Targeting synthetic lethal paralogs in cancer

Trends in Cancer - Tập 9 - Trang 397-409 - 2023
Colm J. Ryan1,2, Ishan Mehta3, Narod Kebabci1,4, David J. Adams3
1Conway Institute and School of Computer Science, University College Dublin, Dublin, Ireland
2Systems Biology Ireland, University College Dublin, Dublin, Ireland
3Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
4Science Foundation Ireland (SFI) Centre for Research Training in Genomics Data Science, University College Dublin, Dublin, Ireland

Tài liệu tham khảo

Huang, 2020, Synthetic lethality as an engine for cancer drug target discovery, Nat. Rev. Drug Discov., 19, 23, 10.1038/s41573-019-0046-z O'Neil, 2017, Synthetic lethality and cancer, Nat. Rev. Genet., 18, 613, 10.1038/nrg.2017.47 Farmer, 2005, Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy, Nature, 434, 917, 10.1038/nature03445 Bryant, 2005, Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase, Nature, 434, 913, 10.1038/nature03443 Lord, 2017, PARP inhibitors: synthetic lethality in the clinic, Science, 355, 1152, 10.1126/science.aam7344 Mullard, 2017, Synthetic lethality screens point the way to new cancer drug targets, Nat. Rev. Drug Discov., 16, 589, 10.1038/nrd.2017.165 Muller, 2015, Collateral lethality: a new therapeutic strategy in oncology, Trends Cancer Res., 1, 161, 10.1016/j.trecan.2015.10.002 Kuzmin, 2022, Retention of duplicated genes in evolution, Trends Genet., 38, 59, 10.1016/j.tig.2021.06.016 Kaessmann, 2009, RNA-based gene duplication: mechanistic and evolutionary insights, Nat. Rev. Genet., 10, 19, 10.1038/nrg2487 Carelli, 2016, The life history of retrocopies illuminates the evolution of new mammalian genes, Genome Res., 26, 301, 10.1101/gr.198473.115 Dehal, 2005, Two rounds of whole genome duplication in the ancestral vertebrate, PLoS Biol., 3, 10.1371/journal.pbio.0030314 Vilella, 2009, EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates, Genome Res., 19, 327, 10.1101/gr.073585.107 Yates, 2020, Ensembl 2020, Nucleic Acids Res., 48, D682 De Kegel, 2021, Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines, Cell Syst., 12, 1144, 10.1016/j.cels.2021.08.006 Dean, 2008, Pervasive and persistent redundancy among duplicated genes in yeast, PLoS Genet., 4, 10.1371/journal.pgen.1000113 Costanzo, 2016, A global genetic interaction network maps a wiring diagram of cellular function, Science, 353, aaf1420, 10.1126/science.aaf1420 Musso, 2008, The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast, Genome Res., 18, 1092, 10.1101/gr.076174.108 DeLuna, 2008, Exposing the fitness contribution of duplicated genes, Nat. Genet., 40, 676, 10.1038/ng.123 Tischler, 2006, Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution, Genome Biol., 7, R69, 10.1186/gb-2006-7-8-r69 Fisher, 2013, Cancer heterogeneity: implications for targeted therapeutics, Br. J. Cancer, 108, 479, 10.1038/bjc.2012.581 Sondka, 2018, The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers, Nat. Rev. Cancer, 18, 696, 10.1038/s41568-018-0060-1 Frei, 1993, Gene deletion: a new target for cancer chemotherapy, Lancet, 342, 662, 10.1016/0140-6736(93)91764-D De Kegel, 2022, Paralog dispensability shapes homozygous deletion patterns in tumor genomes, bioRxiv Muller, 2012, Passenger deletions generate therapeutic vulnerabilities in cancer, Nature, 488, 337, 10.1038/nature11331 Pacini, 2021, Integrated cross-study datasets of genetic dependencies in cancer, Nat. Commun., 12, 1661, 10.1038/s41467-021-21898-7 Meyers, 2017, Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells, Nat. Genet., 49, 1779, 10.1038/ng.3984 Behan, 2019, Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens, Nature, 568, 511, 10.1038/s41586-019-1103-9 Viswanathan, 2018, Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer, Nat. Genet., 