Whole genome doubling drives oncogenic loss of chromatin segregation [WGS]

Whole genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies. However, the 3D organization of the chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here, we show that in p53 deficient cells WGD induces loss of chromatin segregation (LCS), characterized by reduced segregation between short and long chromosomes, A and B sub-compartments, and adjacent chromatin domains. LCS is driven by downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primed genomic regions for sub-compartment repositioning in WGD cells, which resulted in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Importantly, sub-compartment repositioning events were largely independent of chromosomal alterations, indicating that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, suggesting that chromatin evolution is a hallmark of WGD-driven cancer. Overall design: For mutational and copy number change analyses in post-WGD cells in RPE TP53-/- line, whole genome sequencing was performed in RPE TP53-/- control, WGD, and 6w and 20w pWGD cells grown in vitro and in vivo. Biological replicates for 6w pWGD were considered and are denoted as experiment 1-4 based on multiple WGD inductions. RPE cells with a TP53 wild type background were considered as reference for calling mutations and copy number changes.