Gene essentiality and synthetic lethality in haploid human cells

Blomen, Vincent A.; Marynen, Peter; Jae, Lucas T.; Bigenzahn, Johannes W.; Nieuwenhuis, Joppe; Staring, Jacqueline; Sacco, Roberto; Diemen, Ferdy R. van; Olk, Nadine; Stukalov, Alexey; Marceau, Caleb; Janssen, Hans; Carette, Jan E.; Bennett, Keiryn L.; Colinge, Jacques; Superti‐Furga, Giulio; Brummelkamp, Thijn R.

doi:10.1126/science.aac7557

Cited by 774 publications

(933 citation statements)

References 62 publications

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“…We first excluded the possibility that cancer cells containing the CRISPR library were engrafted unsuccessfully, because the tumor size and growth were similar in both screens. We also confirmed that essential genes, identified by previously reported CRISPR screens (29,30), were significantly more depleted than nonessential genes in peritoneal tumors in our CRISPR screen [depletion rate; essential genes vs. nonessential genes defined by Blomen et al (29) , respectively], suggesting that genes were not depleted randomly but by in vivo selective pressure. The shRNA generally induces partial gene knockdown, and the residual activity of the wild-type protein may thus prevent a knockdown phenotype from being observed.…”

Section: Discussionsupporting

confidence: 76%

In vivo loss-of-function screens identify KPNB1 as a new druggable oncogene in epithelial ovarian cancer

Kodama

Newberg

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Epithelial ovarian cancer (EOC) is a deadly cancer, and its prognosis has not been changed significantly during several decades. To seek new therapeutic targets for EOC, we performed an in vivo dropout screen in human tumor xenografts using a pooled shRNA library targeting thousands of druggable genes. Then, in follow-up studies, we performed a second screen using a genome-wide CRISPR/Cas9 library. These screens identified 10 high-confidence drug targets that included well-known oncogenes such as ERBB2 and RAF1, and novel oncogenes, notably KPNB1, which we investigated further. Genetic and pharmacological inhibition showed that KPNB1 exerts its antitumor effects through multiphase cell cycle arrest and apoptosis induction. Mechanistically, proteomic studies revealed that KPNB1 acts as a master regulator of cell cycle-related proteins, including p21, p27, and APC/ C. Clinically, EOC patients with higher expression levels of KPNB1 showed earlier recurrence and worse prognosis than those with lower expression levels of KPNB1. Interestingly, ivermectin, a Food and Drug Administration-approved antiparasitic drug, showed KPNB1-dependent antitumor effects on EOC, serving as an alternative therapeutic toward EOC patients through drug repositioning. Last, we found that the combination of ivermectin and paclitaxel produces a stronger antitumor effect on EOC both in vitro and in vivo than either drug alone. Our studies have thus identified a combinatorial therapy for EOC, in addition to a plethora of potential drug targets.ovarian cancer | KPNB1 | loss-of-function screen | CRISPR/Cas | RNAi

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Section: Discussionsupporting

confidence: 76%

In vivo loss-of-function screens identify KPNB1 as a new druggable oncogene in epithelial ovarian cancer

Kodama

Newberg

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Moreover, complementation assays can also be carried out in other model systems including human cells (Hart et al , 2015). Based on only three large‐scale CRISPR studies (Wang et al , 2014; Blomen et al , 2015; Hart et al , 2015), cellular growth phenotypes (which might serve as the basis for an en masse selection) have already been observed in at least one cell line for 29% of human disease genes. Beyond complementation, assays of protein interaction can, in addition to identifying variants directly impacting interaction, can detect variants ablating overall function through effects on protein folding or stability.…”

Section: Resultsmentioning

confidence: 99%

A framework for exhaustively mapping functional missense variants

Weile

Sun

Coté

et al. 2017

Molecular Systems Biology

157

285

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Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin‐like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.

