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Abstract
Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma with a single driver BRAF rearrangement. Here, we perform scRNAseq in six PAs using methods that enabled detection of the rearrangement. When compared to higher-grade gliomas, a strikingly higher proportion of the PA cancer cells exhibit a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibit a progenitor-like phenotype with evidence of proliferation. These express a mitogen-activated protein kinase (MAPK) programme that was absent from higher-grade gliomas. Immune cells, especially microglia, comprise 40% of all cells in the PAs and account for differences in bulk expression profiles between tumor locations and subtypes. These data indicate that MAPK signaling is restricted to relatively undifferentiated cancer cells in PA, with implications for investigational therapies directed at this pathway.
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1 Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
2 Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
3 Hoffmann-La Roche, Product Development, Innovative Pediatric Oncology Drug Discovery, Basel, Switzerland; Centre Hospitalier Universitaire Strasbourg, Service Hématologie-Oncologie Pédiatrique, Strasbourg, France
4 Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, USA
5 Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
6 Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
7 Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA, USA
8 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
9 Broad Institute of MIT and Harvard, Cambridge, MA, USA
10 Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
11 Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
12 Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
13 Broad Institute of MIT and Harvard, Cambridge, MA, USA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Biology, Howard Hughes Medical Institute, Koch Institute, MIT, Cambridge, MA, USA
14 Department of Pediatric Oncology, Dana-Farber Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Bristol-Myers Squibb, Boston, Devens, MA, USA; Bristol-Myers Squibb, Lawrenceville, NJ, USA
15 Department of Neurosurgery, Boston Children’s Hospital, Boston, MA, USA
16 Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, USA
17 Broad Institute of MIT and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA, USA
18 Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA