Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Its Role in Drug Resistance

Abstract

Although B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy in children and while highly curable, it remains a leading cause of cancer-related mortality. The outgrowth of tumor subclones carrying mutations in genes responsible for resistance to therapy has led to a Darwinian model of clonal selection. Previous work has indicated that alterations in the epigenome might contribute to clonal selection, yet the extent to which the chromatin state is altered under the selective pressures of therapy is unknown. To address this, we performed chromatin immunoprecipitation, gene expression analysis, and enhanced reduced representation bisulfite sequencing on a cohort of paired diagnosis and relapse samples from individual patients who all but one relapsed within 36 months of initial diagnosis. The chromatin state at diagnosis varied widely among patients, while the majority of peaks remained stable between diagnosis and relapse. Yet a significant fraction was either lost or newly gained, with some patients showing few differences and others showing massive changes of the epigenetic state. Evolution of the epigenome was associated with pathways previously linked to therapy resistance as well as novel candidate pathways through alterations in pyrimidine biosynthesis and downregulation of polycomb repressive complex 2 targets. Three novel, relapse-specific superenhancers were shared by a majority of patients including one associated with S100A8, the top upregulated gene seen at relapse in childhood B-ALL. Overall, our results support a role of the epigenome in clonal evolution and uncover new candidate pathways associated with relapse.Significance: This study suggests a major role for epigenetic mechanisms in driving clonal evolution in B-ALL and identifies novel pathways associated with drug resistance.

NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization

“…3e). Interestingly, cancer-related pathways previously identified by RNA-seq or ChIP-seq analysis 5,22 were also found in our compartment-based analysis including Rap1, Ras, Phosphatidylinositol 3-kinase, and calcium signaling. Furthermore, these pathways were shared by at least two of the three cell lines providing evidence that the existence of a core of compacting loci can explain previously described shared phenotypes such as proliferation 5 .…”

Activation of the mitogen‐activated protein kinase–extracellular signal‐regulated kinase pathway in childhood B‐cell acute lymphoblastic leukemia

“…7 We previously demonstrated epigenetically activated MAPK pathway at relapse and a genome-wide shRNA screen-validated MAPK as a driver of clonal evolution and drug resistance. 6,12,16 mutations undetected in some of our WT patients as the lower limit of detection for Sanger sequencing is 15%-20% VAF. In contrast to previous studies with smaller cohorts and specific subtypes of B-ALL, 8,17,18 not all RAS mutated samples in our cohort demonstrated sensitivity to MEKi, but there was a trend toward higher inhibition indexes in mutant cases.…”

“…showed enrichment of RAS mutations at relapse from the outgrowth of a small subclone in the diagnostic sample using diagnosis/relapse pairs 7 . We previously demonstrated epigenetically activated MAPK pathway at relapse and a genome‐wide shRNA screen‐validated MAPK as a driver of clonal evolution and drug resistance 6,12,16 . Likewise, Ma et al.…”

“…We have demonstrated MAPK activation can occur through epigenetic mechanisms in the absence of RAS pathway mutations. 12 Extracellular signals, including stromal interaction, also lead to activation of MAPK, which might be especially relevant in epigenetically primed cells.…”

Single-Cell Sequencing: Biological Insight and Potential Clinical Implications in Pediatric Leukemia

“…Characteristic methylation signatures largely matching the underlying genetic background have been identified and provided basis for DNA methylation-based subtype prediction classifiers, contributing to the clarification of cytogenetically undefined ALL patient groups and facilitating the identification of novel gene fusions [ 90 ]. Some studies suggested that DNA methylation-based biomarkers are not independent predictive markers of patient outcome [ 91 ], while the combined analysis of methylation, DNA-protein interaction, and gene expression in a recent study has uncovered relapse-specific super-enhancers shared by a majority of patients [ 92 ], demonstrating the potential of integrative omic approaches. Large microarray and NGS-based transcriptomic studies identified novel subgroups of ALL patients previously not categorized by more conventional cytogenetic and molecular genetic methods.…”