Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR screens identify EXO1 as a therapeutic target for cancers with Fanconi anemia pathway and BRCA1-A complex deficiencies [PM20138]

ABSTRACT: EXO1 is a conserved multi-functional exonuclease that performs roles in mismatch repair, homologous recombination, nucleotide excision repair, translesion DNA synthesis, resection of stalled replication forks and processing of Okazaki fragments. However, EXO1 loss is well tolerated, suggesting the existence of compensatory mechanisms that could be exploited therapeutically in DNA damage repair (DDR) deficient cancers. Using CRISPR screening, we find that EXO1 loss is synthetic lethal with many somatically inactivated DDR genes identified as frequent vulnerabilities in cancers, including Fanconi anemia (FA) pathway and BRCA1-A complex genes. We also identify the spliceosome factor and tumour suppressor ZRSR2 as synthetic lethal with loss of EXO1 and show that ZRSR2-deficient cells are attenuated for FA-pathway activation, exhibiting cisplatin sensitivity and radial chromosome formation, which we attribute to discreet splicing defects that compromise FA pathway genes. Finally, we show that vulnerabilities caused by mutations in FA or ZRSR2 genes depend on the catalytic activity of EXO1 and can be further sensitised in combination with either PARP inhibitors or ionising radiation. Altogether, we establish the rationale for development of EXO1 inhibitors for treatment across a broad spectrum of cancers with distinct DDR vulnerabilities, which are not effectively targeted with current therapeutic approaches.

ORGANISM(S): Homo sapiens

PROVIDER: GSE255664 | GEO | 2025/07/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CRISPR screens identify EXO1 as a therapeutic target for cancers with Fanconi anemia pathway and BRCA1-A complex deficiencies [PM22329]

Project description:EXO1 is a conserved multi-functional exonuclease that performs roles in mismatch repair, homologous recombination, nucleotide excision repair, translesion DNA synthesis, resection of stalled replication forks and processing of Okazaki fragments. However, EXO1 loss is well tolerated, suggesting the existence of compensatory mechanisms that could be exploited therapeutically in DNA damage repair (DDR) deficient cancers. Using CRISPR screening, we find that EXO1 loss is synthetic lethal with many somatically inactivated DDR genes identified as frequent vulnerabilities in cancers, including Fanconi anemia (FA) pathway and BRCA1-A complex genes. We also identify the spliceosome factor and tumour suppressor ZRSR2 as synthetic lethal with loss of EXO1 and show that ZRSR2-deficient cells are attenuated for FA-pathway activation, exhibiting cisplatin sensitivity and radial chromosome formation, which we attribute to discreet splicing defects that compromise FA pathway genes. Finally, we show that vulnerabilities caused by mutations in FA or ZRSR2 genes depend on the catalytic activity of EXO1 and can be further sensitised in combination with either PARP inhibitors or ionising radiation. Altogether, we establish the rationale for development of EXO1 inhibitors for treatment across a broad spectrum of cancers with distinct DDR vulnerabilities, which are not effectively targeted with current therapeutic approaches.

