Beyond Synthetic Lethality: Charting the Landscape of Clinically Relevant Genetic Interactions in Cancer

2019 ◽  
Author(s):  
Assaf Magen ◽  
Avinash Das ◽  
Joo Sang Lee ◽  
Mahfuza Sharmin ◽  
Alexander Lugo ◽  
...  
Keyword(s):  
Synthetic Lethality ◽  
Genetic Interactions

scholarly journals Synthetic Lethality with the dut Defect in Escherichia coli Reveals Layers of DNA Damage of Increasing Complexity Due to Uracil Incorporation

2008 ◽  
Vol 190 (17) ◽  
pp. 5841-5854 ◽  
Author(s):  
Helen Ting ◽  
Elena A. Kouzminova ◽  
Andrei Kuzminov
Keyword(s):  
Escherichia Coli ◽  
Dna Repair ◽  
Metabolic Pathways ◽  
Synthetic Lethality ◽  
Nucleotide Metabolism ◽  
Genetic Interactions ◽  
Single Defect ◽  
Damage Repair ◽  
Mutant Combination ◽  
Dna Incorporation

ABSTRACT Synthetic lethality is inviability of a double-mutant combination of two fully viable single mutants, commonly interpreted as redundancy at an essential metabolic step. The dut-1 defect in Escherichia coli inactivates dUTPase, causing increased uracil incorporation in DNA and known synthetic lethalities [SL(dut) mutations]. According to the redundancy logic, most of these SL(dut) mutations should affect nucleotide metabolism. After a systematic search for SL(dut) mutants, we did identify a single defect in the DNA precursor metabolism, inactivating thymidine kinase (tdk), that confirmed the redundancy explanation of synthetic lethality. However, we found that the bulk of mutations interacting genetically with dut are in DNA repair, revealing layers of damage of increasing complexity that uracil-DNA incorporation sends through the chromosomal metabolism. Thus, we isolated mutants in functions involved in (i) uracil-DNA excision (ung, polA, and xthA); (ii) double-strand DNA break repair (recA, recBC, and ruvABC); and (iii) chromosomal-dimer resolution (xerC, xerD, and ftsK). These mutants in various DNA repair transactions cannot be redundant with dUTPase and instead reveal “defect-damage-repair” cycles linking unrelated metabolic pathways. In addition, two SL(dut) inserts (phoU and degP) identify functions that could act to support the weakened activity of the Dut-1 mutant enzyme, suggesting the “compensation” explanation for this synthetic lethality. We conclude that genetic interactions with dut can be explained by redundancy, by defect-damage-repair cycles, or as compensation.

scholarly journals Mapping genetic interactions in cancer: a road to rational combination therapies

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Beril Tutuncuoglu ◽  
Nevan J. Krogan
Keyword(s):  
Anticancer Drugs ◽  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Parp Inhibitors ◽  
Genetic Interactions ◽  
Parp Inhibition ◽  
Functional Dependencies ◽  
Combination Therapies ◽  
Systematic Screening ◽  
Rational Combination

Abstract The discovery of synthetic lethal interactions between poly (ADP-ribose) polymerase (PARP) inhibitors and BRCA genes, which are involved in homologous recombination, led to the approval of PARP inhibition as a monotherapy for patients with BRCA1/2-mutated breast or ovarian cancer. Studies following the initial observation of synthetic lethality demonstrated that the reach of PARP inhibitors is well beyond just BRCA1/2 mutants. Insights into the mechanisms of action of anticancer drugs are fundamental for the development of targeted monotherapies or rational combination treatments that will synergize to promote cancer cell death and overcome mechanisms of resistance. The development of targeted therapeutic agents is premised on mapping the physical and functional dependencies of mutated genes in cancer. An important part of this effort is the systematic screening of genetic interactions in a variety of cancer types. Until recently, genetic-interaction screens have relied either on the pairwise perturbations of two genes or on the perturbation of genes of interest combined with inhibition by commonly used anticancer drugs. Here, we summarize recent advances in mapping genetic interactions using targeted, genome-wide, and high-throughput genetic screens, and we discuss the therapeutic insights obtained through such screens. We further focus on factors that should be considered in order to develop a robust analysis pipeline. Finally, we discuss the integration of functional interaction data with orthogonal methods and suggest that such approaches will increase the reach of genetic-interaction screens for the development of rational combination therapies.

scholarly journals Genetic evidence for functional interactions between actin noncomplementing (Anc) gene products and actin cytoskeletal proteins in Saccharomyces cerevisiae.

