Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells

Zachary J Reitman,Rosalind A Segal,Alex K Shalek,Claire Sinai ,Mariella G Filbin,Brenton R Paolella,Mario L Suvà ,Mark W Kieran,Alexandra L Condurat,Orit Rozenblatt-Rosen,Zachary T Herbert,Yu Sun,Charles D Stiles,Hayley Malkin,John Daley ,John A Alberta,Robert T Jones ,Daphne A Haas‐Kogan ,Kenin Qian,Ying Huang,Guillaume Bergthold,Sarah Becker,Leslie Grimmet,Aviv Regev,Jessica L Weatherbee,Keith L Ligon,Kristine Pelton,Prasidda Khadka,Pratiti Bandopadhayay,Liliana Goumnerova,Rameen Beroukhim

doi:10.1038/s41467-019-11493-2

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.

Highlights

Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma with a single driver BRAF rearrangement
We found oligodendrocyte precursor cell (OPC) signatures derived from additional independent normal brain single cell atlases to be the most highly enriched within the PA cancer cells (Supplementary Fig. 8b, c)
We found that BRAF normalized read counts were higher in cancer cells expressing the mitogen-activated protein kinase (MAPK) gene programme compared to those expressing the AC-like gene programme (Supplementary Fig. 10, P = 0.003 using Fisher’s method)

Summary

Introduction

Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma with a single driver BRAF rearrangement. 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. Recent efforts have characterized cellular heterogeneity within WHO grade II–IV adult and pediatric gliomas by single cell RNA sequencing (scRNAseq) These studies revealed hierarchical relationships between cancer cells that mimic normal differentiation of brain cells from neural stem cells or glial progenitor cells into mature glia[1,2,3,4]. Unlike higher-grade gliomas, which usually exhibit multiple driver mutations[9,10,11], most PAs exhibit a single driver somatic genetic alteration[12,13,14] These almost always activate the MAPK pathway, with rearrangements generating the KIAA1549-BRAF fusion oncogene accounting for ~70% of PAs15. It has been unclear whether these differences were due to different contributions of cancer cells and immune cells, or due to different gene programme being expressed in the cancer cells

Methods

Results

Conclusion