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Glucocorticoids (GCs) are a mainstay of contemporary, multidrug chemotherapy in the treatment of childhood acute lymphoblastic leukemia (ALL), and resistance to GCs remains a major clinical concern. Resistance to GCs is predictive of ALL relapse and poor clinical outcome, and therefore represents a major hurdle limiting further improvements in survival rates. While advances have been made in identifying genes implicated in GC resistance, there remains an insufficient understanding of the impact of cis-regulatory disruptions in resistance. To address this, we mapped the gene regulatory response to GCs in two ALL cell lines using functional genomics and high-throughput reporter assays and identified thousands of GC-responsive changes to chromatin state, including the formation of over 250 GC-responsive super-enhancers and a depletion of AP-1 bound cis-regulatory elements implicated in cell proliferation and anti-apoptotic processes. By integrating our GC response maps with genetic and epigenetic datasets in primary ALL cells from patients, we further uncovered cis-regulatory disruptions at GC-responsive genes that impact GC resistance in childhood ALL. Overall, these data indicate that GCs initiate pervasive effects on the leukemia epigenome, and that alterations to the GC gene regulatory network contribute to GC resistance.

Vincristine is one of the most widely prescribed medications for treating solid tumors and acute lymphoblastic leukemia (ALL) in children and adults. However, its major dose-limiting toxicity is peripheral neuropathy that can disrupt curative therapy. Peripheral neuropathy can also persist into adulthood, compromising quality of life of childhood cancer survivors. Reducing vincristine-induced neurotoxicity without compromising its anticancer effects would be ideal. Here we show that low expression of NHP2L1 is associated with increased sensitivity of primary leukemia cells to vincristine, and that concomitant administration of vincristine with inhibitors of NHP2L1 increases vincristine cytotoxicity in leukemia cells, prolongs survival of ALL xenograft mice, but decreases vincristine effects on human induced pluripotent stem cell (hiPSC)-derived neurons and mitigates neurotoxicity in mice. These findings offer a strategy for increasing vincristine's antileukemic effects while reducing peripheral neuropathy in patients treated with this widely prescribed medication.

Acute lymphoblastic leukemia (ALL) is a hematopoietic malignancy comprised of molecular subtypes largely characterized by aneuploidy or recurring chromosomal rearrangements. Despite extensive information on the ALL transcriptome and methylome, there is limited understanding of the ALL chromatin landscape. We therefore mapped accessible chromatin in 24 primary ALL cell biospecimens comprising three common molecular subtypes (DUX4/ERG, ETV6-RUNX1 and hyperdiploid) from patients treated at St. Jude Children's Research Hospital. Our findings highlight extensive chromatin reprogramming in ALL, including the identification ALL subtype-specific chromatin landscapes that are additionally modulated by genetic variation. Chromatin accessibility differences between ALL and normal B-cells implicate the activation of B-cell repressed chromatin domains and detail the disruption of normal B-cell development in ALL. Among ALL subtypes, we uncovered roles for basic helix-loop-helix, homeodomain and activator protein 1 transcription factors in promoting subtype-specific chromatin accessibility and distinct gene regulatory networks. In addition to chromatin subtype-specificity, we further identified over 3500 DNA sequence variants that alter the ALL chromatin landscape and contribute to inter-individual variability in chromatin accessibility. Collectively, our data suggest that subtype-specific chromatin landscapes and gene regulatory networks impact ALL biology and contribute to transcriptomic differences among ALL subtypes.

