study the expansion of T cell clonotypes inflitrating both ectopic cholangiocarcinoma (CCA) and liver tissues in a mouse suffering from primary biliary cholangitis (PBC) (Paillet et al, J Exp Med, 2021). We wondered whether the specificity of T cells found in PBC livers and tumors developing post-PBC might be shared to some extent, comparing them to circulating T cells from the blood (Paillet et al, J Exp Med, 2021). Single-cell TCR sequencing coupled to single-cell RNA sequencing (scTCR/RNA-seq) led to the identification of 8112 distinct clonotypes with a hierarchy of clonotypes enrichment that was significantly higher in PBC livers than in peripheral blood, as well as in CCA compared to blood and liver. Indeed, 12 distinct clonotypes accounted for ~20% of the tumor T cell infiltrate. The overlap of clonotypes between liver and tumor was superior to the overlap between blood and liver, or blood and tumor. Among the 128 clonotypes enriched (i.e. accounting for > 0.1% of total T cells infiltrating the tissue) in the tumor, 25 were also detected and enriched in the liver. Two clonotypes (#2 and #13) were particularly expanded, each representing over 0.5% of the total T cell population in both liver and tumor post-PBC (Paillet et al, J Exp Med, 2021). Bioinformatic analysis of the scRNA-seq data of total T cells isolated from the liver and tumor of a PBC mouse revealed a net distinction between the transcriptome of T lymphocytes located in the two organs. Only one phenotypic cluster (h) was observed in both liver and tumor. The 25 liver/tumor dual-enriched (>0.1%) clonotypes were spread across few clusters (mostly c, j, k in the tumor; b and i in the liver). Among these clusters, three corresponded to CD8+ T cells (c, i, k) and two corresponded to CD4+ T cells (b, j). They exhibited a preponderant Tc1/Th1 polarization as illustrated by the expression of the enhancers Tbx21 and/or Eomes, and of effector molecules, namely IFNγ for Th1 (b, j), or the cytotoxic markers granzymes B and K for Tc1 (c, i, k) (Paillet et al, J Exp Med, 2021). Interestingly, the two clusters containing most of the enriched CD4+ T cell clonotypes presented a multifunctional signature characterized by the co-expression of IFNγ along with either IL4 (cluster b in the liver) or GzmB and KLRG1 (cluster j in the tumor). Clearly, the two most enriched clonotypes shared between CCA tumor and PBC liver belonged to the category of CD8+ cytotoxic T lymphocytes (clusters c + k in tumor, and cluster i in the liver). Moreover, they showed signs of prolonged activation/exhaustion with the expression of Pdcd1 (encoding PD-1), Lag3, Harvc2/Tim3 and Tigit, yet in a lesser extent than another cluster of CD8+ T cells (tumor cluster f) that contains only little shared clonotypes (Paillet et al, J Exp Med, 2021).
2021-09-03 | GSE180288 | GEO
Project description:The goal of the study was to compare the transcriptomic signature (by bulk RNA-sequencing) of hepatic tissues of mice either healthy/normal or affected with primary sclerosing cholangitis (PSC) or primary biliary cholangitis mouse (PBC) (Paillet et al, J Exp Med, 2021). Transcriptomic analyses revealed mostly convergent alterations in the gene expression patterns when PBC and PSC were compared to normal, age- and sex-matched controls. Gene Ontology (GO) term analyses of the modulated mRNAs revealed a significant enrichment of genes involved in inflammation, immune response and chemotaxis of different leukocyte subsets . The expression of genes listed under the GO terms “inflammation” and “neutrophil” was not significantly different (p>0.5, Student t-test) between PBC and PSC. In sharp contrast, genes listed under the GO terms “T cell” and “B cell” were significantly (p<0.05, Student t-test) upregulated in PBC compared to PSC livers. Deeper analysis of the aforementioned liver RNA-seq dataset indicated that several genes specifically involved in Th1 and Tc1 responses were upregulated in PBC livers with respect to controls and, in some cases also with respect to PSC. Especially, this applies to Tc1-related genes encoding the markers CD8a, CD274 (best known as PD-L1), UL16 binding protein 1 (ULBP1), IFNγ, G Protein-Coupled Receptor 18 (GPR18), the transcription factor suppressor of cytokine signaling 1 (SOCS1), and the cytotoxic protease granzyme B (GzmB) (Paillet et al, J Exp Med, 2021).
2021-08-28 | GSE179993 | GEO