Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PPP2R1A mutations cause ATR inhibitor synthetic lethality in ARID1A deficient ovarian clear cell carcinoma

ABSTRACT: Ovarian clear cell carcinoma (OCCC) is a cancer of unmet need characterized by ARID1A mutation. Prior work identified an ARID1A/ATR synthetic lethality, information that led to phase II clinical trials. Using genome-wide CRISPR-Cas9 mutagenesis and interference screens, we identified protein phosphatase 2A (PP2A) subunits, including PPP2R1A, as determinants of ATRi sensitivity in ARID1A mutant OCCC. Analysis of an OCCCs cohort indicated that >1/3 possessed both PPP2R1A and ARID1A loss-of-function mutations. CRISPR-prime editing demonstrated that oncogenic PPP2R1A p.R183 missense mutations enhance in vitro and in vivo ATRi sensitivity in ARID1A mutant OCCC. OCCC patients with both ARID1A and PPP2R1A mutations also showed clinical responses to ATRi in a phase II trial. Mechanistically, this synthetic lethal effect is dependent upon WNK1 kinase, which opposes PP2A function. This data suggests that co-occurrence of PPP2R1A and ARID1A mutations in OCCC should be assessed as a biomarker of ATRi response in on-going clinical trials.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Graeme Benstead-Hume

LAB HEAD: Jyoti Choudhary

PROVIDER: PXD040422 | Pride | 2023-05-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20201207_JS_Lord_lab_LMS03_set02_IMAC_01.raw	Raw
	20201207_JS_Lord_lab_LMS03_set02_IMAC_02.raw	Raw
	20201207_JS_Lord_lab_LMS03_set02_IMAC_03.raw	Raw
	20201207_JS_Lord_lab_LMS03_set02_IMAC_04.raw	Raw
	20201207_JS_Lord_lab_LMS03_set02_IMAC_05.raw	Raw

Items per page:

1 - 5 of 106

Similar Datasets

Cancer-associated FBXW7 loss is synthetic lethal with pharmacological targeting of CDC

Project description:The FBXW7 tumour suppressor is commonly mutated, deleted or hypermethylated in a variety of cancer histologies. The tumour suppressive role of the FBXW7 protein has been ascribed to its ability to drive the ubiquitination and degradation of oncoproteins via its role as a substrate recognition subunit of SCF complexes that mediate E3 ubiquitin ligation. Despite this molecular understanding, therapeutic approaches that target tumoural FBXW7 defects do not exist. To identify candidate vulnerabilities put in place by FBXW7 dysfunction, we carried out genome-wide CRISPR-Cas9 screens, focussed RNA interference screens and whole proteome mass spectrometry profiling in multiple FBXW7 wild type and defective isogenic cell systems. These identified candidate FBXW7 synthetic lethal effects, including those involving SCF-related proteins (e.g. CAND1), proteins involved in the response to replication fork stress (ATR, RAD9A and CHEK1) and also proteins involved in replication licencing such as CDC7 and its substrate GINS4. The ATR, CHEK1 and CDC7 synthetic lethal effects were confirmed using drug-like small molecule inhibitors. Integration of proteomic profiling data indicated that FBXW7 defective cells express elevated levels of the replication factor RIF1. Functional experiments showed that FBXW7 vs. CDC7 synthetic lethality is RIF1 dependent and explained by RIF1 being required for CDC7 inhibitor-induced replication fork stalling. The delineation of FBXW7 synthetic lethal effects we describe here could serve as the starting point for subsequent drug discovery and/or development in this area.

2024-06-16 | PXD043904 | Pride

Structural basis for the modulation of MRP2 activity by phosphorylation and drugs

Project description:Chemotherapy resistance by ABC transporters and secondary transporters is well established. Liver cancer is hard to treat by chemotherapy due to the presence of the multidrug resistance-associated protein 2 (MRP2/ABCC2) in addition to other transporters. The activity of MRP2 can be modulated by phosphorylation of its regulatory domain but also by drug-drug interactions. Here, we have determined the cryo-EM structure of MRP2 from Rattus norvegicus in an autoinhibited state (nucleotide-free) and in the presence of the drug modulator probenecid (uricosuric agent). The autoinhibited conformation is caused by the partially phosphorylated regulatory domain that folds within the transmembrane domain. Combining, in vitro phosphorylation of MRP2, mass spectrometry and kinetics, we show that full phosphorylation of the regulatory domain is required to relieve the autoinhibitory state due to steric clashes between the phosphate groups and the transmembrane domain. The drug bound state, has identified two drug binding sites that has allowed us to propose how probenecid modulates the activity of the transporter in addition to drug-drug interactions. Overall, we have structurally characterised the clinically relevant transporter MRP2, and we provide evidence on its modulation by intracellular kinases but also in the presence of external drugs. Finally, we mapped the mutations that cause Dubin–Johnson syndrome onto the structure and gain an understanding on their contribution in MRP2 dysfunction.

