Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature

Abstract

Simple Summary Retinoblastoma, a childhood cancer of the eye, is thought to be caused by inactivating mutations of both copies of the RB1 gene. The majority of RB1 mutations can be detected by clinical screening. However, retinoblastoma cases exist where mutations in RB1 have not been detected. We used whole-genome sequencing to investigate the landscape of mutations in a cohort of sporadic retinoblastomas, including cases where mutations in both copies of RB1 had not been previously identified. We looked for mutations in cancer driver genes and revealed a wide variety of structural rearrangements disrupting RB1. In addition, we investigated mutation burden and specific mutation patterns (mutational signatures), uncovering a treatment-related mutational signature in a tumour exposed to chemotherapy. The power of whole-genome sequencing to identify RB1 mutations of all mutation types can have significant relevance to the clinical management of retinoblastoma patients and genetic counselling of their families. Abstract The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We used whole-genome sequencing (WGS) and transcriptomics to investigate the landscape of sporadic retinoblastomas derived from twenty patients, sought RB1 and other driver mutations and investigated mutational signatures. At least one RB1 mutation was identified in all retinoblastomas, including new mutations in addition to those previously identified by clinical screening. Ten tumours carried structural rearrangements involving RB1 ranging from relatively simple to extremely complex rearrangement patterns, including a chromothripsis-like pattern in one tumour. Bilateral tumours obtained from one patient harboured conserved germline but divergent somatic RB1 mutations, indicating independent evolution. Mutational signature analysis showed predominance of signatures associated with cell division, an absence of ultraviolet-related DNA damage and a profound platinum-related mutational signature in a chemotherapy-exposed tumour. Most RB1 mutations are identifiable by clinical screening. However, the increased resolution and ability to detect otherwise elusive rearrangements by WGS have important repercussions on clinical management and advice on recurrence risks.