PDF(Pubmed)
Abstract：
Retinoblastomas form in response to biallelic RB1 mutations or MYCN amplification and progress to more aggressive and therapy-resistant phenotypes through accumulation of secondary genomic changes. Progression-related changes include recurrent somatic copy number alterations and typically non-recurrent nucleotide variants, including synonymous and non-coding variants, whose significance has been unclear. To determine if nucleotide variants recurrently affect specific biological processes, we identified altered genes and over-represented variant gene ontologies in 168 exome or whole-genome-sequenced retinoblastomas and 12 tumor-matched cell lines. In addition to RB1 mutations, MYCN amplification, and established retinoblastoma somatic copy number alterations, the analyses revealed enrichment of variant genes related to diverse biological processes including histone monoubiquitination, mRNA processing (P) body assembly, and mitotic sister chromatid segregation and cytokinesis. Importantly, non-coding and synonymous variants increased the enrichment significance of each over-represented biological process term. To assess the effects of such mutations, we examined the consequences of a 3\' UTR variant of PCGF3 (a BCOR-binding component of Polycomb repressive complex I), dual 3\' UTR variants of CDC14B (a regulator of sister chromatid segregation), and a synonymous variant of DYNC1H1 (a regulator of P-body assembly). One PCGF3 and one of two CDC14B 3\' UTR variants impaired gene expression whereas a base-edited DYNC1H1 synonymous variant altered protease sensitivity and stability. Retinoblastoma cell lines retained only ~50% of variants detected in tumors and enriched for new variants affecting p53 signaling. These findings reveal potentially important differences in retinoblastoma cell lines and tumors and implicate synonymous and non-coding variants, along with non-synonymous variants, in retinoblastoma oncogenesis.
摘要：
视网膜母细胞瘤响应于双等位基因RB1突变或MYCN扩增而形成,并通过次级基因组变化的积累发展为更具侵袭性和治疗抗性的表型。进展相关的变化包括复发性体细胞拷贝数改变和典型的非复发性核苷酸变异，包括同义词和非编码变体，其意义尚不清楚。为了确定核苷酸变异是否会反复影响特定的生物过程，我们在168个外显子组或全基因组测序的视网膜母细胞瘤和12个肿瘤匹配细胞系中鉴定了改变的基因和过度表达的变异基因本体.除了RB1突变，MYCN扩增,并建立了视网膜母细胞瘤SCNA，分析揭示了与多种生物过程相关的变异基因的富集，包括组蛋白单同质化，mRNA加工（P）体组装，有丝分裂姐妹染色单体分离和胞质分裂。重要的是,非编码和同义变体增加了每个过度表示的生物过程术语的富集显著性.为了评估这种突变的影响，我们检查了PCGF3的3'UTR变体（Polycomb阻遏复合物I的BCOR结合成分）的后果，CDC14B的双3UTR变体（姐妹染色单体分离的调节剂），以及DYNC1H1（P体组件的调节器）的同义变体。一个PCGF3和两个CDC14B3'UTR变体之一损害了基因表达，而碱基编辑的DYNC1H1同义变体改变了蛋白酶的敏感性和稳定性。视网膜母细胞瘤细胞系仅保留了在肿瘤中检测到的约50％的变体，并富集了影响p53信号传导的新变体。这些发现揭示了视网膜母细胞瘤细胞系和肿瘤的潜在重要差异，并暗示了同义和非编码变体。与非同义变体一起，视网膜母细胞瘤的肿瘤发生。
