Abstract

The Bruton tyrosine kinase (BTK) inhibitor ibrutinib has substantially improved therapeutic options for chronic lymphocytic leukemia (CLL). Although ibrutinib is not curative, it has a profound effect on CLL cells and may create new pharmacologically exploitable vulnerabilities. To identify such vulnerabilities, we developed a systematic approach that combines epigenome profiling (charting the gene-regulatory basis of cell state) with single-cell chemosensitivity profiling (quantifying cell-type-specific drug response) and bioinformatic data integration. By applying our method to a cohort of matched patient samples collected before and during ibrutinib therapy, we identified characteristic ibrutinib-induced changes that provide a starting point for the rational design of ibrutinib combination therapies. Specifically, we observed and validated preferential sensitivity to proteasome, PLK1, and mTOR inhibitors during ibrutinib treatment. More generally, our study establishes a broadly applicable method for investigating treatment-specific vulnerabilities by integrating the complementary perspectives of epigenetic cell states and phenotypic drug responses in primary patient samples.

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Data availability

The ATAC-seq and pharmacoscopy data are available from http://cll-combinations.computational-epigenetics.org. The ATAC-seq data are also available from NCBI GEO under accession number GSE100672. The source code for ATAC-seq data processing is available from a Github repository linked on the above website.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Acknowledgements

We thank all patients who have donated their samples for this study. We also thank the Biomedical Sequencing Facility at CeMM for assistance with next generation sequencing and J. Bigenzahn, M. Rebsamen as well as the G.S.-F. and C.B. labs for help and advice. This work was performed in the context of the following grants and fellowships: WWTF LS16-034 to G.S.-F. and U.J.; FWF SFB F 4711-B20 to G.S.-F.; EMBO Long-Term Fellowship 1543-2012 to G.I.V. and 733-2016 to T.P.; Swiss National Science Foundation Fellowship P300P3_147897 and PP00P3_163961 to B.S.; Marie-Sklodowska Curie Action Fellowship 703668 to N.K.; Feodor Lynen Fellowship of the Alexander von Humboldt Foundation to C. Schmidl; Marie Curie Action International Outgoing Fellowship (PIOF-2013-624924) to M.G.; Initiative Krebsforschung (UE71104017, UE71104005, UE71504001, and UE711043037), Austrian Society of Hematology and Oncology (ÖGHO AP00359OFF), and Anniversary Fund of the Austrian National Bank (OeNB AP130120ONB) to M.S.; Austrian Academy of Sciences New Frontiers Group Award and ERC Starting Grant (European Union’s Horizon 2020 research and innovation programme) 679146 to C.B.

Author information

Author notes

    • Christian Schmidl

    Present address: Regensburg Centre for Interventional Immunology and University Medical Center of Regensburg, Regensburg, Germany

    • Gregory I. Vladimer
    • , Nikolaus Krall
    •  & Oscar Lopez de la Fuente

    Present address: Allcyte GmbH, Vienna, Austria

    • Berend Snijder

    Present address: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

  1. These authors contributed equally: Christian Schmidl, Gregory I. Vladimer, André F. Rendeiro, Susanne Schnabl.

  2. These authors jointly supervised this work: Medhat Shehata, Giulio Superti-Furga, Ulrich Jäger, Christoph Bock.

Affiliations

  1. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

    • Christian Schmidl
    • , Gregory I. Vladimer
    • , André F. Rendeiro
    • , Thomas Krausgruber
    • , Nikolaus Krall
    • , Tea Pemovska
    • , Berend Snijder
    • , Anna Ringler
    • , Kathrin Runggatscher
    • , Oscar Lopez de la Fuente
    • , Michaela Gruber
    • , Stefan Kubicek
    • , Giulio Superti-Furga
    •  & Christoph Bock
  2. Department of Medicine I, Division of Hematology and Hemostaseology, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria

    • Susanne Schnabl
    • , Mohammad Araghi
    • , Rainer Hubmann
    • , Dita Demirtas
    • , Martin Hilgarth
    • , Cathrin Skrabs
    • , Edit Porpaczy
    • , Michaela Gruber
    • , Philipp B. Staber
    • , Medhat Shehata
    •  & Ulrich Jäger
  3. Allcyte GmbH, Vienna, Austria

    • Christina Taubert
  4. Christian Doppler Laboratory for Chemical Epigenetics and Anti-Infectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

    • Anna Ringler
    • , Kathrin Runggatscher
    •  & Stefan Kubicek
  5. Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria

    • Gregor Hoermann
    •  & Christoph Bock
  6. Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria

    • Giulio Superti-Furga
  7. Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany

    • Christoph Bock
  8. Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria

    • Christoph Bock

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Contributions

C. Schmidl and T.K. performed ATAC-seq experiments; G.I.V., C.T., A.R., and K.R. performed image-based chemosensitivity experiments; C. Schmidl, G.I.V., A.F.R., N.K., B.S., O.L.d.l.F., and S.K. analyzed the ATAC-seq and image-based chemosensitivity data; S.S., C.T., T.P., M.A., R.H., D.D., M.H., and M.S. handled patient samples and performed validation experiments; M.S. and U.J. were responsible for study ethics; C. Skrabs, E.P., M.G., G.H., P.B.S., M.S., and U.J. provided and analyzed clinical data or oversaw patient care and ethics; C. Schmidl, G.I.V., A.F.R., T.P., M.S., G.S.-F., U.J., and C.B. wrote the manuscript; M.S., G.S.-F., U.J., and C.B. oversaw the project.

Competing interests

G.I.V., N.K., B.S., G.S.-F. are co-founders of Allcyte GmbH, which has licensed the pharmacoscopy technology, and they are listed as inventors on patent applications for the pharmacoscopy / single-cell imaging methodology. G.I.V. and N.K. have become employees of Allcyte GmbH during the course of this study. U.J. received research grants and honoraria from Janssen Cilag, Abbvie, Novartis, and Roche Austria.

Corresponding author

Correspondence to Christoph Bock.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–7

  2. Reporting Summary

  3. Source Data for figures

    Source data for figures

  4. Supplementary Table 1

    Overview and clinical annotation of patient samples included in this study

  5. Supplementary Table 2

    Sample-specific sequencing statistics for the ATAC-seq experiments

  6. Supplementary Table 3

    List of all chromatin accessible regions detected in the ATAC-seq dataset

  7. Supplementary Table 4

    List of genomic regions with differential chromatin accessibility upon ibrutinib treatment

  8. Supplementary Table 5

    List of drugs and small molecules for the pharmacoscopy experiments

  9. Supplementary Table 6

    Selectivity scores before and during ibrutinib treatment for 131 drugs

About this article

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DOI

https://doi.org/10.1038/s41589-018-0205-2