scholarly journals Integration of pathway, cellular and genetic context reveals principles of synthetic lethality that affect reproducibility

2019 ◽  
Author(s):  
Angel A. Ku ◽  
Sameera Kongara ◽  
Hsien-Ming Hu ◽  
Xin Zhao ◽  
Di Wu ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Synthetic Lethal ◽  
Testing Framework ◽  
Gene Level ◽  
Cancer Mutations ◽  
Experimental Approaches ◽  
Interaction Map ◽  
Mutant Cells ◽  
Genetic Context

ABSTRACTSynthetic lethal screens have the potential to identify new vulnerabilities incurred by specific cancer mutations but have been hindered by lack of agreement between studies. Using KRAS as a model, we identified that published synthetic lethal screens significantly overlap at the pathway rather than gene level. Analysis of pathways encoded as protein networks identified synthetic lethal candidates that were more reproducible than those previously reported. Lack of overlap likely stems from biological rather than technical limitations as most synthetic lethal phenotypes were strongly modulated by changes in cellular conditions or genetic context, the latter determined using a pairwise genetic interaction map that identified numerous interactions that suppress synthetic lethal effects. Accounting for pathway, cellular and genetic context nominates a DNA repair dependency in KRAS-mutant cells, mediated by a network containing BRCA1. We provide evidence for why most reported synthetic lethals are not reproducible which is addressable using a multi-faceted testing framework.STATEMENT OF SIGNIFICANCESynthetic lethal screens have the power to identify new targets in cancer, although have thus far come up short of expectation. We use computational and experimental approaches to delineate principles for identifying robust synthetic lethal targets that could aid in the development of effective new therapeutic strategies for genetically defined cancers.

A Screen for Dynein Synthetic Lethals in Aspergillus nidulans Identifies Spindle Assembly Checkpoint Genes and Other Genes Involved in Mitosis

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 101-116
Author(s):  
Vladimir P Efimov ◽  
N Ronald Morris
Keyword(s):  
Aspergillus Nidulans ◽  
Spindle Assembly Checkpoint ◽  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Spindle Assembly ◽  
Nuclear Migration ◽  
Cytoplasmic Dynein ◽  
Vesicle Transport ◽  
Synthetic Lethal ◽  
Checkpoint Genes

Abstract Cytoplasmic dynein is a ubiquitously expressed microtubule motor involved in vesicle transport, mitosis, nuclear migration, and spindle orientation. In the filamentous fungus Aspergillus nidulans, inactivation of cytoplasmic dynein, although not lethal, severely impairs nuclear migration. The role of dynein in mitosis and vesicle transport in this organism is unclear. To investigate the complete range of dynein function in A. nidulans, we searched for synthetic lethal mutations that significantly reduced growth in the absence of dynein but had little effect on their own. We isolated 19 sld (synthetic lethality without dynein) mutations in nine different genes. Mutations in two genes exacerbate the nuclear migration defect seen in the absence of dynein. Mutations in six other genes, including sldA and sldB, show a strong synthetic lethal interaction with a mutation in the mitotic kinesin bimC and, thus, are likely to play a role in mitosis. Mutations in sldA and sldB also confer hypersensitivity to the microtubule-destabilizing drug benomyl. sldA and sldB were cloned by complementation of their mutant phenotypes using an A. nidulans autonomously replicating vector. Sequencing revealed homology to the spindle assembly checkpoint genes BUB1 and BUB3 from Saccharomyces cerevisiae. Genetic interaction between dynein and spindle assembly checkpoint genes, as well as other mitotic genes, indicates that A. nidulans dynein plays a role in mitosis. We suggest a model for dynein motor action in A. nidulans that can explain dynein involvement in both mitosis and nuclear distribution.

scholarly journals Cohesin mutations are synthetic lethal with stimulation of WNT signaling

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Chue Vin Chin ◽  
Jisha Antony ◽  
Sarada Ketharnathan ◽  
Anastasia Labudina ◽  
Gregory Gimenez ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Therapeutic Strategy ◽  
Synthetic Lethality ◽  
Mcf10a Cell ◽  
Synthetic Lethal ◽  
Deletion Mutations ◽  
Damage Repair ◽  
Genes Encoding ◽  
Mutant Cells ◽  
Gsk3 Inhibitor

