Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry

Abstract

We have performed an in-depth single-cell phenotypic characterization of high-grade serous ovarian cancer (HGSOC) by multiparametric mass cytometry (CyTOF). Using a CyTOF antibody panel to interrogate features of HGSOC biology, combined with unsupervised computational analysis, we identified noteworthy cell types co-occurring across the tumors. In addition to a dominant cell subset, each tumor harbored rarer cell phenotypes. One such group co-expressed E-cadherin and vimentin (EV), suggesting their potential role in epithelial mesenchymal transition, which was substantiated by pairwise correlation analyses. Furthermore, tumors from patients with poorer outcome had an increased frequency of another rare cell type that co-expressed vimentin, HE4, and cMyc. These poorer-outcome tumors also populated more cell phenotypes, as quantified by Simpson's diversity index. Thus, despite the recognized genomic complexity of the disease, the specific cell phenotypes uncovered here offer a focus for therapeutic intervention and disease monitoring.

Mapping Lung Cancer Epithelial-Mesenchymal Transition States and Trajectories with Single-Cell Resolution

“…Five fresh NSCLC adenocarcinoma samples were obtained immediately after patient resection under IRB approval and underwent immediate dissociation for single-cell suspension. For mass cytometry analysis, we used the antibody panel developed for our time-course analysis, augmented with antibodies to sort out immune (CD45 + ), endothelial (CD31 + ) and stromal fibroblast (FAP + ) populations 13 . With this, we were able to discriminate immune, endothelial and stromal cells from cells that were of varying levels of cytokeratins 7 and 8, while at the same time negative for CD45, CD31 and FAP ( Supplementary Fig.…”

“…Pastushenko et al demonstrated the existence of partial EMT states in mammary and skin cancer by examining a large number of surface markers with flow cytometry and sc-RNAseq 12 . Gonzalez et al identified partial EMT states in clinical ovarian cancer samples with mass cytometry 13 . While these studies provide important insights, they did not directly relate their findings to EMT states that have been well characterized in cell lines or preclinical reference in vitro models.…”

Critical questions in ovarian cancer research and treatment: Report of an American Association for Cancer Research Special Conference

“…NMD inhibition triggers cell death through activation of the unfolded protein response. Recent studies of HGSOC with multiparametric mass spectrometry have identified rare cell phenotypes within ovarian tumors in addition to the dominant cell subset . Rare populations included ovarian cancer cells that coexpressed vimentin and E‐cadherin, which may play a role in epithelial mesenchymal transition, as well as populations that coexpressed vimentin, HE4, and c‐myc, which were associated with poor patient outcome.…”

High risk glioblastoma cells revealed by machine learning and single cell signaling profiles

“…CellCNN is another supervised analysis tool that requires prospective assignment of samples to categories and uses convolutional neural networks to learn a filter that predicts whether new cells match one of the groups 15 . Other cell subset discovery approaches do not supervise the analysis with knowledge of clinical outcomes but do use prior biological knowledge to identify cell subpopulations and then test whether differential outcomes are associated these cell subsets 5,6,16 . In mass cytometry analysis, another common approach is to use tools for automated, unsupervised cell discovery and characterization, including SPADE 17 , t-SNE 18 , UMAP 19 , FlowSOM 20 , and Marker Enrichment Modeling (MEM 21 ).…”

“…Mass cytometry has recently been developed for human solid tumors 11,16,24,25 , including glioblastoma, the most common primary malignant brain tumor in adults 26 . The median survival of glioblastoma patients after diagnosis has remained approximately 12-15 months for over a decade 27,28 .…”