Extending the Lymphoblastoid Cell Line Model for Drug Combination Pharmacogenomics

References

• Jia J , ZhuF , MaX , CaoZW , LiYX , ChenYZ. Mechanisms of drug combinations: interaction and network perspectives. Nat. Rev. Drug Discov.8(2), 111–128 (2009).
   PubMed Web of Science ®Google Scholar
• Lin A , GiulianoCJ , PalladinoAet al. Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. Sci. Transl. Med.11(509), 1–18 (2019).
   Web of Science ®Google Scholar
• Palmer AC , SorgerPK. Combination cancer therapy can confer benefit via patient-to-patient variability without drug additivity or synergy. Cell171(7), 1678–1691.e1613 (2017).
   PubMed Web of Science ®Google Scholar
• Jack J , RotroffD , Motsinger-ReifA. Lymphoblastoid cell lines models of drug response: successes and lessons from this pharmacogenomic model. Curr. Mol. Med.14(7), 833–840 (2014).
   PubMed Web of Science ®Google Scholar
• Hussain T , MulherkarR. Lymphoblastoid cell lines: a continuous in vitro source of cells to study carcinogen sensitivity and DNA repair. Int. J. Mol. Cell. Med.1(2), 75–87 (2012).
   PubMedGoogle Scholar
• Wheeler HE , DolanME. Lymphoblastoid cell lines in pharmacogenomic discovery and clinical translation. Pharmacogenomics13(1), 55–70 (2012).
   PubMed Web of Science ®Google Scholar
• Ellsworth KA , EckloffBW , LiLet al. Contribution of FKBP5 genetic variation to gemcitabine treatment and survival in pancreatic adenocarcinoma. PLoS ONE8(8), e70216 (2013).
   PubMed Web of Science ®Google Scholar
• Huang RS , JohnattySE , GamazonERet al. Platinum sensitivity-related germline polymorphism discovered via a cell-based approach and analysis of its association with outcome in ovarian cancer patients. Clin. Cancer Res.17(16), 5490–5500 (2011).
   PubMed Web of Science ®Google Scholar
• Jeon J-P . Chapter 6 – Human Lymphoblastoid Cell Lines in Pharmacogenomics. In: Handbook of Pharmacogenomics and Stratified Medicine.PadmanabhanS ( Ed.). Academic Press, CA, USA, 89–110 (2014).
   Google Scholar
• Li L , FridleyB , KalariKet al. Gemcitabine and cytosine arabinoside cytotoxicity: association with lymphoblastoid cell expression. Cancer Res.68(17), 7050–7058 (2008).
   PubMed Web of Science ®Google Scholar
• Medina MW , GaoF , RuanW , RotterJI , KraussRM. Alternative splicing of 3-hydroxy-3-methylglutaryl coenzyme A reductase is associated with plasma low-density lipoprotein cholesterol response to simvastatin. Circulation118(4), 355–362 (2008).
   PubMed Web of Science ®Google Scholar
• Brown CC , HavenerTM , MedinaMWet al. Genome-wide association and pharmacological profiling of 29 anticancer agents using lymphoblastoid cell lines. Pharmacogenomics15(2), 137–146 (2014).
   PubMed Web of Science ®Google Scholar
• Brown CC , HavenerTM , MedinaMWet al. A genome-wide association analysis of temozolomide response using lymphoblastoid cell lines shows a clinically relevant association with MGMT. Pharmacogenet. Genomics22(11), 796–802 (2012).
   PubMed Web of Science ®Google Scholar
• Wheeler HE , GamazonER , StarkALet al. Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. Pharmacogenomics J.13(1), 35–43 (2013).
   PubMed Web of Science ®Google Scholar
• Motsinger-Reif AA , RotroffDM. Leveraging lymphoblastoid cell lines for drug response modeling. J. Data Min. Genomics Proteomics6(3), 1 (2015).
   Google Scholar
• Niu N , WangL. In vitro human cell line models to predict clinical response to anticancer drugs. Pharmacogenomics16(3), 273–285 (2015).
   PubMed Web of Science ®Google Scholar
• Stark AL , DolanME. Lymphoblastoid cell lines in pharmacogenomics: how applicable are they to clinical outcomes?Pharmacogenomics14(5), 447–450 (2013).
   PubMed Web of Science ®Google Scholar
• Fridley BL , GhoshTM , WangAet al. Genome-wide study of response to platinum, taxane, and combination therapy in ovarian cancer: in vitro phenotypes, inherited variation, and disease recurrence. Front Genet7, 37 (2016).
