Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell mass cytometry and transcriptomic profiling of circulating immune cells identifies an expansion of CD25hi switched memory B cells in Osteoarthritis

ABSTRACT: Osteoarthritis (OA) is a chronic, debilitating disease with no available disease-modifying drugs with end-stage surgery being the only treatment option. Biomarker identification in blood specimens of OA patients has hitherto been limited to serum proteins and bulk transcriptomics and epigenomic feature identification. We sought to capitalize on high resolution, single-cell techniques of mass cytometry by time-of-flight (cyTOF) and sc-RNA-seq to identify OA-associated features in the immune cells of the patients’ peripheral blood. Comparison of healthy donors and OA patients’ peripheral blood mononuclear cells (PBMC) revealed that frequencies of specific subpopulations of B cells, monocytes, CD4+ and CD8+T cells were distinctly perturbed in OA. While many immune subtypes were depleted, a CD25hiCD27+IgD- switched memory B cell population was identified to be significantly expanded in OA blood. Sc-RNA seq revealed a dysfunction of IL2/Stat3 and Notch signaling in the switched memory B cells expanded in OA. Upon profiling peripheral blood of patients with degenerative meniscal tears (DMT), a population known to be at enhanced risk for OA, we observed a similar expansion of CD25hiCD27+IgD- switched memory B cells suggesting that it can be a biomarker of early and late OA. Unsupervised clustering utilizing immune cell correlates stratified the profiled OA patients into three distinct subsets. Development of such single cell platforms can be a powerful clinical tool for OA prognosis as well as precision therapeutics.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253539 | GEO | 2025/05/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

BCR repertoire analyis of class-switched and non-switched thymic B cells

Project description:We report that a large percentage of thymic B cells undergo class switching intrathymically. Thymic B cell class switching requires cognate T-B interaction. To determine whether B cell specificity was also important for thymic B cell class-switching, we sorted class-switched thymic B cells (CD19+B220+IgM-IgD-), unswitched B cells (CD19+B220+IgM+IgD+) and bulk splenic B cells in 3H9 heavy chain-fixed mice and performed high throughput sequencing analysis of the light chain of these populations. Results of this analysis indicated that class-switched thymic B cells have a distinct repertoire compared with unswitched thymic B cells and splenic B cells. Further reactivity tests indicated that a large part of BCRs enriched in class-switched thymic B cells are autoreactive. These data suggest that autoreactive B cells are selected into class-switched population and expanded in the thymus.

2016-08-10 | GSE85366 | GEO

BCR repertoire analyis of class-switched and non-switched thymic B cells

2016-08-10 | E-GEOD-85366 | biostudies-arrayexpress

Two distinct durable human switched memory B cell populations are induced by vaccination and infection

Project description:The traditional definition of memory lymphocytes encompasses antigen-experienced, durable subsets that persist in the absence of antigen and are capable of responding to the antigen on subsequent encounters. We examined the relative durability of eight different non-overlapping class-switched human B cell sub-populations (excluding plasmablasts) that together encompass 100% of all human class switched B cells and identified only two long-lived B cell populations that persist after vaccination in the relative absence of their cognate antigen. In addition to canonical switched memory B cells (SWM) with an IgD- CD27+ CXCR5+ phenotype, a second, non-canonical but distinct memory population of IgD- CD27- CXCR5+ (double negative 1, DN1) B cells is also durable. Beyond surface phenotyping, DN1 memory B cells intriguingly exhibit lower levels of replacement mutations in complementarity determining as well as framework regions of their B cell receptors and have longer CDRH3 sequences relative to canonical SWM B cells. This non-canonical, human memory B cell subset is distinguished by a distinct TP63 driven transcriptional signature that has been linked to extended cell survival and these B cells persist in the circulation at least as long as canonical SWM B cells. Non-canonical human DN1 memory B cells therefore represent a second, distinct, durable, less somatically hypermutated, class-switched human memory B cell subset defined by a unique transcriptomic signature, that likely arises outside germinal centers and may have evolved to preserve immunological breadth.

2025-03-20 | GSE278378 | GEO

Transcriptomic analysis of double-negative B cell subsets in IgG4-related disease

Project description:IgD-CD27- “double negative” (DN) B cells are known to be expanded in the blood in many disease contexts and the IgD-CD27-CXCR5-CD11c+ DN2 B cell subset has been most widely studied in autoimmune diseases. In addition to DN2 B cells, a distinct IgD-CD27-CXCR5-CD11c- DN3 B cell subset accumulates in the blood both in IgG4-related disease, an autoimmune disease in which inflammation and fibrosis can be reversed by B cell depletion, and in severe COVID-19. DN3 B cells, but not DN2 B cells, prominently accumulate in the blood and end-organs of IgG4-related disease.

2023-06-08 | GSE220582 | GEO

ATAC-seq analysis of quiescent human splenic B cell populations

Project description:Memory B cells represent one of the pillar of humoral protection and are found in the circulation and secondary lymphoid organs several decades after initial pathogen or vaccine encounter. The exact cellular and biological mechanisms allowing long-term survival of quiescent cells in such a fluctuating microenvironment remain poorly understood. scRNA-seq analysis of long-lived Vaccinia-specific and total IgG+ memory B cells had helped us identify two subsets of quiescent switched memory B cells in the spleen of adult donors, separated by the expression of CR2(CD21). To better understand the relationship between these two resting splenic memory B cell subsets, we sorted CD21hiCD20hi and CD21intCD20int IgG+ memory B cells from the live IgD-CD27+IgG+CD20+CD3-CD14-CD16- compartment of the spleen of four organ donors, collected between 2015 and 2019. For all donors, both IgG+ memory B cell subsets were sorted alongside naïve B cells (IgD+CD27-CD38-CD24-CD20+CD3-CD14-CD16-). Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on 50000 cells of each sorted population, according to published methods (Buenrostro, Nature Methods, 2013, PMID: 24097267) and sent for library sequencing by Integragen (Evry, France). In parallel, RNA was extracted from remaining cells and sent for library preparation and sequencing by Integragen (Evry, France) (see related accession number).

