Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell transcriptomics of Cxcl13+ LN stromal cells

ABSTRACT: Purpose: The goal of this study is to characterise the follicular dendritic cells (FDCs) upon antigen-immunocomplex immunisation. Methods: FACS sorting of Live/Death- Podoplanin+ CD31- CD45- CXCL13-TdTomato+ after LN disgregation of CXCL13-CreTdTomato mice. Mice has been previously immunised with antigen-Ics at different time-points. Cells were loaded into 10x Genomics Chromium Platform, and sequenced using Illumina HiSeq 4000. Conclusions: Our study detects previously identified stromal cell populations and shows the heterogeneity present on the FDCs. We detect 3 different FDC clusters.

ORGANISM(S): Mus musculus

PROVIDER: GSE213254 | GEO | 2023/06/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Distinctive Histogenesis and Immunological Microenvironment Based on Transcriptional Profiles of Follicular Dendritic Cell Sarcomas

Project description:Follicular dendritic cell (FDC) sarcomas are rare mesenchymal tumours (MTs) with variable clinical, morphologic and phenotypic characteristics. We investigated the transcriptome of 29 FDC sarcomas and compared it with that of other MTs, microdissected Castleman FDCs, and normal fibroblasts. On unsupervised analysis, FDC sarcoma clustered with microdissected FDCs, distinct from other MTs and fibroblasts. The specific endowment of FDC-related programs in FDC sarcomas emerged by applying a gene signature consisting of 1,289 genes differentially expressed between microdissected FDCs and fibroblasts. Supervised analysis comparing FDC sarcomas with microdissected FDCs and other MTs identified 370 and 2,927 differentially expressed transcripts, respectively, which pathway enrichment analysis mainly ascribed to signal transduction, chromatin organization, and extracellular matrix organization programs. Since the transcriptome of FDC sarcomas retained similarity with that of FDCs, we investigated the immune landscape of FDC sarcoma by applying the CIBERSORT analysis to FDC sarcomas and non-FDC MTs, and demonstrated that FDC sarcomas were enriched in TFH and TREG populations, as confirmed in situ by immunohistochemistry. The enrichment in specific T-cell subsets prompted investigating the mRNA expression of the inhibitory immune receptor PD-1 and of its ligands PD-L1 and PD-L2, which were found to be significantly more expressed in FDC sarcomas as compared with other MTs, a finding also confirmed in situ. We demonstrated for the first time the transcriptional relationship of FDC sarcomas with non-malignant FDCs and their distinction from other MTs. Furthermore, we provided evidence of a peculiar immunological microenvironment associated with FDC sarcomas.

2017-04-07 | GSE90592 | GEO

Expression data from murine follicular dendritic cells

Project description:Germinal centers (GCs) are clusters of activated B cells built on stromal cells known as follicular dendritic cells (FDCs). In the Peyerâs patches (PPs), GCs are chronically induced by bacteria and are the major sites for generation of gut IgA immune responses. Whether FDCs directly contribute to the IgA production in PP GCs is unknown. To investigate the role FDCs in gut immune system, we examined comprehensive gene profiles of FDCs purified from PPs or perypheral lymph nodes (pLNs) with or without immunization. We also tried to reconstitute the PP FDC signature in vitro by pulsed or continuous stimulation of pLN FDCs through TLRs, RARs or simultaneously through TLRs and RARs. The number of samples is as follows; ex vivo naÃ¯ve pLN FDC=3, ex vivo immunized pLN FDC=2, ex vivo PP FDCs=3, in vitro without stimulation=2, in vitro with LPS stimulation for 5 hours=1, in vitro with LPS stimulation for 72h=1, in vitro with Pam2CSK4 (Pam) stimulation for 96h=2, in vitro with retinoic acid(RA) stimulation for 96h=2,in vitro with RA+Pam stimulation for 96h=2. In addition, ex vivo FDCs with or without immunizations were compared (3 samples), or in vitro cultured FDCs with or without various stimulations were compared (6 samples)

2010-07-30 | E-GEOD-19401 | biostudies-arrayexpress

Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells [Affymetrix]

Project description:Stromal-derived follicular dendritic cells (FDCs) are essential for germinal centers (GCs), the site where B cells maturate their antibodies. FDCs present native antigen to B cells and maintain a CXCL13 gradient to form the B cell follicle. Yet despite their essential role, the transcriptome of human FDCs remains undefined. Using single-cell RNA sequencing and microarray, we provided the transcriptome of these enigmatic cells as a comprehensive resource. Key genes were validated by flow cytometry and microscopy. Surprisingly, marginal reticular cells (MRCs) rather than FDCs expressed B cell activating factor (BAFF). Furthermore, we found that human FDCs expressed TLR4 and can alter antigen availability in response to pathogen-associated molecular patterns (PAMPs). High expression of PD-L1 and PD-L2 on FDCs activated PD1 on T cells. In addition, we found expression of genes related to T cell regulation, such as HLA-DR, CD40, and others. These data suggest intimate contact between human FDCs and T cells.

