Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profile of CD8+ circulating tumor-reactive lymphocytes (CTRL) isolated by MHC multimers

ABSTRACT: Transcriptomic profile of CD8+ circulating tumor-reactive lymphocytes (CTRL) isolated by MHC multimers

PROVIDER: PRJNA944679 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Transcriptomic profile of CD8+ circulating tumor-reactive lymphocytes (CTRL) isolated by MHC multimers

Project description:Circulating tumor-reactive lymphocytes (CTRL) present in blood circulation at a very low frequency. We efficiently isolated them based on high-performance microfluidics and MHC multimer binding assay. Using an ultra-low input bulk RNAseq workflow, we systematically characterize the transcriptomic profile of tumor-reactive lymphocytes and identified novel biomarkers for multimer-free isolation. Two animal models were studied - B16 melanoma model and CT-26 colon cancer model.

2023-04-09 | GSE227345 | GEO

DNA accessibility in reactive and non-reactive CMV specific CD8+ lymphocytes

Project description:Poor immune reconstitution following haematopoietic stem cell transplantation (HSCT) can cause unwanted and harmful sequelae in recipients with chronic cytomegalovirus (CMV) infection. To understand the molecular mechanisms underlying poor reconstitution, we profiled the transcriptome-chromatin accessibility landscape of CMV-specific CD8+ memory lymphocytes from HCST recipients with different reconstitution efficiencies. Although the transcriptional and epigenomic signatures in non-reactive lymphocytes were not naïve or classic ‘exhaustion’ profiles, some gene expression was common to lymphocytes from other non-resolving infections. Reactive lymphocytes expressed higher levels of interferon/defence response and cell cycle genes in an interconnected network involving PI3KCG, STAT5B, NFAT, RBPJ, and NR3C1, increasing chromatin accessibility at the enhancer regions of immune and T cell receptor signalling pathway genes. We propose that increased HDAC6 expression in non-reactive lymphocytes decreases accessibility at particular enhancers including PI3KCG. Non-reactive cells also expressed higher levels of EGR and KLF factors that, along with lower expression of JARID2, maintained higher accessibility at promoter and CpG-rich regions of genes associated with apoptosis. Together, transcription factors and chromatin modulators create a different chromatin accessibility landscape in reactive and non-reactive cells that not only affects immediate gene expression but differentially primes the cells for responses to additional signals.

2018-04-09 | GSE104750 | GEO

DNA accessibility in reactive and non-reactive CMV specific CD8+ lymphocytes

Project description:DNA accessibility in reactive and non-reactive CMV specific CD8+ lymphocytes

| PRJNA413763 | ENA

Single-cell ATAC sequencing of SIINFEKL-reactive T cells in GL261 murine brain tumors in MHC class II deficient tumor-mircoenvironments

Project description:Single cell ATAC sequencing of SIINFEKL-reactive immune cell from intracranial murine GL261-SIINFEKL tumors 20 days after inoculation. SIINFEKL-reactive T cells were sorted based on dextramer staining. We show that loss of major histocompatibility complex (MHC) class II (MHCII)-restricted antigen presentation on bbm drives dysfunctional intratumoral tumor-reactive CD8+ T cell states through increased chromatin accessibility and expression of Tox, a critical regulator of T cell exhaustion.

2023-01-11 | E-MTAB-12512 | biostudies-arrayexpress

Transcriptional Reprogramming of Mature CD4 T helper Cells generates distinct MHC class II restricted Cytotoxic T Lymphocytes

Project description:We show here that the T helper-fate is not fixed and that mature antigen-stimulated CD4 T cells can switch off Thpok expression and reactivate CD8- lineage genes. This unexpected plasticity results in the post-thymic termination of the T helper- program and the functional differentiation of distinct MHC class II restricted CD4 cytotoxic T lymphocytes Small intestine CD4 intraepithelial T lymphocytes from ThPOK-GFP reposter mice were isolated and sorted (FACS Aria) based on ThPOK and CD8aa expression. Cell were isolated either from non-experimental ThPOK-GFP reporter mice (WT) or after transfering CD4 naive T cells from ThPOK-GFP reporter mice to RAG-/-recipient animals (TR) as an experimental colitis model. Experimet was done in duplicate.

2012-12-10 | E-GEOD-42277 | biostudies-arrayexpress

Transcriptional Reprogramming of Mature CD4 T helper Cells generates distinct MHC class II restricted Cytotoxic T Lymphocytes

2012-12-10 | GSE42277 | GEO

Single cell analysis of circulating B lymphocytes and myocardial B lymphocytes in naïve C57/B6 mice

Project description:Single cell analysis of circulating B lymphocytes and myocardial B lymphocytes in naïve C57/B6 mice

| PRJNA597288 | ENA

CD8+ T lymphocytes in hypopigmented mycosis fungoides: malignant cells or reactive clone?

Project description:CD8+ T lymphocytes in hypopigmented mycosis fungoides: malignant cells or reactive clone?

| PRJNA874095 | ENA

Transcriptional profiling of paired ccRCC patient CD8+ and CD19+ lymphocytes isolated from tumors, normal tissues, and circulating peripheral blood

Project description:Tumor infiltrating lymphocytes are widely associated with positive outcomes, but are still markers of a systemic failed immune response against unresolved cancer. Cancer immunotherapies can reverse their tolerance phenotypes, while preserving tumor-reactivity and neoantigen-specificity shared with circulating immune cells. We performed comprehensive transcriptomic analyses to identify gene signatures common to circulating and tumor infiltrating lymphocytes in the context of clear cell renal cell carcinoma. Modulated genes also associated with disease outcome were validated in other cancer types. Using bioinformatics we identified practical diagnostic markers and actionable targets of the failed immune response. On circulating lymphocytes, three genes could efficiently stratify patients from healthy control donors. From their associations with resistance to cancer immunotherapies as well as viral and bacterial infections, we have uncovered not only pan-cancer, but pan-pathology failed immune response gene signatures.

2020-10-17 | GSE117230 | GEO

Single cell analysis of circulating B lymphocytes and myocardial B lymphocytes in naïve C57/B6 mice

Project description:Perfused naïve murine hearts harbor a sizeable population of B lymphocytes. In order to assess any differences between "myocardial" B cells and circulating B cells we FACS sorted B cells collected from the peripheral blood via cheek bleed and B cells isoalted from the heart after enzymatic digestion. CD45+, CD19+, Aqua- cells were facs sorted into PBS - with 0.04% BSA and processed for single cell RNA sequencing. Peripheral blood was colelcted immediately prior to sacrificing mice in a CO2 chamber. the blood and heart of 3 10 weeks old female mice was pooled together prior to FACS sorting.

2019-12-24 | GSE142515 | 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