Integrated single-cell whole genome sequencing and spatial transcriptomics reveal intra-tumoral heterogeneity in ovarian cancer

Abstract The mortality rate of ovarian cancer remains disproportionately high compared to its incidence. This is partly due to a high level of intra-tumoral heterogeneity, driven by genomic instability, that promotes disease recurrence and treatment failure. In this study, we describe degrees of heterogeneity revealed by single-cell whole genome sequencing and spatial transcriptomics of five late-stage, treatment-naïve primary epithelial ovarian carcinomas, including high grade serous and clear cell subtypes. All samples exhibited widespread copy number aberrations, with greatest intra-specimen diversification in regions of copy number gain. Diversification was also associated with whole genome doubling in all samples. In two samples, we identify persistent, clonal pseudo-diploid cells evolutionarily consistent with a pre-malignant phenotype. In multi-clonal samples, we interpret clonal evolution in the context of single cell copy number, loss of heterozygosity analysis, and somatic mutations, and correlate these with tissue histology and gene expression programs. In one high grade serious carcinoma, we identify functionally consequential copy number alterations that contribute to molecular diversity, cell proliferation, and inflammation in a minor clone that persisted without major expansion alongside a more complex major clone. In another clear cell carcinoma, we describe a complex evolutionary history including a spontaneous functional reversion of a CTNNB1 driver mutation in a secondary clone, which correlated with a switch in oncogenic expression programs. These examples highlight various consequences of genomic instability on clonal heterogeneity and plasticity in ovarian cancer.