Genetics ◽  
1993 ◽  
Vol 135 (2) ◽  
pp. 275-286
Author(s):  
D B Vinh ◽  
M D Welch ◽  
A K Corsi ◽  
K F Wertman ◽  
D G Drubin
Keyword(s):  
Synthetic Lethality ◽  
Binding Protein ◽  
Cytoskeletal Proteins ◽  
Genetic Interactions ◽  
Null Alleles ◽  
Actin Binding ◽  
Gene Products ◽  
Actin Binding Protein ◽  
Functional Interactions ◽  
Allele Specific

Abstract We describe here genetic interactions between mutant alleles of Actin-NonComplementing (ANC) genes and actin (ACT1) or actin-binding protein (SAC6, ABP1, TPM1) genes. The anc mutations were found to exhibit allele-specific noncomplementing interactions with different act1 mutations. In addition, mutant alleles of four ANC genes (ANC1, ANC2, ANC3 and ANC4) were tested for interactions with null alleles of actin-binding protein genes. An anc1 mutant allele failed to complement null alleles of the SAC6 and TPM1 genes that encode yeast fimbrin and tropomyosin, respectively. Also, synthetic lethality between anc3 and sac6 mutations, and between anc4 and tpm1 mutations was observed. Taken together, the above results strongly suggest that the ANC gene products contribute to diverse aspects of actin function. Finally, we report the results of tests of two models previously proposed to explain extragenic noncomplementation.

scholarly journals Shuffle-Seq: En masse combinatorial encoding for n-way genetic interaction screens

2019 ◽  
Author(s):  
Atray Dixit ◽  
Olena Kuksenko ◽  
David Feldman ◽  
Aviv Regev
Keyword(s):  
Large Scale ◽  
Genetic Interaction ◽  
Synthetic Lethality ◽  
Genetic Interactions ◽  
Pairwise Interactions ◽  
Affect Cell Viability ◽  
Melanoma Model ◽  
Dividing Cells ◽  
Combinatorial Encoding ◽  
Massive Number

AbstractGenetic interactions, defined as the non-additive phenotypic impact of combinations of genes, are a hallmark of the mapping from genotype to phenotype. However, genetic interactions remain challenging to systematically test given the massive number of possible combinations. In particular, while large-scale screening efforts in yeast have quantified pairwise interactions that affect cell viability, or synthetic lethality, between all pairs of genes as well as for a limited number of three-way interactions, it has previously been intractable to perform the large screens needed to comprehensively assess interactions in a mammalian genome. Here, we develop Shuffle-Seq, a scalable method to assay genetic interactions. Shuffle-Seq leverages the co-inheritance of genetically encoded barcodes in dividing cells and can scale in proportion to sequencing throughput. We demonstrate the technical validity of Shuffle-Seq and apply it to screening for mechanisms underlying drug resistance in a melanoma model. Shuffle-Seq should allow screens of hundreds of millions of combinatorial perturbations and facilitate the understanding of genetic dependencies and drug sensitivities.

scholarly journals Common computational tools for analyzing CRISPR screens

2021 ◽  
Author(s):  
Medina Colic ◽  
Traver Hart
Keyword(s):  
Drug Resistance ◽  
Genome Editing ◽  
Analytical Methods ◽  
Computational Analysis ◽  
Synthetic Lethality ◽  
Genetic Interactions ◽  
Computational Tools ◽  
Genome Regulation ◽  
Rna Targeting ◽  
State Of Art

CRISPR–Cas technology offers a versatile toolbox for genome editing, with applications in various cancer-related fields such as functional genomics, immunotherapy, synthetic lethality and drug resistance, metastasis, genome regulation, chromatic accessibility and RNA-targeting. The variety of screening platforms and questions in which they are used have caused the development of a wide array of analytical methods for CRISPR analysis. In this review, we focus on the algorithms and frameworks used in the computational analysis of pooled CRISPR knockout (KO) screens and highlight some of the most significant target discoveries made using these methods. Lastly, we offer perspectives on the design and analysis of state-of-art multiplex screening for genetic interactions.

scholarly journals Genetic interactions among Chlamydomonas reinhardtii mutations that confer resistance to anti-microtubule herbicides.

