Skip to main content

Advertisement

Log in

Molecular determinants of drug response in TNBC cell lines

  • Preclinical study
  • Published:
Breast Cancer Research and Treatment Aims and scope Submit manuscript

Abstract

Purpose

There is a need for biomarkers of drug efficacy for targeted therapies in triple-negative breast cancer (TNBC). As a step toward this, we identify multi-omic molecular determinants of anti-TNBC efficacy in cell lines for a panel of oncology drugs.

Methods

Using 23 TNBC cell lines, drug sensitivity scores (DSS3) were determined using a panel of investigational drugs and drugs approved for other indications. Molecular readouts were generated for each cell line using RNA sequencing, RNA targeted panels, DNA sequencing, and functional proteomics. DSS3 values were correlated with molecular readouts using a FDR-corrected significance cutoff of p* < 0.05 and yielded molecular determinant panels that predict anti-TNBC efficacy.

Results

Six molecular determinant panels were obtained from 12 drugs we prioritized based on their efficacy. Determinant panels were largely devoid of DNA mutations of the targeted pathway. Molecular determinants were obtained by correlating DSS3 with molecular readouts. We found that co-inhibiting molecular correlate pathways leads to robust synergy across many cell lines.

Conclusions

These findings demonstrate an integrated method to identify biomarkers of drug efficacy in TNBC where DNA predictions correlate poorly with drug response. Our work outlines a framework for the identification of novel molecular determinants and optimal companion drugs for combination therapy based on these correlates.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Pareja F, Reis-Filho JS (2018) Triple-negative breast cancers—a panoply of cancer types. Nat Rev Clin Oncol 15(6):347–348

    CAS  PubMed  Google Scholar 

  2. Wahba HA, El-Hadaad HA (2015) Current approaches in treatment of triple-negative breast cancer. Cancer Biol Med 12(2):106–116

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Kalimutho M, Parsons K, Mittal D, Lopez JA, Srihari S, Khanna KK (2015) Targeted therapies for triple-negative breast cancer: combating a stubborn disease. Trends Pharmacol Sci 36(12):822–846

    CAS  PubMed  Google Scholar 

  4. Le Du F, Ueno NT (2015) Targeted therapies in triple-negative breast cancer: failure and future. Womens Health (Lond) 11(1):1–5

    Google Scholar 

  5. Yam C, Mani SA, Moulder SL (2017) Targeting the molecular subtypes of triple negative breast cancer: understanding the diversity to progress the field. Oncologist 22(9):1086–1093

    PubMed  PubMed Central  Google Scholar 

  6. Pellegrino B, Mateo J, Serra V, Balmana J (2019) Controversies in oncology: are genomic tests quantifying homologous recombination repair deficiency (HRD) useful for treatment decision making? Esmo Open. https://doi.org/10.1136/esmoopen-2018-000480

    Article  PubMed  PubMed Central  Google Scholar 

  7. Mayer EL, Abramson VG, Jankowitz RC, Falkson CI, Marcom PK, Traina TA, Carey LA, Rimawi MF, Specht JM, Miller K et al (2019) TBCRC 030: a randomized phase II study of preoperative cisplatin versus paclitaxel in TNBC—evaluating the homologous recombination deficiency (HRD) biomarker. J Clin Oncol 37(15_suppl):507

    Google Scholar 

  8. Schmid P, Adams S, Rugo HS, Schneeweiss A, Barrios CH, Iwata H, Dieras V, Hegg R, Im SA, Shaw Wright G et al (2018) Atezolizumab and Nab-paclitaxel in advanced triple-negative breast cancer. N Engl J Med 379(22):2108–2121

    CAS  PubMed  Google Scholar 

  9. Heimes AS, Schmidt M (2019) Atezolizumab for the treatment of triple-negative breast cancer. Expert Opin Investig Drugs 28(1):1–5

    CAS  PubMed  Google Scholar 

  10. Griguolo G, Dieci MV, Guarneri V, Conte P (2018) Olaparib for the treatment of breast cancer. Expert Rev Anticancer Ther 18(6):519–530

