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Mol Syst Biol. 2016 Nov 25;12(11):889. doi: 10.15252/msb.20166969.

Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas.

Author information

1
Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
2
Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
3
Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
4
Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA daniel.lim@ucsf.edu aaron.diaz@ucsf.edu.
5
Veterans Affairs Medical Center, San Francisco, CA, USA.

Abstract

Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain tumor. Epidermal growth factor (EGF) and platelet-derived growth factor (PDGF) receptors are frequently amplified and/or possess gain-of-function mutations in GBM However, clinical trials of tyrosine-kinase inhibitors have shown disappointing efficacy, in part due to intra-tumor heterogeneity. To assess the effect of clonal heterogeneity on gene expression, we derived an approach to map single-cell expression profiles to sequentially acquired mutations identified from exome sequencing. Using 288 single cells, we constructed high-resolution phylogenies of EGF-driven and PDGF-driven GBMs, modeling transcriptional kinetics during tumor evolution. Descending the phylogenetic tree of a PDGF-driven tumor corresponded to a progressive induction of an oligodendrocyte progenitor-like cell type, expressing pro-angiogenic factors. In contrast, phylogenetic analysis of an EGFR-amplified tumor showed an up-regulation of pro-invasive genes. An in-frame deletion in a specific dimerization domain of PDGF receptor correlates with an up-regulation of growth pathways in a proneural GBM and enhances proliferation when ectopically expressed in glioma cell lines. In-frame deletions in this domain are frequent in public GBM data.

KEYWORDS:

PDGFRA ; copy‐number variation; glioblastoma; single‐cell RNA‐sequencing; tumor phylogeny

PMID:
27888226
PMCID:
PMC5147052
DOI:
10.15252/msb.20166969
[Indexed for MEDLINE]
Free PMC Article

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