INTEGRATED ATAC-SEQ AND SINGLE-CELL SYNERGISTIC CHEMOSENSITIVITY PROFILING IDENTIFIES RATIONAL DRUG COMBINATIONS IN IBRUTINIB-TREATED CLL PATIENTS
Author(s): ,
Gregory Vladimer
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria;Allcyte GmbH,Vienna,Austria
,
Christian Schmidl
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria
,
Andre Renderio
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria
,
Susanne Schnabl
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Christina Taubert
Affiliations:
Allcyte GmbH,Vienna,Austria
,
Tea Pemovska
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria
,
Mohammad Araghi
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Thomas Krausgruber
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria
,
Nikolaus Krall
Affiliations:
Allcyte GmbH,Vienna,Austria;CeMM Center for Molecular Medicine,Vienna,Austria
,
Berend Snijder
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria;ETH Zurich,Zurich,Switzerland
,
Rainer Hubmann
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Anna Ringler
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria;Christian Doppler Laboratory for Chemical Epigenetics and Anti-Infectives,CeMM Center for Molecular Medicine,Vienna,Austria
,
Dita Demirtas
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Oscar Lopez
Affiliations:
Allcyte GmbH,Vienna,Austria;CeMM Center for Molecular Medicine,Vienna,Austria
,
Kathrin Runggatscher
Affiliations:
Christian Doppler Laboratory for Chemical Epigenetics and Anti-Infectives,CeMM Center for Molecular Medicine,Vienna,Austria
,
Cathrin Skrabs
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Edit Porpaczy
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Michaela Gruber
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria;CeMM Center for Molecular Medicine,Vienna,Austria
,
Stefan Kubicek
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria;Christian Doppler Laboratory for Chemical Epigenetics and Anti-Infectives,CeMM Center for Molecular Medicine,Vienna,Austria
,
Gregor Hoermann
Affiliations:
Department of Laboratory Medicine, Medical University of Vienna,Medical University of Vienna,Vienna,Austria
,
Philipp Staber
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Medhat Shehata
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
,
Giulio Superti-Furga
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria;Center for Physiology and Pharmacology,Medical University of Vienna,Vienna,Austria
,
Christoph Bock
Affiliations:
CeMM Center for Molecular Medicine,Vienna,Austria;Department of Laboratory Medicine,Medical University of Vienna,Vienna,Austria;Max Planck Institute for Informatics,Saarbrücken,Germany
Ulrich Jäger
Affiliations:
Department of Hematology,Medical University of Vienna,Vienna,Austria
EHA Library. Vladimer G. Jun 17, 2018; 214638; S1572
Gregory Vladimer
Gregory Vladimer
Contributions
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Abstract

Abstract: S1572

Type: Oral Presentation

Presentation during EHA23: On Sunday, June 17, 2018 from 08:30 - 08:45

Location: Room A6

Background

Chronic lymphocytic leukemia (CLL) is characterized by proliferation and accumulation of malignant B cells, where this process is associated with constitutively activated B cell receptor (BCR) signaling, and interference with BCR signaling provides therapeutic benefit. Specifically, the Bruton’s Tyrosine Kinase (BTK) inhibitor ibrutinib prevents BTK tyrosine phosphorylation and thereby interferes with the pathway. It has shown high clinical response rates in patients with relapsed and refractory CLL, including patients with adverse cytogenetic profiles.

Despite high responses achieved by ibrutinib, it has important limitations such as inducing CLL cell redistribution from protected niches to the periphery, and the clinical response to ibrutinib is slow and often incomplete. Further, there is no evidence that a cure can be achieved, even among patients that tolerate long-term treatment with ibrutinib, a considerable percentage develops drug resistance, BTK independent disease progression, or Richter’s transformation, indicating drug synergies with ibrutinib may increase prognosis.

Recent studies have explored combined use of ibrutinib with inhibitors for the proteasome (carfilzomib), BCL2i (venetoclax), and HDAC (abexinostat) in preclinical models, which has shown promising initial results. However, these approaches were largely empirical, and do not have systamatic rational.

Aims

We charted the ibrutinib-induced chromatin regulatory landscape of CLL, and in parallel mapped targetable pathways for synergistic combination therapies that could potentially improve disease control. Peripheral blood from 24 fully characterized CLL cases were collected before and during therapy with ibrutinib. Chromatin accessibility was measured by ATAC-seq to gather the genome-wide regulatory landscape, and ex vivo chemosensitivity to >140 drugs on paired CLL samples was measured using Pharmacoscopy, a translatable method for ex vivo single-cell drug cytotoxicity profiling in primary samples (Snijder et al.Lancet Haematology, 2017;NCT03096821).

Methods

We bioinformatically integrated these datasets, establishing a comprehensive picture of the cellular responses to ibrutinib, and to prioritize targets, we performed secondary differential synergy screening of 21 drugs in combination with Ibrutinib in 8 CLL patient samples taken prior to clinical Ibrutinib treatment, with the goal to visualize changes in the targeted sensitivity of key drugs with and without Ibrutinib treatment.

Results
ATACseq identified increases in chromatin accessibility and chemosensitivity in proteasome, inflammatory NF-κB/TNF signaling, CoA biosynthesis, PI3K/Akt, pathways, along with changes affecting genes such as FOXO3 and IκBa, and both the ex vivo drug testing of samples from patients after clinical ibrutinb and ex vivo synergy screening revealed that ibrutinib treatment in vivo and in vitro sensitizes CLL cells to compounds such as the proteasome inhibitor bortezomib, the JAK inhibitor ruxolitinib, the bisphosphate zoledronate, and the aurora kinase inhibitor ZM447439.

Conclusion

Our results show that synergistic combination and informatics-integration of chromatin profiling with functional drug screening is a powerful tool to identify targetable pathways in CLL. This approach may be useful for designing personalized therapies as well as providing planning for clinical studies. Our approach is directly transferable to other leukemia where malignant cells can be obtained for chromatin profiling and drug sensitivity analysis, thus providing a widely applicable tool for the rational development of combination therapies.

Session topic: 5. Chronic lymphocytic leukemia and related disorders – Biology & Translational Research

Keyword(s): Drug sensitivity, Ex vivo, ibrutinib, Synergy

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