Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic regulation during the pathologic process from human primary Sjögren’s syndrome to mucosa-associated lymphoid tissue lymphoma

ABSTRACT: Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized by reduced activity of the exocrine glands (principally the salivary and lacrimal glands) due to chronic lymphocytic infiltration. pSS has been closely associated with an enhanced risk of mucosa-associated lymphoid tissue (MALT) lymphoma. However, the dynamic epigenetic changes in gland cells accompanied with this pathogenesis are not fully understood. In present study, the labial gland (LG) and parotid gland (PG) tissues from two pSS patients with lymphoma were harvested including LG with negative anti-SSA/SSB and LG with positive anti-SSA/SSB at the first diagnosis of pSS, as well as PG with and without lymphoma tissues at the second diagnosis of MALT. ChIP-seq of H3K4/9/27/36/79me3 were performed. This data is benefit to advanced understanding the dynamic development of MALT from pSS, emphasizing the importance of epigenetic alterations in regulating transcription during the pathologic process.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Chuangqi Yu

PROVIDER: E-MTAB-10340 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Epigenetic regulation during the pathologic process from human primary Sjögren’s syndrome to mucosa-associated lymphoid tissue lymphoma

Project description:Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized by reduced activity of the exocrine glands (principally the salivary and lacrimal glands) due to chronic lymphocytic infiltration. pSS has been closely associated with an enhanced risk of mucosa-associated lymphoid tissue (MALT) lymphoma. However, the dynamic epigenetic changes in gland cells accompanied with this pathogenesis are not fully understood. In present study, the labial gland (LG) and parotid gland (PG) tissues from two pSS patients with lymphoma were harvested including LG with negative antinuclear antibodies (ANA) and LG with positive ANA at the first diagnosis of pSS, as well as PG with and without lymphoma tissues at the second diagnosis of MALT. RNA-seq of these tissues were studied. This data is benefit to advanced understanding the dynamic development of MALT from pSS, emphasizing the importance of epigenetic alterations in regulating transcription during the pathologic process.

2021-04-17 | E-MTAB-10339 | biostudies-arrayexpress

Multi-modal single cell sequencing of B cells in primary Sjögren’s Syndrome

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

Deciphering the role of cDC2s in Sjogren’s Syndrome: transcriptomic profile reveals altered antigen processing and uptake associated with IFN-signatures and autoimmunity

Project description:Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease characterized by lymphocytic infiltration of the exocrine glands. Conventional dendritic cells (cDCs)-2 play a critical role in T and B cell activation, leading to germinal centre formation and autoantibody production. To understand the mechanisms underlying cDC2 dysregulation in pSS we performed RNA-sequencing analysis and functional validation on circulating cDC2s from pSS, non-Sjögren’s sicca (nSS) patients and healthy controls (HC). Two independent cohorts were established to identify reproducible dysregulated signatures, which included the interferon (IFN), toll-like receptors (TLR) signaling and antigen processing and presentation pathways. We confirm by flow cytometry that pSS-cDC2s were less efficient to degrade BSA but more efficient to uptake BSA both linked with the presence of anti-SSA antibodies. As the majority of the SSA+ pSS patients exhibit an IFN-signature, we tested whether IFNα priming would influence cDC2s antigen-uptake and processing. IFNα priming increased cDC2s uptake capacity, but not antigen processing. Additionally, pSS-cDC2s showed an increased uptake capacity of apoptotic salivary gland epithelial cells. Finally, pSS-cDC2s increased the proliferation of HC CD4+ T cells and the expression of CXCR3 and CXCR5 on the proliferating HC CD4+ T cells, contributing to T cell migration into the inflamed salivary glands. Here we provide the first in-depth molecular characterization of pSS-cDC2s and show that the transcriptomic and functional alterations observed in pSS-cDC2s are linked to IFN-signature. In view of its role in pSS immunopathology, delineating the molecular networks that drive cDC2s holds promise for targeting these cells in pSS.

