Siegel RL, Giaquinto AN, Jemal A (2024) Cancer statistics, 2024. CA Cancer J Clin 74(1):12–49

PubMed  Google Scholar 

Behan FM, Iorio F, Picco G, Goncalves E, Beaver CM, Migliardi G et al (2019) Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature 568(7753):511–516

Article  PubMed  CAS  Google Scholar 

Ghandi M, Huang FW, Jane-Valbuena J, Kryukov GV, Lo CC, McDonald ER 3rd et al (2019) Next-generation characterization of the cancer cell line encyclopedia. Nature 569(7757):503–508

Article  PubMed  PubMed Central  CAS  Google Scholar 

Chan EM, Shibue T, McFarland JM, Gaeta B, Ghandi M, Dumont N et al (2019) WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 568(7753):551–556

Article  PubMed  PubMed Central  CAS  Google Scholar 

Neggers JE, Paolella BR, Asfaw A, Rothberg MV, Skipper TA, Yang A et al (2020) Synthetic lethal interaction between the ESCRT paralog enzymes VPS4A and VPS4B in cancers harboring loss of chromosome 18q or 16q. Cell Rep 33(11):108493

Article  PubMed  PubMed Central  CAS  Google Scholar 

Gillani R, Seong BKA, Crowdis J, Conway JR, Dharia NV, Alimohamed S et al (2021) Gene fusions create partner and collateral dependencies essential to cancer cell survival. Cancer Res 81(15):3971–3984

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bondeson DP, Paolella BR, Asfaw A, Rothberg MV, Skipper TA, Langan C et al (2022) Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer. Nat Cancer 3(6):681–695

Article  PubMed  PubMed Central  CAS  Google Scholar 

Zhou J, Wu Z, Zhang Z, Goss L, McFarland J, Nagaraja A et al (2022) Pan-ERBB kinase inhibition augments CDK4/6 inhibitor efficacy in oesophageal squamous cell carcinoma. Gut 71(4):665–675

Article  PubMed  Google Scholar 

Adane B, Alexe G, Seong BKA, Lu D, Hwang EE, Hnisz D et al (2021) STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma. Cancer Cell 39(6):827–44 e10

Article  PubMed  PubMed Central  CAS  Google Scholar 

Sannigrahi MK, Cao AC, Rajagopalan P, Sun L, Brody RM, Raghav L et al (2024) A novel pipeline for prioritizing cancer type-specific therapeutic vulnerabilities using depmap identifies PAK2 as a target in head and neck squamous cell carcinomas. Mol Oncol 18(2):336–349

Article  PubMed  CAS  Google Scholar 

Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H et al (2017) Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet 49(12):1779–1784

Article  PubMed  PubMed Central  CAS  Google Scholar 

Jiang G, Zhang S, Yazdanparast A, Li M, Pawar AV, Liu Y et al (2016) Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer. BMC Genomics 17(Suppl 7):525

Article  PubMed  PubMed Central  Google Scholar 

Sharpe R, Pearson A, Herrera-Abreu MT, Johnson D, Mackay A, Welti JC et al (2011) Fgfr signaling promotes the growth of triple-negative and basal-like breast cancer cell lines both in vitro and in vivo. Clin Cancer Res 17(16):5275–5286

Article  PubMed  PubMed Central  CAS  Google Scholar 

Finn RS, Dering J, Conklin D, Kalous O, Cohen DJ, Desai AJ et al (2009) PD 0332991, a selective cyclin D kinase 4/6 inhibitor, preferentially inhibits proliferation of luminal estrogen receptor-positive human breast cancer cell lines in vitro. Breast Cancer Res 11(5):R77

Article  PubMed  PubMed Central  Google Scholar 

Sun R, Ge W, Zhu Y, Sayad A, Luna A, Lyu M et al (2023) Proteomic dynamics of breast cancer cell lines identifies potential therapeutic protein targets. Mol Cell Proteomics 22(8):100602

Article  PubMed  PubMed Central  CAS  Google Scholar 

Dai X, Cheng H, Bai Z, Li J (2017) Breast cancer cell line classification and its relevance with breast tumor subtyping. J Cancer 8(16):3131–3141

Article  PubMed  PubMed Central  Google Scholar 

Pacini C, Duncan E, Goncalves E, Gilbert J, Bhosle S, Horswell S et al (2024) A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization. Cancer Cell 42(2):301–16 e9

Article  PubMed  CAS  Google Scholar 

Polanski A, Marczyk M, Pietrowska M, Widlak P, Polanska J (2018) Initializing the EM algorithm for univariate Gaussian, multi-component, heteroscedastic mixture models by dynamic programming partitions. Int J Comput Methods. https://doi.org/10.1142/S0219876218500123

Article  Google Scholar 

Dempster JM, Pacini C, Pantel S, Behan FM, Green T, Krill-Burger J et al (2019) Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets. Nat Commun 10(1):5817

Article  PubMed  PubMed Central  CAS  Google Scholar 

Blomen VA, Majek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J et al (2015) Gene essentiality and synthetic lethality in haploid human cells. Science 350(6264):1092–1096

Article  PubMed  CAS  Google Scholar 

Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G et al (2015) High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163(6):1515–1526

Article  PubMed  CAS  Google Scholar 

Freshour SL, Kiwala S, Cotto KC, Coffman AC, McMichael JF, Song JJ et al (2021) Integration of the drug-gene interaction database (DGIdb 4.0) with open crowdsource efforts. Nucleic Acids Res 49(D1):D1144–D1151

Article  PubMed  CAS  Google Scholar 

Ochoa D, Hercules A, Carmona M, Suveges D, Baker J, Malangone C et al (2023) The next-generation open targets platform: reimagined, redesigned, rebuilt. Nucleic Acids Res 51(D1):D1353–D1359

Article  PubMed  Google Scholar 

Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z et al (2021) Clusterprofiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb) 2(3):100141

PubMed  CAS  Google Scholar 

Gu Z, Eils R, Schlesner M (2016) Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32(18):2847–2849

Article  PubMed  CAS  Google Scholar 

Li J, He D, Li S, Xiao J, Zhu Z (2023) Ferroptosis: the emerging player in remodeling triple-negative breast cancer. Front Immunol 14:1284057

Article  PubMed  PubMed Central  CAS  Google Scholar 

Fulda S (2013) Targeting c-FLICE-like inhibitory protein (CFLAR) in cancer. Expert Opin Ther Targets 17(2):195–201

Article  PubMed  CAS  Google Scholar 

Yang JS, Cao JM, Sun R, Zhou XJ, Chen ZH, Liu BW et al (2025) SMYD4 promotes MYH9 ubiquitination through lysine monomethylation modification to inhibit breast cancer progression. Breast Cancer Res 27(1):20

Article  PubMed  PubMed Central  CAS  Google Scholar 

Seachrist DD, Anstine LJ, Keri RA (2021) FOXA1: a pioneer of nuclear receptor action in breast cancer. Cancers (Basel). https://doi.org/10.3390/cancers13205205

Article  PubMed  Google Scholar 

Bianco G, Coto-Llerena M, Gallon J, Kancherla V, Taha-Mehlitz S, Marinucci M et al (2022) GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers. Commun Biol 5(1):373

Article