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Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor

Abstract

Broad and deep tumour genome sequencing has shed new light on tumour heterogeneity and provided important insights into the evolution of metastases arising from different clones1,2. There is an additional layer of complexity, in that tumour evolution may be influenced by selective pressure provided by therapy, in a similar fashion to that occurring in infectious diseases. Here we studied tumour genomic evolution in a patient (index patient) with metastatic breast cancer bearing an activating PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha, PI(3)Kα) mutation. The patient was treated with the PI(3)Kα inhibitor BYL719, which achieved a lasting clinical response, but the patient eventually became resistant to this drug (emergence of lung metastases) and died shortly thereafter. A rapid autopsy was performed and material from a total of 14 metastatic sites was collected and sequenced. All metastatic lesions, when compared to the pre-treatment tumour, had a copy loss of PTEN (phosphatase and tensin homolog) and those lesions that became refractory to BYL719 had additional and different PTEN genetic alterations, resulting in the loss of PTEN expression. To put these results in context, we examined six other patients also treated with BYL719. Acquired bi-allelic loss of PTEN was found in one of these patients, whereas in two others PIK3CA mutations present in the primary tumour were no longer detected at the time of progression. To characterize our findings functionally, we examined the effects of PTEN knockdown in several preclinical models (both in cell lines intrinsically sensitive to BYL719 and in PTEN-null xenografts derived from our index patient), which we found resulted in resistance to BYL719, whereas simultaneous PI(3)K p110β blockade reverted this resistance phenotype. We conclude that parallel genetic evolution of separate metastatic sites with different PTEN genomic alterations leads to a convergent PTEN-null phenotype resistant to PI(3)Kα inhibition.

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Figure 1: Clinical response of index patient treated with BYL719.
Figure 2: Loss of PTEN upon BYL719 resistance.
Figure 3: Loss of PTEN by different genetic alterations.
Figure 4: Loss of PTEN expression and sensitivity to PI(3)Kα and PI(3)Kβ blockade.

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Data deposits

DNA sequences have been deposited in the European Genome-phenome Archive with accession number EGAS00001000991.

References

  1. Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012)

    Article  CAS  Google Scholar 

  2. Swanton, C. Intratumor heterogeneity: evolution through space and time. Cancer Res. 72, 4875–4882 (2012)

    Article  CAS  Google Scholar 

  3. Juric, D. BYL719, a next generation PI3K alpha specific inhibitor: preliminary safety, PK, and efficacy results from the first-in-human study. Cancer Res. 72, Abstr. CT-01 (2012)

    Google Scholar 

  4. Engelman, J. A., Luo, J. & Cantley, L. C. The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nature Rev. Genet. 7, 606–619 (2006)

    Article  CAS  Google Scholar 

  5. Cantley, L. C. The phosphoinositide 3-kinase pathway. Science 296, 1655–1657 (2002)

    Article  ADS  CAS  Google Scholar 

  6. Engelman, J. A. Targeting PI3K signalling in cancer: opportunities, challenges and limitations. Nature Rev. Cancer 9, 550–562 (2009)

    Article  CAS  Google Scholar 

  7. Brachmann, S. M., Ueki, K., Engelman, J. A., Kahn, R. C. & Cantley, L. C. Phosphoinositide 3-kinase catalytic subunit deletion and regulatory subunit deletion have opposite effects on insulin sensitivity in mice. Mol. Cell. Biol. 25, 1596–1607 (2005)

    Article  CAS  Google Scholar 

  8. Zhao, L. & Vogt, P. K. Helical domain and kinase domain mutations in p110alpha of phosphatidylinositol 3-kinase induce gain of function by different mechanisms. Proc. Natl Acad. Sci. USA 105, 2652–2657 (2008)

