Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations

// Susanne Lorenz 1,5 , Tale Baroy 1,14 , Jinchang Sun 2,5 , Torfinn Nome 3,10 , Daniel Vodak 1 , Jan-Christian Bryne 1,2 , Anne-Mari Hakelien 1 , Lynnette Fernandez-Cuesta 6,7 , Birte Mohlendick 8 , Harald Rieder 8 , Karoly Szuhai 9 , Olga Zaikova 4 , Terje C. Ahlquist 3,10 , Gard O. S. Thomassen 3,10 , Rolf I. Skotheim 3,10 , Ragnhild A. Lothe 3,10 , Patrick S. Tarpey 11 , Peter Campbell 11 , Adrienne Flanagan 12,13 , Ola Myklebost 1,5,* and Leonardo A. Meza-Zepeda 1,2,5,* 1 Department of Tumor Biology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway 2 Genomics Core Facility, Department of Core Facilities, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway 3 Department of Molecular Oncology, Institute for Cancer research, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway 4 Clinic for Cancer, Surgery and Transplantation, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway 5 Norwegian Cancer Genomics Consortium, Norway 6 Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, Cologne, Germany 7 Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC-WHO), Lyon, France 8 Institute for Human Genetics, University Hospital Dusseldorf, Dusseldorf, Germany 9 Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands 10 Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway 11 Wellcome Trust Sanger Institute, Hinxton, UK 12 Royal National Orthopaedic Hospital, Middlesex, UK 13 UCL Cancer Institute, University College London, London, UK 14 Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway * These authors shared last authorship Correspondence to: Leonardo A. Meza-Zepeda, email: // Keywords : bone cancer, osteosarcomas, gene fusion, trans-splicing, DNA repair Received : July 16, 2015 Accepted : November 15, 2015 Published : December 11, 2015 Abstract In contrast to many other sarcoma subtypes, the chaotic karyotypes of osteosarcoma have precluded the identification of pathognomonic translocations. We here report hundreds of genomic rearrangements in osteosarcoma cell lines, showing clear characteristics of microhomology-mediated break-induced replication (MMBIR) and end-joining repair (MMEJ) mechanisms. However, at RNA level, the majority of the fused transcripts did not correspond to genomic rearrangements, suggesting the involvement of trans-splicing, which was further supported by typical trans-splicing characteristics. By combining genomic and transcriptomic analysis, certain recurrent rearrangements were identified and further validated in patient biopsies, including a PMP22-ELOVL5 gene fusion, genomic structural variations affecting RB1, MTAP/CDKN2A and MDM2 , and, most frequently, rearrangements involving TP53. Most cell lines (7/11) and a large fraction of tumor samples (10/25) showed TP53 rearrangements, in addition to somatic point mutations (6 patient samples, 1 cell line) and MDM2 amplifications (2 patient samples, 2 cell lines). The resulting inactivation of p53 was demonstrated by a deficiency of the radiation-induced DNA damage response. Thus, TP53 rearrangements are the major mechanism of p53 inactivation in osteosarcoma. Together with active MMBIR and MMEJ, this inactivation probably contributes to the exceptional chromosomal instability in these tumors. Although rampant rearrangements appear to be a phenotype of osteosarcomas, we demonstrate that among the huge number of probable passenger rearrangements, specific recurrent, possibly oncogenic, events are present. For the first time the genomic chaos of osteosarcoma is characterized so thoroughly and delivered new insights in mechanisms involved in osteosarcoma development and may contribute to new diagnostic and therapeutic strategies.