Multiomic analysis of subtype evolution and heterogeneity in high-grade serous ovarian carcinoma

Ludwig Geistlinger, Sehyun Oh, Marcel Ramos, Lucas Schiffer, Rebecca S LaRue, Christy Henzler, Sarah A. Munro, Claire Daughters, Andrew C. Nelson, Boris J Winterhoff, Zenas Chang, Shobhana Talukdar, Mihir Shetty, Sally A Mullany, Martin Morgan, Giovanni Parmigiani, Michael J. Birrer, Li Xuan Qin, Markus Riester, Timothy K. StarrLevi Waldron

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1 Scopus citations

Abstract

Multiple studies have identified transcriptome subtypes of high-grade serous ovarian carcinoma (HGSOC), but their interpretation and translation are complicated by tumor evolution and polyclonality accompanied by extensive accumulation of somatic aberrations, varying cell type admixtures, and different tissues of origin. In this study, we examined the chronology of HGSOC subtype evolution in the context of these factors using a novel integrative analysis of absolute copy-number analysis and gene expression in The Cancer Genome Atlas complemented by single-cell analysis of six independent tumors. Tumor purity, ploidy, and subclonality were reliably inferred from different genomic platforms, and these characteristics displayed marked differences between subtypes. Genomic lesions associated with HGSOC subtypes tended to be subclonal, implying subtype divergence at later stages of tumor evolution. Subclonality of recurrent HGSOC alterations was evident for proliferative tumors, characterized by extreme genomic instability, absence of immune infiltration, and greater patient age. In contrast, differentiated tumors were characterized by largely intact genome integrity, high immune infiltration, and younger patient age. Single-cell sequencing of 42,000 tumor cells revealed widespread heterogeneity in tumor cell type composition that drove bulk subtypes but demonstrated a lack of intrinsic subtypes among tumor epithelial cells. Our 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 tumor stage and tissue of origin, and evolution between properties previously associated with discrete subtypes.

Original languageEnglish (US)
Pages (from-to)4335-4345
Number of pages11
JournalCancer Research
Volume80
Issue number20
DOIs
StatePublished - Oct 15 2021

Bibliographical note

Funding Information:
L. Geistlinger was supported by a research fellowship from the German Research Foundation (GE3023/1-1 and GE3023/1-2). R.S. LaRue, C.M. Henzler, A.C. Nelson, B.J. Winterhoff, and T.K. Starr were supported by grants from the Jan Chorzempa Cancer Research Endowed Fund (to T.K. Starr), the Masonic Cancer Center's Translational Working Group Grant (to T.K. Starr), University of MN Grand Challenges grant (to B.J. Winterhoff, A.C. Nelson, and T.K. Starr), the American Cancer Society CSDG (#132574-CSDG-18-139-01-CSM to A.C. Nelson), and institutional grants to the University of Minnesota from NIH/NCI P30CA07759821 and CTSI NCATS UL1TR00249402. G. Parmigiani was supported by grant 5P30CA006516-53, and L. Waldron by grants U24CA180996 and 1R03CA191447-01A1 from the NCI of the NIH.

Funding Information:
employee of Novartis outside the submitted work. T.K. Starr reports grants from Ovarian Cancer Research Alliance (The Ovarian Cancer Research Alliance provided funding for experiments reported in this article) during the conduct of the study. No potential conflicts of interest were disclosed by the other authors.

Funding Information:
B.J. Winterhoff reports grants from Ovarian Cancer Research Alliance (Liz Tilberis Early Career Award) and University of Minnesota (Grand Challenges Research Program) during the conduct of the study. S.A. Mullany reports grants from OCRA during the conduct of the study. M. Morgan reports grants from US NIH during the conduct of the study. G. Parmigiani reports a patent for WO2014153442A2 Methods and systems for treatment of ovarian cancer issued. L.-X. Qin reports grants from NIH (R21 CA214845) during the conduct of the study. M. Riester is a full-time

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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