Non-Synonymous, Synonymous, and Non-Coding Nucleotide Variants Contribute to Recurrently Altered Biological Processes During Retinoblastoma Progression

Stachelek, K.; Harutyunyan, N.; Lee, S.; Beck, A.; Kim, J.; Xu, L.; Berry, J.; Nagiel, A.; Reynolds, C. P.; Murphree, A. L.; Lee, T.; Aparicio, J.; Cobrinik, D.

doi:10.1101/2022.10.27.512289

bioRxiv · 10.1101/2022.10.27.512289

Non-Synonymous, Synonymous, and Non-Coding Nucleotide Variants Contribute to Recurrently Altered Biological Processes During Retinoblastoma Progression

Stachelek, K.·Harutyunyan, N.·Lee, S.·Beck, A.·Kim, J.·Xu, L.·Berry, J.·Nagiel, A.·Reynolds, C. P.·Murphree, A. L.·Lee, T.·Aparicio, J.·Cobrinik, D.

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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 assess synonymous and non-coding variant contributions to recurrently altered 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 initiating RB1 mutations, MYCN amplification, and established retinoblastoma SCNAs, 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, inclusion of non-coding and synonymous variants increased the enrichment significance of each over-represented biological process term. To assess the effects of such mutations, we performed functional tests of 3 UTR variants of PCGF3 (a BCOR-binding component of Polycomb repressive complex I) and CDC14B (a regulator of sister chromatid segregation) and a synonymous variant of DYNC1H1 (a regulator of P-body assembly). PCGF3 and CDC14B 3 UTR variants impaired gene expression whereas a base-edited DYNC1H1 synonymous variant altered protein structure and stability. Compared to tumors, retinoblastoma cell lines had a partially overlapping variant gene spectrum and enrichment for p53 pathway mutations. These findings reveal potentially important differences in retinoblastoma cell lines and antecedent tumors and implicate synonymous and non-coding variants, along with non-synonymous variants, in retinoblastoma oncogenesis.

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Stachelek, K., Harutyunyan, N., Lee, S., Beck, A., Kim, J., Xu, L., Berry, J., Nagiel, A., Reynolds, C. P., Murphree, A. L., Lee, T., Aparicio, J., Cobrinik, D.. 2022-10-28. Non-Synonymous, Synonymous, and Non-Coding Nucleotide Variants Contribute to Recurrently Altered Biological Processes During Retinoblastoma Progression. https://doi.org/10.1101/2022.10.27.512289

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