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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single cell RNA-seq of sorted Tfh cells from C57BL/6 Foxp3-GFP mice immunized with OVA-IFA and OVA-CpG

ABSTRACT: The aim of the project was the identification of the transcriptional signature of Tfh cells that emerge following immunization with different adjuvants. For this purpose C57Bl/6 mice, bearing a Foxp3-GFP reporter system, were immunized with OVA-IFA or OVA-CpG. At day 11 post-immunization, Foxp3 negative Tfh cells were FACS-sorted from the draining lymph nodes and processed for single cell RNA sequencing.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Saumya Kumar

PROVIDER: E-MTAB-12085 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-seq of Tfh cells from BALB/c and C57Bl/6 mice immunized with OVA-IFA or OVA-CpG

Project description:The aim of the project was the identification of the transcriptional signature of effector T cells and Tfh cells that emerge following immunization with different adjuvants. For this purpose OVA-specific TCR-transgenic cells (from DO11.10 or OT-II mice) were adoptively transferred into congenic BALB/c or C57Bl/6 mice, subsequently immunized with OVA-IFA or OVA-CpG. At day 11, the OVA-specific T effector and Tfh cells were FACS sorted from the draining lymph nodes for RNA sequencing.

2023-04-15 | E-MTAB-12086 | biostudies-arrayexpress

Expression data from BCL6-YFP-positive Tfh cells, BCL6-YFP-negative Tfh cells, non-Tfh cells, and naïve helper T cells.

Project description:We found that a number of Tfh cells downmodulated BCL6 protein after their development, and we sought to compare the gene expression between BCL6-hi Tfh cells and BCL6-low Tfh cells. CD4+ T cells were sorted from immunized and non-immunized mice for RNA extraction and hybridization on Affymetrix microarrays. Bcl6yfp/+ OT-II cells were transferred to congenic recipient mice, and immunized with NP-OVA in CFA subcutaneously. Seven or ten days after immunization, cells were collected from draining lymph nodes, and sorted on FACSAria by the expression of CXCR5, PD-1 and BCL6-YFP. Naive CD4+ T cells were CD4+ CD44lo CD62Lhi cells from unimmunized mice.

2011-06-02 | E-GEOD-24574 | biostudies-arrayexpress

Transcription profiling of mouse Splenic CD4+CXCR5+ T (TFH) cells

Project description:After activation, CD4+ helper T (Th) cells differentiate; into distinct effector subsets. Although chemokine; (C-X-C motif) receptor 5-expressing T follicular; helper (Tfh) cells are important in humoral immunity,; their developmental regulation is unclear. Here we; show that Tfh cells had a distinct gene expression; profile and developed in vivo independently of the; Th1 or Th2 cell lineages. Tfh cell generation was regulated; by ICOS ligand (ICOSL) expressed on B cells; and was dependent on interleukin-21 (IL-21), IL-6,; and signal transducer and activator of transcription; 3. However, unlike Th17 cells, differentiation of Tfh; cells did not require transforming growth factor; b (TGF-b) or Th17-specific orphan nuclear receptors; RORa and RORg in vivo. Finally, naive T cells activated; in vitro in the presence of IL-21 but not; TGF-b signaling preferentially acquired Tfh gene; expression and promoted germinal-center reactions; in vivo. This study thus demonstrates that Tfh is a; distinct Th cell lineage. Experiment Overall Design: Splenic CD4+CXCR5+ T cells were isolated from KLH-immunized mice and restimulated with anti-CD3 for 4 hours before total RNA preparation. Affymetrix gene chips were used to analyze their gene expression.

2008-10-21 | E-GEOD-11924 | biostudies-arrayexpress

Gene expression of T follicular helper (TFH) cells 6 h after ICOS-L blockade

Project description:The maintenance of the TFH phenotype depends on continuous signals via ICOS. For a global assessment of differences in gene expression after interruption of the ICOS pathway a genome wide transcriptome analysis was performed. We used the OT-II adoptive transfer system to isolate antigen-specific TFH cells (day 6 after immunization) after short-term (6 hours) blockade of the ICOS pathway using a monoclonal antibody against ICOS-L. Gene expression profiles of TFH cells with or without ICOS-L blockade. Affymetrix MG 430 2.0 whole genome arrays were performed in duplicates for the control and blockade group (4 arrays in total). To obtain genes significantly regulated upon ICOS L blockade, the expression profiles of TFH cells treated with an isotype control or anti-ICOS-L antibody were compared to each other. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 M-BM-5g cRNA hybridized in duplicates for each of the two groups to the 4 GeneChip arrays: Group1 TFH cells control, Group2 TFH cells ICOS-L blockade.

