RB1 gene inactivation by chromothripsis in human retinoblastoma

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 identifed 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 identifed recurrent focal amplification of OTX2, a transcription factor required for retinal photoreceptor development. We identifed 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.

A mouse model of MYCN-driven retinoblastoma reveals MYCN-independent tumor reemergence

“…In one study, high-level MYCN amplifications were found only in those retinoblastomas in which RB mutations were undetected (3). In a more recent study, however, 8 of 94 retinoblastomas had more than 10 MYCN copies, and 6 of 8 of these MYCN-amplified retinoblastomas had at least 1 hit in the RB gene detected (2). Thus, a subset of retinoblastomas shows MYCN amplification, even in the absence of detected RB mutation, while in other retinoblastomas, MYCN amplification and RB mutations co-occur.…”

“…RB deletion and MYCN amplification are the two most frequent focal alterations occurring in human retinoblastoma, and these alterations often co-occur in the same tumor (2). MYCN amplifications in the absence of RB mutations or deletions have been described previously (2,3).…”

“…MYCN amplifications have long been known to contribute to human retinoblastoma, often together with retinoblastoma (RB) loss (1,2). MYCN is also amplified in a small subset of human retinoblastomas harboring an intact RB gene (3).…”

“…MYCN is the most frequently focally altered gene in human retinoblasto- , referred to hereafter as Rb/ p107 mice), retinoblastomas arose with long latency. MYCN was ma beyond RB (2), and so we sought to control MYCN expression in the mouse retina harboring Rb family member deletion. We report a model of retinoblastoma that precisely mimics key genetic alterations in human retinoblastoma tumors and obviates any need to genetically inactivate Rb family members beyond Rb.…”

Retinoblastoma and Neuroblastoma Predisposition and Surveillance

“…About 1% of RB (usually unilateral) is due to somatic MYCN amplification rather than loss of RB1 function (4). Another study demonstrated three RBs with focal chromothripsis in the tumor tissue disrupting the RB1 locus, suggesting that somatic acquisition of these complex structural rearrangements can play a role in RB1 tumor-suppressor inactivation (5).…”