Mutations in genes encoding subunits of the cohesin complex are common in several cancers, but may also expose druggable vulnerabilities. We generated isogenic MCF10A cell lines with deletion mutations of genes encoding cohesin subunits SMC3, RAD21, and STAG2 and screened for synthetic lethality with 3009 FDA-approved compounds. The screen identified several compounds that interfere with transcription, DNA damage repair and the cell cycle. Unexpectedly, one of the top ‘hits’ was a GSK3 inhibitor, an agonist of Wnt signaling. We show that sensitivity to GSK3 inhibition is likely due to stabilization of β-catenin in cohesin-mutant cells, and that Wnt-responsive gene expression is highly sensitized in STAG2-mutant CMK leukemia cells. Moreover, Wnt activity is enhanced in zebrafish mutant for cohesin subunits stag2b and rad21. Our results suggest that cohesin mutations could progress oncogenesis by enhancing Wnt signaling, and that targeting the Wnt pathway may represent a novel therapeutic strategy for cohesin-mutant cancers.

scholarly journals Cohesin mutations are synthetic lethal with stimulation of WNT signaling

2020 ◽  
Author(s):  
Chue Vin Chin ◽  
Jisha Antony ◽  
Sarada Ketharnathan ◽  
Gregory Gimenez ◽  
Kate M. Parsons ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Synthetic Lethality ◽  
Mcf10a Cell ◽  
Synthetic Lethal ◽  
Deletion Mutations ◽  
Damage Repair ◽  
Genes Encoding ◽  
Cohesin Subunit ◽  
Mutant Cells ◽  
Gsk3 Inhibitor

AbstractMutations in genes encoding subunits of the cohesin complex are common in several cancers, but may also expose druggable vulnerabilities. We generated isogenic MCF10A cell lines with deletion mutations of genes encoding cohesin subunits SMC3, RAD21 and STAG2 and screened for synthetic lethality with 3,009 FDA-approved compounds. The screen identified several compounds that interfere with transcription, DNA damage repair and the cell cycle. Unexpectedly, one of the top ‘hits’ was a GSK3 inhibitor, an agonist of Wnt signaling. We show that sensitivity to GSK3 inhibition is likely due to stabilization of β-catenin in cohesin mutant cells, and that Wnt-responsive gene expression is highly sensitized in STAG2-mutant CMK leukemia cells. Moreover, Wnt activity is enhanced in zebrafish mutant for cohesin subunit rad21. Our results suggest that cohesin mutations could progress oncogenesis by enhancing Wnt signaling, and that targeting the Wnt pathway may represent a novel therapeutic strategy for cohesin mutant cancers.

scholarly journals Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Salvatore Benfatto ◽  
Özdemirhan Serçin ◽  
Francesca R. Dejure ◽  
Amir Abdollahi ◽  
Frank T. Zenke ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cancer Genomics ◽  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Interacting Protein ◽  
Synthetic Lethal ◽  
Damage Repair ◽  
Genome Wide ◽  
Machine Learning Approach ◽  
Transcriptomics Data

Abstract Background Synthetic lethality describes a genetic interaction between two perturbations, leading to cell death, whereas neither event alone has a significant effect on cell viability. This concept can be exploited to specifically target tumor cells. CRISPR viability screens have been widely employed to identify cancer vulnerabilities. However, an approach to systematically infer genetic interactions from viability screens is missing. Methods Here we describe PAn-canceR Inferred Synthetic lethalities (PARIS), a machine learning approach to identify cancer vulnerabilities. PARIS predicts synthetic lethal (SL) interactions by combining CRISPR viability screens with genomics and transcriptomics data across hundreds of cancer cell lines profiled within the Cancer Dependency Map. Results Using PARIS, we predicted 15 high confidence SL interactions within 549 DNA damage repair (DDR) genes. We show experimental validation of an SL interaction between the tumor suppressor CDKN2A, thymidine phosphorylase (TYMP) and the thymidylate synthase (TYMS), which may allow stratifying patients for treatment with TYMS inhibitors. Using genome-wide mapping of SL interactions for DDR genes, we unraveled a dependency between the aldehyde dehydrogenase ALDH2 and the BRCA-interacting protein BRIP1. Our results suggest BRIP1 as a potential therapeutic target in ~ 30% of all tumors, which express low levels of ALDH2. Conclusions PARIS is an unbiased, scalable and easy to adapt platform to identify SL interactions that should aid in improving cancer therapy with increased availability of cancer genomics data.

scholarly journals Sli15 Associates with the Ipl1 Protein Kinase to Promote Proper Chromosome Segregation in Saccharomyces cerevisiae

1999 ◽  
Vol 145 (7) ◽  
pp. 1381-1394 ◽  
Author(s):  
Jae-hyun Kim ◽  
Jung-seog Kang ◽  
Clarence S.M. Chan
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Kinase ◽  
Chromosome Segregation ◽  
Genetic Interaction ◽  
Spindle Pole ◽  
Mutant Phenotype ◽  
Yeast Saccharomyces Cerevisiae ◽  
Synthetic Lethal ◽  
Mutant Cells

