Construction of a novel Escherichia coli expression system: relocation of lpxA from chromosome to a constitutive expression vector.
Zhao Lei,Hu Xiaoqing,Li Ye,Wang Zhen,Wang Xiaoyuan
Applied microbiology and biotechnology
The selective marker in the plasmid-based expression system is usually a gene that encodes an antibiotic-resistant protein; therefore, the antibiotic has to add to maintain the plasmid when growing the bacteria. This antibiotic addition would lead to increase of production cost and the environment contamination. In this study, a novel Escherichia coli expression system, the lpxA deletion mutant harboring an lpxA-carrying vector, was developed. To develop this system, three plasmids pCas9Cre, pTF-A-UD, and pRSFCmlpxA were constructed. The plasmid pCas9Cre produces enzymes Cas9, λ-Red, and Cre and can be cured by growing at 42 °C; pTF-A-UD contains several DNA fragments required for deleting the chromosomal lpxA and can be cured by adding isopropyl-D-thiogalactopyranoside; pRSFCmlpxA contains the lpxA mutant lpxA123 and CamR. When E. coli were transformed with these three plasmids, the chromosomal lpxA and the CamR in pRSFCmlpxA can be efficiently removed, resulting in an E. coli lpxA mutant harboring pRSFlpxA. The lpxA is essential for the growth of E. coli; its relocation from chromosome to a constitutive expression vector is an ideal strategy to maintain the vector without antibiotic addition. The lpxA123 in pRSFlpxA can complement the deletion of the chromosomal lpxA and provide a strong selective pressure to maintain the plasmid pRSFlpxA. This study provides an experimental evidence that this novel expression system is convenient and efficient to use and can be used to improve L-threonine biosynthesis in the wild type E. coli MG1655 and an L-threonine producing E. coli TWF006.
Drug delivery with living cells.
Fliervoet Lies A L,Mastrobattista Enrico
Advanced drug delivery reviews
The field of drug delivery has grown tremendously in the past few decades by developing a wide range of advanced drug delivery systems. An interesting category is cell-based drug delivery, which includes encapsulation of drugs inside cells or attached to the surface and subsequent transportation through the body. Another approach involves genetic engineering of cells to secrete therapeutic molecules in a controlled way. The next-generation systems integrate expertise from synthetic biology to generate therapeutic gene networks for highly advanced sensory and output devices. These developments are very exciting for the drug delivery field and could radically change the way we administer biological medicines to chronically ill patients. This review is covering the use of living cells, either as transport system or production-unit, to deliver therapeutic molecules and bioactive proteins inside the body. It describes a wide range of approaches in cell-based drug delivery and highlights exceptional examples.
The Future Is Synthetic Biology.
Increasingly, synthetic biological systems and molecules are being used to drive biological applications and discovery. At the 2018 Fall Meeting of the American Chemical Society, Cell's Andrew Rennekamp met up with John Glass, Jim Collins, and Floyd Romesberg to discuss synthetic biology as a discipline and to get their take on where it's headed. Annotated excerpts from this conversation are presented below, and the full conversation is available with the article online.
Realizing the potential of synthetic biology.
Church George M,Elowitz Michael B,Smolke Christina D,Voigt Christopher A,Weiss Ron
Nature reviews. Molecular cell biology
Synthetic biology, despite still being in its infancy, is increasingly providing valuable information for applications in the clinic, the biotechnology industry and in basic molecular research. Both its unique potential and the challenges it presents have brought together the expertise of an eclectic group of scientists, from cell biologists to engineers. In this Viewpoint article, five experts discuss their views on the future of synthetic biology, on its main achievements in basic and applied science, and on the bioethical issues that are associated with the design of new biological systems.
Synthetic biology in cell-based cancer immunotherapy.
Chakravarti Deboki,Wong Wilson W
Trends in biotechnology
The adoptive transfer of genetically engineered T cells with cancer-targeting receptors has shown tremendous promise for eradicating tumors in clinical trials. This form of cellular immunotherapy presents a unique opportunity to incorporate advanced systems and synthetic biology approaches to create cancer therapeutics with novel functions. We first review the development of synthetic receptors, switches, and circuits to control the location, duration, and strength of T cell activity against tumors. In addition, we discuss the cellular engineering and genome editing of host cells (or the chassis) to improve the efficacy of cell-based cancer therapeutics, and to reduce the time and cost of manufacturing.