2024-02-05 | PXD045845 | Pride

Proteomic characterisation of triple negative breast cancer cells following CDK4/6 inhibition

Project description:CDK4/6 inhibitor, Palbociclib, has shown a high success in breast cancer subtypes however it is often accompanied by a dependency on mutation status of cell lines. Consequently, there has been speculation on the breast cancer subtypes which should be offered treatment with specific CDK4/6 inhibitors and the response that can be expected. A common observation has been the induction of a cell programme known as "senescence" whereby cells experience a complete halt in mitosis, however, remaining metabolically active. Therapy-induced senescence markers and its effect on the tumour microenvironment as well as the diversity of this cell state remain unappreciated. In the following proteomics, phosphoproteomics and secretome datasets we focus on MDA-MB-231 cells, a triple negative cell line, to better understand the senescence-like cell state which arises after treatment. Ultimately, the dataset encompasses the population that arises upon Palbociclib treatment and highlights potential signatures and biomarkers of the cell state which could provide information on the use of CDK4/6 inhibitors in triple negative breast cancer subtypes.

2022-01-28 | PXD030407 | Pride

K562 SF3B1 Mutants and Splicing

Project description:This project containins data for K562 cell line experiments with SF3B1 Mutations

2024-11-20 | PXD030127 | Pride

Gene expression data ARID1A knockdown OE33 cells versus mock OE33 cells

Project description:A nonsense mutation in ARID1A was identified by next generation sequencing in non-dysplastic Barrett's esophagus [BE] tissue and esophageal adenocarcinoma [EAC] tissue of a patient diagnosed with EAC. Immunohistochemistry performed on an independent archival cohort demonstrated ARID1A protein loss in 0% (0/76), 4.9% (2/40), 14.3% (4/28), 16.0% (8/50), and 12.2% (12/98) of normal squamous epithelium, BE, low-, high-grade dysplasia, and EAC tissues, respectively. Enhanced cell growth, proliferation and invasion were observed upon ARID1A knockdown in EAC cells. ARID1A was knocked down in OE33 cells (Sample MS_1 and MS_3) using on-TARGET smartpool ARID1A siRNA. At the same time, OE33 cells were transfected with a non-targeting siRNA, and these experiments (Samples MS_2 and MS_4) functioned as mock controls. Cells were harvested after 48 hours and total RNA was extracted using the Rneasy kit (Qiagen) Aim Affymetrix Human PrimeView Gene Expression Array : to determine the downstream effectors of ARID1A that are likely to contribute to the oncogenic phenotype caused by ARID1A down-regulation. Two biological replicates of each condition (2x ARID1A knockdown, and 2x Mock) were used for the microarray experiment.

2012-05-31 | E-GEOD-38380 | biostudies-arrayexpress

Genomic determinants of protein abundance variation in colorectal cancer cell lines

Project description:Assessing the impact of genomic alterations on protein networks is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labelling to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the functional consequences of somatic genomic variants. The robust quantification of over 9,000 proteins and 11,000 phosphopeptides on average, enabled the de novo construction of a functional protein correlation network which ultimately exposed the collateral effects of mutations on protein complexes. CRISPR-cas9 deletion of key chromatin modifiers confirmed that the consequences of genomic alterations can propagate through protein interactions in a transcript-independent manner. Lastly, we leveraged the quantified proteome to perform unsupervised classification of the cell lines and to build predictive models of drug response in colorectal cancer. Overall, we provide a deep integrative view of the functional network and the molecular structure underlying the heterogeneity of colorectal cancer cells.

2017-08-09 | PXD005235 | Pride

CytoScanHD array Data for 15 normal, 15 primary colorectal carcinomas and their 15 matched liver metastases

Project description:We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss (SCNAs). The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. TP53 mutation was observed in 47% of the primary samples and 67% in liver metastatic samples. The grouped pairs, in hierarchical clustering showed similar SCNA patterns, in contrast to the ungrouped pairs. Many mutations (including those of known key cancer driver genes) were shared in the grouped pairs. The ungrouped pairs exhibited distinct mutation patterns with no shared mutations in key driver genes. Four ungrouped liver metastasis samples had mutations in DNA mismatch repair genes along with hypermutations and a substantial number of copy number of alterations. Genomically, colorectal and metastatic liver tumors were very similar. However, in a subgroup of patients, there were genetic variations in liver metastases in the loss of DNA mismatch repair genes. Copy number analysis of Affymetrix CytoScanHD arrays was performed for 15 primary colorectal carcinoma and 15 samples of their matched liver metastases. 15 normal samples prepared from each of the patient was used as the reference for the study. Nexus Copy number 6.1 software was used for somatic copy number alteration analysis.

