Study: single-cell analysis in pediatric midline gliomas with histone H3K27M mutation 4058 cells

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science, in press.

Filbin MG*, Tirosh I*, Hovestadt V*, Shaw ML, Escalante LE, Mathewson ND, Neftel C, Frank N, Pelton K, Hebert CM, Haberler C, Yizhak K, Gojo J, Egervari K, Mount C, van Galen P, Bonal D, Nguyen QD, Beck A, Sinai C, Czech T, Dorfer C, Goumnerova L, Lavarino C, Carcaboso AM, Mora J, Mylvaganam R, Luo CC, Peyrl A, Popović M, Azizi A, Batchelor TT, Frosch MP, Martinez-Lage M, Kieran MW, Bandopadhayay P, Beroukhim R, Fritsch G, Getz G, Rozenblatt-Rosen O, Wucherpfennig KW, Louis DN, Monje M, Slavc I, Ligon KL, Golub TR, Regev A*, Bernstein BE*, Suvà ML*.



Gliomas with histone H3 lysine27-to-methionine mutations (H3K27M-glioma) arise primarily in the midline of the central nervous system of young children, suggesting a cooperation between genetics and cellular context in tumorigenesis. While the genetics of H3K27M-glioma are well-characterized, their cellular architecture remains uncharted. Here, we performed single-cell RNA-seq in 3,321 cells from six primary H3K27M-glioma and matched models. We found that H3K27M-glioma primarily contain cells resembling oligodendrocyte precursor cells (OPC-like), while more differentiated malignant cells are a minority. Importantly, OPC-like cells exhibit greater proliferation and tumor-propagating potential than their more differentiated counterparts, and are at least in part sustained by PDGFRA signaling. Our study characterizes oncogenic and developmental programs in H3K27M-glioma at single-cell resolution and across genetic subclones, suggesting potential therapeutic targets in this disease.

Sample Collection and Processing Workflow

Workflow. Samples are collected at the time of surgery, freshly dissociated to single-cell suspensions and sorted based on viability markers into 96-well plates. Processing to full-length scRNA-seq is performed following the Smart-Seq2 protocol. Data from H3K27M patient samples and models are analyzed and compared to other classes of gliomas profiled by scRNA-seq.