RB1 gene inactivation by chromothripsis in human retinoblastoma

// Justina McEvoy 1,* , Panduka Nagahawatte 2,* , David Finkelstein 2 , Jennifer Richards-Yutz 6 , Marcus Valentine 13 , Jing Ma 14 , Charles Mullighan 14 , Guangchun Song 14 , Xiang Chen 2 , Matthew Wilson 4 , Rachel Brennan 12 , Stanley Pounds 3 , Jared Becksfort 2 , Robert Huether 2 , Charles Lu 7 , Robert S. Fulton 7,8 , Lucinda L. Fulton 7,8 , Xin Hong 7,8 , David J. Dooling 7,8 , Kerri Ochoa 7,8 , Elaine R. Mardis 7,8,9 , Richard K.Wilson 7,8,10 , John Easton 2 , Jinghui Zhang 2 , James R. Downing 14 , Arupa Ganguly 5,6,* and Michael A. Dyer 1,4,11 for the St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project 1 Departments of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA. 2 Computational Biology and Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA. 3 Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN, USA. 4 Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN 5 Department of Genetics, School of Medicine, Philadelphia, PA, USA 6 Genetic Diagnostic Laboratory at University of Pennsylvania, School of Medicine, Philadelphia, PA, USA. 7 The Genome Institute, Washington University School of Medicine in St Louis, St Louis, Missouri, USA. 8 Department of Genetics, Washington University School of Medicine in St Louis, St Louis, Missouri, USA. 9 Siteman Cancer Center, Washington University School of Medicine in St Louis, St Louis, Missouri, USA. 10 Department of Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA 11 Howard Hughes Medical Institute, Chevy Chase, MD 12 Oncology, St. Jude Children’s Research Hospital, Memphis, TN, USA. 13 Cytogenetics, St. Jude Children’s Research Hospital, Memphis, TN, USA. 14 Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA. * These authors contributed equally to this work. Correspondence: Michael A. Dyer , email: // Keywords : chromothripsis, retinoblastoma, RB1, MYCN Received : December 13, 2013 Accepted : January 7, 2014 Published : January 11, 2014 Abstract Retinoblastoma is a rare childhood cancer of the developing retina. Most retinoblastomas initiate with biallelic inactivation of the RB1 gene through diverse mechanisms including point mutations, nucleotide insertions, deletions, loss of heterozygosity and promoter hypermethylation. Recently, a novel mechanism of retinoblastoma initiation was proposed. Gallie and colleagues discovered that a small proportion of retinoblastomas lack RB1 mutations and had MYCN amplification 1 . In this study, we identified recurrent chromosomal, regional and focal genomic lesions in 94 primary retinoblastomas with their matched normal DNA using SNP 6.0 chips. We also analyzed the RB1 gene mutations and compared the mechanism of RB1 inactivation to the recurrent copy number variations in the retinoblastoma genome. In addition to the previously described focal amplification of MYCN and deletions in RB1 and BCOR , we also identified recurrent focal amplification of OTX2 , a transcription factor required for retinal photoreceptor development. We identified 10 retinoblastomas in our cohort that lacked RB1 point mutations or indels. We performed whole genome sequencing on those 10 tumors and their corresponding germline DNA. In one of the tumors, the RB1 gene was unaltered, the MYCN gene was amplified and RB1 protein was expressed in the nuclei of the tumor cells. In addition, several tumors had complex patterns of structural variations and we identified 3 tumors with chromothripsis at the RB1 locus. This is the first report of chromothripsis as a mechanism for RB1 gene inactivation in cancer.