A Meta-Analysis of Retinoblastoma Copy Numbers Refines the List of Possible Driver Genes Involved in Tumor Progression

• Published in: PloS one Vol. 11; no. 4; p. e0153323
• Main Authors: Kooi, Irsan E., Mol, Berber M., Massink, Maarten P. G., de Jong, Marcus C., de Graaf, Pim, van der Valk, Paul, Meijers-Heijboer, Hanne, Kaspers, Gertjan J. L., Moll, Annette C., te Riele, Hein, Cloos, Jacqueline, Dorsman, Josephine C.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 26.04.2016; Public Library of Science (PLoS)
• Subjects: Algorithms; Analysis; Arrays; Bioinformatics; Biology and Life Sciences; Cancer; Cell Line, Tumor; Chromosome 1; Chromosome 13; Chromosome 2; Copy number; Deoxyribonucleic acid; Development and progression; Disease Progression; DNA; DNA microarrays; Gene Dosage; Gene expression; Gene Expression Profiling; Genes; Genetic aspects; Genetic variation; Genetics; Genomes; Hematology; Heterogeneity; Homozygosity; Humans; Medical diagnosis; Medicine and Health Sciences; Meta-analysis; Mutation; Nuclear medicine; Oligonucleotide Array Sequence Analysis; Oncogenes; Pediatrics; Physical Sciences; Physiological aspects; Research and Analysis Methods; Retina; Retinal Neoplasms - genetics; Retinoblastoma; Retinoblastoma - genetics; Retinoblastoma Binding Proteins - genetics; Revisions; Risk factors; Sample size; Statistics; Studies; Tumors; Ubiquitin-Protein Ligases - genetics; Netherlands
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0153323

While RB1 loss initiates retinoblastoma development, additional somatic copy number alterations (SCNAs) can drive tumor progression. Although SCNAs have been identified with good concordance between studies at a cytoband resolution, accurate identification of single genes for all recurrent SCNAs is still challenging. This study presents a comprehensive meta-analysis of genome-wide SCNAs integrated with gene expression profiling data, narrowing down the list of plausible retinoblastoma driver genes. We performed SCNA profiling of 45 primary retinoblastoma samples and eight retinoblastoma cell lines by high-resolution microarrays. We combined our data with genomic, clinical and histopathological data of ten published genome-wide SCNA studies, which strongly enhanced the power of our analyses (N = 310). Comprehensive recurrence analysis of SCNAs in all studies integrated with gene expression data allowed us to reduce candidate gene lists for 1q, 2p, 6p, 7q and 13q to a limited gene set. Besides the well-established driver genes RB1 (13q-loss) and MYCN (2p-gain) we identified CRB1 and NEK7 (1q-gain), SOX4 (6p-gain) and NUP205 (7q-gain) as novel retinoblastoma driver candidates. Depending on the sample subset and algorithms used, alternative candidates were identified including MIR181 (1q-gain) and DEK (6p gain). Remarkably, our study showed that copy number gains rarely exceeded change of one copy, even in pure tumor samples with 100% homozygosity at the RB1 locus (N = 34), which is indicative for intra-tumor heterogeneity. In addition, profound between-tumor variability was observed that was associated with age at diagnosis and differentiation grades. Since focal alterations at commonly altered chromosome regions were rare except for 2p24.3 (MYCN), further functional validation of the oncogenic potential of the described candidate genes is now required. For further investigations, our study provides a refined and revised set of candidate retinoblastoma driver genes.