Multi-omic analysis of subtype evolution and heterogeneity in high-grade serous ovarian carcinoma
Authors: Geistlinger Ludwig , Oh Sehyun , Ramos Marcel , Schiffer Lucas , LaRue Rebecca , Henzler Christine , Munro Sarah , Daughters Claire , Nelson Andrew C. , Winterhoff Boris , Chang Zenas , Talukdar Shobhana , Shetty Mihir , Mullaney Sally , Morgan Martin , Parmigiani Giovanni , Birrer Michael , Qin Li-Xuan , Riester Markus , Starr Timothy K. , Waldron Levi 
Published: February 2019

Multiple studies have identified transcriptome subtypes of high-grade serous ovarian carcinoma (HGSOC), but these have yet to impact clinical practice. Interpretation and translation of HGSOC subtypes are complicated by tumor evolution and polyclonality accompanied by accumulation of somatic aberrations, varying cell type admixtures, and different tissues of origin. The chronology of HGSOC subtype evolution was examined in the context of these factors by a novel integrative analysis of bulk absolute somatic copy number analysis and gene expression in The Cancer Genome Atlas, complemented by single-cell RNA-seq analysis of six independent tumors. The approach was validated by contrast to soft-tissue sarcoma. Genomic lesions associated with HGSOC subtypes tend to be subclonal, implying subtype divergence at later stages of tumor evolution. Subclonality of recurrent HGSOC alterations is particularly evident for proliferative tumors, characterized by extreme genomic instability, absence of immune infiltration, and greater patient age. In contrast, differentiated tumors are characterized by largely intact genome integrity, high immune infiltration, and younger patient age. We propose an alternative model to discrete subtypes of HGSOC, in which tumors develop from an early differentiated spectrum to a late proliferative spectrum, along a timeline characterized by increasing genomic instability and subclonal expansion. The proposed methods provide a new approach to investigating tumor evolution through multi-omic analysis.

Statement of Significance

This study proposes a method to infer whether transcriptome-based groupings of tumors differentiate early in carcinogenesis and are therefore potentially appropriate targets for therapy, and demonstrates that this is not the case for high-grade serous ovarian carcinoma (HGSOC). Significant findings for HGSOC include:

Tumor purity, ploidy, and subclonality can be reliably inferred from different genomic platforms and show marked differences between subtypes

Recurrent DNA alterations are associated with subtypes and tend to occur more frequently in subclones

Single-cell sequencing of 42,000 tumor cells reveals widespread heterogeneity in tumor cell type composition that drives bulk subtype calls, but demonstrates a lack of intrinsic subtypes among tumor epithelial cells

Findings prompt the dismissal of discrete transcriptome subtypes for HGSOC and replacement by a more realistic model of continuous tumor development that includes mixtures of subclones, accumulation of somatic aberrations, infiltration of immune and stromal cells in proportions correlated with tissue of origin and tumor stage, and evolution between properties previously associated with discrete subtypes