title: Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis.
abstract: Retroviral insertional mutagenesis (RIM) is a powerful tool for cancer genomics that was combined in this study with deep sequencing (RIM/DS) to facilitate a comprehensive analysis of lymphoma progression. Transgenic mice expressing two potent collaborating oncogenes in the germ line (CD2-MYC, -Runx2) develop rapid onset tumours that can be accelerated and rendered polyclonal by neonatal Moloney murine leukaemia virus (MoMLV) infection. RIM/DS analysis of 28 polyclonal lymphomas identified 771 common insertion sites (CISs) defining a 'progression network' that encompassed a remarkably large fraction of known MoMLV target genes, with further strong indications of oncogenic selection above the background of MoMLV integration preference. Progression driven by RIM was characterised as a Darwinian process of clonal competition engaging proliferation control networks downstream of cytokine and T-cell receptor signalling. Enhancer mode activation accounted for the most efficiently selected CIS target genes, including Ccr7 as the most prominent of a set of chemokine receptors driving paracrine growth stimulation and lymphoma dissemination. Another large target gene subset including candidate tumour suppressors was disrupted by intragenic insertions. A second RIM/DS screen comparing lymphomas of wild-type and parental transgenics showed that CD2-MYC tumours are virtually dependent on activation of Runx family genes in strong preference to other potent Myc collaborating genes (Gfi1, Notch1). Ikzf1 was identified as a novel collaborating gene for Runx2 and illustrated the interface between integration preference and oncogenic selection. Lymphoma target genes for MoMLV can be classified into (a) a small set of master regulators that confer self-renewal; overcoming p53 and other failsafe pathways and (b) a large group of progression genes that control autonomous proliferation in transformed cells. These findings provide insights into retroviral biology, human cancer genetics and the safety of vector-mediated gene therapy.
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Camille A
authors.initials: CA
authors.lastname: Huser
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Gilroy
authors.affiliation: Delft Bioinformatics Lab, Faculty of EEMCS, TU Delft, Delft, The Netherlands.
authors.forename: Jeroen
authors.initials: J
authors.lastname: de Ridder
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Anna
authors.initials: A
authors.lastname: Kilbey
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Gillian
authors.initials: G
authors.lastname: Borland
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Nancy
authors.initials: N
authors.lastname: Mackay
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Alma
authors.initials: A
authors.lastname: Jenkins
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Margaret
authors.initials: M
authors.lastname: Bell
authors.affiliation: Glasgow Polyomics, Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Pawel
authors.initials: P
authors.lastname: Herzyk
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Louise
authors.initials: L
authors.lastname: van der Weyden
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: David J
authors.initials: DJ
authors.lastname: Adams
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Alistair G
authors.initials: AG
authors.lastname: Rust
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Ewan
authors.initials: E
authors.lastname: Cameron
authors.affiliation: Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
authors.forename: James C
authors.initials: JC
authors.lastname: Neil
mesh_terms: D000818:Animals; D063646:Carcinogenesis; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D020570:Genes, myb / Q000235:genetics*; D005854:Germ Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051740:Ikaros Transcription Factor / Q000096:biosynthesis / Q000235:genetics; D008223:Lymphoma / Q000235:genetics* / Q000473:pathology / Q000821:virology; D051379:Mice; D008979:Moloney murine leukemia virus / Q000235:genetics*; D016254:Mutagenesis, Insertional / Q000235:genetics*; D016159:Tumor Suppressor Protein p53 / Q000235:genetics*
chemical_list: D016159:Tumor Suppressor Protein p53; C497238:Zfpn1a1 protein, mouse; D051740:Ikaros Transcription Factor