2015-01-19 | E-GEOD-49314 | biostudies-arrayexpress

Single-cell immune repertoire sequencing of bone marrow plasma cells following infection and immunizations

Project description:We performed single-cell transcriptome and antibody repertoire sequencing of bone marrow plasma cells following protein (OVA and TNFR2) immunizations or infection with high dose LCMV clone 13.

2021-12-01 | E-MTAB-11096 | biostudies-arrayexpress

Single-cell RNA-seq of tumor-infiltrating lymphocytes in metastatic uveal melanoma

Project description:Metastatic uveal melanoma generally responds poorly to immunotherapy. The aim here was to sequence tumor-infiltrating lymphocytes from uveal melanoma metastases to study their phenotypes and T-cell receptor (TCR) clonotypes. We performed paired single-cell transcriptome and TCR sequencing using the 10x Genomics platform of IL2-expanded tumor-infiltrating lymphocytes from 7 liver and 1 subcutaneous metastasis.

2020-03-16 | E-MTAB-8846 | biostudies-arrayexpress

Gene expression in adoptively transferred OT-II cells isolated from mesenteric lymph nodes of control or MHCIIB-/- chimeras 5 days post-immunization with OVA and polyI:C.

Project description:To gain insight into the transcriptional program conferred to Th cells by B cells, we conducted microarray gene expression analyses of adoptively transferred OT-II cells sorted from the mesenteric lymph nodes of bone marrow chimeric control and MHCIIB-/- mice 5 days after immunization with OVA and polyI:C.

2021-11-11 | E-MTAB-11165 | biostudies-arrayexpress

Germinal center T follicular helper cell IL-4 production is dependent on SLAM receptor (CD150)

Project description:CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation. This SuperSeries is composed of the following subset Series: GSE21379: Expression Data from WT and Sh2d1a-/- in vivo follicular helper CD4 T cells (TFH) versus non follicular helper CD4 T cells (non-TFH) GSE21380: Expression Data from in vivo Tfh vs GC Tfh vs non-Tfh Refer to individual Series

2010-04-28 | E-GEOD-21381 | biostudies-arrayexpress

Expression Data from in vivo Tfh vs GC Tfh vs non-Tfh

Project description:CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation. Analysis of in vivo polyclonal GC Tfh vs Tfh vs Non-Tfh eight days after LCMV viral infection. Analysis of in vivo follicular helper CD4 T cells (CXCR5high GL7low), versus germinal center follicular helper CD4 T cells (CXCR5hi GL7hi), versus non-follicular helper CD4 T cells (CXCR5low) eight days after viral infection.

2010-04-28 | E-GEOD-21380 | biostudies-arrayexpress

T cell UTX promotes Tfh-mediated clearance of persistent virus infection

Project description:Epigenetic changes, including histone methylation, control T cell differentiation and memory formation, though the enzymes that mediate these processes are not clear. We show that UTX, a histone H3 lysine 27 (H3K27) demethylase, promotes the generation of T follicular helper (Tfh) cells, a CD4+ T cell subset essential for B cell antibody generation and clearance of chronic viral infections. Mice with T cell specific UTX deletion (UTX TKO mice) had fewer Tfh cells, showed defective germinal center formation, lacked virus-specific IgG production, and were unable to resolve chronic lymphocytic choriomeningitis virus infection. In UTX TKO T cells, decreased expression of IL-6R±, and other Tfh-related loci, was associated with increased H3K27 methylation. Additionally, Turner Syndrome subjects, who are predisposed to chronic ear infections, have reduced UTX expression in immune cells and decreased Tfh frequency. Thus, we identify a critical link between UTX in T cells and immunity to infection. Mice were infected with chronic LCMV and sorted for Tfh on day 21 pi (sorted for: CD4+CXCR5+CD62Llo T cell). ChIP-Seq and RNA-Seq on WT and Utx KO cells.

2015-09-01 | E-GEOD-64969 | biostudies-arrayexpress

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