LncRNA and mRNA expression profile of peripheral blood mononuclear cells in primary Sjögren’s syndrome patients
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE145065 | GEO | 2020/02/11
REPOSITORIES: GEO
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Project description:Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease characterized by abnormal immune cell activation. This study aimed to investigate differentially expressed long non-coding RNA (lncRNA) in peripheral blood mononuclear cells (PBMCs) in patients with pSS to identify lncRNAs that affect pSS pathogenesis. Transcriptome sequencing detected 38096 lncRNAs and 50869 mRNAs in PBMCs from patients with pSS and healthy individuals. The differentially expressed mRNAs underwent functional enrichment analysis. A protein interaction relationship (PPI) and ceRNA network was constructed. LncRNA expression in patients with pSS and controls was determined using RT-PCR. 1180 lncRNAs and 640 mRNAs were differentially expressed in pSS patients (fold change > 2 in healthy persons). The PPI network was constructed with 640 mRNAs and a ceRNA network with four key lncRNAs (GABPB1-AS1, PSMA3-AS1, LINC00847 and SNHG1). A co-expression relationship was found between GABPB1-AS1 and several upregulated mRNAs (IFI44, IFI44L, IFI6, and EPSTI1). RT-PCR revealed that GABPB1-AS1 and PSMA3-AS1 were significantly upregulated 3.0- and 1.4-fold in the pSS group, respectively. In patients with pSS, the GABPB1-AS1 expression level was positively correlated with B cell and IgG levels. GABPB1-AS1 expression levels are positively correlated with B cell levels and may be involved in the pathogenesis of pSS.
2021-07-28 | GSE164885 | GEO
Project description:Objective: We explored the patterns of long non-coding RNA (lncRNA) expression in peripheral blood mononuclear cells (PBMCs) from patients with non-segmental vitiligo. Methods: We used high-throughput RNA sequencing technology to generate sequence data from five patients with non-segmental vitiligo alongside five normal healthy individuals, and then performed bioinformatics analyses to detect the differential expression of lncRNA in PBMCs. Gene Ontology (GO) and pathway analyses were performed for functional annotation, and quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify gene expression. Target miRNAs and mRNAs of differentially expressed lncRNAs were predicted using bioinformatics analysis. Results: A total of 292 lncRNAs were differentially expressed in non-segmental vitiligo (fold change≥2.0, P<0.05), of which 171 were upregulated and 121 were downregulated. Six differentially expressed lncRNAs were selected , namely ENST00000460164.1, ENST00000393264.2, NR-046211.1, NR-135491.1, NR-135320.1, and ENST00000381108.3, for validation by qRT-PCR. The results showed that ENST00000460164.1 and NR-046211.1 were highly expressed in PBMCs of non-segmental vitiligo. An lncRNA-miRNA-mRNA network containing two lncRNAs, 17 miRNAs, and 223 mRNAs was constructed. Conclusion: Our results revealed patterns of differentially expressed lncRNAs in the PBMCs of non-segmental vitiligo individuals. ENST00000460164.1, and NR-046211.1 may be potential biomarkers and drug targets for the treatment of non-segmental vitiligo.
2021-11-04 | GSE186928 | GEO
Project description:We established m6A modification profiles using MeRIP-seq in peripheral blood mononuclear cells (PBMCs) from systemic lupus erythematosus (SLE) patients and controls (HC), and investigated m6A-related lncRNAs in SLE for novel potential roles in SLE. Compared with controls, m6A level was lower in SLE patients,426 lncRNAs and 2,331 mRNAs were differentially expressed in SLE patients.
2023-01-31 | GSE173312 | GEO
Project description:To reveal the role of DNA methylation in peripheral monocytes (Mo) of primary Sjögren’s syndrome (pSS) patients, monocyte DNAs from 11 pSS patients and 5 matched controls were analyzed by methylation microarray. In total, we identified 1977 hypomethylated and 842 hypermethylated differentially methylated positions (DMPs) in Mo from pSS patients compared to healthy controls.