    Article  ADS  CAS  Google Scholar 

  9. Miller, T. W., Rexer, B. N., Garrett, J. T. & Arteaga, C. L. Mutations in the phosphatidylinositol 3-kinase pathway: role in tumor progression and therapeutic implications in breast cancer. Breast Cancer Res. 13, 224–235 (2011)

    Article  CAS  Google Scholar 

  10. Samuels, Y. et al. High frequency of mutations of the PIK3CA gene in human cancers. Science 304, 554 (2004)

    Article  CAS  Google Scholar 

  11. Sequist, L. V. et al. Implementing multiplexed genotyping of non-small-cell lung cancers into routine clinical practice. Ann. Oncol. 22, 2616–2624 (2011)

    Article  CAS  Google Scholar 

  12. Therasse, P. et al. New guidelines to evaluate the response to treatment in solid tumors. European Organization for Research and Treatment of Cancer, National Cancer Institute of the United States, National Cancer Institute of Canada. J. Natl. Cancer Inst. 92, 205–216 (2000)

    Article  CAS  Google Scholar 

  13. Toy, W. et al. ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. Nature Genet. 45, 1439–1445 (2013)

    Article  CAS  Google Scholar 

  14. Won, H. H., Scott, S. N., Brannon, A. R., Shah, R. H. & Berger, M. F. Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. J. Visual. Expts e50710 (2013)

  15. Yang, Z. Q., Liu, G., Bollig-Fischer, A., Giroux, C. N. & Ethier, S. P. Transforming properties of 8p11-12 amplified genes in human breast cancer. Cancer Res. 70, 8487–8497 (2010)

    Article  CAS  Google Scholar 

  16. Karlsson, E. et al. High-resolution genomic analysis of the 11q13 amplicon in breast cancers identifies synergy with 8p12 amplification, involving the mTOR targets S6K2 and 4EBP1. Genes Chromosom. Cancer 50, 775–787 (2011)

    Article  CAS  Google Scholar 

  17. Fritsch, C. et al. Characterization of the novel and specific PI3Kα inhibitor NVP-BYL719 and development of the patient stratification strategy for clinical trials. Mol. Cancer Ther. 13, 1117–1129 (2014)

    Article  CAS  Google Scholar 

  18. Stambolic, V. et al. Negative regulation of PKB/Akt-dependent cell survival by the tumor suppressor PTEN. Cell 95, 29–39 (1998)

    Article  CAS  Google Scholar 

  19. Jia, S. et al. Essential roles of PI(3)K-p110β in cell growth, metabolism and tumorigenesis. Nature 454, 776–779 (2008)

    Article  ADS  CAS  Google Scholar 

  20. Edgar, K. A. et al. Isoform-specific phosphoinositide 3-kinase inhibitors exert distinct effects in solid tumors. Cancer Res. 70, 1164–1172 (2010)

    Article  CAS  Google Scholar 

  21. Elkabets, M. et al. mTORC1 inhibition is required for sensitivity to PI3K p110a inhibitors in PIK3CA-mutant breast cancer. Sci. Transl. Med. 5, 196ra199 (2013)

    Article  Google Scholar 

  22. Lemey, P. et al. Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain. J. Virol. 79, 11981–11989 (2005)

    Article  CAS  Google Scholar 

  23. Li, S. et al. Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Rep. 4, 1116–1130 (2013)

    Article  ADS  CAS  Google Scholar 

  24. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

    Article  CAS  Google Scholar 

  25. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491–498 (2011)

    Article  CAS  Google Scholar 

  26. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nature Biotechnol. 31, 213–219 (2013)

    Article  CAS  Google Scholar 

  27. Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2, 82–93 (2012)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank members of the MSKCC Diagnostic Molecular Pathology Laboratory and the MSK Maria-Josée and Henry Kravis Center for Molecular Oncology for assistance with sequencing. We thank M. Asher and U. Bhanot from the MSKCC Pathology Core for assistance with tissue staining. This work was funded by a “Stand Up to Cancer” Dream Team Translational Research Grant, a Program of the Entertainment Industry Foundation (SU2C-AACR-DT0209), the Breast Cancer Research Foundation, the Geoffrey Beene Cancer Research Center, the Starr Cancer Consortium and an MMHCC grant (CA105388). D.J. is also funded by a National Institutes of Health Training Grant (T32 CA-71345-15) and by philanthropic support from Stephen and Kathleen Chubb.

