Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

Abstract

Summary Neuroblastoma is a pediatric malignancy that typically arises in early childhood and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumors with excellent outcomes to widely metastatic disease where long-term survival is approximately 40% despite intensive therapy1. A previous genome-wide association study (GWAS) identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumor cells2. Here we sought to discover the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation, and transcription factor binding sites. SNP rs2168101 G>T was the most highly associated variant (combined P=7.47×10-29, Odds Ratio 0.65, 95% CI: 0.60-0.70) and resided in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G-allele that is associated with tumor formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P=0.028) in neuroblastoma primary tumors and ablates GATA3 binding (P<0.0001). We demonstrate allelic imbalance favoring the G-containing strand in tumors heterozygous for this SNP as demonstrated both by RNA sequencing (P<0.0001) and reporter assays (P=0.002). These findings show that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumor cells.

Hmga2 collaborates with JAK2V617F in the development of myeloproliferative neoplasms

“…[51][52][53] Therefore, targets of Ezh2 other than Hmga2 may play a greater role in fibrosis in this context. RNA-seq also revealed that an Ezh2 deletion and overexpression of Hmga2 share deregulated oncogenic targets such as Lmo1 [54][55][56] in the presence of JAK2V617F. These observations give rise to the hypothesis that when the loss of Ezh2 and/or MIRlet-7 block the inhibition of some oncogenes, Hmga2 may synergistically accelerate such upregulation in the MPN stem cells.…”

The temporal requirements for Isl1 in sympathetic neuron proliferation, differentiation and diversification

“…However, the role of ISL1 in neuroblastoma tumorigenesis is unknown. We found that a number of genes implicated in neuroblastoma pathogenesis are downstream of ISL1 (e.g., Lmo1, Ccnd1, Tfap2b, Prox1, Casz1, Foxm1, Lin28b, Ccnd1, and Alk) [20][21][22][23]34,[36][37][38] , many of which are direct targets of ISL1. Notably, LMO1 is a neuroblastoma oncogene associated with more proliferative and aggressive phenotype 39 .…”

“…Notably, a number of targets of ISL1 downregulated in Isl1 CKO mutants were implicated in neuroblastoma pathogenesis [20][21][22][23] , including Lmo1, Gata3, Prox1, Lin28b, and Alk. We found that ISL1 binds to an evolutionary conserved region within the first intron of Lmo1 (mm9: chr7:116289070-116289656) in mouse sympathetic neurons that, by whole-genome alignment, overlaps with the super-enhancer of LMO1 identified in human neuroblastoma 20 .…”

“…A polymorphism within a super-enhancer in the first intron of LMO1 that preserves an evolutionarily conserved GATA factor binding motif predisposes to neuroblastoma. Knockdown of GATA3 results in decreased LMO1 expression and suppression of neuroblastoma cell growth 20 . We found that ISL1 binds to an evolutionary conserved region within the first intron of Lmo1 (chr7:116289070-116289656) in mouse sympathetic neurons that overlaps with the super-enhancer of LMO1 identified in human neuroblastoma, suggesting coregulation of LMO1 expression by ISL1 and GATA3 and a potential role of ISL1 in controlling neuroblastoma cell proliferation.…”

Whole-genome noncoding sequence analysis in T-cell acute lymphoblastic leukemia identifies oncogene enhancer mutations

“…6,7 There is growing evidence implicating noncoding genetic variation in human diseases, either by modulating transcriptional regulatory elements of protein-coding genes or by altering noncoding RNAs themselves. 8,[9][10][11] Somatically acquired promoter and/or enhancer mutations have also been identified that profoundly change oncogene expression and drive tumorigenesis (eg, TAL1 enhancer mutation in T-ALL). 6 In this study, we systematically searched for functional noncoding genomic alterations in T-ALL by whole-genome and transcriptome sequencing.…”