   PubMed Web of Science ®Google Scholar
• Pinto R , AssisJ , NogueiraAet al. Pharmacogenomics in epithelial ovarian cancer first-line treatment outcome: validation of GWAS-associated NRG3 rs1649942 and BRE rs7572644 variants in an independent cohort. Pharmacogenomics J.19(1), 25–32 (2019).
   PubMed Web of Science ®Google Scholar
• Bansal M , YangJ , KaranCet al. A community computational challenge to predict the activity of pairs of compounds. Nat. Biotechnol.32(12), 1213–1222 (2014).
   PubMed Web of Science ®Google Scholar
• Menden MP , WangD , MasonMJet al. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nat. Commun.10(1), 2674 (2019).
   PubMedGoogle Scholar
• O’Neil J , BenitaY , FeldmanIet al. An unbiased oncology compound screen to identify novel combination strategies. Mol. Cancer Ther.15(6), 1155–1162 (2016).
   PubMed Web of Science ®Google Scholar
• Menden MP , CasaleFP , StephanJet al. The germline genetic component of drug sensitivity in cancer cell lines. Nat. Commun.9(1), 3385 (2018).
   PubMedGoogle Scholar
• Moen EL , GodleyLA , ZhangW , DolanME. Pharmacogenomics of chemotherapeutic susceptibility and toxicity. Genome Med.4(11), 90 (2012).
   PubMedGoogle Scholar
• Dolan ME , NewboldKG , NagasubramanianRet al. Heritability and linkage analysis of sensitivity to cisplatin-induced cytotoxicity. Cancer Res.64(12), 4353–4356 (2004).
   PubMed Web of Science ®Google Scholar
• Wheeler HE , MaitlandML , DolanME , CoxNJ , RatainMJ. Cancer pharmacogenomics: strategies and challenges. Nat. Rev. Genet.14(1), 23–34 (2013).
   PubMed Web of Science ®Google Scholar
• Relling MV , SchwabM , Whirl-CarrilloMet al. Clinical pharmacogenetics implementation consortium guideline for thiopurine dosing based on TPMT and NUDT 15 genotypes: 2018 update. Clin. Pharmacol. Ther.105(5), 1095–1105 (2019).
   PubMed Web of Science ®Google Scholar
• Gillet JP , VarmaS , GottesmanMM. The clinical relevance of cancer cell lines. J. Natl Cancer Inst.105(7), 452–458 (2013).
   PubMedGoogle Scholar
• Hussain T , KotnisA , SarinR , MulherkarR. Establishment & characterization of lymphoblastoid cell lines from patients with multiple primary neoplasms in the upper aero-digestive tract & healthy individuals. Indian J. Med. Res.135(6), 820–829 (2012).
   PubMed Web of Science ®Google Scholar
• Hynds RE , VladimirouE , JanesSM. The secret lives of cancer cell lines. Dis. Model Mech.11(11), dmm037366 (2018).
   PubMed Web of Science ®Google Scholar
• Chou TC . Drug combination studies and their synergy quantification using the Chou-Talalay method. Cancer Res.70(2), 440–446 (2010).
   PubMed Web of Science ®Google Scholar
• Roell KR , HavenerTM , ReifDMet al. Synergistic chemotherapy drug response is a genetic trait in lymphoblastoid cell lines. Front. Genet.10, 829 (2019).
   PubMed Web of Science ®Google Scholar
• Crystal AS , ShawAT , SequistLVet al. Patient-derived models of acquired resistance can identify effective drug combinations for cancer. Science346(6216), 1480–1486 (2014).
   PubMed Web of Science ®Google Scholar
• Gayvert KM , AlyO , PlattJ , BosenbergMW , SternDF , ElementoO. A computational approach for identifying synergistic drug combinations. PLoS Comput. Biol.13(1), e1005308 (2017).
   PubMed Web of Science ®Google Scholar
• Holbeck SL , CamalierR , CrowellJAet al. The National Cancer Institute ALMANAC: a comprehensive screening resource for the detection of anticancer drug pairs with enhanced therapeutic activity. Cancer Res.77(13), 3564–3576 (2017).
   PubMed Web of Science ®Google Scholar
• Roell KR , ReifDM , Motsinger-ReifAA. An introduction to terminology and methodology of chemical synergy-perspectives from across disciplines. Front. Pharmacol.8, 158 (2017).
   PubMed Web of Science ®Google Scholar
• Jonsson VD , BlakelyCM , LinLet al. Novel computational method for predicting polytherapy switching strategies to overcome tumor heterogeneity and evolution. Sci. Rep.7, 44206 (2017).