Programming gene and engineered-cell therapies with synthetic biology.
Kitada Tasuku,DiAndreth Breanna,Teague Brian,Weiss Ron
Science (New York, N.Y.)
Gene and engineered-cell therapies promise to treat diseases by genetically modifying cells to carry out therapeutic tasks. Although the field has had some success in treating monogenic disorders and hematological malignancies, current approaches are limited to overexpression of one or a few transgenes, constraining the diseases that can be treated with this approach and leading to potential concerns over safety and efficacy. Synthetic gene networks can regulate the dosage, timing, and localization of gene expression and therapeutic activity in response to small molecules and disease biomarkers. Such "programmable" gene and engineered-cell therapies will provide new interventions for incurable or difficult-to-treat diseases.
From DNA to targeted therapeutics: bringing synthetic biology to the clinic.
Chen Yvonne Y,Smolke Christina D
Science translational medicine
Synthetic biology aims to make biological engineering more scalable and predictable, lowering the cost and facilitating the translation of synthetic biological systems to practical applications. Increasingly sophisticated, rationally designed synthetic systems that are capable of complex functions pave the way to translational applications, including disease diagnostics and targeted therapeutics. Here, we provide an overview of recent developments in synthetic biology in the context of translational research and discuss challenges at the interface between synthetic biology and clinical medicine.
Can Bottom-Up Synthetic Biology Generate Advanced Drug-Delivery Systems?
Lussier Felix,Staufer Oskar,Platzman Ilia,Spatz Joachim P
Trends in biotechnology
Creating a magic bullet that can selectively kill cancer cells while sparing nearby healthy cells remains one of the most ambitious objectives in pharmacology. Nanomedicine, which relies on the use of nanotechnologies to fight disease, was envisaged to fulfill this coveted goal. Despite substantial progress, the structural complexity of therapeutic vehicles impedes their broad clinical application. Novel modular manufacturing approaches for engineering programmable drug carriers may be able to overcome some fundamental limitations of nanomedicine. We discuss how bottom-up synthetic biology principles, empowered by microfluidics, can palliate current drug carrier assembly limitations, and we demonstrate how such a magic bullet could be engineered from the bottom up to ultimately improve clinical outcomes for patients.
Synthetic Posttranslational Modifications: Chemical Catalyst-Driven Regioselective Histone Acylation of Native Chromatin.
Amamoto Yoshifumi,Aoi Yuki,Nagashima Nozomu,Suto Hiroki,Yoshidome Daisuke,Arimura Yasuhiro,Osakabe Akihisa,Kato Daiki,Kurumizaka Hitoshi,Kawashima Shigehiro A,Yamatsugu Kenzo,Kanai Motomu
Journal of the American Chemical Society
Posttranslational modifications (PTMs) of histones play an important role in the complex regulatory mechanisms governing gene transcription, and their dysregulation can cause diseases such as cancer. The lack of methods for site-selectively modifying native chromatin, however, limits our understanding of the functional roles of a specific histone PTM, not as a single mark, but in the intertwined PTM network. Here, we report a synthetic catalyst DMAP-SH (DSH), which activates chemically stable thioesters (including acetyl-CoA) under physiological conditions and transfers various acyl groups to the proximate amino groups. Our data suggest that DSH, conjugated with a nucleosome ligand, such as pyrrole-imidazole-polyamide and LANA (latency-associated nuclear antigen)-peptide, promotes both natural (including acetylation, butyrylation, malonylation, and ubiquitination) and non-natural (azido- and phosphoryl labeling) PTMs on histones in recombinant nucleosomes and/or in native chromatin, at lysine residues close to the DSH moiety. To investigate the validity of our method, we used LANA-DSH to promote histone H2B lysine-120 (K120) acylation, the function of which is largely unknown. H2BK120 acetylation and malonylation modulated higher-order chromatin structures by reducing internucleosomal interactions, and this modulation was further enhanced by histone tail acetylation. This approach, therefore, may have versatile applications for dissecting the regulatory mechanisms underlying chromatin function.
Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions.
Han Kyuho,Jeng Edwin E,Hess Gaelen T,Morgens David W,Li Amy,Bassik Michael C
Identification of effective combination therapies is critical to address the emergence of drug-resistant cancers, but direct screening of all possible drug combinations is infeasible. Here we introduce a CRISPR-based double knockout (CDKO) system that improves the efficiency of combinatorial genetic screening using an effective strategy for cloning and sequencing paired single guide RNA (sgRNA) libraries and a robust statistical scoring method for calculating genetic interactions (GIs) from CRISPR-deleted gene pairs. We applied CDKO to generate a large-scale human GI map, comprising 490,000 double-sgRNAs directed against 21,321 pairs of drug targets in K562 leukemia cells and identified synthetic lethal drug target pairs for which corresponding drugs exhibit synergistic killing. These included the BCL2L1 and MCL1 combination, which was also effective in imatinib-resistant cells. We further validated this system by identifying known and previously unidentified GIs between modifiers of ricin toxicity. This work provides an effective strategy to screen synergistic drug combinations in high-throughput and a CRISPR-based tool to dissect functional GI networks.
Gene expression and mutation-guided synthetic lethality eradicates proliferating and quiescent leukemia cells.
Nieborowska-Skorska Margaret,Sullivan Katherine,Dasgupta Yashodhara,Podszywalow-Bartnicka Paulina,Hoser Grazyna,Maifrede Silvia,Martinez Esteban,Di Marcantonio Daniela,Bolton-Gillespie Elisabeth,Cramer-Morales Kimberly,Lee Jaewong,Li Min,Slupianek Artur,Gritsyuk Daniel,Cerny-Reiterer Sabine,Seferynska Ilona,Stoklosa Tomasz,Bullinger Lars,Zhao Huaqing,Gorbunova Vera,Piwocka Katarzyna,Valent Peter,Civin Curt I,Muschen Markus,Dick John E,Wang Jean Cy,Bhatia Smita,Bhatia Ravi,Eppert Kolja,Minden Mark D,Sykes Stephen M,Skorski Tomasz
The Journal of clinical investigation
Quiescent and proliferating leukemia cells accumulate highly lethal DNA double-strand breaks that are repaired by 2 major mechanisms: BRCA-dependent homologous recombination and DNA-dependent protein kinase-mediated (DNA-PK-mediated) nonhomologous end-joining, whereas DNA repair pathways mediated by poly(ADP)ribose polymerase 1 (PARP1) serve as backups. Here we have designed a personalized medicine approach called gene expression and mutation analysis (GEMA) to identify BRCA- and DNA-PK-deficient leukemias either directly, using reverse transcription-quantitative PCR, microarrays, and flow cytometry, or indirectly, by the presence of oncogenes such as BCR-ABL1. DNA-PK-deficient quiescent leukemia cells and BRCA/DNA-PK-deficient proliferating leukemia cells were sensitive to PARP1 inhibitors that were administered alone or in combination with current antileukemic drugs. In conclusion, GEMA-guided targeting of PARP1 resulted in dual cellular synthetic lethality in quiescent and proliferating immature leukemia cells, and is thus a potential approach to eradicate leukemia stem and progenitor cells that are responsible for initiation and manifestation of the disease. Further, an analysis of The Cancer Genome Atlas database indicated that this personalized medicine approach could also be applied to treat numerous solid tumors from individual patients.
Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.
Behan Fiona M,Iorio Francesco,Picco Gabriele,Gonçalves Emanuel,Beaver Charlotte M,Migliardi Giorgia,Santos Rita,Rao Yanhua,Sassi Francesco,Pinnelli Marika,Ansari Rizwan,Harper Sarah,Jackson David Adam,McRae Rebecca,Pooley Rachel,Wilkinson Piers,van der Meer Dieudonne,Dow David,Buser-Doepner Carolyn,Bertotti Andrea,Trusolino Livio,Stronach Euan A,Saez-Rodriguez Julio,Yusa Kosuke,Garnett Mathew J
Functional genomics approaches can overcome limitations-such as the lack of identification of robust targets and poor clinical efficacy-that hamper cancer drug development. Here we performed genome-scale CRISPR-Cas9 screens in 324 human cancer cell lines from 30 cancer types and developed a data-driven framework to prioritize candidates for cancer therapeutics. We integrated cell fitness effects with genomic biomarkers and target tractability for drug development to systematically prioritize new targets in defined tissues and genotypes. We verified one of our most promising dependencies, the Werner syndrome ATP-dependent helicase, as a synthetic lethal target in tumours from multiple cancer types with microsatellite instability. Our analysis provides a resource of cancer dependencies, generates a framework to prioritize cancer drug targets and suggests specific new targets. The principles described in this study can inform the initial stages of drug development by contributing to a new, diverse and more effective portfolio of cancer drug targets.
Mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer.
Lissanu Deribe Yonathan,Sun Yuting,Terranova Christopher,Khan Fatima,Martinez-Ledesma Juan,Gay Jason,Gao Guang,Mullinax Robert A,Khor Tin,Feng Ningping,Lin Yu-Hsi,Wu Chia-Chin,Reyes Claudia,Peng Qian,Robinson Frederick,Inoue Akira,Kochat Veena,Liu Chang-Gong,Asara John M,Moran Cesar,Muller Florian,Wang Jing,Fang Bingliang,Papadimitrakopoulou Vali,Wistuba Ignacio I,Rai Kunal,Marszalek Joseph,Futreal P Andrew
Lung cancer is a devastating disease that remains a top cause of cancer mortality. Despite improvements with targeted and immunotherapies, the majority of patients with lung cancer lack effective therapies, underscoring the need for additional treatment approaches. Genomic studies have identified frequent alterations in components of the SWI/SNF chromatin remodeling complex including SMARCA4 and ARID1A. To understand the mechanisms of tumorigenesis driven by mutations in this complex, we developed a genetically engineered mouse model of lung adenocarcinoma by ablating Smarca4 in the lung epithelium. We demonstrate that Smarca4 acts as a bona fide tumor suppressor and cooperates with p53 loss and Kras activation. Gene expression analyses revealed the signature of enhanced oxidative phosphorylation (OXPHOS) in SMARCA4 mutant tumors. We further show that SMARCA4 mutant cells have enhanced oxygen consumption and increased respiratory capacity. Importantly, SMARCA4 mutant lung cancer cell lines and xenograft tumors have marked sensitivity to inhibition of OXPHOS by a novel small molecule, IACS-010759, that is under clinical development. Mechanistically, we show that SMARCA4-deficient cells have a blunted transcriptional response to energy stress creating a therapeutically exploitable synthetic lethal interaction. These findings provide the mechanistic basis for further development of OXPHOS inhibitors as therapeutics against SWI/SNF mutant tumors.
Collateral sensitivity of natural products in drug-resistant cancer cells.
Efferth Thomas,Saeed Mohamed E M,Kadioglu Onat,Seo Ean-Jeong,Shirooie Samira,Mbaveng Armelle T,Nabavi Seyed Mohammad,Kuete Victor
Cancer chemotherapy is frequently hampered by drug resistance. Concepts to combine anticancer drugs with different modes of action to avoid the development of resistance did not provide the expected success in the past, because tumors can be simultaneously non-responsive to many drugs (e.g. the multidrug resistance phenotype). However, tumors may be specifically hypersensitive to other drugs - a phenomenon also termed collateral sensitivity. This seems to be a general biological mechanism, since it also occurs in drug-resistant Escherichia coli and Saccharomyces cerevisiae. Here, we give a timely and comprehensive overview on hypersensitivity in resistant cancer cells towards natural products and their derivatives. Since the majority of clinically established anticancer drugs are natural products or are in one way or another derived from them, it is worth hypothesizing that natural products may deliver promising lead compounds for the development of collateral sensitive anticancer drugs. Hypersensitivity occurs not only in classical ABC transporter-mediated multidrug resistance, but also in many other resistance phenotypes. Resistant cancers can be hypersensitive to natural compounds from diverse classes and origins (i.e. mitotic spindle poisons, DNA topoisomerase 1 and 2 inhibitors, diverse phytochemicals isolated from medicinal plants, (semi)synthetic derivatives of phytochemicals, antibiotics, marine drugs, recombinant therapeutic proteins and others). Molecular mechanisms of collateral sensitivity include (1) increased ATP hydrolysis and reactive oxygen species production by futile cycling during ABC transporter-mediated drug efflux, (2) inhibition of ATP production, and (3) alterations of drug target proteins (e.g. increased expression of topoisomerases and heat shock proteins, inhibition of Wnt/β-catenin pathway, mutations in β-tubulin). The phenomenon of hypersensitivity needs to be exploited for clinical oncology by the development of (1) novel combination protocols that include collateral sensitive drugs and (2) novel drugs that specifically exhibit high degrees of hypersensitivity in resistant tumors.
Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras.
Wang Tim,Yu Haiyan,Hughes Nicholas W,Liu Bingxu,Kendirli Arek,Klein Klara,Chen Walter W,Lander Eric S,Sabatini David M
The genetic dependencies of human cancers widely vary. Here, we catalog this heterogeneity and use it to identify functional gene interactions and genotype-dependent liabilities in cancer. By using genome-wide CRISPR-based screens, we generate a gene essentiality dataset across 14 human acute myeloid leukemia (AML) cell lines. Sets of genes with correlated patterns of essentiality across the lines reveal new gene relationships, the essential substrates of enzymes, and the molecular functions of uncharacterized proteins. Comparisons of differentially essential genes between Ras-dependent and -independent lines uncover synthetic lethal partners of oncogenic Ras. Screens in both human AML and engineered mouse pro-B cells converge on a surprisingly small number of genes in the Ras processing and MAPK pathways and pinpoint PREX1 as an AML-specific activator of MAPK signaling. Our findings suggest general strategies for defining mammalian gene networks and synthetic lethal interactions by exploiting the natural genetic and epigenetic diversity of human cancer cells.
A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation.
Michel Brittany C,D'Avino Andrew R,Cassel Seth H,Mashtalir Nazar,McKenzie Zachary M,McBride Matthew J,Valencia Alfredo M,Zhou Qianhe,Bocker Michael,Soares Luis M M,Pan Joshua,Remillard David I,Lareau Caleb A,Zullow Hayley J,Fortoul Nora,Gray Nathanael S,Bradner James E,Chan Ho Man,Kadoch Cigall
Nature cell biology
Mammalian SWI/SNF chromatin remodelling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF and a newly characterized non-canonical complex (ncBAF). However, their complex-specific targeting on chromatin, functions and roles in disease remain largely undefined. Here, we comprehensively mapped complex assemblies on chromatin and found that ncBAF complexes uniquely localize to CTCF sites and promoters. We identified ncBAF subunits as synthetic lethal targets specific to synovial sarcoma and malignant rhabdoid tumours, which both exhibit cBAF complex (SMARCB1 subunit) perturbation. Chemical and biological depletion of the ncBAF subunit, BRD9, rapidly attenuates synovial sarcoma and malignant rhabdoid tumour cell proliferation. Importantly, in cBAF-perturbed cancers, ncBAF complexes maintain gene expression at retained CTCF-promoter sites and function in a manner distinct from fusion oncoprotein-bound complexes. Together, these findings unmask the unique targeting and functional roles of ncBAF complexes and present new cancer-specific therapeutic targets.
HIF activation causes synthetic lethality between the tumor suppressor and the histone methyltransferase.
Chakraborty Abhishek A,Nakamura Eijiro,Qi Jun,Creech Amanda,Jaffe Jacob D,Paulk Joshiawa,Novak Jesse S,Nagulapalli Kshithija,McBrayer Samuel K,Cowley Glenn S,Pineda Javier,Song Jiaxi,Wang Yaoyu E,Carr Steven A,Root David E,Signoretti Sabina,Bradner James E,Kaelin William G
Science translational medicine
Inactivation of the von Hippel-Lindau tumor suppressor protein (pVHL) is the signature lesion in the most common form of kidney cancer, clear cell renal cell carcinoma (ccRCC). pVHL loss causes the transcriptional activation of hypoxia-inducible factor (HIF) target genes, including many genes that encode histone lysine demethylases. Moreover, chromatin regulators are frequently mutated in this disease. We found that ccRCC displays increased H3K27 acetylation and a shift toward mono- or unmethylated H3K27 caused by an HIF-dependent increase in H3K27 demethylase activity. Using a focused short hairpin RNA library, as well as CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) and a pharmacological inhibitor, we discovered that pVHL-defective ccRCC cells are hyperdependent on the H3K27 methyltransferase EZH1 for survival. Therefore, targeting EZH1 could be therapeutically useful in ccRCC.
Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data.
Sinha Subarna,Thomas Daniel,Chan Steven,Gao Yang,Brunen Diede,Torabi Damoun,Reinisch Andreas,Hernandez David,Chan Andy,Rankin Erinn B,Bernards Rene,Majeti Ravindra,Dill David L
Two genes are synthetically lethal (SL) when defects in both are lethal to a cell but a single defect is non-lethal. SL partners of cancer mutations are of great interest as pharmacological targets; however, identifying them by cell line-based methods is challenging. Here we develop MiSL (Mining Synthetic Lethals), an algorithm that mines pan-cancer human primary tumour data to identify mutation-specific SL partners for specific cancers. We apply MiSL to 12 different cancers and predict 145,891 SL partners for 3,120 mutations, including known mutation-specific SL partners. Comparisons with functional screens show that MiSL predictions are enriched for SLs in multiple cancers. We extensively validate a SL interaction identified by MiSL between the IDH1 mutation and ACACA in leukaemia using gene targeting and patient-derived xenografts. Furthermore, we apply MiSL to pinpoint genetic biomarkers for drug sensitivity. These results demonstrate that MiSL can accelerate precision oncology by identifying mutation-specific targets and biomarkers.
Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality.
Gogola Ewa,Duarte Alexandra A,de Ruiter Julian R,Wiegant Wouter W,Schmid Jonas A,de Bruijn Roebi,James Dominic I,Guerrero Llobet Sergi,Vis Daniel J,Annunziato Stefano,van den Broek Bram,Barazas Marco,Kersbergen Ariena,van de Ven Marieke,Tarsounas Madalena,Ogilvie Donald J,van Vugt Marcel,Wessels Lodewyk F A,Bartkova Jirina,Gromova Irina,Andújar-Sánchez Miguel,Bartek Jiri,Lopes Massimo,van Attikum Haico,Borst Piet,Jonkers Jos,Rottenberg Sven
Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have recently entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, drug resistance is a clinical hurdle, and we poorly understand how cancer cells escape the deadly effects of PARPi without restoring the HR pathway. By combining genetic screens with multi-omics analysis of matched PARPi-sensitive and -resistant Brca2-mutated mouse mammary tumors, we identified loss of PAR glycohydrolase (PARG) as a major resistance mechanism. We also found the presence of PARG-negative clones in a subset of human serous ovarian and triple-negative breast cancers. PARG depletion restores PAR formation and partially rescues PARP1 signaling. Importantly, PARG inactivation exposes vulnerabilities that can be exploited therapeutically.
A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy.
Srivas Rohith,Shen John Paul,Yang Chih Cheng,Sun Su Ming,Li Jianfeng,Gross Andrew M,Jensen James,Licon Katherine,Bojorquez-Gomez Ana,Klepper Kristin,Huang Justin,Pekin Daniel,Xu Jia L,Yeerna Huwate,Sivaganesh Vignesh,Kollenstart Leonie,van Attikum Haico,Aza-Blanc Pedro,Sobol Robert W,Ideker Trey
An emerging therapeutic strategy for cancer is to induce selective lethality in a tumor by exploiting interactions between its driving mutations and specific drug targets. Here we use a multi-species approach to develop a resource of synthetic lethal interactions relevant to cancer therapy. First, we screen in yeast ∼169,000 potential interactions among orthologs of human tumor suppressor genes (TSG) and genes encoding drug targets across multiple genotoxic environments. Guided by the strongest signal, we evaluate thousands of TSG-drug combinations in HeLa cells, resulting in networks of conserved synthetic lethal interactions. Analysis of these networks reveals that interaction stability across environments and shared gene function increase the likelihood of observing an interaction in human cancer cells. Using these rules, we prioritize ∼10(5) human TSG-drug combinations for future follow-up. We validate interactions based on cell and/or patient survival, including topoisomerases with RAD17 and checkpoint kinases with BLM.