Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNAseq of CD19-CAR-T cells generated in presence or absence of vitamin C

ABSTRACT: CD19-CAR-T cells were generated from human primary CD3+ T cells of three donors in presence or absence of vitamin C. RNA was isolated after 24h of co-culture with Nalm-6 cells. Details of experimental design can be found in the M&M section of the manuscript.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER: Agnes Bonifacius

PROVIDER: E-MTAB-15718 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-seq analysis of bone marrow (BM) samples of patients with B-Cell Acute Lymphoblastic Leukemia treated with anti CD19 CAR T cells

Project description:Single-cell RNA sequencing of BM resident immune cells of patients undergoing CAR T-cell infusion and their Infusion Product (IP). Data in this study were generated from a patients enrolled in the FT01CARCIK Phase I/IIb clinical trial (NCT03389035) and two patients treated with autologous commercial CAR T cells (tisagenlecleucel). BM samples have been collected before CAR T treatment (pre) and at early time points (1-2 months) after treatment (post). CD45+CD3+ T cells, and CD45+/lowCD3-, encompassing the hematopoietic immune niche of the TME cells, have been separated by flow cytometry-based cell sorting and compared to cells of the corresponding patient’s BM before CAR T-cell treatment at the moment of relapse. In parallel, CAR T-cell infusion products (IP) have been sorted according to the surface CAR expression. Significance: This study highlights the critical role of the tumor microenvironment on CAR T-cell fate and endogenous immunity in B-cell acute lymphoblastic leukemia. We demonstrate that IFN response, hypoxia, and TGF-b signaling lead to general immune suppression, resulting in endogenous T-cell exhaustion and compromising CAR T-cell efficacy

2025-12-31 | E-MTAB-14549 | biostudies-arrayexpress

Single-cell RNA sequencing and single-cell CRISPR screens of interacting natural killer and blood cancer cells

Project description:To profile the cell states of interacting natural killer (NK) cells and blood cancer cells, we cultured 26 different cell lines representing diverse hematologic neoplasms either alone or with NK cells derived from three healthy human donors. After 24 h co-culture, we labeled the cells from each monoculture or co-culture condition with oligonucleotide-conjugated antibodies against ubiquitously expressed surface proteins (with different oligonucleotide for each mono- or co-culture), enabling multiplexing in the scRNA-seq using the cell hashing method. We additionally performed pooled CRISPR screens with a single-cell transcriptome readout using the CROP-seq platform in blood cancer cells cultured either alone or in the presence of NK cells to study the effects of perturbing genes that influenced sensitivity to NK cell killing in genome-scale CRISPR screens.

2023-07-24 | E-MTAB-13204 | biostudies-arrayexpress

Generation of clinical grade CD19-specific CAR-modified CD8+ memory stem cells for the treatment of B-cell malignancies

Project description:Long-lived, self-renewing, multipotent T memory stem cells (TSCM) can trigger profound and sustained tumor regression but their rareness poses a major hurdle to their clinical application. Presently, clinically compliant procedures to generate relevant numbers of this T cell population are undefined. Here, we provide a strategy for deriving large numbers of clinical grade tumor-redirected TSCM cells starting from naÃ¯ve precursors. CD8+CD62L+CD45RA+ naÃ¯ve T cells enriched by streptamer-based serial positive selection were activated by CD3/CD28 engagement in the presence of IL-7, IL-21 and the glycogen synthase-3Î² inhibitor TWS119, and genetically engineered to express a CD19-specific chimeric antigen receptor (CD19-CAR). These conditions allowed for the generation of CD19-CAR modified TSCM cells that were phenotypically, functionally and transcriptomically equivalent to their naturally occurring counterpart. Compared with T cell products currently under clinical investigation, CD19-CAR modified TSCM cells exhibit enhanced metabolic fitness, persistence and anti-tumor activity against systemic acute lymphoblastic leukemia xenografts. Based on these findings, we have initiated a phase 1 clinical study to evaluate the activity of CD19-CAR modified TSCM in patients with B-cell malignancies refractory to prior allogeneic hematopoietic stem cell transplantation. Three healthy human blood donors provided lymphocyte-enriched apheresis blood for this study after informed consent. From all samples, total RNA was isolated using an miRNeasy Mini Kit (Qiagen), processed by Ambionâ??s WT expression kit, fragmented and labeled with a WT Terminal Labeling Kit (Affymetrix), hybridized to WT Human Gene 1.0 ST arrays (Affymetrix) and stained on a Genechip Fluidics Station 450 (Affymetrix), all according to the respective manufacturer's instructions. Samples represent exon-level and gene-level analyses.

