title: MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia.
abstract: Understanding the underlying molecular mechanisms of defined cancers is crucial for effective personalized therapies. Translocations of the mixed-lineage leukemia (MLL) gene produce fusion proteins such as MLL-AF4 that disrupt epigenetic pathways and cause poor-prognosis leukemias. Here, we find that at a subset of gene targets, MLL-AF4 binding spreads into the gene body and is associated with the spreading of Menin binding, increased transcription, increased H3K79 methylation (H3K79me2/3), a disruption of normal H3K36me3 patterns, and unmethylated CpG regions in the gene body. Compared to other H3K79me2/3 marked genes, MLL-AF4 spreading gene expression is downregulated by inhibitors of the H3K79 methyltransferase DOT1L. This sensitivity mediates synergistic interactions with additional targeted drug treatments. Therefore, epigenetic spreading and enhanced susceptibility to epidrugs provides a potential marker for better understanding combination therapies in humans.
authors.affiliation: MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
authors.forename: Jon
authors.initials: J
authors.lastname: Kerry
authors.affiliation: MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
authors.forename: Laura
authors.initials: L
authors.lastname: Godfrey
authors.affiliation: Computational Biology Research Group, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
authors.forename: Emmanouela
authors.initials: E
authors.lastname: Repapi
authors.affiliation: MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
authors.forename: Marta
authors.initials: M
authors.lastname: Tapia
authors.affiliation: Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Neil P
authors.initials: NP
authors.lastname: Blackledge
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Helen
authors.initials: H
authors.lastname: Ma
authors.affiliation: MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
authors.forename: Erica
authors.initials: E
authors.lastname: Ballabio
authors.affiliation: Department of Paediatrics, University of Oxford, Children's Hospital, John Radcliffe, Oxford OX3 9DU, UK.
authors.forename: Sorcha
authors.initials: S
authors.lastname: O'Byrne
authors.affiliation: Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK.
authors.forename: Frida
authors.initials: F
authors.lastname: Ponthan
authors.affiliation: Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK.
authors.forename: Olaf
authors.initials: O
authors.lastname: Heidenreich
authors.affiliation: Department of Paediatrics, University of Oxford, Children's Hospital, John Radcliffe, Oxford OX3 9DU, UK.
authors.forename: Anindita
authors.initials: A
authors.lastname: Roy
authors.affiliation: MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Department of Paediatrics, University of Oxford, Children's Hospital, John Radcliffe, Oxford OX3 9DU, UK.
authors.forename: Irene
authors.initials: I
authors.lastname: Roberts
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
authors.forename: Marina
authors.initials: M
authors.lastname: Konopleva
authors.affiliation: Laboratory of Chromatin Biology and Transcription, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Klose
authors.affiliation: Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
authors.forename: Huimin
authors.initials: H
authors.lastname: Geng
authors.affiliation: MRC, Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK. Electronic address: thomas.milne@imm.ox.ac.uk.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Milne
mesh_terms: D001665:Binding Sites; D045744:Cell Line, Tumor; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D015973:Gene Expression Regulation, Leukemic; D015894:Genome, Human; D011495:Histone-Lysine N-Methyltransferase; D006657:Histones / Q000378:metabolism; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000378:metabolism; D007938:Leukemia / Q000235:genetics* / Q000473:pathology*; D008239:Lysine / Q000378:metabolism; D008780:Methyltransferases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D051788:Myeloid-Lymphoid Leukemia Protein / Q000378:metabolism*; D015514:Oncogene Proteins, Fusion / Q000378:metabolism*; D011379:Prognosis; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000378:metabolism
chemical_list: D006657:Histones; D036341:Intercellular Signaling Peptides and Proteins; C105373:MEN1 protein, human; C113855:MLL-AF4 fusion protein, human; D015514:Oncogene Proteins, Fusion; D011518:Proto-Oncogene Proteins; C119380:lens epithelium-derived growth factor; D051788:Myeloid-Lymphoid Leukemia Protein; C473477:DOT1L protein, human; D008780:Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; D008239:Lysine
keywords: DOT1L; H3K79me2; MLL; MLL-AF4; drug combination therapy; epigenetic spreading; epigenetic therapy; leukemia