Abstract C12: Identification of biomarkers and pathways associated with response to the DOT1L inhibitor Pinometostat (EPZ-5676) in MLL-r leukemia
Authors: Daigle Scott , McDonald Alice , Thomson Ty M. , Drubin David A. , Maria Michael , Carson A. , Patay Brad , Keats Jeff , Klaus Christine , Raimondi Alejandra , Garcia-Manero G. , Rizzieri D. A. , Tibes Raoul , Berdeja Jesus , Stein Eytan M. , Thomson Blythe , Blakemore Stephen J. 
Published: May 2016

Abstract
Pinometostat is a highly selective first in class DOT1L inhibitor currently in Phase 1 clinical trials in adult and pediatric leukemia patients (pts) with MLL rearrangements (MLL-r or MLL-PTD). Preliminary results of the adult trial have demonstrated clinical activity including complete remissions in a subset of patients (Stein, 2014). Investigation and identification of candidate molecular correlates of pinometostat response in both pt samples and cell lines are reported.
RNA and DNA were isolated from PBMCs and/or bone marrow collected prior to treatment from 18 pts enrolled in the adult pinometostat Phase 1 study (CT.gov: NCT01684150), at the following doses 24 (n = 2), 36 (n = 3), 54 (n = 6), 80 (n = 3) and 90 mg/m2/day doses (n = 4). mRNA transcript abundance was assessed using whole genome RNASeq and DNA variants were determined using a 194 gene panel, MyAML (Genection Inc.). Correlations of transcript abundance and DNA variants detected with categorical (responder = CR or PR [n = 3], or no response [n = 16]) and continuous response parameters (time on study [TOS], mean = 59 days: range = 8-196 days) were performed. For cell lines, whole genome RNASeq data was generated from 14 cell lines (MLL-r or MLL-PTD) with a range of in vitro sensitivity to pinometostat (cell proliferation IC50 2 nM to &gt; 10 μM) and RNA transcripts identified as correlated with IC50 were submitted for pathway analysis.
Univariate analyses revealed no DNA variants to be associated with either response category (FDR adjusted P &lt; 0.05), however, a statistical association (unadjusted P = 0.05) was identified between increased TOS and those pts harboring t(11:19). Indicating that specific MLL fusion partners may elicit differential sensitivity to pinometostat therapy (2/2 CR pts had t(11:19)). Analysis of the baseline PBMC RNASeq data revealed 201 genes as significantly correlated with TOS (FDR adjusted P&lt;0.05), these data were further analyzed using the Selventa causal modelling platform to identify pathways associated with TOS. Increased activity in pathways leading to differentiation, oxidative stress, inflammation, ras activation and decreased activities of PPAR-γ, DNA methylation and stem cell renewal were associated with increased TOS. Independent analysis of the cell line response data identified pathways that significantly overlapped with those observed in pt samples, with 4/7 of the pt derived mechanisms identified (PPAR-γ activity, inflammation, stem cell renewal and ras activation). In all cases directionality of pathway activity relative to pinometostat sensitivity were concordant between pt and cell line data. Based on these results the effect of a PPAR-γ agonist e.g. rosiglitazone, would be predicted to be antagonistic to pinometostat activity. Results of experiments investigating the effects of combination of rosiglitazone and pinometostat in MOLM-13 cell lines demonstrated that the combination was significantly less effective at inhibiting cell proliferation than pinometostat alone (IC50 shift of 2 fold (n = 2)).
MLL-r fusion partner (e.g. t(11:19)) may influence clinical response to pinometostat. In addition RNASeq based characterization of patient samples and cell lines revealed candidate pathways that may cooperate with or antagonize pinometostat activity that warrant further investigation.
Citation Format: Scott Daigle, Alice McDonald, Ty M. Thomson, David A. Drubin, Michael Maria, A. Carson, Brad Patay, Jeff Keats, Christine Klaus, Alejandra Raimondi, G. Garcia-Manero, D. A. Rizzieri, Raoul Tibes, Jesus Berdeja, Eytan M. Stein, Blythe Thomson, Stephen J. Blakemore. Identification of biomarkers and pathways associated with response to the DOT1L inhibitor Pinometostat (EPZ-5676) in MLL-r leukemia. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C12.