Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR activation and interference screens decode stimulation responses in primary human T cells [CRISPR]

ABSTRACT: Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. We now report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin 2 and interferon gamma production. Arrayed CRISPRa confirmed key hits and enabled multiplexed secretome characterization, revealing reshaped cytokine responses. Coupling CRISPRa screening with single-cell RNA-seq enabled deep molecular characterization of screen hits, revealing how perturbations tuned T cell activation and promoted cell states characterized by distinct cytokine expression profiles. Together, these screens reveal genes that reprogram critical immune cell functions, which could inform the design of immunotherapies.

ORGANISM(S): unidentified plasmid Homo sapiens

PROVIDER: GSE174255 | GEO | 2021/05/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CRISPR activation and interference screens decode stimulation responses in primary human T cells [Supplemental CRISPR]

Project description:Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. We now report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin 2 and interferon gamma production. Arrayed CRISPRa confirmed key hits and enabled multiplexed secretome characterization, revealing reshaped cytokine responses. Coupling CRISPRa screening with single-cell RNA-seq enabled deep molecular characterization of screen hits, revealing how perturbations tuned T cell activation and promoted cell states characterized by distinct cytokine expression profiles. Together, these screens reveal genes that reprogram critical immune cell functions, which could inform the design of immunotherapies.

2022-02-04 | GSE190846 | GEO

CRISPR activation and interference screens decode stimulation responses in primary human T cells [CRISPRa Perturb-seq]

2022-02-04 | GSE190604 | GEO

CRISPR activation and interference screens decode stimulation responses in primary human T cells [Bulk RNA-seq]

2021-05-13 | GSE174284 | GEO

CRISPR-based epigenome editing screens identify transcriptional and epigenetic regulators of human CD8 T cell function [Sorting-based CRISPR screens]

Project description:All bulk CRISPR based screens CD2 and B2M CRISPRi tiling screens (primary human CD8 T cells), IL2RA CRISPRa tiling screens (Jurkats), CRISPRi/a TF screens (primary human CD8 T cells), and CRISPR TFome KO (primary human T cells)

2023-08-31 | GSE241933 | GEO

Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements

Project description:Pooled CRISPR-Cas9 screens have recently emerged as a powerful method for functionally characterizing regulatory elements in the non-coding genome, but off-target effects in these experiments have not been systematically evaluated. Here, we conducted multiple genome-scale CRISPR screens for essential CTCF loop anchors in the human K562 erythroid cell line. Surprisingly, the primary drivers of apparent ``hits'' in this screen were single guide RNAs (sgRNAs) with low sequence specificity. After removing these confounders, we found that no CTCF loop anchors among the ones we screened are essential for cell growth in culture. We also observed analogous effects in independent non-coding screens densely tiling regulatory elements and genomic neighborhoods near previously known essential genes. Strikingly, we found that low-specificity guides also result in strong confounding growth effects in screens employing epigenetic perturbations that do not cause DNA damage, such as CRISPRi and CRISPRa. Remarkably, the set of confounded guides is distinct for each perturbation mode. Promisingly, strict filtering of CRISPRi libraries using GuideScan-aggregate specificity scores removed these confounded sgRNAs and allowed for the identification of essential enhancers, which we validated extensively. Our stduy presents the first genome-scale functional characterization of CTCF binding sites in the human genome, while also identifying the limitations on and outlining the future prospects for the detailed functional dissection of regulatory elements in the genome using Cas9.

2019-07-01 | GSE131349 | GEO

Genome-wide CRISPR/Cas9 Screens Reveal Shared and Bespoke Mechanisms of Resistance to SHP2 inhibition [CRISPR genomic screen]

Project description:CRISPR/Cas9 screens identified unexpected hits in human AML cell lines whose loss of function causes resistance to SHP2 inhibition

2023-02-20 | GSE218488 | GEO

Genome-wide CRISPR/Cas9 Screens Reveal Shared and Bespoke Mechanisms of Resistance to SHP2 inhibition [CRISPR mini screen]

Project description:CRISPR/Cas9 screens identified unexpected hits in human AML cell lines whose loss of function causes resistance to SHP2 inhibition

2023-02-20 | GSE218489 | GEO

CRISPR activation and interference screens decode stimulation responses in primary human T cells [CRISPRa Perturb-seq]

Project description:CRISPR activation and interference screens decode stimulation responses in primary human T cells [CRISPRa Perturb-seq]

| PRJNA787633 | ENA

Genome-wide CRISPR/Cas9 Screens Reveal Shared and Bespoke Mechanisms of Resistance to SHP2 Inhibition [RNA-seq]

Project description:CRISPR/Cas9 screens identified unexpected hits in human AML cell lines whose loss of function causes resistance to SHP2 inhibition.

2023-02-20 | GSE212231 | GEO

Genome-wide CRISPR-Cas9 screens reveal loss of redundancy between PKMYT1 and WEE1 in Glioblastoma stem-like cells

Project description:To identify new therapeutic targets for Glioblastoma (GBM), we performed genome-wide CRISPR-Cas9 "knockout" (KO) screens in patient-derived GBM stem-like cells (GSCs) and human neural stem/progenitors (NSCs), non-neoplastic stem cell controls, for genes required for their in vitro growth. Surprisingly, the vast majority GSC-lethal hits were found outside of molecular networks commonly altered in GBM and GSCs (e.g., oncogenic drivers). In vitro and in vivo validation of GSC-specific targets revealed several strong hits, including the wee1-like kinase, PKMYT1/Myt1. Mechanistic studies demonstrated that PKMYT1 acts redundantly with WEE1 to inhibit Cyclin B-CDK1 activity via CDK1-Tyr15 phosphorylation and to promote timely completion of mitosis in NSCs. However, in GSCs, this redundancy is lost, likely as a result of oncogenic signaling, causing GBM-specific lethality. A whole-genome CRISPR-Cas9 knockout screens targeting over 18,000 genes using the all-in-one LV-sgRNA:Cas9 platform system were performed using a âshot gunâ approach by transducing 2 GBM patient-derived isolates and 2 human neural stem cell isolates with the pool library (2 biological replicates), and cultures were outgrown for ~3 weeks. The end time point of each screen was compared to day 0 in order to determine which sgRNAs were overrepresented or underrepresented in the population.

2016-02-15 | E-GEOD-70038 | 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