Ibrutinib induces chromatin reorganisation of chronic lymphocytic leukaemia cells

Abstract

Chronic lymphocytic leukaemia (CLL) is the most common leukaemia in Western countries. It has recently been shown that the homogeneity of the chromatin landscape between CLL cells contrasts with the important observed genetic heterogeneity of the disease. To gain further insight into the consequences of disease evolution on the epigenome’s plasticity, we monitored changes in chromatin structure occurring in vivo in CLL cells from patients receiving continuous Ibrutinib treatment. Ibrutinib, an oral inhibitor of the Bruton’s tyrosine kinase (BTK) has proved to be remarkably efficient against treatment naïve (TN), heavily pre-treated and high-risk chronic lymphocytic leukaemia (CLL), with limited adverse events. We established that the chromatin landscape is significantly and globally affected in response to Ibrutinib. However, we observed that prior to treatment, CLL cells show qualitative and quantitative variations in chromatin structure correlated with both EZH2 protein level and cellular response to external stimuli. Then, under prolonged exposure to Ibrutinib, a loss of the two marks associated with lysine 27 (acetylation and trimethylation) was observed. Altogether, these data indicate that the epigenome of CLL cells from the peripheral blood change dynamically in response to stimuli and suggest that these cells might adapt to the Ibrutinib “hit” in a process leading toward a possible reduced sensitivity to treatment.

Epigenomic evolution in chronic lymphocytic leukaemia cells from patients treated with ibrutinib and showing disease progression

“…In contrast with genetic abnormalities, the specificity of the chromatin landscape for a given individual correlates with cell phenotype and is, consequently, relevant for this particular individual when compared to clinical outcome. This study, combined with gene expression analysis, suggests coordinated phenotypic variations of CLL cells independent of disease evolution, characteristic of either cell activation or quiescence, consistent with our previous observations (17), and not explained by technical variability. We also determined that WNT5A might participate in the mechanism of relapse in a patient with no detectable mutation of either the BTK or PLCg2 genes.…”

“…Longer exposure to ibrutinib induces erosion of CLL identity correlated with a quiescent-like gene expression signature (14), global loss of both H3K27 acetylation (activating) and trimethylation (repressive) marks (17). Furthermore, while H3K4me3 stays globally relatively stable with time on ibrutinib, this histone PTM is distinctly reduced in regions identified as bivalent (H3K4me3+/H3K27me3+) before treatment (17). All of these observations indicate an important epigenomic plasticity of CLL cells in response to ibrutinib treatment.…”

“…We have previously analysed the evolution of the chromatin structure in CLL cells from patients enrolled in the IcICLLe trial, a feasibility study investigating the mechanism of action of ibrutinib. Patients received continuous oral therapy with ibrutinib (420 mg OD) and CLL cells were collected from PB before and at regular time points during treatment (17). From this trial, we identified a CLL patient (IbruR3) who progressed after 24 months of ibrutinib therapy ( Supplementary Fig.…”

“…These cells are typically over-expressing genes related to proliferation pathways and cell cycle (16). Accordingly, epigenomic analysis of these cells reveals transient increases in histone H3 lysine 4 trimethylation (H3K4me3), a histone post-translational modification (PTM) associated with open chromatin at cis-elements targeted by lineage defining transcription factors providing a signature of activation (17). Longer exposure to ibrutinib induces erosion of CLL identity correlated with a quiescent-like gene expression signature (14), global loss of both H3K27 acetylation (activating) and trimethylation (repressive) marks (17).…”

“…Accordingly, epigenomic analysis of these cells reveals transient increases in histone H3 lysine 4 trimethylation (H3K4me3), a histone post-translational modification (PTM) associated with open chromatin at cis-elements targeted by lineage defining transcription factors providing a signature of activation (17). Longer exposure to ibrutinib induces erosion of CLL identity correlated with a quiescent-like gene expression signature (14), global loss of both H3K27 acetylation (activating) and trimethylation (repressive) marks (17). Furthermore, while H3K4me3 stays globally relatively stable with time on ibrutinib, this histone PTM is distinctly reduced in regions identified as bivalent (H3K4me3+/H3K27me3+) before treatment (17).…”