Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR knockout screen implicates three genes in lysosome function

ABSTRACT: CRISPR knockout screen implicates three genes in lysosome function

PROVIDER: PRJNA530740 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8842510.fastq.gz	Fastqsanger.gz
	SRR8842511.fastq.gz	Fastqsanger.gz
	SRR8842512.fastq.gz	Fastqsanger.gz
	SRR8842513.fastq.gz	Fastqsanger.gz
	SRR8842514.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

CRISPR knockout screen implicates three genes in lysosome function

Project description:Defective biosynthesis of the phospholipid PI(3,5)P2 underlies neurological disorders characterized by cytoplasmic accumulation of large acidic vacuoles. To identify novel genetic causes of lysosomal vacuolization, we developed an assay for enlargement of the lysosome compartment that is amenable to cell sorting and pooled screens. After calibration on cells lacking FIG4, a known PI(3,5)P2 biosynthetic factor, we carried out a genome-wide knockout screen that captured fifteen genes, including VAC14 which is known to cause endosomal vacuolization. We selected three genes not previously associated with lysosome dysfunction for validation: C10orf35, LRRC8A, and MARCH7. We isolated two clonal knockout cell lines for each gene and confirmed loss of protein expression. The knockout lines contained enlarged acidic vesicles with surface labeling of the endolysosomal marker LAMP2. This assay will be useful for characterizing variants of unknown significance in patients with neuromuscular or lysosomal storage disorders. This genome-wide strategy for identification of genes with lysosomal function can also be adapted for drug screens to identify small molecules that correct vacuolization.

2019-05-01 | GSE129282 | GEO

CRISPR knockout screen implicates three genes in lysosome function.

Project description:Defective biosynthesis of the phospholipid PI(3,5)P2 underlies neurological disorders characterized by cytoplasmic accumulation of large lysosome-derived vacuoles. To identify novel genetic causes of lysosomal vacuolization, we developed an assay for enlargement of the lysosome compartment that is amenable to cell sorting and pooled screens. We first demonstrated that the enlarged vacuoles that accumulate in fibroblasts lacking FIG4, a PI(3,5)P2 biosynthetic factor, have a hyperacidic pH compared to normal cells'. We then carried out a genome-wide knockout screen in human HAP1 cells for accumulation of acidic vesicles by FACS sorting. A pilot screen captured fifteen genes, including VAC14, a previously identified cause of endolysosomal vacuolization. Three genes not previously associated with lysosome dysfunction were selected to validate the screen: C10orf35, LRRC8A, and MARCH7. We analyzed two clonal knockout cell lines for each gene. All of the knockout lines contained enlarged acidic vesicles that were positive for LAMP2, confirming their endolysosomal origin. This assay will be useful in the future for functional evaluation of patient variants in these genes, and for a more extensive genome-wide screen for genes required for endolysosome function. This approach may also be adapted for drug screens to identify small molecules that rescue endolysosomal vacuolization.

| S-EPMC6610096 | biostudies-literature

Three-way combinatorial CRISPR screen for analyzing interactions among druggable targets

Project description:Three-way combinatorial CRISPR screen for analyzing interactions among druggable targets

| PRJNA645143 | ENA

Genome-scale CRISPR knockout screen for a Dengue virus mutant

Project description:Unbiased forward genetic screen to identify host factors for a Dengue virus mutant

2023-06-30 | E-MTAB-11119 | biostudies-arrayexpress

CRISPR screen

Project description:CRISPR screen

2023-04-25 | OEX00023089 | NODE

CRISPR-screen

Project description:CRISPR screen

2025-03-27 | OEX00031362 | NODE

CRISPR-screen

Project description:CRISPR screen

2025-05-29 | OEX00031508 | NODE

Maintenance of neuronal TDP-43 expression requires axonal lysosome transport

Project description:TDP-43 mislocalization and pathology occurs across a range of neurodegenerative diseases, but the pathways that modulate TDP-43 in neurons are not well understood. We generated a Halo-TDP-43 knock-in iPSC line and performed a genome-wide CRISPR interference FACS-based screen to identify modifiers of TDP-43 levels in neurons. A meta-analysis of our screen and publicly available screens identified both specific hits and pathways present across multiple screens, the latter likely responsible for generic protein level maintenance. We identified BORC, a complex required for anterograde lysosome transport, as a specific modifier of TDP-43 protein, but not mRNA, levels in neurons. BORC loss led to longer half-life of TDP-43 and other proteins, suggesting lysosome location is required for proper protein turnover. As such, lysosome location and function are crucial for maintaining TDP-43 protein levels in neurons.

2025-07-01 | GSE299976 | GEO

CRISPR screen for rAAV production implicates genes associated with infection.

Project description:Recombinant adeno-associated virus (rAAV) vectors are an effective and well-established tool in the growing gene therapy field, with five FDA-approved AAV-mediated gene therapies already on the market and numerous more in clinical trials. However, manufacturing rAAV vectors is an expensive, timely, and labor-intensive process that limits the commercial use of AAV-mediated gene therapies. To address this limitation, we screened producer cells for genes that could be targeted to increase rAAV yield. Specifically, we performed a CRISPR-based genome-wide knockout screen in HEK 293 cells using an antibody specific to intact AAV2 capsids coupled with flow cytometry to identify genes that modulate rAAV production. We discovered that the knockout of a group of heparan sulfate biosynthesis genes previously implicated in rAAV infectivity decreased rAAV production. Additionally, we identified several vesicular trafficking proteins for which knockout in HEK 293 cells increased rAAV yields. Our findings provide evidence that host proteins associated with viral infection may have also been co-opted for viral assembly and that the genetic makeup of viral producer cells can be manipulated to increase particle yield.

| S-EPMC11429925 | biostudies-literature

Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [scCRISPR screen]

Project description:Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [scCRISPR screen]

| PRJNA1086393 | ENA

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