    CAS  PubMed  Google Scholar 

  11. Romero D (2019) Benefit in patients with PD-L1-positive TNBC. Nat Rev Clin Oncol 16(1):6

    PubMed  Google Scholar 

  12. Bareche Y, Venet D, Ignatiadis M, Aftimos P, Piccart M, Rothe F, Sotiriou C (2018) Unravelling triple-negative breast cancer molecular heterogeneity using an integrative multiomic analysis. Ann Oncol 29(4):895–902

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Chiu AM, Mitra M, Boymoushakian L, Coller HA (2018) Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer. Sci Rep 8(1):11807

    PubMed  PubMed Central  Google Scholar 

  14. Davis SL, Eckhardt SG, Tentler JJ, Diamond JR (2014) Triple-negative breast cancer: bridging the gap from cancer genomics to predictive biomarkers. Ther Adv Med Oncol 6(3):88–100

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W et al (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921

    CAS  PubMed  Google Scholar 

  16. Saito M, Momma T, Kono K (2018) Targeted therapy according to next generation sequencing-based panel sequencing. Fukushima J Med Sci 64(1):9–14

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, Harris PL, Haserlat SM, Supko JG, Haluska FG et al (2004) Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 350(21):2129–2139

    CAS  PubMed  Google Scholar 

  18. Garrido-Castro AC, Lin NU, Polyak K (2019) Insights into molecular classifications of triple-negative breast cancer: improving patient selection for treatment. Cancer Discov 9(2):176–198

    PubMed  PubMed Central  Google Scholar 

  19. Mardis E (2018) Many mutations in one clinical-trial basket. Nature 554(7691):173–175

    CAS  PubMed  Google Scholar 

  20. Renfro LA, Sargent DJ (2017) Statistical controversies in clinical research: basket trials, umbrella trials, and other master protocols: a review and examples. Ann Oncol 28(1):34–43

    CAS  PubMed  Google Scholar 

  21. Wheler J, Lee JJ, Kurzrock R (2014) Unique molecular landscapes in cancer: implications for individualized, curated drug combinations. Cancer Res 74(24):7181–7184

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Roerink SF, Sasaki N, Lee-Six H, Young MD, Alexandrov LB, Behjati S, Mitchell TJ, Grossmann S, Lightfoot H, Egan DA et al (2018) Intra-tumour diversification in colorectal cancer at the single-cell level. Nature 556(7702):457–462

    CAS  PubMed  Google Scholar 

  23. Hodson R (2016) Precision medicine. Nature 537(7619):S49

    CAS  PubMed  Google Scholar 

  24. Dugger SA, Platt A, Goldstein DB (2018) Drug development in the era of precision medicine. Nat Rev Drug Discov 17(3):183–196

    CAS  PubMed  Google Scholar 

  25. Yadav B, Pemovska T, Szwajda A, Kulesskiy E, Kontro M, Karjalainen R, Majumder MM, Malani D, Murumagi A, Knowles J et al (2014) Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Sci Rep 4:5193

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Chou TC (2010) Drug combination studies and their synergy quantification using the Chou–Talalay method. Cancer Res 70(2):440–446

    CAS  PubMed  Google Scholar 

  27. Chou TC (2006) Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharmacol Rev 58(3):621–681

    CAS  PubMed  Google Scholar 

  28. Morpheus

  29. Chou TC, Talalay P (1984) Quantitative analysis of dose–effect relationships: the combined effects of multiple drugs or enzyme inhibitors. Adv Enzyme Regul 22:27–55

    CAS  PubMed  Google Scholar 

  30. Brower V (2015) NCI-MATCH pairs tumor mutations with matching drugs. Nat Biotechnol 33(8):790–791

    CAS  PubMed  Google Scholar 

  31. Fan J, Upadhye S, Worster A (2006) Understanding receiver operating characteristic (ROC) curves. CJEM 8(1):19–20

    PubMed  Google Scholar 

  32. Hammerman PS, Sos ML, Ramos AH, Xu C, Dutt A, Zhou W, Brace LE, Woods BA, Lin W, Zhang J et al (2011) Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer. Cancer Discov 1(1):78–89

