Chromatin Accessibility Landscapes of B-Cell Acute Lymphoblastic Leukemia Identify Extensive Epigenomic Reprogramming and Heterogeneity Among Subtypes

Acute lymphoblastic leukemia (ALL) is the most common malignancy in pediatric patients and represents about a quarter of all pediatric malignancies. Past work has characterized B-cell lineage ALL (B-ALL) into molecular subtypes spanning a range of aberrant chromosomal rearrangements and oncogene chimeric fusions driving malignancy. While transcriptional and DNA methylome profiling of these subtypes has been extensively examined, the accompanying chromatin landscape and corresponding gene regulatory repertoire are not well characterized for many B-ALL subtypes. To better profile the B-ALL epigenome and gene regulatory networks we examined chromatin accessibility of 11 distinct molecular subtypes (BCR-ABL1, DUX4/ERG, ETV6-RUNX1, Hyperdiploid, Low hypodiploid, KMT2A-rearranged, Ph-like, PAX5-altered, TCF3-PBX1, ZNF384-rearranged and B-other) using 154 primary patient samples from across the United States with assay for transposase-accessible chromatin and high-throughput sequencing (ATAC-seq). We mapped extensive chromatin reprogramming when comparing B-ALL and normal B-cells that drive oncogenic signaling pathways and inhibit normal B-cell functions. Strikingly, we also uncovered chromatin accessibility sites in B-ALL (42,457 sites) with distinct subtype-specific enrichment. A classification model utilizing subtype distinct loci was able to accurately predict B-ALL subtypes with 87% cross-validation accuracy. Transcription factor (TF) footprint profiling and transcriptomic information further identified candidate subtype-enriched TFs, such as DUX4, ZNF384, HOXA9, MEIS1, GATA3 and RARA, along with subtype distinct gene regulatory networks. In connecting these findings with genetic variation, we identified 9080 inherited DNA sequence variants that act as ATAC-seq chromatin accessibility quantitative trait loci (ATAC-QTLs) and contribute to variability in chromatin accessibility among patient samples. Nearly one-third of ATAC-QTLs map to TF footprints and commonly altered DNA consensus motifs impacting chromatin accessibility include ETS family TFs (PU.1, SPI-B, ELF3, EHF), ZNF family (ZNF263, ZNF460) and CTCF. Collectively, using the largest B-ALL chromatin accessibility dataset to date, our investigation offers a unique window into the gene regulatory landscape that highlights the complexity and heterogeneity of chromatin accessibility among B-ALL molecular subtypes.

Stock:Pfizer: Consultancy, Honoraria, Research Funding; Kite: Honoraria; Amgen: Honoraria; Jazz Pharmaceuticals: Honoraria; Kura Oncology: Honoraria; MorphoSys: Honoraria; Pluristem: Consultancy, Honoraria; Servier: Honoraria; Syndax: Consultancy, Honoraria; Newave Pharmaceuticals: Consultancy; Agios: Honoraria. Inaba:Servier: Other: Grants and Personal Fees; Amgen: Other: Grants and Personal Fees; Incyte: Other: Grants; JAZZ: Other: Personal Fees; Chugai: Other: Personal Fees. Pui:Adaptive Biotechnologies: Membership on an entity's Board of Directors or advisory committees; Novartis: Other: Data monitoring committee. Relling:Servier: Research Funding; BioSkryb: Other: Spouse has equity interest in bioskryb. Evans:Princess Maxima Centre for Childhood Cancer: Membership on an entity's Board of Directors or advisory committees; BioSkryb Genomics Inc: Membership on an entity's Board of Directors or advisory committees. Yang:Takeda Pharmaceutical Company: Research Funding.