Author information

Authors and Affiliations

Authors

Contributions

D.J., P.C., M.F.B., J.B. and M.S. conceived the project, designed and analysed the experiments, and wrote the manuscript. M.G., O.L.G., B.J.A., A.R. and E.R.M. performed and analysed the WGS and WES data. T.H., M.M.-K., D.S., S.I., A.T., L.E., C.Q., M.P., A.D., R.B. and A.H. collected and analysed patients’ samples. P.C., H.E., S.H.E. and S.W.L. performed and supervised the laboratory experiments. H.H.W., G.I., R.H.S., D.B.S. and M.F.B. performed and supervised the IMPACT sequencing and analysis.

Corresponding authors

Correspondence to Michael F. Berger, José Baselga or Maurizio Scaltriti.

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Competing interests

C.Q., M.P., A.D. and A.H. are Novartis employees. D.J., D.B.S. and J.B. consult for Novartis.

Extended data figures and tables

Extended Data Figure 1 CT scan of index patient.

CT scan showing a liver lesion (baseline) experiencing a partial response after 8 cycles (cycle 8) of BYL719.

Extended Data Figure 2 Gene copy number variation in both primary tumour and lung metastasis.

Extended Data Figure 3 Representative exon-level copy number profiles for genes on chromosome 10 in all 14 metastases collected from the index patient.

Exons in PTEN are shown in red.

Extended Data Figure 4 Loss-of-function mutations in PTEN detected by IMPACT in metastases M06 and M10.

Mutations were visualized by the Integrative Genomics Viewer (IGV).

Extended Data Figure 5 PTEN immunostaining of the 14 metastases collected during the autopsy.

Haematoxylin and eosin (H&E) and PTEN expression detected by IHC in 14 metastases collected during the autopsy of the index patient. PTEN staining in PTEN negative samples is only present in stromal cells.

Extended Data Figure 6 PTEN immunostaining in patients treated with BYL719.

PTEN expression detected by IHC in paired samples from six additional patients treated with BYL719. Specimens before starting BYL719 therapy (baseline) and at time of disease progression (post-treatment) are compared.

Extended Data Figure 7 Inducible loss of PTEN and sensitivity to BYL719 and BKM120.

a. Cell viability assay in MCF7 cells with inducible PTEN knockdown treated with increasing concentrations of either BYL719 or BKM120. Error bars, s.e.m. b, Cell viability assay in MDA-MB-453 (MDA453) cells with constitutive PTEN knockdown treated with increasing concentrations of either BYL719 or BKM120. Error bars, s.e.m. c, Quantification of pAKT (S473) and pS6 (S240/4) from Fig. 4d. Student’s t-test was used and P values are indicated. d, Western blot from the PDXs treated as indicated.

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Extended Data Figure 8 Constitutive loss of PTEN and sensitivity to BYL719 and AZD6482.

a, Cell viability assay in T47D cells with inducible PTEN knockdown (no. 2) treated with increasing concentrations of either BYL719 or AZD6482 in the presence of doxycycline 1 μg ml−1. Error bars, s.e.m. b, Quantification of pAKT (S473) and pS6 (S240/4) from Fig. 4g. Student’s t-test was used and P values are indicated. Error bars, s.e.m. c, Western blot from the PDXs treated as indicated.

Extended Data Table 1 Samples analysed from the index patient

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Juric, D., Castel, P., Griffith, M. et al. Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor. Nature 518, 240–244 (2015). https://doi.org/10.1038/nature13948

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