2025-07-11 | GSE255579 | GEO

Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice

Project description:DNA damage response pathways rely extensively on nuclease activity to process DNA intermediates. Exonuclease 1 (EXO1) is a pleiotropic evolutionary conserved DNA exonuclease. In mammals, it is involved in various DNA repair pathways, replication, antibody diversification, and meiosis. But, whether EXO1 facilitates these DNA metabolic processes through its enzymatic or scaffolding functions remains unclear. Here we dissect the contribution of EXO1 enzymatic versus scaffolding activity by comparing Exo1DA/DA mice expressing a proven nuclease-dead mutant form of EXO1 to entirely EXO1-deficient Exo1-/- and EXO1 wild type Exo1+/+ mice. We show that Exo1DA/DA and Exo1-/- mice are compromised in canonical DNA repair processing, suggesting that the EXO1 enzymatic role is important for error-free DNA mismatch and double-strand break repair pathways. However, in non-canonical repair pathways, EXO1 appears to have a more nuanced function. Next-generation sequencing of heavy chain V region in B cells showed the mutation spectra of Exo1DA/DA mice to be intermediate between Exo1+/+ and Exo1-/- mice, suggesting that both catalytic and scaffolding roles of EXO1 are important for somatic hypermutation. Similarly, while overall class switch recombination in Exo1DA/DA and Exo1-/- mice was comparably defective, switch-switch junction analysis suggests that EXO1 might fulfill an additional scaffolding function downstream of class switching. In contrast to Exo1-/- mice that are infertile, meiosis progressed normally in Exo1DA/DA and Exo1+/+ cohorts, indicating that a structural but not the nuclease function of EXO1 is critical for meiosis. However, both Exo1DA/DA and Exo1-/- mice displayed similar mortality and cancer predisposition profiles. Taken together, these data demonstrate that EXO1 has both scaffolding and enzymatic functions in distinct DNA repair processes and suggest a more composite and intricate role for EXO1 in DNA metabolic processes and disease.

2022-07-11 | GSE183344 | GEO

Mechanism of in vivo activation of the MutLgamma-Exo1 complex for meiotic crossover formation

Project description:Programmed DNA double-strand breaks (DSBs) initiate meiotic recombination and their subsequent repair culminates in crossover (CO) formation. COs result from the asymmetric cleavage of double-Holliday junction (dHJ) intermediates, that requires the MutLγ complex together with a non-catalytic function of Exo1, an activity essential for fertility but at risk of generating unwanted chromosome rearrangements. Here we show how crossover formation by MutLγ is activated at the right time and at the right place. MutLγ forms a constitutive complex with Exo1, and in meiotic cells transiently contacts the upstream MutSγ (Msh4-Msh5) heterodimer. MutLγ associates with DSB hotspots at a late step in the recombinational repair, once recombination intermediates have been stabilized and engaged in the crossover repair pathway. MutLγ-Exo1 is recruited to DSB hotspots independently of the polo-like Cdc5 kinase, but to activate dHJ resolution, Cdc5 is recruited to the recombination intermediates and interacts individually with both MutLγ and Exo1, suggesting their direct modification. in vivo, MutLγ occupancy is restrained on recombination intermediates, and genome-wide, MutLγ associates with the vast majority of DSB hotspots, but at a lower frequency in centromeres, consistent with a strategy to reduce at-risk crossover events in these regions, and in late replicating regions. Our data highlight the highly temporally and spatially control of the activity of this constitutive, potentially harmful, nuclease

2019-12-01 | GSE132850 | GEO

Mechanism of in vivo activation of the MutL-Exo1 complex for meiotic crossover formation

Project description:Programmed DNA double-strand breaks (DSBs) initiate meiotic recombination and their subsequent repair culminates in crossover (CO) formation. COs result from the asymmetric cleavage of double-Holliday junction (dHJ) intermediates, that requires the MutLγ endonuclease and a non-catalytic function of Exo1, an activity essential for fertility but at risk of generating unwanted chromosome rearrangements. Here we show how crossover formation by MutLγ is activated at the right time and at the right place. MutLγ forms a constitutive complex with Exo1, and in meiotic cells transiently contacts the upstream MutSγ (Msh4-Msh5) heterodimer. MutLγ associates with DSB hotspots only once recombination intermediates have been stabilized and engaged in the crossover repair pathway. MutLγ-Exo1 is recruited to DSB hotspots independently of the polo-like Cdc5 kinase, but to activate dHJ resolution, Cdc5 is recruited to the recombination intermediates and interacts individually with both MutLγ and Exo1, suggesting their direct modification. in vivo, MutLγ occupancy is restrained on recombination intermediates, and MutLγ associates with the vast majority of DSB hotspots, but at a lower frequency in centromeres, consistent with a strategy to reduce at-risk crossover events in these regions, and in late replicating regions. Our data highlight the tight temporal and spatial control of the activity of this constitutive, potentially harmful, nuclease.

