title: Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism.
abstract: Neuroblastoma is a paediatric malignancy that typically arises in early childhood, and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumours with excellent outcomes to widely metastatic disease in which long-term survival is approximately 40% despite intensive therapy. A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumour cells. Here we investigate 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. We show that SNP rs2168101 G>T is the most highly associated variant (combined P = 7.47 × 10(-29), odds ratio 0.65, 95% confidence interval 0.60-0.70), and resides 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 tumour 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 tumours, and ablates GATA3 binding (P < 0.0001). We demonstrate allelic imbalance favouring the G-containing strand in tumours heterozygous for this SNP, as demonstrated both by RNA sequencing (P < 0.0001) and reporter assays (P = 0.002). These findings indicate 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 tumour cells.
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.|Medical Scientist Training Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Derek A
authors.initials: DA
authors.lastname: Oldridge
authors.affiliation: Department of Molecular Medicine and Pathology, University of Auckland, Auckland, Auckland Region 1142, New Zealand.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Wood
authors.affiliation: Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.|Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
authors.forename: Nina
authors.initials: N
authors.lastname: Weichert-Leahey
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Ian
authors.initials: I
authors.lastname: Crimmins
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Robyn
authors.initials: R
authors.lastname: Sussman
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Winter
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Lee D
authors.initials: LD
authors.lastname: McDaniel
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Maura
authors.initials: M
authors.lastname: Diamond
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Lori S
authors.initials: LS
authors.lastname: Hart
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA.
authors.forename: Shizhen
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.|Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
authors.forename: Adam D
authors.initials: AD
authors.lastname: Durbin
authors.affiliation: Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Abraham
authors.affiliation: Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA.
authors.forename: Lars
authors.initials: L
authors.lastname: Anders
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Lifeng
authors.initials: L
authors.lastname: Tian
authors.affiliation: Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA.
authors.forename: Shile
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA.
authors.forename: Jun S
authors.initials: JS
authors.lastname: Wei
authors.affiliation: Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA.
authors.forename: Javed
authors.initials: J
authors.lastname: Khan
authors.affiliation: Thermo Fisher Scientific, Austin, Texas 78744, USA.
authors.forename: Kelli
authors.initials: K
authors.lastname: Bramlett
authors.affiliation: The Institute of Cancer Research, London SM2 5NG, UK.
authors.forename: Nazneen
authors.initials: N
authors.lastname: Rahman
authors.affiliation: University of Naples Federico II, 80131 Naples, Italy.|CEINGE Biotecnologie Avanzate, 80131 Naples, Italy.
authors.forename: Mario
authors.initials: M
authors.lastname: Capasso
authors.affiliation: University of Naples Federico II, 80131 Naples, Italy.|CEINGE Biotecnologie Avanzate, 80131 Naples, Italy.
authors.forename: Achille
authors.initials: A
authors.lastname: Iolascon
authors.affiliation: Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA.
authors.forename: Daniela S
authors.initials: DS
authors.lastname: Gerhard
authors.affiliation: Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA.
authors.forename: Jaime M
authors.initials: JM
authors.lastname: Guidry Auvil
authors.affiliation: Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
authors.affiliation: Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.|Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Hakon
authors.initials: H
authors.lastname: Hakonarson
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.|Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.|Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Diskin
authors.affiliation: Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.|Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.
authors.forename: A Thomas
authors.initials: AT
authors.lastname: Look
authors.affiliation: Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.|Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.|Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Maris
mesh_terms: D000107:Acetylation; D000483:Alleles; D022981:Allelic Imbalance; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D057890:Epigenomics; D050990:GATA3 Transcription Factor / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007438:Introns / Q000235:genetics; D060588:LIM Domain Proteins / Q000235:genetics*; D008239:Lysine / Q000378:metabolism; D009447:Neuroblastoma / Q000235:genetics*; D009928:Organ Specificity; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D050990:GATA3 Transcription Factor; C494749:GATA3 protein, human; D006657:Histones; D060588:LIM Domain Proteins; C065072:LMO1 protein, human; D014157:Transcription Factors; D008239:Lysine