Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide CRISPR Knockout Screen in HAP1 MTHFD1-K56R cells to identify genes which confer to resistance to adenosine toxicity

ABSTRACT: This dataset contains sequencing data from a pooled CRISPR knockout screen performed in HAP1 MTHFD1K56R (i.e. harbouring a K56R mutation in MTHFD1) cells. Cells were transduced with a lentiviral genome-wide sgRNA knockout library (Brunello, Addgene #73179) followed by puromycin selection. The screen was then performed in IMDM medium with dialysed FBS supplemented with 50µM adenosine (ADE). Under these conditions, HAP1 MTHFD1K56R usually die. Dialysed medium (DIA) was used as control conditions. Cells were expanded for 14 days and surviving cells were collected for subsequent sequencing analyses. The screen aimed to identify genes whose loss would confer to adenosine resistance in HAP1 MTHFD1-K56R cells. Sequencing was performed to identify sgRNA abundances between adenosine treatment and control. Data was analyzed using PinAPL-Py.

ORGANISM(S): Homo sapiens

PROVIDER: GSE306775 | GEO | 2025/11/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

BFP pulldown of BFP-NUDT5 HAP1 MTHFD1-K56R cells

Project description:We performed BFP pulldowns with BFP-tagged NUDT5 in HAP1 harboring the MTHFD1 K56R mutation to find interactors of NUDT5. We performed the study under various medium conditions, including full IMDM medium (FULL), IMDM with dialysed FBS (DIA) and DIA supplemented with 50µM adenosine to investigate potential changes of interactors upon different medium conditions. Additionally, we performed Pulldowns with a catalytic inactive NUDT5 variant (E112Q), to check whether its catalytic activity has an influence in the interactome. As a control, we used HAP1 MTHFD1 K56R NUDT5 KO cells. Experiments were performed in duplicates

2025-11-07 | PXD067739 | Pride

Effect of adenosine treatment on HAP1 cells with a knockout of MTHFD1

Project description:Folate metabolism provides the building blocks of many classes of biomolecules including purine nucleotides, thymidylate, serine and methionine and is an important target of antimetabolite drugs. A central enzyme in the pathway is the trifunctional MTHFD1, that catalyzes the interconversion of folates by its formyltetrahydrofolate synthetase and methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase domains. Here, we employ large-scale chemical and genome-wide genetic screens to investigate the chemical and genetic dependencies caused by MTHFD1 loss-of-function and uncover a central role of the enzyme in balancing the response to extracellular adenosine. We show that adenosine is essential in MTHFD1KO cells, where adenine-containing compounds counter AMPK activation and increase proliferation in a PARP8, ATF7 and PML-dependent manner. In contrast, adenosine supplementation causes strong toxicity in patient-derived MTHFD1-derived cells harboring dehydrogenase/cyclohydrolase domain mutations. This response, mediated by replication stress and activation of the DNA damage response, is dependent on the nucleotide salvage enzyme HRPT1 and on NUDT5, an enzyme involved in nuclear ATP generation. Our findings suggest an evolutionary rationale for integrating three distinct enzymatic activities within the single MTHFD1 protein and propose the application of dehydrogenase/cyclohydrolase inhibitors in tumors located in an adenosine-rich microenvironment.

2023-04-26 | GSE201334 | GEO

Effect of adenosine treatment on HAP1 cells with a knockout of MTHFD1

Project description:Effect of adenosine treatment on HAP1 cells with a knockout of MTHFD1

| PRJNA830886 | ENA

Mthfd1 is a modifier of intestinal carcinogenesis

Project description:The metabolic pathways that underlie the association between folate deficiency and increased risk for colorectal cancer (CRC) remain unclear. We have studied the effect of C1THF synthase (encoded by the Mthfd1 gene) and dietary folate and choline on intestinal tumor development in Apcmin/+ mice and azoxymethane (AOM)-induced colon cancer in mice. Mthfd1 deficiency did not alter tumor number or load in Apcmin/+ mice, but did result in a decreased incidence of colon tumors. Conversely, Mthfd1 deficiency increased tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. Here we tested colons isolated from wildtype and Mthfd1-deficient animals for alterations in gene expression. Keywords: genetic modification RNA was isolated from proximal colons of MTHFD heterozygous and wild-type mice raised on a control diet. Three colon samples were isolated from each genotype to provide biological replication.

