Loss of polycomb repressive complex 1 activity and chromosomal instability drive uveal melanoma progression

Chromosomal instability (CIN) and epigenetic alterations have been implicated in tumor progression and metastasis; yet how these two hallmarks of cancer are related remains poorly understood. By integrating genetic, epigenetic, and functional analyses at the single cell level, we show that progression of uveal melanoma (UM), the most common intraocular primary cancer in adults, is driven by loss of Polycomb Repressive Complex 1 (PRC1) in a subpopulation of tumor cells. This leads to transcriptional de-repression of PRC1-target genes and mitotic chromosome segregation errors. Ensuing CIN leads to the formation of rupture-prone micronuclei, exposing genomic double-stranded DNA (dsDNA) to the cytosol. This provokes tumor cell-intrinsic inflammatory signaling, mediated by aberrant activation of the cGAS-STING pathway. PRC1 inhibition promotes nuclear enlargement, induces a transcriptional response that is associated with significantly worse patient survival and clinical outcomes, and enhances migration that is rescued upon pharmacologic inhibition of CIN or STING. Thus, deregulation of PRC1 can promote tumor progression by inducing CIN and represents an opportunity for early therapeutic intervention.

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Software and code
Policy information about availability of computer code Data collection Data analysis Ashley Laughney, PhD, Samuel Bakhoum, MD, PhD, Paul Mischel, MD and Mathieu Bakhoum, MD, PhD 07/16/2021 No Software was used Partek flow software, version 10.0 (Partek) for bulk RNA sequencing and CUT&RUN analysis, Python 3.6.9 for single cell analysis. For manuscripts utilizing custom algorithms or software that are central to the research but not yet described in published literature, software must be made available to editors/reviewers. We strongly encourage code deposition in a community repository (e.g. GitHub). See the Nature Research guidelines for submitting code & software for further information.

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Life sciences study design
All studies must disclose on these points even when the disclosure is negative.    A custom GSEA annotation file, assembled to query cell types and pathways related to UM, PRC1/2 transcriptional signature and aneuploidy, as well as hallmark genesets is provided in Supplementary Data File 3.
No sample size calculation was performed. Six enucleation specimens were obtained with at least one sample from each prognostic class based on bulk assessment from Castle Biosciences (GEP1 (n=2) and GEP2 (n=4)). For all experimental conditions, a minimum of biological or technical triplicates were used.
No Data were excluded from the analysis Experimental and biological replicates were done for all experiments as indicated in the figure legend.
Not applicable to this study as there was no interventions Investigators were blinded to all experimental conditions including migration assays, growth assays, counting micronuclei, measuring nuclear size or counting patterns of chromosome missegregation.