Leveraging synthetic lethality to uncover potential therapeutic target in gastric cancer

Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. Ca-a Cancer J Clinicians. 2018;68:394–424.

Article  Google Scholar 

Zhang PH, Zheng ZG, Ling L, Yang XH, Zhang N, Wang X, et al. w09, a novel autophagy enhancer, induces autophagy-dependent cell apoptosis via activation of the EGFR-mediated RAS-RAF1-MAP2K-MAPK1/3 pathway. Autophagy. 2017;13:1093–112.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chung HC, Bang YJ, Fuchs CS, Qin SK, Satoh T, Shitara K, et al. First-line pembrolizumab/placebo plus trastuzumab and chemotherapy in HER2-positive advanced gastric cancer: KEYNOTE-811. Future Oncol. 2021;17:491–501.

Article  CAS  PubMed  Google Scholar 

Wang DS, Liu ZX, Lu YX, Bao H, Wu X, Zeng ZL, et al. Liquid biopsies to track trastuzumab resistance in metastatic HER2-positive gastric cancer. Gut. 2019;68:1152–61.

Article  CAS  PubMed  Google Scholar 

Lord CJ, Ashworth A. PARP inhibitors: Synthetic lethality in the clinic. Science. 2017;355:1152–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fong PC, Boss DS, Yap TA, Tutt A, Wu PJ, Mergui-Roelvink M, et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med. 2009;361:123–34.

Article  CAS  PubMed  Google Scholar 

Yeoh KG, Tan PT. Mapping the genomic diaspora of gastric cancer. Nat Rev Cancer. 2022;22:71–84.

Article  CAS  PubMed  Google Scholar 

Kroll ES, Hyland KM, Hieter P, Li JJ. Establishing genetic interactions by a synthetic dosage lethality phenotype. Genetics. 1996;143:95–102.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zecchini V, Frezza C. Metabolic synthetic lethality in cancer therapy. Biochimica Et Biophysica Acta-Bioenerg. 2017;1858:723–31.

Article  CAS  Google Scholar 

Muller FL, Aquilanti EA, DePinho RA. Collateral lethality: a new therapeutic strategy in oncology. Trends Cancer. 2015;1:161–73.

Article  PubMed  PubMed Central  Google Scholar 

Jerby-Arnon L, Pfetzer N, Waldman YY, McGarry L, James D, Shanks E, et al. Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality. Cell. 2014;158:1199–209.

Article  CAS  PubMed  Google Scholar 

Wang J, Zhang Q, Han J, Zhao Y, Zhao C, Yan B, et al. Computational methods, databases and tools for synthetic lethality prediction. Brief Bioinform. 2022;23:bbac106.

Article  PubMed  PubMed Central  Google Scholar 

Sinha S, Thomas D, Chan S, Gao Y, Brunen D, Torabi D, et al. Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data. Nat Commun. 2017;8:13.

Article  Google Scholar 

Lee JS, Das A, Jerby-Arnon L, Arafeh R, Auslander N, Davidson M, et al. Harnessing synthetic lethality to predict the response to cancer treatment. Nat Commun. 2018;9:12.

Google Scholar 

Das S, Deng X, Camphausen K, Shankavaram U. DiscoverSL: an R package for multi-omic data driven prediction of synthetic lethality in cancers. Bioinformatics. 2019;35:701–2.

Article  CAS  PubMed  Google Scholar 

Bass AJ, Thorsson V, Shmulevich I, Reynolds SM, Miller M, Bernard B, et al. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513:202–9.

Article  Google Scholar 

Cristescu R, Lee J, Nebozhyn M, Kim KM, Ting JC, Wong SS, et al. Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes. Nat Med. 2015;21:449–U217.

Article  CAS  PubMed  Google Scholar 

Lei ZD, Tan IB, Das K, Deng NT, Zouridis H, Pattison S, et al. Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil. Gastroenterology. 2013;145:554–65.

Article  CAS  PubMed  Google Scholar 

Yoon SJ, Park J, Shin Y, Choi Y, Park SW, Kang SG, et al. Deconvolution of diffuse gastric cancer and the suppression of CD34 on the BALB/c nude mice model. Bmc Cancer. 2020;20:10.

Article  Google Scholar 

Ghandi M, Huang FW, Jane-Valbuena J, Kryukov GV, Lo CC, McDonald ER, et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. 2019;569:503–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, et al. Missing value estimation methods for DNA microarrays. Bioinformatics. 2001;17:520–5.

Article  CAS  PubMed  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.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, et al. Defining a Cancer Dependency Map. Cell. 2017;170:564–76.e16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bashashati A, Haffari G, Ding JR, Ha G, Lui K, Rosner J, et al. DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer. Genome Biol. 2012;13:14.

Article  Google Scholar 

Wu GM, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol. 2010;11:23.

Article  Google Scholar 

He CY, Qiu MZ, Yang XH, Zhou DL, Ma JJ, Long YK, et al. Classification of gastric cancer by EBV status combined with molecular profiling predicts patient prognosis. Clin Transl Med. 2020;10:353–62.

Article  PubMed  PubMed Central  Google Scholar 

Ge S, Xia X, Ding C, Zhen B, Zhou Q, Feng J, et al. A proteomic landscape of diffuse-type gastric cancer. Nat Commun. 2018;9:1012.

Article  PubMed  PubMed Central  Google Scholar 

Wang K, Yuen ST, Xu J, Lee SP, Yan HH, Shi ST, et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet. 2014;46:573–82.

Article  CAS  PubMed  Google Scholar 

Lee YS, Cho YS, Lee GK, Lee S, Kim YW, Jho S, et al. Genomic profile analysis of diffuse-type gastric cancers. Genome Biol. 2014;15:R55.

Article  PubMed  PubMed Central  Google Scholar 

Cancer Genome Atlas Research, N. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513:202–9.

Article  Google Scholar 

Jeong SH, Park M, Park SY, Park J, Kim TH, Lee YJ, et al. Transcriptome analysis and the prognostic role of NUDC in diffuse and intestinal gastric cancer. Technol Cancer Res Treat. 2021;20:15330338211019501.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, et al. A census of human cancer genes. Nat Rev Cancer. 2004;4:177–83.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, et al. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013;10:1081–2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vogelstein B, Papadopoulos N, Velculescu VE, Zhou SB, Diaz LA, Kinzler KW. Cancer Genome Landscapes. Science. 2013;339:1546–58.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nat Methods. 2013;10:1108–15.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang JK, Jia TQ, Carlin DE, Ideker T. pyNBS: a Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018;34:2859–61.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tan IB, Ivanova T, Lim KH, Ong CW, Deng NT, Lee J, et al. Intrinsic subtypes of gastric cancer, based on gene expression pattern, predict survival and respond differently to chemotherapy. Gastroenterology. 2011;141:476–U551.

Article  PubMed  Google Scholar 

Cao J, Gong J, Li XH, Hu ZX, Xu YJ, Shi H, et al. Unsupervised hierarchical clustering identifies immune gene subtypes in gastric cancer. Front Pharmacol. 2021;12:12.

Article  Google Scholar 

Hanzelmann S, C

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