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Thota R, Johnson DB, Sosman JA (2015) Trametinib in the treatment of melanoma. Expert Opin Biol Ther 15(5):735–747

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Hassan B, Akcakanat A, Sangai T, Evans KW, Adkins F, Eterovic AK, Zhao H, Chen K, Chen H, Do KA et al (2014) Catalytic mTOR inhibitors can overcome intrinsic and acquired resistance to allosteric mTOR inhibitors. Oncotarget 5(18):8544–8557

    PubMed  PubMed Central  Google Scholar 

  35. Guo Y, Kwiatkowski DJ (2013) Equivalent benefit of rapamycin and a potent mTOR ATP-competitive inhibitor, MLN0128 (INK128), in a mouse model of tuberous sclerosis. Mol Cancer Res 11(5):467–473

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Tetsu O, McCormick F (2017) ETS-targeted therapy: can it substitute for MEK inhibitors? Clin Transl Med 6(1):16

    PubMed  PubMed Central  Google Scholar 

  37. Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB et al (2015) Dual roles of RNF2 in melanoma progression. Cancer Discov 5(12):1314–1327

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Xu J, Pfarr N, Endris V, Mai EK, Md Hanafiah NH, Lehners N, Penzel R, Weichert W, Ho AD, Schirmacher P et al (2017) Molecular signaling in multiple myeloma: association of RAS/RAF mutations and MEK/ERK pathway activation. Oncogenesis 6(5):e337

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Diamond JR, Eckhardt SG, Pitts TM, van Bokhoven A, Aisner D, Gustafson DL, Capasso A, Sams S, Kabos P, Zolman K et al (2018) A phase II clinical trial of the Aurora and angiogenic kinase inhibitor ENMD-2076 for previously treated, advanced, or metastatic triple-negative breast cancer. Breast Cancer Res 20(1):82

    PubMed  PubMed Central  Google Scholar 

  40. Chang Q, Jorgensen C, Pawson T, Hedley DW (2008) Effects of dasatinib on EphA2 receptor tyrosine kinase activity and downstream signalling in pancreatic cancer. Br J Cancer 99(7):1074–1082

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Shi H, Zhang CJ, Chen GY, Yao SQ (2012) Cell-based proteome profiling of potential dasatinib targets by use of affinity-based probes. J Am Chem Soc 134(6):3001–3014

    CAS  PubMed  Google Scholar 

  42. Yang W, Soares J, Greninger P, Edelman EJ, Lightfoot H, Forbes S, Bindal N, Beare D, Smith JA, Thompson IR et al (2013) Genomics of drug sensitivity in cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res 41(Database issue):D955–D961

    CAS  PubMed  Google Scholar 

  43. Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R et al (2018) Genetic and transcriptional evolution alters cancer cell line drug response. Nature 560(7718):325–330

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Kim SB, Dent R, Im SA, Espie M, Blau S, Tan AR, Isakoff SJ, Oliveira M, Saura C, Wongchenko MJ et al (2017) Ipatasertib plus paclitaxel versus placebo plus paclitaxel as first-line therapy for metastatic triple-negative breast cancer (LOTUS): a multicentre, randomised, double-blind, placebo-controlled, phase 2 trial. Lancet Oncol 18(10):1360–1372

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Tamura S, Wang Y, Veeneman B, Hovelson D, Bankhead A 3rd, Broses LJ, Lorenzatti Hiles G, Liebert M, Rubin JR, Day KC et al (2018) molecular correlates of in vitro responses to dacomitinib and afatinib in bladder cancer. Bladder Cancer 4(1):77–90

    PubMed  PubMed Central  Google Scholar 

  46. Nagamine A, Araki T, Nagano D, Miyazaki M, Yamamoto K (2019) l-Lactate dehydrogenase B may be a predictive marker for sensitivity to anti-EGFR monoclonal antibodies in colorectal cancer cell lines. Oncol Lett 17(5):4710–4716

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Oztop S, Isik A, Guner G, Gurdal H, Karabulut E, Yilmaz E, Akyol A (2019) Class III beta-tubulin expression in colorectal neoplasms is a potential predictive biomarker for paclitaxel response. Anticancer Res 39(2):655–662

