Investigator
University Of Southern California
OvaPrint—A Cell-free DNA Methylation Liquid Biopsy for the Risk Assessment of High-grade Serous Ovarian Cancer
Abstract Purpose: High-grade serous ovarian carcinoma (HGSOC) is the most lethal epithelial ovarian cancer (EOC) and is often diagnosed at late stage. In women with a known pelvic mass, surgery followed by pathologic assessment is the most reliable way to diagnose EOC and there are still no effective screening tools in asymptomatic women. In the current study, we developed a cell-free DNA (cfDNA) methylation liquid biopsy for the risk assessment of early-stage HGSOC. Experimental Design: We performed reduced representation bisulfite sequencing to identify differentially methylated regions (DMR) between HGSOC and normal ovarian and fallopian tube tissue. Next, we performed hybridization probe capture for 1,677 DMRs and constructed a classifier (OvaPrint) on an independent set of cfDNA samples to discriminate HGSOC from benign masses. We also analyzed a series of non-HGSOC EOC, including low-grade and borderline samples to assess the generalizability of OvaPrint. A total of 372 samples (tissue n = 59, plasma n = 313) were analyzed in this study. Results: OvaPrint achieved a positive predictive value of 95% and a negative predictive value of 88% for discriminating HGSOC from benign masses, surpassing other commercial tests. OvaPrint was less sensitive for non-HGSOC EOC, albeit it may have potential utility for identifying low-grade and borderline tumors with higher malignant potential. Conclusions: OvaPrint is a highly sensitive and specific test that can be used for the risk assessment of HGSOC in symptomatic women. Prospective studies are warranted to validate OvaPrint for HGSOC and further develop it for non-HGSOC EOC histotypes in both symptomatic and asymptomatic women with adnexal masses.
Integrated Single-Cell Whole-Genome Sequencing and Spatial Transcriptomics Reveal Intratumoral Heterogeneity in Ovarian Cancer.
The mortality rate of ovarian cancer remains disproportionately high compared with its incidence. This is partly due to a high level of intratumoral 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 (ST) of five late-stage, treatment-naïve primary epithelial ovarian carcinomas, including high-grade serous and clear-cell subtypes. All samples exhibited widespread copy-number (CN) aberrations, with the greatest intraspecimen diversification in regions of CN gain. Diversification was also associated with whole-genome doubling in all samples. In two samples, we identify persistent, clonal pseudodiploid cells evolutionarily consistent with a premalignant phenotype. In multiclonal samples, we interpret clonal evolution in the context of single-cell CN, loss of heterozygosity analysis, and somatic mutations and correlate these with tissue histology and gene expression programs. In one high-grade serous carcinoma, we identify functionally consequential CN 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. We utilize single-cell DNA sequencing and ST to illustrate the wide extent of intratumoral heterogeneity within late-stage ovarian tumors. We describe several consequences of chromosomal instability, including divergent biology in multiclonal tumors, persistence of a premalignant cell population, and functional reversion of an oncogenic driver mutation.