2014-03-01 | E-GEOD-53799 | biostudies-arrayexpress

Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer

Project description:Many cell types exhibit remarkable size homogeneity through successive divisions. In both yeast and humans, size homogeneity during division cycles is a result of tight control on the concentration of cell-cycle inhibitors such as WHI5 or RB1 (Retinoblastoma 1) proteins respectively. However, size control is often lost during oncogenesis, correlating with aggression. How size control is affected by mutations which drive proliferation, such as those of the RAS-ERK pathway, or even loss of RB1 itself, is poorly understood. Using quantitative single cell imaging of different melanoma cell lines, we show that melanoma cells exhibit both inter- and intra-line size variability. Integration of imaging with multi-omic data demonstrates that the translation machinery, G2 regulators, inflammatory mediators and growth-regulatory proteins are key determinants of size in melanoma. Theoretical modelling suggests that the cell size of daughter cells is determined by biosynthetic processes and engagement of stress responses in the mother. Biosynthesis and stress in mother cells impacts the synthesis of heritable prodivision factors like Cyclin D1 (CCND1) which control cell progression by inhibiting RB1 in concentration dependent fashions Small cell sizes and uniform populations are driven by robust DNA repair and increased levels of biosynthetic factors which promote CCDN1 accumulation. We propose that increased size and size-heterogeneity in BRAF and NRAS mutated cells is determined by stress or DNA damage in mother’s division cycle that slows cycle progression in the daughters. Such events lead to increased size and senescent-like states. Taken together our data suggest that oncogenic events, such as the dysregulation of MAPK signalling, provide a means to circumvent normal mechanisms of size regulation and increase cell-to-cell variations in size which may drive disease.

2023-01-03 | PXD028339 | Pride

A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant

Project description:Although PARP inhibitors (PARPi) now form part of the standard-of-care for the treatment of homologous recombination defective cancers, de novo and acquired resistance limits their overall effectiveness. Previously, overexpression of the BRCA1-∆11q splice variant has been shown to cause PARPi resistance. How cancer cells achieve increased BRCA1-∆11q expression has remained unclear. Using isogenic cells with different BRCA1 mutations, we show that reduction in HUWE1 leads to increased levels of BRCA1-∆11q and PARPi resistance. This effect is specific to cells able to express BRCA1-∆11q (e.g. BRCA1 exon 11 mutant cells) and is not seen in BRCA1 mutants that cannot express BRCA1-∆11q, nor in BRCA2 mutant cells. As well as increasing levels of BRCA1-∆11q protein in exon 11 mutant cells, HUWE1 silencing also restores RAD51 nuclear foci and platinum salt resistance. HUWE1 catalytic domain mutations were also seen in a case of PARPi resistant, BRCA1 exon 11 mutant, high grade serous ovarian cancer. These results suggest how elevated levels of BRCA1-∆11q and PARPi resistance can be achieved, identify HUWE1 as a candidate biomarker of PARPi resistance for assessment in future clinical trials and illustrate how some PARPi resistance mechanisms may only operate in patients with particular BRCA1 mutations.

2023-07-18 | PXD040430 | Pride

scRNA-seq of mESC and mouse CD4+ cells using different buffers and enzymes

Project description:Existing protocols for full-length single-cell RNA sequencing (scRNA-seq) produce libraries of high complexity (thousands of distinct genes) with outstanding sensitivity and specificity of transcript quantification. These full-length libraries have the advantage of allowing probing of transcript isoforms, are informative regarding single nucleotide polymorphisms, and allow assembly of the VDJ region of the T- and B-cell receptor sequences. Since full length protocols are mostly plate-based at present, they are also suited to profiling cell types where cell numbers are limiting, such as rare cell types during development for instance. A disadvantage of these methods has been the scalability and cost of the experiments, which has limited their popularity as compared to droplet-based and nanowell approaches. Here, we describe an automated protocol for full-length scRNA-seq, including both an in-house automated SMART-seq2 protocol, and a commercial kit-based workflow. We discuss these two protocols in terms of ease-of-use, equipment requirements, running time, cost per sample and sequencing quality. By benchmarking the lysis buffers, reverse transcription enzymes and their combinations, we propose an optimized in-house automated protocol with dramatically reduced cost. These pipelines have been employed successfully for several research projects allied with the Human Cell Atlas initiative (www.humancellatlas.org) and are available on protocols.io.

2020-12-31 | E-MTAB-9345 | 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