    PubMed  Google Scholar 

  48. Wallden B, Storhoff J, Nielsen T, Dowidar N, Schaper C, Ferree S, Liu S, Leung S, Geiss G, Snider J et al (2015) Development and verification of the PAM50-based Prosigna breast cancer gene signature assay. BMC Med Genomics 8:54

    PubMed  PubMed Central  Google Scholar 

  49. Costa RLB, Han HS, Gradishar WJ (2018) Targeting the PI3 K/AKT/mTOR pathway in triple-negative breast cancer: a review. Breast Cancer Res Treat 169(3):397–406

    CAS  PubMed  Google Scholar 

  50. Ganesan P, Moulder S, Lee JJ, Janku F, Valero V, Zinner RG, Naing A, Fu S, Tsimberidou AM, Hong D et al (2014) Triple-negative breast cancer patients treated at MD Anderson Cancer Center in phase I trials: improved outcomes with combination chemotherapy and targeted agents. Mol Cancer Ther 13(12):3175–3184

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Ibrahim YH, Garcia-Garcia C, Serra V, He L, Torres-Lockhart K, Prat A, Anton P, Cozar P, Guzman M, Grueso J et al (2012) PI3 K inhibition impairs BRCA1/2 expression and sensitizes BRCA-proficient triple-negative breast cancer to PARP inhibition. Cancer Discov 2(11):1036–1047

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Shimoi T, Hamada A, Yamagishi M, Hirai M, Yoshida M, Nishikawa T, Sudo K, Shimomura A, Noguchi E, Yunokawa M et al (2018) PIK3CA mutation profiling in patients with breast cancer, using a highly sensitive detection system. Cancer Sci 109(8):2558–2566

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Basho RK, Gilcrease M, Murthy RK, Helgason T, Karp DD, Meric-Bernstam F, Hess KR, Herbrich SM, Valero V, Albarracin C et al (2017) Targeting the PI3 K/AKT/mTOR pathway for the treatment of mesenchymal triple-negative breast cancer: evidence from a phase 1 trial of mTOR inhibition in combination with liposomal doxorubicin and bevacizumab. JAMA Oncol 3(4):509–515

    PubMed  Google Scholar 

  54. Fouque A, Jean M, Weghe P, Legembre P (2016) Review of PI3 K/mTOR inhibitors entering clinical trials to treat triple negative breast cancers. Recent Pat Anticancer Drug Discov 11(3):283–296

    CAS  PubMed  Google Scholar 

  55. Stanfield Z, Coskun M, Koyuturk M (2017) Corrigendum: drug response prediction as a link prediction problem. Sci Rep 7:44961

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Groenendijk FH, Bernards R (2014) Drug resistance to targeted therapies: deja vu all over again. Mol Oncol 8(6):1067–1083

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Wein L, Loi S (2017) Mechanisms of resistance of chemotherapy in early-stage triple negative breast cancer (TNBC). Breast 34(Suppl 1):S27–S30

    PubMed  Google Scholar 

  58. Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J et al (2018) Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3 K inhibition in triple-negative breast cancers. Cancer Res 78(10):2732–2746

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Wu ZH, Lin C, Liu MM, Zhang J, Tao ZH, Hu XC (2016) Src inhibition can synergize with gemcitabine and reverse resistance in triple negative breast cancer cells via the AKT/c-Jun pathway. PLoS ONE 11(12):e0169230

    PubMed  PubMed Central  Google Scholar 

  60. Mumin NH, Drobnitzky N, Patel A, Lourenco LM, Cahill FF, Jiang Y, Kong A, Ryan AJ (2019) Overcoming acquired resistance to HSP90 inhibition by targeting JAK-STAT signalling in triple-negative breast cancer. BMC Cancer 19(1):102

    PubMed  PubMed Central  Google Scholar 

  61. Miles D, von Minckwitz G, Seidman AD (2002) Combination versus sequential single-agent therapy in metastatic breast cancer. Oncologist 7(Suppl 6):13–19

    CAS  PubMed  Google Scholar 

  62. Lee J, Yesilkanal AE, Wynne JP, Frankenberger C, Liu J, Yan J, Elbaz M, Rabe DC, Rustandy FD, Tiwari P et al (2019) Effective breast cancer combination therapy targeting BACH1 and mitochondrial metabolism. Nature 568(7751):254–258

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We kindly thank Rork Kuick (University of Michigan) for his insight on statistical analysis and careful editing of this manuscript. We thank the MD Anderson RPPA core for protein analysis, TIGEM in Naples, Italy for RNA sequencing, and the University of Michigan sequencing core for DNA sequencing.

