Abstract 319: Integrated ATAC-seq and single-cell synergistic chemosensitivity profiling identifies rational drug combinations in ibrutinib treated CLL patients
Authors: Vladimer Gregory I. , Schmidl Christoph , Renderio Andre , Schnabl Susanne , Shehata Medhat , Superti-Furga Giulio , Jäger Ulrich , Bock Christoph 
Published: August 2019

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 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 Richters 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 systematic rational.

We charted the ibrutinib-induced chromatin regulatory landscape of CLL, and in parallel mapped targetable pathways for combination therapies that could potentially improve disease control. Peripheral blood from 24 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 &gt;130 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 Haemato, 2017).

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

Specifically we observed gained sensitivity to proteasome, PLK1, and mTOR inhibitors during ibrutinib treatment. Validations of both combination screening through image based screening and also classical CLL co-culture models confirmed the findings. 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.

Citation Format: Gregory I. Vladimer, Christoph Schmidl, Andre Renderio, Susanne Schnabl, Medhat Shehata, Giulio Superti-Furga, Ulrich Jäger, Christoph Bock. Integrated ATAC-seq and single-cell synergistic chemosensitivity profiling identifies rational drug combinations in ibrutinib treated CLL patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 319.