Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells

Boris J. Winterhoff, Makayla Maile, Amit Kumar Mitra, Attila Sebe, Martina Bazzaro, Melissa A. Geller, Juan E. Abrahante, Molly Klein, Raffaele Hellweg, Sally A. Mullany, Kenneth Beckman, Jerry Daniel, Timothy K. Starr

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

Abstract

Objectives The purpose of this study was to determine the level of heterogeneity in high grade serous ovarian cancer (HGSOC) by analyzing RNA expression in single epithelial and cancer associated stromal cells. In addition, we explored the possibility of identifying subgroups based on pathway activation and pre-defined signatures from cancer stem cells and chemo-resistant cells. Methods A fresh, HGSOC tumor specimen derived from ovary was enzymatically digested and depleted of immune infiltrating cells. RNA sequencing was performed on 92 single cells and 66 of these single cell datasets passed quality control checks. Sequences were analyzed using multiple bioinformatics tools, including clustering, principle components analysis, and geneset enrichment analysis to identify subgroups and activated pathways. Immunohistochemistry for ovarian cancer, stem cell and stromal markers was performed on adjacent tumor sections. Results Analysis of the gene expression patterns identified two major subsets of cells characterized by epithelial and stromal gene expression patterns. The epithelial group was characterized by proliferative genes including genes associated with oxidative phosphorylation and MYC activity, while the stromal group was characterized by increased expression of extracellular matrix (ECM) genes and genes associated with epithelial-to-mesenchymal transition (EMT). Neither group expressed a signature correlating with published chemo-resistant gene signatures, but many cells, predominantly in the stromal subgroup, expressed markers associated with cancer stem cells. Conclusions Single cell sequencing provides a means of identifying subpopulations of cancer cells within a single patient. Single cell sequence analysis may prove to be critical for understanding the etiology, progression and drug resistance in ovarian cancer.

Original languageEnglish (US)
Pages (from-to)598-606
Number of pages9
JournalGynecologic oncology
Volume144
Issue number3
DOIs
StatePublished - Mar 1 2017

Bibliographical note

Funding Information:
This work was supported by the following funding sources: Masonic Cancer Center, University of Minnesota (TWG grant to TKS, MB, and MAB); NCI/NIH Project grant ( P30-CA77598 ); The National Center for Advancing Translational Sciences of the NIH ( UL1TR000114 ). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Keywords

  • Molecular subtypes
  • Ovarian cancer
  • Single cell sequencing and cancer stem cells

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