title: Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors.
abstract: Cancer develops through a multistep process in which normal cells progress to malignant tumors via the evolution of their genomes as a result of the acquisition of mutations in cancer driver genes. The number, identity and mode of action of cancer driver genes, and how they contribute to tumor evolution is largely unknown. This study deployed the Mouse Mammary Tumor Virus (MMTV) as an insertional mutagen to find both the driver genes and the networks in which they function. Using deep insertion site sequencing we identified around 31000 retroviral integration sites in 604 MMTV-induced mammary tumors from mice with mammary gland-specific deletion of Trp53, Pten heterozygous knockout mice, or wildtype strains. We identified 18 known common integration sites (CISs) and 12 previously unknown CISs marking new candidate cancer genes. Members of the Wnt, Fgf, Fgfr, Rspo and Pdgfr gene families were commonly mutated in a mutually exclusive fashion. The sequence data we generated yielded also information on the clonality of insertions in individual tumors, allowing us to develop a data-driven model of MMTV-induced tumor development. Insertional mutations near Wnt and Fgf genes mark the earliest "initiating" events in MMTV induced tumorigenesis, whereas Fgfr genes are targeted later during tumor progression. Our data shows that insertional mutagenesis can be used to discover the mutational networks, the timing of mutations, and the genes that initiate and drive tumor evolution.
authors.affiliation: Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands ; Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: Christiaan
authors.initials: C
authors.lastname: Klijn
authors.forename: Marco J
authors.initials: MJ
authors.lastname: Koudijs
authors.forename: Jaap
authors.initials: J
authors.lastname: Kool
authors.forename: Jelle
authors.initials: J
authors.lastname: ten Hoeve
authors.forename: Mandy
authors.initials: M
authors.lastname: Boer
authors.forename: Joost
authors.initials: J
authors.lastname: de Moes
authors.forename: Waseem
authors.initials: W
authors.lastname: Akhtar
authors.forename: Martine
authors.initials: M
authors.lastname: van Miltenburg
authors.forename: Annabel
authors.initials: A
authors.lastname: Vendel-Zwaagstra
authors.forename: Marcel J T
authors.initials: MJ
authors.lastname: Reinders
authors.forename: David J
authors.initials: DJ
authors.lastname: Adams
authors.forename: Maarten
authors.initials: M
authors.lastname: van Lohuizen
authors.forename: John
authors.initials: J
authors.lastname: Hilkens
authors.forename: Lodewyk F A
authors.initials: LF
authors.lastname: Wessels
authors.forename: Jos
authors.initials: J
authors.lastname: Jonkers
mesh_terms: D000818:Animals; D063646:Carcinogenesis / Q000235:genetics; D045744:Cell Line, Tumor; D018450:Disease Progression; D005260:Female; D053263:Gene Regulatory Networks / Q000235:genetics*; D052138:Genes, Neoplasm / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008325:Mammary Neoplasms, Experimental / Q000235:genetics* / Q000473:pathology* / Q000821:virology; D008324:Mammary Tumor Virus, Mouse / Q000502:physiology*; D051379:Mice; D016254:Mutagenesis, Insertional; D051059:PTEN Phosphohydrolase / Q000235:genetics; D017422:Sequence Analysis, DNA; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D016159:Tumor Suppressor Protein p53; D051059:PTEN Phosphohydrolase