2022-09-19 | E-MTAB-11625 | biostudies-arrayexpress

RNA-seq analysis of quiescent human splenic B cell populations

Project description:Memory B cells represent one of the pillar of humoral protection and are found in the circulation and secondary lymphoid organs several decades after initial pathogen or vaccine encounter. The exact cellular and biological mechanisms allowing long-term survival of quiescent cells in such a fluctuating microenvironment remain poorly understood. scRNA-seq analysis of long-lived Vaccinia-specific and total IgG+ memory B cells had helped us identify two subsets of quiescent switched memory B cells in the spleen of adult donors, separated by the expression of CR2(CD21). To better understand the relationship between these two resting splenic memory B cell subsets, we sorted CD21hiCD20hi and CD21intCD20int IgG+ memory B cells from the live IgD-CD27+IgG+CD20+CD3-CD14-CD16- compartment of the spleen of four organ donors, collected between 2015 and 2019. For all donors, both IgG+ memory B cell subsets were sorted alongside naïve B cells (IgD+CD27-CD38-CD24-CD20+CD3-CD14-CD16-). Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on 50000 cells of each sorted population, according to published methods (Buenrostro, Nature Methods, 2013, PMID: 24097267) and sent for library sequencing by Integragen (Evry, France) (See linked experiment). RNA was extracted from remaining cells and sent for library preparation and sequencing by Integragen (Evry, France).

2022-09-19 | E-MTAB-11622 | biostudies-arrayexpress

Transcriptome data of B cells in patients with primary Sjögren's syndrome

Project description:We compared subsets of B cells as follows: Bm1 cells; CD38-IgD+, naïve B cells; CD38+IgD+, pre-germinal centre B cells; CD38highIgD+ and memory B cells; CD38±IgD that were collected from patients with primary Sjögren's syndrome. As a result, list of 623 differentially expressed genes was created. We found interferon signature genes and HLA genes were mostly up-regulated in patients compared to healthy controls.

2019-09-03 | GSE135809 | GEO

RNA sequencing of B cell subsets (CD11c hi IgD+ B cells, CD11c hi IgD- B cells, Memory B cells and Naïve B cells) from healthy subjects and subjects with Systemic lupus erythematosus (SLE) or Rheumatoid arthritis (RA)

Project description:CD11c+ B cells (IgD+ and IgD-) are pathogenic B cells expanded in autoimmune disease. The purpose of this study is to identify the pathways unique to IgD+ CD11c B cells and IgD- CD11c B cells.

2018-02-23 | GSE110999 | GEO

Increased CD226 Expression on CD8+ T cells in Patients with Systemic Sclerosis

Project description:Systemic sclerosis (SSc) is an autoimmune disease characterized by vascular damage, and fibrosis of the skin and internal organs. Because activated and oligoclonally expanded CD8+ T cells can be detected in peripheral blood and lung of SSc patients, effector memory CD8+ T cells may play a critical role for organ involvement in SSc; however, the pathogenic functions of effector memory CD8+ T cells remain incompletely understood. Here we performed DNA microarray analysis of the sort-purified effector memory CD8+ T cells from SSc patients and healthy controls, and showed that the expression of genes related to immune response and cell adhesion, including CD226 (also known as DNAX accessory molecule-1, DNAM-1), was significantly altered. Moreover, detailed analysis of CD226 revealed that CD226highCD8+ T cells were increased in SSc patients (mean, 50.7%) compared with healthy controls (32.9%) and were appreciably associated with the severity of skin sclerosis and interstitial lung disease. Further, CD226highCD8+ T cells from SSc patients produced abundant IL-13 and were positively correlated with the cytotoxic capacity of CD8+ T cells against HUVECs. Finally, the neutralization of CD226 impaired IL-13 production and cytolysis against HUVECs. These findings indicate that upregulated CD226 expression on CD8+ T cells reflects disease severity and are involved in SSc pathogenesis via the production of profibrotic IL-13 and endothelial cell injury, and that CD226 may be a useful target in the treatment of SSc. We first purified effector memory CD8+ T cells (CD3+CD8+CD45RO+CD62L+ cells) from peripheral blood by cell sorting and subsequently performed cDNA microarray analysis of the sort-purified effector memory CD8+ T cells from 9 SSc patients and 5 healthy controls.

2014-12-06 | E-GEOD-63903 | biostudies-arrayexpress

CD49f defines a subset of dysfunctional regulatory T cells circulating in the human peripheral blood

Project description:The therapeutic use of regulatory T cells (Tregs) in patients with autoimmune disorders has been hampered by the biological variability of memory Treg populations in the peripheral blood. In this study, we reveal through a combination of quantitative proteomic, multiparametric flow cytometry, RNA-seq data analysis and functional assays, that CD49f is heterogeneously expressed among human Tregs and impacts their immunomodulatory function. High expression of CD49f defines a subset of dysfunctional Tregs in the human blood characterized by a Th17-like phenotype and impaired suppressive capacity. CD49f is similarly distributed between naïve and memory Tregs and impacts the expression of CD39, CTLA-4, FoxP3 and CCR6 specifically in the memory compartment. Accumulation of CD49f high memory Tregs in the blood of ulcerative colitis patients correlates with disease severity. Our results highlight important considerations for Treg immunotherapy design in patients with inflammatory bowel disease which could possibly extend to other autoimmune disorders.

2021-08-06 | PXD022095 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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