title: Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas.
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.
authors.affiliation: Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.|Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Sören
authors.initials: S
authors.lastname: Müller
authors.affiliation: Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.|Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Siyuan John
authors.initials: SJ
authors.lastname: Liu
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.|Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Di Lullo
authors.affiliation: Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.|Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Martina
authors.initials: M
authors.lastname: Malatesta
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.|Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Alex A
authors.initials: AA
authors.lastname: Pollen
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.|Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Tomasz J
authors.initials: TJ
authors.lastname: Nowakowski
authors.affiliation: Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Kohanbash
authors.affiliation: Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Manish
authors.initials: M
authors.lastname: Aghi
authors.affiliation: Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.|Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Arnold R
authors.initials: AR
authors.lastname: Kriegstein
authors.affiliation: Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA daniel.lim@ucsf.edu aaron.diaz@ucsf.edu.|Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.|Veterans Affairs Medical Center, San Francisco, CA, USA.
authors.forename: Daniel A
authors.identifier: http://orcid.org/0000-0001-7221-3425
authors.initials: DA
authors.lastname: Lim
authors.affiliation: Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA daniel.lim@ucsf.edu aaron.diaz@ucsf.edu.|Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA.
authors.forename: Aaron
authors.identifier: http://orcid.org/0000-0001-9059-9501
authors.initials: A
authors.lastname: Diaz
mesh_terms: D001932:Brain Neoplasms; D066246:ErbB Receptors / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D018740:Genetic Heterogeneity; D005909:Glioblastoma; D006801:Humans; D009154:Mutation; D017479:Receptors, Platelet-Derived Growth Factor / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: C512478:EGFR protein, human; D066246:ErbB Receptors; D017479:Receptors, Platelet-Derived Growth Factor
keywords: 
  PDGFRA
  ; copy‐number variation; glioblastoma; single‐cell RNA‐sequencing; tumor phylogeny