   PubMed Web of Science ®Google Scholar
• Komarova NL , WodarzD. Drug resistance in cancer: principles of emergence and prevention. Proc. Natl Acad. Sci. USA102(27), 9714–9719 (2005).
   PubMed Web of Science ®Google Scholar
• Anchang B , DavisKL , FienbergHGet al. DRUG-NEM: optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity. Proc. Natl Acad. Sci. USA115(18), E4294–E4303 (2018).
   PubMed Web of Science ®Google Scholar
• Hoffman JA , PapasBN , TrotterKW , ArcherTK. Single-cell RNA sequencing reveals a heterogeneous response to glucocorticoids in breast cancer cells. Commun. Biol.3(1), 126 (2020).
   PubMed Web of Science ®Google Scholar
• Zhao B , HemannMT , LauffenburgerDA. Intratumor heterogeneity alters most effective drugs in designed combinations. Proc. Natl Acad. Sci. USA111(29), 10773–10778 (2014).
   PubMed Web of Science ®Google Scholar
• Zhao B , PritchardJR , LauffenburgerDA , HemannMT. Addressing genetic tumor heterogeneity through computationally predictive combination therapy. Cancer Discov.4(2), 166–174 (2014).
   PubMed Web of Science ®Google Scholar
• Chen SH , YangW , FanYet al. A genome-wide approach identifies that the aspartate metabolism pathway contributes to asparaginase sensitivity. Leukemia25(1), 66–74 (2011).
   PubMed Web of Science ®Google Scholar
• Dzamko N , DeakM , HentatiFet al. Inhibition of LRRK2 kinase activity leads to dephosphorylation of Ser(910)/Ser(935), disruption of 14-3-3 binding and altered cytoplasmic localization. Biochem. J.430(3), 405–413 (2010).
   PubMedGoogle Scholar
• Gamazon ER , HuangRS , CoxNJ , DolanME. Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Proc. Natl Acad. Sci. USA107(20), 9287–9292 (2010).
   PubMed Web of Science ®Google Scholar
• Hartford CM , DuanS , DelaneySMet al. Population-specific genetic variants important in susceptibility to cytarabine arabinoside cytotoxicity. Blood113(10), 2145–2153 (2009).
   PubMed Web of Science ®Google Scholar
• Kotaki R , KawashimaM , YamamotoYet al. Dasatinib exacerbates splenomegaly of mice inoculated with Epstein-Barr virus-infected lymphoblastoid cell lines. Sci. Rep.10(1), 4355 (2020).
   PubMed Web of Science ®Google Scholar
• Loomis R , CarboneR , ReissM , LacyJ. Bcl-2 antisense (G3139, Genasense) enhances the in vitro and in vivo response of Epstein-Barr virus-associated lymphoproliferative disease to rituximab. Clin. Cancer Res.9(5), 1931–1939 (2003).
   PubMed Web of Science ®Google Scholar
• Mitra AK , CrewsK , PoundsSet al. Impact of genetic variation in FKBP5 on clinical response in pediatric acute myeloid leukemia patients: a pilot study. Leukemia25(8), 1354–1356 (2011).
   PubMed Web of Science ®Google Scholar
• O’Donnell PH , GamazonE , ZhangWet al. Population differences in platinum toxicity as a means to identify novel genetic susceptibility variants. Pharmacogenet. Genomics20(5), 327–337 (2010).
   PubMed Web of Science ®Google Scholar
• Peters EJ , KrajaAT , LinSJet al. Association of thymidylate synthase variants with 5-fluorouracil cytotoxicity. Pharmacogenet. Genomics19(5), 399–401 (2009).
   PubMed Web of Science ®Google Scholar
• Shan D , LedbetterJA , PressOW. Apoptosis of malignant human B cells by ligation of CD20 with monoclonal antibodies. Blood91(5), 1644–1652 (1998).
   PubMed Web of Science ®Google Scholar
• Tan XL , MoyerAM , FridleyBLet al. Genetic variation predicting cisplatin cytotoxicity associated with overall survival in lung cancer patients receiving platinum-based chemotherapy. Clin. Cancer Res.17(17), 5801–5811 (2011).
   PubMed Web of Science ®Google Scholar
• Ziliak D , O’DonnellPH , ImHKet al. Germline polymorphisms discovered via a cell-based, genome-wide approach predict platinum response in head and neck cancers. Transl. Res.157(5), 265–272 (2011).