Funding

This research was supported by the National Institutes of Health (1R21CA218498 to M.B.S. and S.D.M.), the Breast Cancer Research Foundation (to S.D.M.), Tempting Tables (to S.D.M.), The Rose Run (to S.D.M.), and the Kathy Bruk Pearce Research Fund of the University of Michigan Rogel Cancer Center (to M.B.S.).

Author information

Authors and Affiliations

Authors

Contributions

Study concept and design: M.B.S., N.M.M. Acquisition of data: N.M.M., N.M.V., E.J.L., L.W.B. Drafting the manuscript: N.M.M., J.A.Y., M.B.S., S.D.M. Analysis and interpretation of data: N.M.M., M.B.S., P.J.L, J.P.L., S.D.M. Experimentation: N.M.M., N.M.V., E.J.L., L.W.B. Statistical analysis: N.M.M., P.U.L., J.P.L. Administrative, technical, or material support: J.A.Y., A.M. Study supervision: M.B.S., S.D.M. All authors reviewed and approved the final version of the manuscript.

Corresponding authors

Correspondence to Sofia D. Merajver or Matthew B. Soellner.

Ethics declarations

Conflicts of interest

All authors declare that they have no conflicts of interest related to this work.

Research involving human and animal participants

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 14 kb)

10549_2019_5473_MOESM2_ESM.eps

Supplementary material 2 Candidate molecular correlates in TNBC cell lines. Examples of compounds with significant correlates include: A. temsirolimus and B. docetaxel. All molecular marker readouts have a FDR-adjusted p*-value < 0.05. Top bars depict DSS3, with dark green representing the most sensitive lines and white representing the least sensitive. Orange labeled readouts are derived from DNA variants. Black labeled readouts are derived from targeted RNA expression levels (EPS 656 kb)

Supplementary material 3 Strong agreement between nanostring and RNA sequencing results for Copanlisib (EPS 2418 kb)

10549_2019_5473_MOESM4_ESM.docx

Supplementary material 4 Cell culture conditions. When comparing the Nanostring readouts with RNA sequencing, we observed strong correlations for A. IL7R, B. ERBB2, C. KIF2C, D. CD164, E. PRR15L. F. CACNB3, G. MYCL, H. EPHA2, I. PIK3CD, J. IGFBP4, and K. IRAK2. We observed poor correlations for L. FOSL1 (DOCX 314 kb)

10549_2019_5473_MOESM5_ESM.pdf

Supplementary material 5 Table showing IC50 values, hill-slopes, max response, dose range, and DSS3 values in individual cell lines. (PDF 312 kb)

10549_2019_5473_MOESM6_ESM.pdf

Supplementary material 6 Individual correlating DNA non-synonymous mutations in the molecular correlate panel. Genes marked with “*” indicate a roll-up of mutations was used for correlations. SIFT, Polyphen2, MutationTaster, MutationAssessor, and FATHMM were used to generate functional predictions. (PDF 25 kb)

Supplementary material 7 (XLSX 304 kb)

Supplementary material 8 (XLSX 67 kb)

Supplementary material 9 (XLSX 12 kb)

Supplementary material 10 (XLSX 953 kb)

Supplementary material 11 (CSV 4768 kb)

Supplementary material 12 (XLSX 109 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Merrill, N.M., Lachacz, E.J., Vandecan, N.M. et al. Molecular determinants of drug response in TNBC cell lines. Breast Cancer Res Treat 179, 337–347 (2020). https://doi.org/10.1007/s10549-019-05473-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10549-019-05473-9

Keywords

Navigation