The conserved Ipl1 protein kinase is essential for proper chromosome segregation and thus cell viability in the budding yeast Saccharomyces cerevisiae. Its human homologue has been implicated in the tumorigenesis of diverse forms of cancer. We show here that sister chromatids that have separated from each other are not properly segregated to opposite poles of ipl1-2 cells. Failures in chromosome segregation are often associated with abnormal distribution of the spindle pole–associated Nuf2-GFP protein, thus suggesting a link between potential spindle pole defects and chromosome missegregation in ipl1 mutant cells. A small fraction of ipl1-2 cells also appears to be defective in nuclear migration or bipolar spindle formation. Ipl1 associates, probably directly, with the novel and essential Sli15 protein in vivo, and both proteins are localized to the mitotic spindle. Conditional sli15 mutant cells have cytological phenotypes very similar to those of ipl1 cells, and the ipl1-2 mutation exhibits synthetic lethal genetic interaction with sli15 mutations. sli15 mutant phenotype, like ipl1 mutant phenotype, is partially suppressed by perturbations that reduce protein phosphatase 1 function. These genetic and biochemical studies indicate that Sli15 associates with Ipl1 to promote its function in chromosome segregation.

scholarly journals Overview of Ferroptosis and Synthetic Lethality Strategies

2021 ◽  
Vol 22 (17) ◽  
pp. 9271
Author(s):  
Yuko Kinowaki ◽  
Towako Taguchi ◽  
Iichiroh Onishi ◽  
Susumu Kirimura ◽  
Masanobu Kitagawa ◽  
...  
Keyword(s):  
Epithelial Mesenchymal Transition ◽  
Synthetic Lethality ◽  
Therapeutic Strategies ◽  
Related Factors ◽  
Synthetic Lethal ◽  
Mesenchymal Transition ◽  
Genetic Abnormalities ◽  
Low Toxicity ◽  
New Research ◽  
Mutant Cells

Ferroptosis, a term first proposed in 2012, is iron-dependent, non-apoptotic regulatory cell death induced by erastin. Ferroptosis was originally discovered during synthetic lethal screening for drugs sensitive to RAS mutant cells, and is closely related to synthetic lethality. Ferroptosis sensitizes cancer stem cells and tumors that undergo epithelial−mesenchymal transition and are resistant to anticancer drugs or targeted therapy. Therefore, ferroptosis-inducing molecules are attractive new research targets. In contrast, synthetic lethal strategies approach mechanisms and genetic abnormalities that cannot be directly targeted by conventional therapeutic strategies, such as RAS mutations, hypoxia, and abnormalities in the metabolic environment. They also target the environment and conditions specific to malignant cells, have a low toxicity to normal cells, and can be used in combination with known drugs to produce new ones. However, the concept of synthetic lethality has not been widely adopted with ferroptosis. In this review, we surveyed the literature on ferroptosis-related factors and synthetic lethality to examine the potential therapeutic targets in ferroptosis-related molecules, focusing on factors related to synthetic lethality, discovery methods, clinical application stages, and issues in drug discovery.

scholarly journals Sirtuin inhibition is synthetic lethal with BRCA1 or BRCA2 deficiency

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Ilirjana Bajrami ◽  
Callum Walker ◽  
Dragomir B. Krastev ◽  
Daniel Weekes ◽  
Feifei Song ◽  
...  
Keyword(s):  
Synthetic Lethality ◽  
Parp Inhibitor ◽  
Lethal Effect ◽  
Synthetic Lethal ◽  
Genetic Ablation ◽  
Adp Ribosylation ◽  
Gene Mutant ◽  
Gene Defects ◽  
Mechanistic Basis ◽  
Mutant Cells

AbstractPARP enzymes utilise NAD+ as a co-substrate for their enzymatic activity. Inhibition of PARP1 is synthetic lethal with defects in either BRCA1 or BRCA2. In order to assess whether other genes implicated in NAD+ metabolism were synthetic lethal with BRCA1 or BRCA2 gene defects, we carried out a genetic screen, which identified a synthetic lethality between BRCA1 and genetic inhibition of either of two sirtuin (SIRT) enzymes, SIRT1 or SIRT6. This synthetic lethal interaction was replicated using small-molecule SIRT inhibitors and was associated with replication stress and increased cellular PARylation, in contrast to the decreased PARylation associated with BRCA-gene/PARP inhibitor synthetic lethality. SIRT/BRCA1 synthetic lethality was reversed by genetic ablation of either PARP1 or the histone PARylation factor-coding gene HPF1, implicating PARP1/HPF1-mediated serine ADP-ribosylation as part of the mechanistic basis of this synthetic lethal effect. These observations suggest that PARP1/HPF1-mediated serine ADP-ribosylation, when driven by SIRT inhibition, can inadvertently inhibit the growth of BRCA-gene mutant cells.

