Morris LGT, Chan TA. Therapeutic targeting of tumor suppressor genes. Cancer. 2015;121:1357–68.
Article CAS PubMed Google Scholar
Wang T, Yu H, Hughes NW, Liu B, Kendirli A, Klein K, et al. Gene essentiality profiling reveals gene networks and synthetic lethal interactions with oncogenic ras. Cell. 2017;168(890–903):e15.
Pan J, Meyers RM, Michel BC, Mashtalir N, Sizemore AE, Wells JN, et al. Interrogation of mammalian protein complex structure, function, and membership using genome-scale fitness screens. Cell Syst. 2018;6:555–568.e7.
Article CAS PubMed PubMed Central Google Scholar
Kim E, Dede M, Lenoir WF, Wang G, Srinivasan S, Colic M, et al. A network of human functional gene interactions from knockout fitness screens in cancer cells. Life Sci Alliance [Internet]. 2019;2. Available from: https://www.ncbi.nlm.nih.gov/pubmed/30979825.
Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, et al. A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. Nat Genet. 2021;53:638–49.
Article CAS PubMed PubMed Central Google Scholar
Takemon Y, LeBlanc VG, Song J, Chan SY, Lee SD, Trinh DL, et al. Multi-omic analysis of CIC’s functional networks reveals novel interaction partners and a potential role in mitotic fidelity. Cancers. 2023;15:2805.
Article CAS PubMed PubMed Central Google Scholar
Mani R, St Onge RP, Hartman JL 4th, Giaever G, Roth FP. Defining genetic interaction. Proc Natl Acad Sci U S A. 2008;105:3461–6.
Article CAS PubMed PubMed Central Google Scholar
Behan FM, Iorio F, Picco G, Gonçalves E, Beaver CM, Migliardi G, et al. Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens. Nature. 2019;568:511–6.
Article CAS PubMed Google Scholar
De Kegel B, Quinn N, Thompson NA, Adams DJ, Ryan CJ. Comprehensive prediction of synthetic lethality between paralog pairs in cancer cell lines [Internet]. Cold Spring Harbor Laboratory. 2020. p. 2020.12.16.423022. Available from: https://www.biorxiv.org/content/https://doi.org/10.1101/2020.12.16.423022v1.
Jiang M, Instrell R, Saunders B, Berven H, Howell M. Tales from an academic RNAi screening facility. FAQs Brief Funct Genomics. 2011;10:227–37.
Article CAS PubMed Google Scholar
Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, et al. High-content CRISPR screening. Nat Rev Methods Primers. 2022;2:1–23.
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333–9.
Article CAS PubMed PubMed Central Google Scholar
Samstein RM, Lee C-H, Shoushtari AN, Hellmann MD, Shen R, Janjigian YY, et al. Tumor mutational load predicts survival after immunotherapy across multiple cancer types. Nat Genet. 2019;51:202–6.
Article CAS PubMed PubMed Central Google Scholar
Laskin J, Jones S, Aparicio S, Chia S, Ch’ng C, Deyell R, et al. Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers. Cold Spring Harb Mol Case Stud. 2015;1:a000570.
Article PubMed PubMed Central Google Scholar
Pleasance E, Titmuss E, Williamson L, Kwan H, Culibrk L, Zhao EY, et al. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. Nat Cancer. 2020;1:452–68.
Article CAS PubMed Google Scholar
Ferretti S, Hamon J, de Kanter R, Scheufler C, Andraos-Rey R, Barbe S, et al. Discovery of WRN inhibitor HRO761 with synthetic lethality in MSI cancers. Nature. 2024;629:443–9.
Article CAS PubMed PubMed Central Google Scholar
Baltgalvis KA, Lamb KN, Symons KT, Wu C-C, Hoffman MA, Snead AN, et al. Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase. Nature. 2024;629:435–42.
Article CAS PubMed Google Scholar
Kim H, Um E, Cho S-R, Jung C, Kim H, Kim J-S. Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat Methods. 2011;8:941–3.
Article CAS PubMed Google Scholar
Engelen E, Brandsma JH, Moen MJ, Signorile L, Dekkers DHW, Demmers J, et al. Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry. Nat Commun. 2015;6:7155.
Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol. 2014;10:757.
Hughes CS, Moggridge S, Müller T, Sorensen PH, Morin GB, Krijgsveld J. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat Protoc. 2019;14:68–85.
Article CAS PubMed Google Scholar
Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat Methods. 2017;14:513–20.
Article CAS PubMed PubMed Central Google Scholar
da Veiga LF, Haynes SE, Avtonomov DM, Chang H-Y, Shanmugam AK, Mellacheruvu D, et al. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 2020;17:869–70.
Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, et al. Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines. Cell Syst. 2018;6:271–281.e7.
Article CAS PubMed PubMed Central Google Scholar
Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011;476:298–303.
Article CAS PubMed PubMed Central Google Scholar
Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, et al. The genetics of nodal marginal zone lymphoma. Blood. 2016;128:1362–73.
Article CAS PubMed PubMed Central Google Scholar
Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, et al. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. Proc Natl Acad Sci U S A. 2013;110:18250–5.
Article PubMed PubMed Central Google Scholar
Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC-H, et al. The genetic landscape of the childhood cancer medulloblastoma. Science. 2011;331:435–9.
Article CAS PubMed Google Scholar
George J, Lim JS, Jang SJ, Cun Y, Ozretić L, Kong G, et al. Comprehensive genomic profiles of small cell lung cancer. Nature. 2015;524:47–53.
Article CAS PubMed PubMed Central Google Scholar
Takemon Y, Marra MA. GRETTA: an R package for mapping in silico genetic interaction and essentiality networks. Bioinformatics. 2023;39. Available from: https://doi.org/10.1093/bioinformatics/btad381.
DepMap B. DepMap 20Q1 Public. figshare; 2020. Available from: https://doi.org/10.6084/M9.FIGSHARE.11791698.V2.
Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER 3rd, et al. Next-generation characterization of the cancer cell line encyclopedia. Nature. 2019;569:503–8.
Article CAS PubMed PubMed Central Google Scholar
Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, et al. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet. 2017;49:1779–84.
留言 (0)