Genetic and Epigenetic Cis-Regulatory Disruptions Impacting the Canonical Wnt Signaling Repressor TLE1 Gene Promote Glucocorticoid Resistance in Childhood Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer and despite improved survival rates, more children die of ALL than any other cancer. Glucocorticoids (GCs) are a mainstay of contemporary, multi-drug chemotherapy in the treatment of childhood ALL. Resistance to GCs is predictive of ALL relapse and poor clinical outcomes, 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 GC resistance. This is particularly relevant for GCs, which function through the activation of the glucocorticoid receptor (GR) nuclear receptor transcription factor. To better understand the role of cis-regulatory disruptions in GC resistance we comprehensively mapped the dynamic gene regulatory response to GCs in two human ALL cell lines using functional genomic (RNA-seq, ChIP-seq, ATAC-seq and HiChIP) and massively parallel reporter (ATAC-STARR-seq) assays at multiple time points within a 24-hour window. In total, over 100 independent datasets were generated and integrated. We identified thousands of GR binding sites and GC-responsive changes to chromatin state, including the formation of over 250 GC-responsive super-enhancers and depletion of AP-1 bound cis-regulatory elements implicated in cell proliferation and anti-apoptotic processes. Our results further show that GR mediates gene regulatory effects in ALL cells at GC-responsive chromatin sites through long-range looping interactions with GC-responsive gene promoters. Notably, GC-responsive chromatin sites were also enriched for functionally active cis-regulatory elements. By integrating our GC response maps with inherited DNA sequence variants and differentially accessible chromatin sites associated with GC resistance in primary ALL cells from patients enrolled on St. Jude clinical trials, we identified two GR-bound cis-regulatory elements at the canonical Wnt signaling repressor TLE1 gene locus that were genetically or epigenetically disrupted in GC-resistant patient samples. Functional evaluation of these two GR binding sites using CRISPR genome or CRISPR interference epigenome editing validated their impact on GC resistance and TLE1 gene expression. To better understand the relationship between GC signaling and canonical Wnt signaling, we further performed TOP-flash luciferase reporter assays, cellular drug viability assays and transcriptomic drug response profiling which identified mutual antagonism between these two signaling pathways. Collectively, these data uncovered genetic and epigenetic cis-regulatory disruptions of canonical Wnt signaling as a novel mechanism impacting GC resistance in childhood ALL and further suggest that therapeutic inhibition of canonical Wnt signaling could improve GC sensitivity in patients with resistant disease.