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer and despite improved survival rates, relapsed ALL is still among the most common causes of cancer death in children. Although changes in the expression of specific genes have been linked to chemotherapeutic resistance, relatively little is understood of the pharmacogenomic impact of the noncoding, cis-regulatory landscape governing gene regulation. Glucocorticoids (GCs; i.e. steroids) are a mainstay of contemporary, multi-drug chemotherapy in ALL, and GC resistance is predictive of both relapse and poor clinical outcome in ALL. Because GCs function through activation of glucocorticoid receptor (GR), a nuclear receptor transcription factor that interacts directly with cis-regulatory elements, unveiling the glucocorticoid gene regulatory network (GC-GRN) in leukemia cells is crucial to understanding not only the biological mechanism of apoptosis, but also illuminating gene regulatory mechanisms contributing to GC resistance. To test the hypothesis that alterations to the GC-GRN are important contributors to steroid resistance in ALL, we comprehensively mapped cellular responses to GCs in human ALL cell lines using >100 independent functional genomic datasets. This comprehensive approach uncovered thousands of genes and cis-regulatory elements that were responsive to GCs, and further identified >38,000 high-confidence glucocorticoid response elements (GREs) in the ALL genome. A closer examination of these data revealed GR binding profiles that were consistent with the long-range flexible billboard model of gene regulation. By further integrating our results with genetic and epigenetic data in primary ALL cells from patients enrolled on St. Jude clinical trials, we identified 45 DNA sequence variants associated with ex vivo GC resistance that map to GREs and functionally validated an associated variant within the TLE1 gene locus. We also uncovered 1929 accessible chromatin sites (FDR10,000 sgRNAs targeting >1000 GR binding events at putative GC-resistance accessible chromatin sites identified a subset of GR binding sites implicated in GC resistance. Overall, these data indicate that GCs initiate pervasive, genome-wide effects on the leukemia epigenome and transcriptome, and that genetic and epigenetic alterations to GREs are mechanisms contributing to GC resistance in childhood ALL. Disclosures Pui: Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; Novartis: Other: Data Monitoring Committee. Evans: Princess Máxima Center for Pediatric Oncology, Scientific Advisory Board, Chair: Membership on an entity's Board of Directors or advisory committees; BioSkryb, Inc.: Membership on an entity's Board of Directors or advisory committees; St. Jude Children's Research Hospital, Emeritus Member (began Jan 2021): Ended employment in the past 24 months.

2594 Background: The anthracycline doxorubicin (DOX) is widely used to treat breast cancer. Doxorubicin is associated with pharmacokinetic and pharmacodynamic variability and despite its use for several years there is limited understanding behind it. Hepatic carbonyl reductases (CBR1 and CBR3) catalyze the reduction of DOX into its main circulating C-13 metabolite doxorubicinol (DOXOL). Polymorphisms in CBR1 and CBR3 influence synthesis of DOXOL, and could potentially play a role in the pharmacokinetic (PK) variability seen with doxorubicin treatment. In this study, we examined the influence of genetic polymorphisms in CBR1 and CBR3 on DOX and DOXOL PK. Methods: DOX was administered IV to 79 breast cancer patients at 60 mg/m2. Population PK modeling was performed on the parent concentration-time profiles with the following patient factors: [BSA (1.4-2.6 m2), weight (40-140 kg), age (25-75), race (78% white), CBR1 rs9024 (78% wild-type), CBR3 V244M (47% wild-type), CBR3 C4Y (20.5% wild-type); followed by model validation. Noncompartmental analysis (NCA) was performed for both DOX and DOXOL and the metabolic ratio was calculated as AUCDOXOL0-24:AUCDOX0-24. Results: A two-compartment model was used to describe DOX PK. Mean predicted (%SEM) clearance (CL), plasma volume (Vp), tissue volume and distribution clearance were 28.1 L/hr (7.72), 22.5 L (3.80), 257 L (13.8) and 13.6L (21.8), respectively. Interpatient variability on CL and Vp were 22.1% and 12.6%, respectively. BSA was found to be a significant predictor of the interpatient variability on CL. No other patient factors were found to be significant on parent drug PK. The metabolic ratio, assessing the conversion of DOX to DOXOL, was stratified by different polymorphisms of CBR1 and CBR3. There were no significant differences in metabolic ratio due to CBR1 and CBR3 genotypes. Conclusions: A PK model was developed that was able to characterize DOX pharmacokinetics. CBR1 and CBR3 polymorphisms were tested as covariates but were not found to be significant contributors to the variable pharmacokinetic profiles of DOX and DOXOL.