2016-06-29 | E-GEOD-68003 | biostudies-arrayexpress

ScRNA/TCR-seq of T cells from EMT6 tumors treated with aTGFb/aPD-L1

Project description:We performed 10x single cell RNA and VDJ sequencing on sorted T cells (7AAD- Calcein blue+ CD45+ THY1.1- TCRb+) in an orthotopic EMT6 tumor model 7 days after treatment initiation in four experimental groups: 1) Control 2) aPD-L1 3) aTGFb 4) aPD-L1 and aTGFb.

2023-06-30 | E-MTAB-13073 | biostudies-arrayexpress

Single nucleus RNA sequencing of human iPSC-derived forebrain organoids to assay cell type composition

Project description:Human iPSC line D1 was differentiated into spheroids. After 21 weeks in culture, single nucei were extracted and assayed using single nucleus RNA sequencing to characterize the spheroids' cell type composition.

2021-12-01 | E-MTAB-10605 | biostudies-arrayexpress

Placental infection single-cell and single-nuclei maps

Project description:This resource comprises a single-cell multi-lineage map of first trimester infected placental cells. We have included data from both uninfected cells and cells infected with three pathogens known to cause maternal and fetal disorders: Plasmodium falciparum, Listeria monocytogenes, and Toxoplasma gondii. We also generated single-nuclei map of infected trophoblasts and their corresponding controls. Furthermore, we created a single-nuclei reference dataset containing information from uninfected primary placental organoids as well as organoids infected with P. falciparum. Additionally, we conducted sequencing at a single-cell level for P. falciparum parasites that were bound to the placenta (pf_b), parasites unbound to the placenta (pf_nb), and parasites that were cultured in vitro (pf_iv).

2024-03-01 | E-MTAB-12795 | biostudies-arrayexpress

Single-cell RNA-seq of Endometrial Superficial biopsies and full depth uterine tissue from organ donors

Project description:We performed single-cell RNA-sequencing to create a cell census of the human endometrium, which is the mucosal lining of the uterus that undergoes dynamic changes throughout the menstrual cycle. We integrated cells that were obtained from 3 superficial biopsies to selected samples that originated from 2 organ donors; this allowed a better representation of cell type diversity found within the full depth of the endometrium.

2021-07-21 | E-MTAB-10287 | biostudies-arrayexpress

Comparison of different hashing methods on human PBMCs and primary mice tissues

Project description:the aim 1 was to evaluate hashing (sample multiplexing) accuracy of TotalSeq-B antibodies and CellPlex (a multiplexing solution from 10x Genomics) on 2 pools of PBMCs from 3 different donors. Thus the genetic difference between donors was used as a ground truth for sample demultiplexing based on antibody or lipid hashing hashing. the aim 2 was to evaluate TotalSeq antibody and lipid hashing on different mice primary tissues using different hashing protocols.

2022-02-12 | E-MTAB-11401 | biostudies-arrayexpress

CAR T cells inhibit B cell activating phosphorylation in their targets

Project description:Adoptive cell therapy, a subset of cancer immunotherapy, is collection of therapeutic approaches which aim to redirect the immune system by reprogramming patient T-cells to target antigenic molecules differentially and specifically expressed in certain cancers. One promising immunotherapy technique is CAR T-cell therapy, where cancer cells are targeted through the expression a chimeric antigen receptor (CAR), a synthetic trans- membrane receptor that functionally compensates for the T-cell receptor (TCR) but targets a tumor associated antigen on the cancer cell surface. While CAR T-cell therapy is promising with two clinically approved second-generation CARs (Kymriah and Yescarta), few studies have investigated the mechanism of signal propagation in T-cells and no studies have investigated the potential signaling response in the target cells. To gain further insight to CAR-based signaling, we stimulated third generation CD19 CAR-expressing Jurkat T-cells by co-culture with SILAC labeled CD19HI Raji B-cells and used two phosphoenrichment strategies coupled with liquid chromatography-tandem mass spec- trometry (LC-MS/MS) to detect and analyze global phosphorylation changes in both cell populations. Analysis of the phosphopeptides originating from the CD19-CAR T cells revealed an increase in many phosphorylation events necessary for canonical TCR signaling. We also observed for the first time a significant decrease in B-cell receptor- related phosphopeptide abundance in CD19HI Raji B-cells after co-culture with CD19-targetted CAR T-cells.

2022-01-28 | PXD028109 | Pride

Monocyte-derived IL-1 and IL-6 are differentially required for cytokine release syndrome and neurotoxicity by CAR-T cells.

Project description:Single-cell transcriptome profiling using a 3' droplet-based platform (Chromium,10x Genomics) of human CD45+ leukocytes isolated from leukemic HuSGM3 mice infused with CD19.28z CAR-T cells, two days after cytokine release syndrome (CRS) onset and 5 days later.

2018-05-24 | E-MTAB-6505 | biostudies-arrayexpress

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