2022-12-14 | GSE200020 | GEO

The transcriptome of paired major and minor salivary gland tissue in patients with primary Sjögren's syndrome

Project description:While all salivary glands (SGs) can be involved in primary Sjögren’s syndrome (pSS), their respective role in pathogenesis remains unclear. To assess immunopathway activation in paired parotid and labial gland tissue from biopsy-positive and biopsy-negative pSS and non-SS sicca patients, paraffin-embedded, paired parotid and labial salivary gland tissue and peripheral blood mononuclear cells were obtained from 39 pSS and 20 non-SS sicca patients. The patients were subdivided based on fulfillment of ACR-EULAR criteria and histopathology and the samples were analyzed for differentially expressed genes (DEGs). The principal component analysis of SG gene expression could only separate biopsy-positive pSS from non-SS sicca patients. However, when comparing the transcriptome of biopsy-positive pSS and biopsy-negative non-SS sicca patients, 1235 and 624 DEGs (FDR<-1 or >1) were identified for parotid and labial glands, respectively. The number of DEGs between biopsy negative pSS and non-SS sicca patients was scarce. The overall, transcript expression levels correlated strongly between parotid and labial glands (R2=0.86, p‐value<0.0001). Gene signatures present in both glands of biopsy‐positive pSS patients included IFN‐α signaling, IL-12/IL-18 signaling, CD3/CD28 T-cell activation, CD40 signaling in B-cells, DN2 B-cells, and FcRL4+ B-cells. Signature scores varied considerably amongst pSS patients. In conclusion, the transcriptomes of paired major and minor SGs in pSS were overall comparable, although significant inter-individual heterogeneity in immunopathway activation existed. The SG transcriptome of biopsy-negative pSS was indistinguishable from non-SS sicca patients. The different patterns of SG immunopathway activation in pSS argue for personalized treatment approaches.

2022-07-16 | GSE208260 | GEO

The transcriptome of paired major and minor salivary gland tissue in patients with primary Sjögren's syndrome

2021-05-05 | GSE173808 | GEO

Transcription profiling by array of parotid tissue from Primary Sjögren’s Syndrome and controls

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

Transcriptome sequencing reveals potential roles of ICOS in primary Sjögren’s syndrome

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

Transcriptomic analysis of B cells from patients with Sjögren’s Syndrome

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).

2022-12-14 | GSE199868 | GEO

Gene expression analysis of human salivary gland and organoid at single cell resolution

Project description:Salivary glands that produce and secret saliva, which is essential for lubrication, digestion, immunity, and oral homeostasis, consist of diverse cells. Maintenance of diverse salivary gland cells in organoids remains problematic. Here, we established human salivary gland organoids, which is composed of multiple cellular subsets, from 3 major salivary glands, including parotid gland (PG), submandibular gland (SMG), and sublingual gland (SLG). Human salivary gland organoids expressed gland-specific genes and proteins of acinar, myoepithelial, and duct cells. Organoids were maintained in growth media (named GEM) and further underwent differentiation in differentiation media (named DAM). Our study will provide an experimental platform for the exploration of mechanisms involvled in tissue regeneration, development, or several salivary gland diseases.

2022-05-05 | GSE184526 | GEO

Gene expression of murine 3 major salivary gland organoids

Project description:Salivary glands that produce and secret saliva, which is essential for lubrication, digestion, immunity, and oral homeostasis, consist of diverse cells. The long-term maintenance of diverse salivary gland cells in organoids remains problematic. Here, we established long-term murine salivary gland organoids from 3 major salivary glands, including parotid gland (PG), submandibular gland (SMG), and sublingual gland (SLG). Murine salivary gland organoids expressed gland-specific genes and proteins of acinar, myoepithelial, and duct cells. Organoids were maintained in growth media (named GEM) and further underwent differentiation in differentiation media (named DAM). Our study will provide an experimental platform for the exploration of mechanisms involvled in tissue regeneration, development, or several salivary gland diseases.

2022-05-05 | GSE184091 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data