title: Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma.
abstract: Despite intensive study, many mysteries remain about the MYCN oncogene's functions. Here we focus on MYCN's role in neuroblastoma, the most common extracranial childhood cancer. MYCN gene amplification occurs in 20% of cases, but other recurrent somatic mutations are rare. This scarcity of tractable targets has hampered efforts to develop new therapeutic options. We employed a multi-level omics approach to examine MYCN functioning and identify novel therapeutic targets for this largely un-druggable oncogene. We used systems medicine based computational network reconstruction and analysis to integrate a range of omic techniques: sequencing-based transcriptomics, genome-wide chromatin immunoprecipitation, siRNA screening and interaction proteomics, revealing that MYCN controls highly connected networks, with MYCN primarily supressing the activity of network components. MYCN's oncogenic functions are likely independent of its classical heterodimerisation partner, MAX. In particular, MYCN controls its own protein interaction network by transcriptionally regulating its binding partners.Our network-based approach identified vulnerable therapeutically targetable nodes that function as critical regulators or effectors of MYCN in neuroblastoma. These were validated by siRNA knockdown screens, functional studies and patient data. We identified β-estradiol and MAPK/ERK as having functional cross-talk with MYCN and being novel targetable vulnerabilities of MYCN-amplified neuroblastoma. These results reveal surprising differences between the functioning of endogenous, overexpressed and amplified MYCN, and rationalise how different MYCN dosages can orchestrate cell fate decisions and cancerous outcomes. Importantly, this work describes a systems-level approach to systematically uncovering network based vulnerabilities and therapeutic targets for multifactorial diseases by integrating disparate omic data types.
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.|The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Duffy
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Krstic
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Melinda
authors.initials: M
authors.lastname: Halasz
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.|European Molecular Biology Laboratory (EMBL), Meyerhofstraße, Heidelberg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schwarzl
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Dirk
authors.initials: D
authors.lastname: Fey
authors.affiliation: VTT Technical Research Centre of Finland, Espoo, Finland.
authors.forename: Kristiina
authors.initials: K
authors.lastname: Iljin
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Jai Prakash
authors.initials: JP
authors.lastname: Mehta
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Kate
authors.initials: K
authors.lastname: Killick
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Jenny
authors.initials: J
authors.lastname: Whilde
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Benedetta
authors.initials: B
authors.lastname: Turriziani
authors.affiliation: VTT Technical Research Centre of Finland, Espoo, Finland.
authors.forename: Saija
authors.initials: S
authors.lastname: Haapa-Paananen
authors.affiliation: VTT Technical Research Centre of Finland, Espoo, Finland.
authors.forename: Vidal
authors.initials: V
authors.lastname: Fey
authors.affiliation: Department of Paediatric Haematology and Oncology and Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Fischer
authors.affiliation: Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Westermann
authors.affiliation: Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Kai-Oliver
authors.initials: KO
authors.lastname: Henrich
authors.affiliation: Division of NB Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Bannert
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.|Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.|School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Desmond G
authors.initials: DG
authors.lastname: Higgins
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland.|Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin, Ireland.|School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland.
authors.forename: Walter
authors.initials: W
authors.lastname: Kolch
mesh_terms: D015153:Blotting, Western; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000502:physiology; D016259:Genes, myc / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D000071447:N-Myc Proto-Oncogene Protein; D009447:Neuroblastoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D009687:Nuclear Proteins / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D015513:Oncogene Proteins / Q000502:physiology*; D016133:Polymerase Chain Reaction; D060066:Protein Interaction Maps / Q000502:physiology*; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction / Q000502:physiology
chemical_list: C459801:MYCN protein, human; D000071447:N-Myc Proto-Oncogene Protein; D009687:Nuclear Proteins; D015513:Oncogene Proteins
keywords: 4sU-seq; MYC (c-MYC); mRNA sequencing (mRNA-seq); neuroblastoma; transcriptional regulation