50, 937, 10.1038/s41588-018-0155-3 De Kegel, 2019, Paralog buffering contributes to the variable essentiality of genes in cancer cell lines, PLoS Genet., 15, 10.1371/journal.pgen.1008466 Dede, 2020, Multiplex enCas12a screens detect functional buffering among paralogs otherwise masked in monogenic Cas9 knockout screens, Genome Biol., 21, 262, 10.1186/s13059-020-02173-2 Köferle, 2022, Interrogation of cancer gene dependencies reveals paralog interactions of autosome and sex chromosome-encoded genes, Cell Rep., 39, 10.1016/j.celrep.2022.110636 Helming, 2014, ARID1B is a specific vulnerability in ARID1A-mutant cancers, Nat. Med., 20, 251, 10.1038/nm.3480 Hoffman, 2014, Functional epigenetics approach identifies BRM/SMARCA2 as a critical synthetic lethal target in BRG1-deficient cancers, Proc. Natl. Acad. Sci. U. S. A., 111, 3128, 10.1073/pnas.1316793111 van der Lelij, 2020, STAG1 vulnerabilities for exploiting cohesin synthetic lethality in STAG2-deficient cancers, Life Sci. Alliance, 3, 10.26508/lsa.202000725 Thompson, 2021, Combinatorial CRISPR screen identifies fitness effects of gene paralogues, Nat. Commun., 12, 1302, 10.1038/s41467-021-21478-9 Parrish, 2021, Discovery of synthetic lethal and tumor suppressor paralog pairs in the human genome, Cell Rep., 36, 10.1016/j.celrep.2021.109597 Gonatopoulos-Pournatzis, 2020, Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform, Nat. Biotechnol., 38, 638, 10.1038/s41587-020-0437-z Ito, 2021, Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers, Nat. Genet., 53, 1664, 10.1038/s41588-021-00967-z Ryan, 2018, Synthetic lethality and cancer – penetrance as the major barrier, Trends Cancer Res., 4, 671, 10.1016/j.trecan.2018.08.003 Lord, 2020, Integrative analysis of large-scale loss-of-function screens identifies robust cancer-associated genetic interactions, eLife, 9, 10.7554/eLife.58925 Guan, 2007, Functional analysis of gene duplications in Saccharomyces cerevisiae, Genetics, 175, 933, 10.1534/genetics.106.064329 VanderSluis, 2010, Genetic interactions reveal the evolutionary trajectories of duplicate genes, Mol. Syst. Biol., 6, 429, 10.1038/msb.2010.82 Downward, 2015, RAS synthetic lethal screens revisited: still seeking the elusive prize?, Clin. Cancer Res., 21, 1802, 10.1158/1078-0432.CCR-14-2180 Henkel, 2019, Context-dependent genetic interactions in cancer, Curr. Opin. Genet. Dev., 54, 73, 10.1016/j.gde.2019.03.004 Ku, 2020, Integration of multiple biological contexts reveals principles of synthetic lethality that affect reproducibility, Nat. Commun., 11, 2375, 10.1038/s41467-020-16078-y Kuzmin, 2020, Exploring whole-genome duplicate gene retention with complex genetic interaction analysis, Science, 368, eaaz5667, 10.1126/science.aaz5667 Kelly, 2020, Combined proteomic and genetic interaction mapping reveals new RAS effector pathways and susceptibilities, Cancer Discov., 10, 1950, 10.1158/2159-8290.CD-19-1274 Wilson, 2014, Residual complexes containing SMARCA2 (BRM) underlie the oncogenic drive of SMARCA4 (BRG1) mutation, Mol. Cell. Biol., 34, 1136, 10.1128/MCB.01372-13 Oike, 2013, A synthetic lethality-based strategy to treat cancers harboring a genetic deficiency in the chromatin remodeling factor BRG1, Cancer Res., 73, 5508, 10.1158/0008-5472.CAN-12-4593 Vangamudi, 2015, The SMARCA2/4 ATPase domain surpasses the bromodomain as a drug target in SWI/SNF-mutant cancers: insights from cDNA rescue and PFI-3 inhibitor studies, Cancer Res., 75, 3865, 10.1158/0008-5472.CAN-14-3798 Munoz, 2016, CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions, Cancer Discov., 6, 900, 10.1158/2159-8290.CD-16-0178 Shi, 2015, Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains, Nat. Biotechnol., 33, 661, 10.1038/nbt.3235 He, 