scholarly journals Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2

2021 ◽  
Vol 4 (11) ◽  
pp. e202101083
Author(s):  
Melanie L Bailey ◽  
David Tieu ◽  
Andrea Habsid ◽  
Amy Hin Yan Tong ◽  
Katherine Chan ◽  
...  
Keyword(s):  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Regulatory Gene ◽  
Chromosome Instability ◽  
Genetic Interactions ◽  
Complex Nature ◽  
Whole Genome ◽  
Cohesin Complex ◽  
Synthetic Lethal ◽  
Cancer Types

STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2. Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.

scholarly journals VRK1 is a Paralog Synthetic Lethal Target in VRK2-methylated Glioblastoma

2022 ◽  
Author(s):  
Julie A Shields ◽  
Samuel R Meier ◽  
Madhavi Bandi ◽  
Maria Dam Ferdinez ◽  
Justin L Engel ◽  
...  
Keyword(s):  
Kinase Activity ◽  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Cancer Therapeutics ◽  
Tumor Growth Inhibition ◽  
Synthetic Lethal Interaction ◽  
Synthetic Lethal ◽  
Aggressive Cancer ◽  
Nuclear Envelope Formation ◽  
Redundant Functions

Synthetic lethality - a genetic interaction that results in cell death when two genetic deficiencies co-occur but not when either deficiency occurs alone - can be co-opted for cancer therapeutics. A pair of paralog genes is among the most straightforward synthetic lethal interaction by virtue of their redundant functions. Here we demonstrate a paralog-based synthetic lethality by targeting Vaccinia-Related Kinase 1 (VRK1) in Vaccinia-Related Kinase 2 (VRK2)-methylated glioblastoma (GBM). VRK2 is silenced by promoter methylation in approximately two-thirds of GBM, an aggressive cancer with few available targeted therapies. Genetic knockdown of VRK1 in VRK2-null or VRK2-methylated cells results in decreased activity of the downstream substrate Barrier to Autointegration Factor (BAF), a regulator of post-mitotic nuclear envelope formation. VRK1 knockdown, and thus reduced BAF activity, causes nuclear lobulation, blebbing and micronucleation, which subsequently results in G2/M arrest and DNA damage. The VRK1-VRK2 synthetic lethal interaction is dependent on VRK1 kinase activity and is rescued by ectopic VRK2 expression. Knockdown of VRK1 leads to robust tumor growth inhibition in VRK2-methylated GBM xenografts. These results indicate that inhibiting VRK1 kinase activity could be a viable therapeutic strategy in VRK2-methylated GBM.

scholarly journals CRISPR editing of sftb-1/SF3B1 in C. elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing

2019 ◽  
Author(s):  
Xènia Serrat ◽  
Dmytro Kukhtar ◽  
Eric Cornes ◽  
Anna Esteve-Codina ◽  
Helena Benlloch ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Synthetic Lethality ◽  
Splicing Factor ◽  
Homogeneous Population ◽  
Synthetic Lethal ◽  
C Elegans ◽  
U2 Snrnp ◽  
Pladienolide B ◽  
Cancer Mutations ◽  
Chemical Inhibition

ABSTRACTSF3B1 is the most frequently mutated splicing factor in cancer. Mutations in SF3B1 confer growth advantages to cancer cells but they may also confer vulnerabilities that can be therapeutically targeted. In contrast to other animal models, SF3B1 cancer mutations can be maintained in homozygosis in C. elegans, allowing synthetic lethal screens with a homogeneous population of animals. These mutations cause alternative splicing (AS) defects in C. elegans, as it occurs in SF3B1-mutated human cells. In a screen, we identified RNAi of U2 snRNP components that cause synthetic lethality with sftb-1/SF3B1 mutations. We also detected synthetic interactions between sftb-1 mutants and cancer-related mutations in uaf-2/U2AF1 or rsp-4/SRSF2, demonstrating that this model can identify interactions between mutations that are mutually exclusive in human tumors. Finally, we have edited an SFTB-1 domain to sensitize C. elegans to the splicing inhibitor pladienolide B. Thus, we have established a multicellular model for SF3B1 mutations amenable for high-throughput genetic and chemical screens.

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