2021-06-16 | GSE146116 | GEO
Project description:Objective Neutrophils and aberrant NETosis have been implicated in the pathogenesis of diverse autoimmune diseases, however, their roles in primary Sjögren’s syndrome (pSS) remain unclear. We aimed to reveal the potential roles of neutrophils and neutrophil extracellular traps (NETs) in this study. Methods pSS patients were enrolled according to the corresponding diagnostic criteria. NETosis markers were measured in plasma and small salivary gland using ELISA and immunofluorescence. The gene signatures of neutrophils were assessed by RNA-Seq and RT-PCR. Reactive oxygen species (ROS), mitochondrial ROS (mitoROS) production and JC-1 was measured by flow cytometry. Results NETosis markers including cell free-DNA (cf-DNA), myeloperoxidase (MPO) in plasma and small salivary gland from pSS patients were significantly higher than healthy controls (HCs) and were associated with disease activity. RNA sequencing and RT-qPCR revealed activated Type I IFN signaling pathway and higher expression of type I interferon related genes in pSS neutrophils. Further stimulating with IFN-α 2a in vitro significantly induced ROS production and JC-1 monomer percentage in pSS neutrophils. Conclusions Our data suggest the involvement of neutrophils and enhanced NETosis in pSS patients. Further mechanism study in vitro revealed that type I IFN activation in pSS neutrophils led to mitochondrial damage and related ROS production which finally result in the generation of NETs.
2022-01-25 | GSE194234 | GEO
Project description:Primary Sjögren’s syndrome (pSS) is a chronic systemic autoimmune disease characterized by exocrine glands damage and extraglandular manifestations. To identify potential biomarkers for the early diagnosis of pSS and further investigate the potential mechanisms in progression of the disease, we combined our previous RNA- sequencing study and four microarrays data to conduct integrative transcriptome analyses in salivary glands (SGs) between the pSS and non-pSS. Differential gene expression analysis, gene co-expression network analysis and pathway analysis were conducted to detect hub gene, which was subsequently validated in peripheral blood. Correlation analysis, single-gene Gene Set Enrichment Analysis (GSEA) and receiver operating characteristic (ROC) curve were applied to investigate the role of ICOS in pSS and its classification capacity for pSS.
2020-12-22 | GSE159574 | GEO
Project description:Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease with complex etiopathogenesis. Here we use Affymetrix U133 plus 2.0 microarray gene expression data from human parotid tissue. Parotid gland tissues were harvested from 17 pSS and 14 14 non-pSS sicca patients and 18 controls. The data were used in the following article: Nazmul-Hossain ANM, Pollard RPE, Kroese FGM, Vissink A, Kallenberg CGM, Spijkervet FKL, Bootsma H, Michie SA, Gorr SU, Peck AB, Cai C, Zhou H, Horvath S, Wong DTW (2012) Systems Analysis of Primary Sjögren’s Syndrome Pathogenesis in Salivary Glands: Comparative Pathways and Molecular Events in Humans and a Mouse Model. Parotid gland tissues were harvested from 17 pSS and 14 non-pSS sicca patients and 18 controls.
2012-09-06 | E-GEOD-40611 | biostudies-arrayexpress
Project description:Primary Sjögren’s syndrome (pSS) is an autoimmune disease characterized by lymphocytic infiltration in the salivary and lacrimal glands, B cell activation, SSA/SSB autoantibodies and an increased risk of B cell lymphoma. By generating sorted B cell single-cell gene expression and BCR libraries from 24 pSS patients stratified by SSA/SSB antibodies and four healthy controls, we defined 16 B cell subtypes. Interferon response genes were upregulated in pSS across all B cell subtypes, with the highest levels in pSS with both SSAB antibodies. The SSAB group showed a higher proportion of naïve B cells and lower proportion of memory B cells compared with controls. Memory B cells from SSAB patients were not class switched and expressed unmutated VDJ sequences. IGHV1-69 repertoire frequencies were higher in pSS patients than controls and 1287 clonotypes were unique for pSS. The present study describes molecular differences which may enable stratification of pSS patients at improved resolution.
2023-09-04 | GSE214974 | GEO
Project description:We investigated the expression profiles of lncRNAs and mRNAs in peripheral blood mononuclear cells (PBMCs) from subjects with 13 Phlegm-dampness constitution (PDC) and nine balanced Balanced constitution (BC). The differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified by the “limma” method. Goal was to determine whether long non-coding RNAs (lncRNAs) play a regulatory role in metabolic disease in subjects with PDC.
2022-01-07 | GSE158042 | GEO
Project description:Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized by lymphocytic infiltration of the exocrine glands and prominent B cell hyperactivity. B cells are crucial in the pathophysiology of pSS through several mechanisms, including cytokine production, exocrine gland destruction, and autoantibody secretion. Considering the central role of B cells we performed RNA-sequencing analysis of circulating CD19+ B cells from patients with pSS, non-Sjögren’s sicca (nSS), and healthy controls (HC).
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