2020-01-15 | GSE133108 | GEO

Kinome profiling of shControl and shFANCA HL60 cells treated with volasertib

Project description:The Fanconi anemia (FA) pathway is a network of proteins critical to the preservation of genomic integrity and the prevention of cancer. FA proteins safeguard the genome by regulating the cell cycle and facilitating error-free repair of DNA damage. Bi-allelic mutation of genes encoding FA pathway proteins causes the cancer predisposition syndrome Fanconi anemia (FA), which is associated with a high incidence of acute myeloid leukemia (AML). Individuals with mono-allelic mutation of a subset FA genes do not develop FA but suffer increased lifetime risk of solid and hematological malignancies. Within the general population, approximately 14% of sporadic AMLs harbor damaging mutations within the FA pathway. Our previous work demonstrated that inhibition of the mitotic kinase PLK1 induced synthetic lethality in cells deficient for FANCA, the gene most frequently lost in FA. This finding corroborates work from others that have identified synthetic lethal interactions between PLK1 and additional FA genes (FANCG, BRCA1, and BRCA2). Together, these findings suggest that FA pathway mutations may serve as biomarkers for sensitivity to PLK1 inhibitors, which have demonstrated therapeutic efficacy in an undefined subset of AML patients. Here, HL60 AML cells were generated with shControl or shFANCA and treated with 10nM volasertib for 24 h prior to kinome profiling.

2024-11-21 | PXD048014 | Pride

Kinome profiling of shControl and shFANCA THP1 cells treated with volasertib

Project description:The Fanconi anemia (FA) pathway is a network of proteins critical to the preservation of genomic integrity and the prevention of cancer. FA proteins safeguard the genome by regulating the cell cycle and facilitating error-free repair of DNA damage. Bi-allelic mutation of genes encoding FA pathway proteins causes the cancer predisposition syndrome Fanconi anemia (FA), which is associated with a high incidence of acute myeloid leukemia (AML). Individuals with mono-allelic mutation of a subset FA genes do not develop FA but suffer increased lifetime risk of solid and hematological malignancies. Within the general population, approximately 14% of sporadic AMLs harbor damaging mutations within the FA pathway. Our previous work demonstrated that inhibition of the mitotic kinase PLK1 induced synthetic lethality in cells deficient for FANCA, the gene most frequently lost in FA. This finding corroborates work from others that have identified synthetic lethal interactions between PLK1 and additional FA genes (FANCG, BRCA1, and BRCA2). Together, these findings suggest that FA pathway mutations may serve as biomarkers for sensitivity to PLK1 inhibitors, which have demonstrated therapeutic efficacy in an undefined subset of AML patients. Here, THP1 AML cells were generated with shControl or shFANCA and treated with 10nM volasertib for 24 h prior to kinome profiling.

2024-11-21 | PXD048057 | Pride

Mapping in silico genetic networks of tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities

Project description:Cancers harbouring loss-of-function (LOF) alterations in tumour suppressor genes lack targeted therapies, thus alternative means to characterise gene function and identify vulnerabilities in these cancer cells are required. Here, we map the in silico genetic networks of KMT2D, a frequently mutated tumour suppressor gene, to demonstrate its utility in uncovering novel functional associations and vulnerabilities in cancer cells with tumour suppressor gene LOF alterations. In silico KMT2D networks revealed associated with histone modification, DNA replication, metabolism, and immune response. We identified synthetic lethal (SL) candidates encoding exising therapeutic targets. Analysing patient data from The Cancer Genome Atlas (TCGA) and the Personalized OncoGenomics Project (NCT021556210), we showed dysregulated pathways associated with SL candidates and elevated immune checkpoint response markers in KMT2DLOF cases, bringing forth evidence supporting KMT2D as a biomarker for immune checkpoint inhibitors. Our study presents a framework for identifying targetable vulnerabilities in cancers with tumour suppressor gene alterations.