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“…To identify the most comprehensive set of EGs in mammals, we combined the set of human orthologs of EGs in the mouse (n = 3,326) (14) with a set of human "core EGs" (n = 956) that were found to be essential in cell-based assays (20)(21)(22). Based on a significant overlap between tested mouse and human EGs (14), we expanded our original set of 3,326 EGs with the addition of nonoverlapping 589 EGs identified only in human cell lines for a total of 3,915 EGs (SI Materials and Methods and Dataset S1).…”

Section: Resultsmentioning

confidence: 99%

“…Recently, three large-scale screens (gene trap and CRISPRCas9) have been performed to assess the effect of single-gene mutations on cell viability or survival of haploid human cancer cell lines ("cell-based essentiality") (20)(21)(22). These studies identified an overlapping core set of genes that were essential in the majority of cell lines tested (n = 956), although a subset of genes were essential in specific cell lines.…”

mentioning

confidence: 99%

“…In addition to their role in defining a "minimal gene set" (16,17), EGs tend to play important roles in protein interaction networks (18). Therefore, one may consider that EGs are involved in rate-limiting steps that affect a range of disease pathways (19).Recently, three large-scale screens (gene trap and CRISPRCas9) have been performed to assess the effect of single-gene mutations on cell viability or survival of haploid human cancer cell lines ("cell-based essentiality") (20)(21)(22). These studies identified an overlapping core set of genes that were essential in the majority of cell lines tested (n = 956), although a subset of genes were essential in specific cell lines.…”

mentioning

confidence: 99%

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Increased burden of deleterious variants in essential genes in autism spectrum disorder

Xiao

Kember

Brown

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication, and repetitive behavior. It is estimated that hundreds of genes contribute to ASD. We asked if genes with a strong effect on survival and fitness contribute to ASD risk. Human orthologs of genes with an essential role in pre-and postnatal development in the mouse [essential genes (EGs)] are enriched for disease genes and under strong purifying selection relative to human orthologs of mouse genes with a known nonlethal phenotype [nonessential genes (NEGs)]. This intolerance to deleterious mutations, commonly observed haploinsufficiency, and the importance of EGs in development suggest a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. With a comprehensive catalog of 3,915 mammalian EGs, we provide compelling evidence for a stronger contribution of EGs to ASD risk compared with NEGs. By examining the exonic de novo and inherited variants from 1,781 ASD quartet families, we show a significantly higher burden of damaging mutations in EGs in ASD probands compared with their non-ASD siblings. The analysis of EGs in the developing brain identified clusters of coexpressed EGs implicated in ASD. Finally, we suggest a high-priority list of 29 EGs with potential ASD risk as targets for future functional and behavioral studies. Overall, we show that large-scale studies of gene function in model organisms provide a powerful approach for prioritization of genes and pathogenic variants identified by sequencing studies of human disease.essential genes | mouse knockouts | mutational burden | autism spectrum disorder | coexpression modules A utism spectrum disorder (ASD) is a heterogeneous, heritable neurodevelopmental syndrome characterized by impaired social interaction, communication, and repetitive behavior (1, 2). The highly polygenic nature of ASD (3-5) suggests that the analysis of the full spectrum of sequence variants in hundreds of genes will be necessary for deeper understanding of disrupted neuronal function. Prioritization of ASD risk genes initially focused on known pathways with recognized relevance to pathogenesis of ASD, such as synaptic function and neuronal development (6). However, combined analyses of de novo, inherited, and case-control variation in over 2,500 ASD parentchild nuclear families identified around 100 genes contributing to ASD risk (7-9), converging on pathways implicated in transcriptional regulation and chromatin modeling in addition to synaptic function.The main challenge in the current understanding of genetic architecture of ASD comes from a need to study the interplay between variants with a high effect (for example, recurrent de novo variants) and a background of variants with an intermediate effect but that nevertheless still disrupt proper neuronal development. Essential genes (EGs) or genes that are necessary for successful completion of pre-and postnatal development are prime candi...

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Gene essentiality and synthetic lethality in haploid human cells

Cited by 774 publications

References 62 publications

In vivo loss-of-function screens identify KPNB1 as a new druggable oncogene in epithelial ovarian cancer

In vivo loss-of-function screens identify KPNB1 as a new druggable oncogene in epithelial ovarian cancer

A framework for exhaustively mapping functional missense variants

Increased burden of deleterious variants in essential genes in autism spectrum disorder

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