   PubMed Web of Science ®Google Scholar
• Chen D , LiuX , YangY , YangH , LuP. Systematic synergy modeling: understanding drug synergy from a systems biology perspective. BMC Syst. Biol.9, 56 (2015).
   PubMed Web of Science ®Google Scholar
• Regan-Fendt KE , XuJ , DivincenzoMet al. Synergy from gene expression and network mining (SynGeNet) method predicts synergistic drug combinations for diverse melanoma genomic subtypes. NPJ Syst. Biol. Appl.5, 6 (2019).
   PubMed Web of Science ®Google Scholar
• Yeh PJ , HegrenessMJ , AidenAP , KishonyR. Drug interactions and the evolution of antibiotic resistance. Nat. Rev. Microbiol.7(6), 460–466 (2009).
   PubMed Web of Science ®Google Scholar
• Zhang Y , SmolenP , BaxterDA , ByrneJH. Computational analyses of synergism in small molecular network motifs. PLoS Comput. Biol.10(3), e1003524 (2014).
   PubMed Web of Science ®Google Scholar
• Yin N , MaW , PeiJ , OuyangQ , TangC , LaiL. Synergistic and antagonistic drug combinations depend on network topology. PLoS ONE9(4), e93960 (2014).
   PubMed Web of Science ®Google Scholar
• Khatri P , SirotaM , ButteAJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol.8(2), e1002375 (2012).
   PubMed Web of Science ®Google Scholar
• Pirkl M , DiekmannM , VanDer Wees M , BeerenwinkelN , FröhlichH , MarkowetzF. Inferring modulators of genetic interactions with epistatic nested effects models. PLoS Comput. Biol.13(4), e1005496 (2017).
   PubMed Web of Science ®Google Scholar
• Van Wageningen S , KemmerenP , LijnzaadPet al. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell143(6), 991–1004 (2010).
   PubMed Web of Science ®Google Scholar
• Alvarez MJ , SubramaniamPS , TangLHet al. A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Nat. Genet.50(7), 979–989 (2018).
   PubMed Web of Science ®Google Scholar
• Baskar R , FienbergHG , KhairZet al. TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis. Life Sci. Alliance2(6), e201900554 (2019).
   PubMed Web of Science ®Google Scholar
• Hong SP , ChanTE , LombardoYet al. Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy. Nat. Commun.10(1), 3840 (2019).
   PubMedGoogle Scholar
• Osorio D , YuX , YuP , SerpedinE , CaiJJ. Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. Sci. Data6(1), 112 (2019).
   PubMedGoogle Scholar
• Borel C , FerreiraPG , SantoniFet al. Biased allelic expression in human primary fibroblast single cells. Am. J. Hum. Genet.96(1), 70–80 (2015).
   PubMed Web of Science ®Google Scholar
• Eyler CE , MatsunagaH , HovestadtV , VantineSJ , Van GalenP , BernsteinBE. Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome Biol.21(1), 174 (2020).
   PubMed Web of Science ®Google Scholar
• Cancer Therapy Advisor . Breast, skin, prostate, lung cancer treatment regimens. Haymarket Media, Inc., NY, USA. https://www.cancertherapyadvisor.com/home/cancer-treatment-regimens/
   Google Scholar
• Ma J , BairE , Motsinger-ReifA. Nonlinear dose-response modeling of high-throughput screening data using an evolutionary algorithm. Dose Response18(2), 1559325820926734 (2020).
   Web of Science ®Google Scholar
• Bates D , WattsD. Nonlinear regression: iterative estimation and linear approximations. In: Nonlinear Regression Analysis and Its Applications.John Wiley & Sons, Inc., NJ, USA, 32–66 (2008).
   Google Scholar
• Meyer CT , WootenDJ , LopezCF , QuarantaV. Charting the fragmented landscape of drug synergy. Trends Pharmacol. Sci.41(4), 266–280 (2020).
   PubMed Web of Science ®Google Scholar
• Bliss CI . The toxicity of poisons applied jointly 1. Ann. Appl. Biol.26(3), 585–615 (1939).
   Google Scholar
• Loewe S . The problem of synergism and antagonism of combined drugs. Arzneimittelforschung3(6), 285–290 (1953).
   PubMed Web of Science ®Google Scholar
• Folkesson E , NiederdorferB , NakstadVTet al. High-throughput screening reveals higher synergistic effect of MEK inhibitor combinations in colon cancer spheroids. Sci. Rep.10(1), 11574 (2020).
   PubMed Web of Science ®Google Scholar