Defining the transcriptional control of pediatric AML highlights RARA as a superenhancer-regulated druggable dependency

Abstract

Somatic mutations are rare in pediatric AML (pAML), indicating alternate strategies are needed to identify targetable dependencies. We performed the first enhancer mapping of 3 pAML in 22 patient samples. Generally, pAML samples were distinct from adult AML 4 samples, and MLL (KMT2A)-rearranged samples were also distinct from non-KMT2A-5 rearranged samples. Focusing specifically on super-enhancers (SEs), we identified SEs 6 associated with many known leukemia regulators. The retinoic acid receptor alpha 7 (RARA) gene was differentially regulated in our cohort, and a RARA associated SE was 8 detected in 64% our cohort across all cyto/molecular subtypes tested. RARA SE-positive 9 pAML cell lines and samples demonstrated high RARA mRNA levels. These samples 10 were specifically sensitive to the synthetic RARA agonist tamibarotene in vitro, with 11 slowed proliferation, apoptosis induction, differentiation, and upregulated retinoid target 12 gene expression, compared to RARA SE-negative samples. Tamibarotene prolonged 13 survival and suppressed the leukemia burden of a RARA SE-positive pAML patient-14 derived xenograft (PDX) mouse model compared to a RARA SE-negative PDX. Our work 15 demonstrates that examining chromatin regulation can identify new, druggable 16 dependencies in pAML and provides rationale for a pediatric tamibarotene trial in children 17 with RARA-high AML.

A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

“…2 A). We assembled a mixed sample cohort with a strong representation of both adult and pediatric KMT2Ar AML, consisting of AML cell lines ( n = 24), patient-derived xenografts (PDXs; n = 38) ( Murakami et al 2015 ), and pediatric primary AMLs ( n = 19) ( Perez et al 2021 ). Additionally, we incorporated a published adult primary AML data set ( n = 49) ( McKeown et al 2017 ), for a total of 130 samples.…”

“…Cells were preserved in conditioned media from the human bone marrow stromal cell line HS5 (collected after 2 d of plating) diluted 1:1 with RPMI + 10% FBS and 1% penicillin/streptomycin. Freshly thawed cells were cross-linked with formaldehyde and used for ChIP-seq ( Perez et al 2021 ).…”

Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors

“…We speculate that p300/CBP restrain MYB function at a subset of target genes and inhibiting their interaction with MYB may result in increased MYB activity. Surprisingly, ATRA, which regulates gene expression through binding to the nuclear retinoid receptor 60,61 , demonstrated a strong enrichment for primary MYB targets and similar functional ambivalence, suggesting a potential interaction between MYB and the retinoid receptor at the enhancer/promoter level. Importantly, the mixed agonism-antagonism of MYB modulators differentially affects distinct MYB-regulated pathways, indicating that any therapeutic use of these molecules would need to be tailored to the specific parts of the MYB program that drive the disease phenotype.…”

Super-Enhancers and Their Parts: From Prediction Efforts to Pathognomonic Status

“…Interestingly, some paediatric tumours were found to differ in the SE landscape [ 173 , 174 ]. Moreover, in infant neuroblastoma 2, major SE-directed molecular subtypes have been described, namely the ADRN and MES subtypes.…”