2010-03-20 | E-GEOD-15419 | biostudies-arrayexpress

MTHFD1 controls DNA methylation in Arabidopsis

Project description:In order to further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. We identified the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me, and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1.

2016-06-07 | GSE77966 | GEO

Mthfd1 is a modifier of intestinal carcinogenesis

2010-03-20 | GSE15419 | GEO

Genome-wide CRISPR Knockout Screen in HAP1 MTHFD1-K56R cells to identify genes which confer to resistance to adenosine toxicity

Project description:Genome-wide CRISPR Knockout Screen in HAP1 MTHFD1-K56R cells to identify genes which confer to resistance to adenosine toxicity

| PRJNA1312086 | ENA

MTHFD1 links folate metabolism to BRD4-mediated transcriptional regulation

Project description:The histone acetyl-reader BRD4 is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for functional regulators and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1. We show that a fraction of MTHFD1 resides in the nucleus, where it is recruited to distinct genomic loci by direct interaction with BRD4. Inhibition of either BRD4 or MTHFD1 results in similar changes in nuclear metabolite composition and gene expression, and pharmacologic inhibitors of the two pathways synergize to impair cancer cell viability in vitro and in vivo. Our finding that MTHFD1 and other metabolic enzymes are chromatin-associated suggests a direct role for nuclear metabolism in the control of gene expression.

2019-04-04 | GSE105786 | GEO

Murine MTHFD1-synthetase deficiency, a model for the human MTHFD1 R653Q polymorphism, decreases tumor growth in males

Project description:[Abstract] The R653Q variant in the synthetase domain of the folate-metabolizing enzyme MTHFD1 has been shown to increase risk for birth defects, but it does not affect risk for development of colorectal cancer (CRC). However, since we have shown that this variant reduces purine synthesis, the goal of this study was to determine whether it could affect tumor growth. Using our mouse model for MTHFD1-synthetase deficiency (Mthfd1S+/-), we induced tumor formation with azoxymethane (AOM) and dextran sodium sulfate (DSS) in male and female wild-type and Mthfd1S+/- mice. Tumor size was significantly smaller due to mutant genotype, particularly in males. Tumor size was increased in female mice compared with males, regardless of genotype. Tumor number was not influenced by genotype and was lower in females. Inflammation within tumors of male Mthfd1S+/- mice was lower than in wild-type mice. Proliferation of mouse embryonic fibroblasts from mutant lines was slower than that in wild-type fibroblasts. Gene expression analysis in tumor adjacent normal (preneoplastic) tissue identified several genes involved in proliferation (Fosb, Fos, Ptk6, Esr2, Atf3) or inflammation (Atf3, Saa1, TNF-α) that were downregulated in mutant male mice. Female mutants did not have changes in expression for those genes, nor in tumor inflammation levels, compared with wild-type, suggesting a different mechanism directing tumor growth in females. We suggest that restriction of purine synthesis and reduced expression of critical tumor-promoting genes leads to slower tumor growth in MTHFD1-synthetase deficiency. These findings may have implications for CRC tumor growth and prognosis in individuals with the R653Q variant.

2017-03-01 | GSE77931 | GEO

Genome-scale CRISPR-Cas9 screen of OVCAR3 and CCL218 cancer cells with or without hydroxychloroquine

Project description:A Brunello CRISPR-Cas9 library screen was performed with OVCAR3 and CCL218 cells in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After each pulse-chase, a pool of cells were collected for sgRNA quantitation. Three pulse chases were performed. Cell pellets were processed for genomic DNA and sgRNA sequences amplified by PCR for NGS-based quantitation. Once quantified by NGS analysis, MAGeCK MLE analysis was performed to determine which sgRNAs were most associated with resistance or sensitization to hydroxychloroquine.

2024-03-18 | GSE245215 | 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