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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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.
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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.
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.
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Supplementary Figures 1–7
Source data for figures
Overview and clinical annotation of patient samples included in this study
Sample-specific sequencing statistics for the ATAC-seq experiments
List of all chromatin accessible regions detected in the ATAC-seq dataset
List of genomic regions with differential chromatin accessibility upon ibrutinib treatment
List of drugs and small molecules for the pharmacoscopy experiments
Selectivity scores before and during ibrutinib treatment for 131 drugs