2024-10-18 | PXD048272 | Pride

DNA Damage Response Deficiency Enhances Neuroblastoma Progression and Sensitivity to Combination PARP and ATR Inhibition

Project description:Next generation sequencing of neuroblastoma (NB) tumors have revealed frequent somatic and germline genetic alterations in genes encoding proteins involved in DNA damage response (DDR) pathways. Despite being well-studied in many adult cancers, roles for DDR disruption in pediatric solid tumors have not been fully elucidated. To address this, patient-relevant loss-of-function mutations in DDR pathway components including Brca2, Atm, and Palb2 were incorporated into an established zebrafish MYCN transgenic model (Tg(dbh:EGFP-MYCN)). These mutations were found to enhance NB formation and metastasis in vivo, and result in upregulation of proliferation, cell cycle checkpoint and DNA damage repair transcriptional signatures, revealing novel molecular vulnerabilities in DDR-deficient NB. Zebrafish DDR-deficient NB and human NB cells with DDR protein knock-down were sensitive to the poly(ADP-ribose)-polymerase (PARP) inhibitor olaparib, and this effect was further enhanced by inhibition of the ataxia telangiectasia and rad3 related (ATR) kinase. Altogether, our data supports a functional role for DDR-deficiency in NB in vivo and therapeutic potential for combination PARP + ATR inhibition in NB patients with alterations in DDR genes.

2025-02-10 | GSE283976 | GEO

The translational repair pathway is a frequent synthetic lethal target in cancer

Project description:Synthetic lethality exploits the genetic vulnerabilities of cancer cells enabling, a targeted, precision approach to treat cancer. Synthetic lethal discovery approaches have led to clinical successes of PARP inhibitors and the progression of several next-generation therapeutic targets such as WRN, USP1, PKMYT1, POLQ, and PRMT5 into the clinic. To date, however, most discovery efforts in the synthetic lethal space have focused on DNA repair. Here, we show, for the first time in humans, a frequent synthetic lethal interaction between two complexes of the translational repair pathway, PELO/HBS1L and the superkiller (SKI) complex. In distinct genetic contexts, either in 9p21.3 (FOCAD) deleted or MSI-H tumors, we found that phenotypically destabilized SKI complex leads to dependence on the PELO/HBS1L ribosomal rescue complex. We estimate that 20% of all tumors have a destabilized SKI complex. The concomitant loss of PELO in a SKI destabilized tumor drives an unfolded protein stress response, cell cycle arrest, and robust tumor growth inhibition. Furthermore, we demonstrate that the loss of HBS1L phenocopies PELO loss, presenting a second potential therapeutic target within the rescue complex. Our results indicate that PELO/HBS1L represent novel therapeutic targets whose dependence converges upon SKI complex destabilization, a common phenotypic biomarker in diverse genetic contexts and a significant patient population.

2024-10-14 | GSE261804 | GEO

Cyclin F - EXO1 axis controls cell cycle dependent execution of double strand break repair

Project description:Ubiquitination is a crucial post-translational modification required for the proper repair of DNA double-strand breaks (DSBs) induced by ionising radiation (IR). DSBs are mainly repaired through homologous recombination (HR) when template DNA is present and non-homologous end joining (NHEJ) in its absence. Additionally, microhomology-mediated end joining (MMEJ) and single strand annealing (SSA) provide back-up DSBs repair pathways. However, the mechanisms controlling their use remain poorly understood. By employing a high-resolution CRISPR screen of the ubiquitin system after IR, we systematically uncover genes required for cell survival and elucidate a critical role of the E3 ubiquitin ligase SCFcyclin F in cell cycle dependent DSB repair. We show that SCFcyclin F -mediated EXO1 degradation prevents DNA end resection in mitosis, allowing MMEJ to take place. Moreover, we identify a conserved cyclin F recognition motif, distinct from the one used by other cyclins, with broad implications in cyclin specificity for cell cycle control.

2024-10-17 | PXD051841 | Pride

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