ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia

Abstract

Distal enhancers play critical roles in sustaining oncogenic gene expression programs. We identify aberrant enhancer-like activation of GGAA tandem repeats as a characteristic feature of B-cell acute lymphoblastic leukemia (B-ALL) with genetic defects of the ETV6 transcriptional repressor, including ETV6-RUNX1+ and ETV6-null B-ALL. We show that GGAA repeat enhancers are direct activators of previously identified ETV6-RUNX1+/-like B-ALL “signature” genes, including the likely leukemogenic driver EPOR. When restored to ETV6-deficient B-ALL cells, ETV6 directly binds to GGAA repeat enhancers, represses their acetylation, downregulates adjacent genes, and inhibits B-ALL growth. In ETV6-deficient B-ALL cells, we find that the ETS transcription factor ERG directly binds to GGAA microsatellite enhancers and is required for sustained activation of repeat enhancer-activated genes. Together, our findings reveal an epigenetic gatekeeper function of the ETV6 tumor suppressor gene and establish microsatellite enhancers as a key mechanism underlying the unique gene expression program of ETV6-RUNX1+/-like B-ALL.

Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators

“…These data also supported a role of DUX4 in DUX4- rearranged ALL, ZNF384 and GATA3 in ZNF384- rearranged ALL, and HOXA9 and MEIS1 in KMT2A- rearranged ALL in the generation of subtype-specific chromatin landscapes ( Figures 5 C and S11 ). Additionally, our subtype versus non-subtype findings for ETV6 :: RUNX1 further confirm the importance of factors binding GGAA DNA-sequence repeats (EWSR1-FLI1, MA0149.1) as previously characterized for the ETV6 :: RUNX1 subtype 27 ( Figure S11 ). In complement to analysis of subtype-enriched DASs, we also examined TF footprints among subtype-depleted DASs by again comparing each B-ALL subtype group and non-subtype group.…”

“… 25 GEO: GSE122989 , GSE74912 B-ALL cell line ATAC-seq and H3K27ac ChIP-seq tracks associated with dCas9-KRAB targeting Kodgule et al. 27 GEO: GSE186942 B-ALL cell sample histone modification ChIP-seq datasets (H3K27ac, H3K4me1 and H3K27me3) Blueprint Epigenome Consortium https://www.blueprint-epigenome.eu/ Patient B-ALL samples (validation cohort) Diedrich et al. 29 GEO: GSE161501 Patient B-ALL cell sample ATAC-seq This paper GEO: GSE211631 Patient B-ALL cell sample ChIP-seq This paper GEO: GSE211631 Patient B-ALL cell sample promoter capture Hi-C This paper GEO: GSE211631 B-ALL cell line promoter capture Hi-C This paper GEO: GSE211631 B-ALL cell line AP-1 factor CUT&RUN This paper GEO: GSE211631 Patient B-ALL cell sample RNA-seq data St. Jude Children’s Research Hospital St. Jude Cloud Patient B-ALL cell sample Variant Call Frequency (VCF) genotyping data St. Jude Children’s Research Hospital St. Jude Cloud Experimental models : Cell lines 697 B-ALL cells DSMZ ACC 42; RRID:CVCL_0079 BALL1 B-ALL cells DSMZ ACC 742; RRID:CVCL_1075 Nalm6 B-ALL cells ATCC CRL-3273; RRID:CVCL_0092 REH B-ALL cells ATCC CRL-8286; RRID:CVCL_1650 RS4; 11 B-ALL cells ATCC CRL-1873; RRID:CVCL_0093 SEM B-ALL cells DSMZ...…”

“…Normal B cell ATAC-seq 10 , 25 were downloaded from NCBI ( GSE122989 and GSE74912 ). B-ALL cell line ATAC-seq and H3K27ac tracks associated with dCas9-KRAB repressor targeting or CRISPR/Cas9 deletions and investigation were downloaded from GEO under accession numbers GSE186942 27 and GSE129066 . 29 B-ALL cell histone modification ChIP-seq datasets (H3K27ac, H3K4me1 and H3K27me3) were downloaded from the Blueprint Epigenome Consortium ( https://www.blueprint-epigenome.eu/ ).…”

Altered enhancer-promoter interaction leads toMNX1expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13)

“…ETV6 is a strong transcriptional repressor, and haploinsufficiency could result in reactivation of its target genes. Recent work highlighted that ETV6 binds GGAA microsatellite enhancers and prevents them from being activated through histone acetylation 37 . Upon ETV6 loss, the ETS transcription factor ERG can bind these sites and activate the target genes.…”

“…ETV6 is a strong transcriptional repressor, and haploinsufficiency could result in reactivation of its target genes. 41…”