2021-08-17 | GSE178271 | GEO

Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells [scRNA-seq]

2021-08-17 | GSE173539 | GEO

Single-cell transcriptomics of Cxcl13+ LN stromal cells

Project description:Single-cell transcriptomics of Cxcl13+ LN stromal cells

| PRJNA880277 | ENA

Transcription profiling of mouse primary splenocytes enriched or depleted of follicular dendritic cells to study the events leading to maturation of follicular dendritic cells and lymphoid germinal centers.

Project description:Comparison of follicular dendritic cell-enriched versus -depleted splenocytes. Affinity maturation and Ab class switches occur in lymphoid germinal centers (GCs), in which differentiation and maintenance depend on lymphotoxin (LT) signaling and include differentiation of follicular dendritic cells (FDCs). The events leading to FDC and GC maturation are poorly defined. Using several approaches of functional genomics, we enumerated transcripts affected in mice by suppressing LT receptor (LTR) signaling and/or overrepresented in FDC-enriched GC isolates. Protein expression analysis of 3 of 12 genes both enriched in FDCs and down-regulated by LTR signaling suppression validated them as FDC markers. Functional analysis of one of these three, clusterin, suggests a role as an FDC-derived trophic factor for GC B cells. Hence, the set of genes presented in this study includes markers emanating from LTR signaling and transcripts relevant to GC and FDC function.

2007-09-21 | E-GEOD-2123 | biostudies-arrayexpress

Expression data from murine follicular dendritic cells

Project description:Germinal centers (GCs) are clusters of activated B cells built on stromal cells known as follicular dendritic cells (FDCs). In the Peyer’s patches (PPs), GCs are chronically induced by bacteria and are the major sites for generation of gut IgA immune responses. Whether FDCs directly contribute to the IgA production in PP GCs is unknown. To investigate the role FDCs in gut immune system, we examined comprehensive gene profiles of FDCs purified from PPs or perypheral lymph nodes (pLNs) with or without immunization. We also tried to reconstitute the PP FDC signature in vitro by pulsed or continuous stimulation of pLN FDCs through TLRs, RARs or simultaneously through TLRs and RARs.

2010-07-05 | GSE19401 | GEO

Using ATAC-Seq to investigate the impact of vaccination on the epigenome

Project description:We used a mouse model to investigate whether live (BCG) and non-live (DTPw) vaccines differentially reprogram trained immune responses and to investigate whether immunisation with DTPw altered susceptibility to sepsis. We found that compared to BCG-immunised mice, DTPw immunisation led to altered monocyte and dendritic cell (DC) cytokine responses to subsequent secondary stimuli, as well as genome-wide changes to chromatin accessibility in DCs. These effects were evident months after immunisation and are consistent with different programs of trained immunity being induced by live versus non-live vaccines.

2021-07-20 | GSE162872 | GEO

miRNA expression profiling divides follicular dendritic cell sarcomas into two groups, related to fibroblasts and myopericytomas or Castleman's disease

Project description:miRNA expression profiling divides 31 follicular dendritic cell (FDC) sarcomas into two subgroups, one group closely related to microdissected FDCs from Castleman´s disease, the other group closely related to fibroblasts and myopericytomas. miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

2017-06-21 | GSE83994 | GEO

Interferon subverts an AHR-JUN axis to promote CXCL13+ T cells in lupus

Project description:SLE is prototypical autoimmune disease driven by pathologic T cell-B cell interactions. Expansion of B cell-helper T cells including T follicular helper (Tfh) and T peripheral helper (Tph) cells is a prominent feature of systemic lupus erythematosus (SLE). Human Tfh and Tph cells characteristically produce high levels of the B cell chemoattractant CXCL13, yet regulation of T cell CXCL13 production and the relationship between CXCL13+ T cells and other T cell states remains unclear. Here, we identify an imbalance in CD4 T cell phenotypes in SLE patients, with expansion of PD-1+/ICOS+ CXCL13+ T cells and reduction of CD96hi IL-22+ T cells. Using CRISPR screens, we identify the aryl hydrocarbon receptor (AHR) as a potent negative regulator of CXCL13 production by human CD4 T cells. Transcriptomic, epigenetic, and functional studies demonstrate that AHR coordinates with AP-1 family member JUN to prevent CXCL13+ Tph/Tfh cell differentiation and promote an IL-22+ phenotype. Type I interferon (IFN), a pathogenic driver of SLE, opposes AHR and JUN to promote T cell production of CXCL13. These results place CXCL13+ Tph/Tfh cells on a polarization axis opposite from Th22 cells and reveal AHR, JUN, and IFN as key regulators of these divergent T cell states.

2024-07-08 | GSE233050 | GEO

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