2019, De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens, Nat. Commun., 10, 4541, 10.1038/s41467-019-12489-8 Bhogal, 2022, The methyltransferase domain of DNMT1 is an essential domain in acute myeloid leukemia independent of DNMT3A mutation, Commun. Biol., 5, 1174, 10.1038/s42003-022-04139-5 Lai, 2017, Induced protein degradation: an emerging drug discovery paradigm, Nat. Rev. Drug Discov., 16, 101, 10.1038/nrd.2016.211 Xiao, 2021, Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer, Nature, 601, 434, 10.1038/s41586-021-04246-z Farnaby, 2019, BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design, Nat. Chem. Biol., 15, 672, 10.1038/s41589-019-0294-6 Kofink, 2022, A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo, Nat. Commun., 13, 5969, 10.1038/s41467-022-33430-6 Kruger, 2012, Global analysis of small molecule binding to related protein targets, PLoS Comput. Biol., 8, 10.1371/journal.pcbi.1002333 Ochoa, 2021, Open Targets Platform: supporting systematic drug-target identification and prioritisation, Nucleic Acids Res., 49, D1302, 10.1093/nar/gkaa1027 Sherr, 2016, Targeting CDK4 and CDK6: from discovery to therapy, Cancer Discov., 6, 353, 10.1158/2159-8290.CD-15-0894 Medina, 2008, Lapatinib: a dual inhibitor of human epidermal growth factor receptor tyrosine kinases, Clin. Ther., 30, 1426, 10.1016/j.clinthera.2008.08.008 Lin, 2013, Targeting activated Akt with GDC-0068, a novel selective Akt inhibitor that is efficacious in multiple tumor models, Clin. Cancer Res., 19, 1760, 10.1158/1078-0432.CCR-12-3072 Flaherty, 2012, Improved survival with MEK inhibition in BRAF-mutated melanoma, N. Engl. J. Med., 367, 107, 10.1056/NEJMoa1203421 Zhao, 2019, A one-step tRNA-CRISPR system for genome-wide genetic interaction mapping in mammalian cells, Sci. Rep., 9, 14499, 10.1038/s41598-019-51090-3 Najm, 2017, Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens, Nat. Biotechnol., 36, 179, 10.1038/nbt.4048 DeWeirdt, 2021, Optimization of AsCas12a for combinatorial genetic screens in human cells, Nat. Biotechnol., 39, 94, 10.1038/s41587-020-0600-6 Ogiwara, 2016, Targeting p300 addiction in CBP-deficient cancers causes synthetic lethality by apoptotic cell death due to abrogation of MYC expression, Cancer Discov., 6, 430, 10.1158/2159-8290.CD-15-0754 van der Lelij, 2017, Synthetic lethality between the cohesin subunits STAG1 and STAG2 in diverse cancer contexts, eLife, 6, 10.7554/eLife.26980 Benedetti, 2017, Synthetic lethal interaction between the tumour suppressor STAG2 and its paralog STAG1, Oncotarget, 8, 37619, 10.18632/oncotarget.16838 Dey, 2017, Genomic deletion of malic enzyme 2 confers collateral lethality in pancreatic cancer, Nature, 542, 119, 10.1038/nature21052 Yoshihama, 2022, Potent and selective PTDSS1 inhibitors induce collateral lethality in cancers with PTDSS2 deletion, Cancer Res., 82, 4031, 10.1158/0008-5472.CAN-22-1006 Szymańska, 2020, Synthetic lethality between VPS4A and VPS4B triggers an inflammatory response in colorectal cancer, EMBO Mol. Med., 12, 10.15252/emmm.201910812 Neggers, 2020, Synthetic lethal interaction between the ESCRT paralog enzymes VPS4A and VPS4B in cancers harboring loss of chromosome 18q or 16q, Cell Rep., 33, 10.1016/j.celrep.2020.108493 Malone, 2021, Selective modulation of a pan-essential protein as a therapeutic strategy in cancer, Cancer Discov., 11, 2282, 10.1158/2159-8290.CD-20-1213 Tsherniak, 2017, Defining a cancer dependency map, Cell, 170, 564, 10.1016/j.cell.2017.06.010 So, 2022, VRK1 as a synthetic lethal target in VRK2 promoter-methylated cancers of the nervous system, JCI Insight, 7, 10.1172/jci.insight.158755 Shields, 2022, VRK1 is a synthetic-lethal target in VRK2-deficient glioblastoma, Cancer Res., 82, 4044, 10.1158/0008-5472.CAN-21-4443