Decitabine and Vorinostat with Chemotherapy in Relapsed Pediatric Acute Lymphoblastic Leukemia: A TACL Pilot Study

Abstract

Purpose: Treatment failure from drug resistance is the primary reason for relapse in acute lymphoblastic leukemia (ALL). Improving outcomes by targeting mechanisms of drug resistance is a potential solution.

Patients and methods: We report results investigating the epigenetic modulators decitabine and vorinostat with vincristine, dexamethasone, mitoxantrone, and PEG-asparaginase for pediatric patients with relapsed or refractory B-cell ALL (B-ALL). Twenty-three patients, median age 12 years (range, 1-21) were treated in this trial.

Results: The most common grade 3-4 toxicities included hypokalemia (65%), anemia (78%), febrile neutropenia (57%), hypophosphatemia (43%), leukopenia (61%), hyperbilirubinemia (39%), thrombocytopenia (87%), neutropenia (91%), and hypocalcemia (39%). Three subjects experienced dose-limiting toxicities, which included cholestasis, steatosis, and hyperbilirubinemia (n = 1); seizure, somnolence, and delirium (n = 1); and pneumonitis, hypoxia, and hyperbilirubinemia (n = 1). Infectious complications were common with 17 of 23 (74%) subjects experiencing grade ≥3 infections including invasive fungal infections in 35% (8/23). Nine subjects (39%) achieved a complete response (CR + CR without platelet recovery + CR without neutrophil recovery) and five had stable disease (22%). Nine (39%) subjects were not evaluable for response, primarily due to treatment-related toxicities. Correlative pharmacodynamics demonstrated potent in vivo modulation of epigenetic marks, and modulation of biologic pathways associated with functional antileukemic effects.

Conclusions: Despite encouraging response rates and pharmacodynamics, the combination of decitabine and vorinostat on this intensive chemotherapy backbone was determined not feasible in B-ALL due to the high incidence of significant infectious toxicities. This study is registered at http://www.clinicaltrials.gov as NCT01483690.

Conflict of interest statement

Conflict-of-interest disclosure: M.J.B. has received honoraria from Shire Pharmaceuticals, Jazz Pharmaceuticals and Amgen. L.G. has received consulting fees from Amgen, Bristol-Myers Squibb, Celgene, Novartis and Genentech/Roche. T.W.L. has consulted for Novartis, Loxo Oncology, Bayer, and Eli Lilly. J.E.O has received honoraria from Shire Pharmaceuticals. S.G.D. has consulted for Loxo Oncology and has received travel expenses from Loxo Oncology and Roche. R.A.G. has received honoraria from Novartis. A.S.W. has received research funding from MedImmune, Kite Pharma, Institut de Recherches Internationales Servier (Servier), and Spectrum Pharmaceuticals and has served on an advisory committee for Servier.

©2020 American Association for Cancer Research.

Figures

Figure 1:

T2009–003 Treatment Schema IT, intrathecal; *CNS positive patients only

Figure 2:. Methylation correlates strongly with gene expression, both before and after epigenetic treatment.

The expression of 22,522 genes was averaged between pre- and post- treatment, ranked from highest to lowest, and split into quintiles in order of highest (Q1) to lowest (Q5). (A) The highly expressed genes (Q1, Q2) had low methylation (

Figure 3:. Epigenetic treatment-induced decreases in gene promoter CpG methylation correlate with increases in RNA transcript expression.

We identified gene promoters with at least 50 CpGs within 1 kilobase upstream or downstream of the transcription start site where the CpGs were at least 40% methylated at baseline (pre-treatment). We then calculated the change in methylation after treatment and correlated with the treatment-induced change in transcript expression of the associated gene. For all 6 cases with both methylation and RNA-seq data, the plot demonstrates the highly significant correlation between the change in methylation of promoter CpGs (x-axis) and log2 fold change in gene transcript expression after decitabine and vorinostat treatment (y-axis). Each dot (n=4749) represents one gene/promoter pair and includes composite data from all 6 cases. The color of each dot indicates the baseline (pre-treatment) methylation level of the gene promoter. Promoters with higher levels of baseline methylation (red/orange) show a greater degree of demethylation and increased expression after treatment relative to those with lower levels of baseline methylation (purple/blue). Plots for the contributions from each individual case are shown in Supplemental Figure 3.

Figure 4:. Epigenetically activated pathways include PRC2 and TP53 targets.

Gene set enrichment analysis on 6 cases with paired WGBS and RNA-seq data showed that genes that had highest promoter hypomethylation and gene upregulation after epigenetic treatment were enriched in sets of genes that are: 1) targets of PRC2 components and chromatin remodeling by H3K27ME3 modifications; and 2) targets of TP53 binding. (A) The top 30 gene sets ranked by combined normalized enrichment score (NES, GSEA v3.0) across the 6 cases. The drug-induced activation of PRC2/H3K27ME3 targets suggests that epigenetic treatment of relapsed ALL may induce differentiation, and the activation of TP53 targets suggests that epigenetic treatment can reactivate tumor suppressor genes. (B, C) Enrichment plots for PRC2 and TP53 gene sets, respectively.