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

Abstract

BackgroundWhile 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.MethodsWe 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).ResultsComprehensive 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.InterpretationSince 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.

Genomic landscape of retinoblastoma in Rb−/−p130−/− mice resembles human retinoblastoma

“…7), based on human-mouse orthology annotation provided by the Ensembl database. For both HMGA1 and SRSF3, a significant relation between increased copy numbers and increased expression was found previously in human retinoblastoma (Kooi et al, 2016b). Frequently altered human chromosome arm 1q is largely syntenic to mouse chromosome 1 that was gained in 3/23 Rb 2/2 p130 2/2 tumors.…”

“…Genes at mouse SCNAs identified in our cohort and the MacPherson cohort were linked to the human orthologs at the frequently altered 1q, 2p, 6p, and 16q arms (Fig. On the contrary, candidate gene identification of human chromosome arm 6p is still challenging, as no focal high-level amplifications have been described (Kooi et al, 2016b). A summary of the number of human genes that were altered similarly in human and mouse retinoblastoma is given per chromosome for both models (Table 2) and further details are given in Supporting Information Table S5.…”

“…The most common SCNAs in human retinoblastoma (>30% of tumors per cohort) include gain of 1q, 2p, and 6p and loss of 16q (Kooi et al, 2016b) Identification of the SCNA target genes at these chromosome arms has however been challenging (Kooi et al, 2016b). Since the murine genome is organized differently from the human genome, intersecting the frequently altered human regions with SCNAs identified in murine retinoblastoma might aid retinoblastoma driver gene discovery.…”

“…For human chromosome arm 2p, it is well established that MYCN is the driver gene, which may explain gain of chromosome 12 seen in many of the murine tumors. On the contrary, candidate gene identification of human chromosome arm 6p is still challenging, as no focal high-level amplifications have been described (Kooi et al, 2016b). Human chromosome arm 6p corresponds to gained mouse chromosomes 1 and 11, including 20 and 3 gene transcripts, respectively.…”

Retinoblastoma, the visible CNS tumor: A review

“…MYCN is the most commonly amplified gene on 2p, while on 6p, the best‐studied genes are the DNA‐binding proto‐oncogene DEK and the transcription factor E2F3 . Genes commonly lost on 16q include CDH11 , encoding the adhesion protein cadherin‐11, and RBL2 , encoding the retinoblastoma family member p130 (Kooi et al, ; Theriault, Dimaras, Gallie, & Corson, ). In addition, aberrant methylation is seen in the retinoblastoma genome (Benavente & Dyer, ), including the oncogenic kinase SYK (spleen tyrosine kinase).…”