Genetics ◽  
1992 ◽  
Vol 130 (2) ◽  
pp. 305-314
Author(s):  
S W James ◽  
P A Lefebvre
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Synthetic Lethality ◽  
Deuterium Oxide ◽  
Genetic Interactions ◽  
Heat Sensitivity ◽  
Recessive Mutations ◽  
Common Structure ◽  
Suppressor Mutations ◽  
Allele Specific ◽  
Interallelic Complementation

Abstract We previously described two types of genetic interactions among recessive mutations in the APM1 and APM2 loci of Chlamydomonas reinhardtii that may reflect a physical association of the gene products or their involvement in a common structure/process: (1) allele-specific synthetic lethality, and (2) unlinked noncomplementation, or dominant enhancement. To further investigate these interactions, we isolated revertants in which the heat sensitivity caused by the apm2-1 mutation is lost. The heat-insensitive revertants were either fully or partially suppressed for the drug-resistance caused by the apm2-1 allele. In recombination tests the revertants behaved as if the suppressing mutation mapped within the APM2 locus; the partial suppressors of apm2-1 herbicide resistance failed to complement apm2-1, leading to the conclusion that they were likely to be intragenic pseudorevertants. The apm2-1 partial suppressor mutations reversed apm1-apm2-1 synthetic lethality in an allele-specific manner with respect both to apm1- alleles and apm2-1 suppressor mutations. Those apm1- apm2-1rev strains that regained viability also regained heat sensitivity characteristic of the original apm2-1 mutation, even though the apm2-1 suppressor strains were fully heat-insensitive. The Hs+ phenotypes of apm2-1 partial suppressors were also reversed by treatment with the microtubule-stabilizing agent deuterium oxide (D2O). In addition to the above interactions, we observed interallelic complementation and phenotypic enhancement of temperature conditionality among apm1- alleles. Evidence of a role for the products of the two genes in microtubule-based processes was obtained from studying flagellar assembly in apm1- and apm2- mutants.

scholarly journals Extensive Genetic Interactions Between PRP8 and PRP17/CDC40, Two Yeast Genes Involved in Pre-mRNA Splicing and Cell Cycle Progression

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 61-71
Author(s):  
Sigal Ben-Yehuda ◽  
Caroline S Russell ◽  
Ian Dix ◽  
Jean D Beggs ◽  
Martin Kupiec
Keyword(s):  
Elevated Temperatures ◽  
Synthetic Lethality ◽  
Splice Junction ◽  
Genetic Interactions ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Permissive Temperature ◽  
Yeast Saccharomyces Cerevisiae ◽  
Prp8 Gene ◽  
Yeast Genes

Abstract Biochemical and genetic experiments have shown that the PRP17 gene of the yeast Saccharomyces cerevisiae encodes a protein that plays a role during the second catalytic step of the splicing reaction. It was found recently that PRP17 is identical to the cell division cycle CDC40 gene. cdc40 mutants arrest at the restrictive temperature after the completion of DNA replication. Although the PRP17/CDC40 gene product is essential only at elevated temperatures, splicing intermediates accumulate in prp17 mutants even at the permissive temperature. In this report we describe extensive genetic interactions between PRP17/CDC40 and the PRP8 gene. PRP8 encodes a highly conserved U5 snRNP protein required for spliceosome assembly and for both catalytic steps of the splicing reaction. We show that mutations in the PRP8 gene are able to suppress the temperature-sensitive growth phenotype and the splicing defect conferred by the absence of the Prp17 protein. In addition, these mutations are capable of suppressing certain alterations in the conserved PyAG trinucleotide at the 3′ splice junction, as detected by an ACT1-CUP1 splicing reporter system. Moreover, other PRP8 alleles exhibit synthetic lethality with the absence of Prp17p and show a reduced ability to splice an intron bearing an altered 3′ splice junction. On the basis of these findings, we propose a model for the mode of interaction between the Prp8 and Prp17 proteins during the second catalytic step of the splicing reaction.

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