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Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

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Science  20 Apr 2018:
Vol. 360, Issue 6386, pp. 331-335
DOI: 10.1126/science.aao4750
  • Fig. 1 Characterization of H3K27M-glioma by means of scRNA-seq.

    (A) Pairwise correlations between the expression profiles of 2458 single cells (rows, column) from six H3K27M-glioma samples (color bar). Two clusters of nonmalignant cells are marked as “NM.” (B) Enrichment score of microglia and oligodendrocyte signatures. (C) Inferred CNV profiles. Black indicates CNV present (fig. S4). (D) Gene mutations. (Top) H3K27M.; (Bottom) All other mutations identified per sample by means of WGS/WES. Black line indicates at least one mutated gene identified (fig. S6).

  • Fig. 2 Intratumor heterogeneity in H3K27M-glioma.

    (A and B) Relative expression (color bar) across 2259 malignant cells (columns) of the top 30 genes for each of the combined expression programs P1, P2, and P3 [(A), rows] or 19 genes [(B), P4] that are preferentially expressed in cells with low expression of P1, P2, and P3 (8). (C) Plot of the lineage (x axis) and stemness (y axis) scores for each of 2259 malignant cells (dots). Red dots indicate positive score for the cell cycle program. (D) In situ RNA hybridization of H3K27M glioma for astrocytic-like (APOE), OPC-like (PDGFRA), and proliferation (Ki-67) markers. Arrow highlights cell coexpressing PDGFRA and Ki-67.

  • Fig. 3 Cellular hierarchies of H3K27M-glioma and IDH-mutant gliomas.

    (A, C, and E) Malignant cells (dots) from H3K27M, IDH-A, and IDH-O scored for the (A) AC-like, (C) OC-like, and (E) stem-like signatures of H3K27M-glioma (x axis) and of IDH-mutant gliomas (y axis). Correlation values are in the bottom right quadrant. (B, D, and F) Relative expression in (B) AC-like, (D) OC-like, and (F) stem-like cells in each glioma class (rows) of genes with preferential expression in the respective cell subset (8), with genes ordered into those common to H3K27M and IDH-mutant gliomas, or specific to either tumor type. (G) Relative expression (color bar) of OC-like and stem-like genes shared between (common) or specific to H3K27M and IDH-mutant gliomas in nonmalignant oligodendrocytes, OPCs, and NPCs (5). (H) Percentage of cycling cells (x axis) and undifferentiated cells (y axis) in each glioma sample, marked by type and grade. (I) CNVs, (J) haplotype frequencies, and (K) point mutations in selected genes identified with WGS (columns) inferred for individual malignant cells (rows) from BCH869. Dashed lines indicate four subclones based on CNV and haplotype profiles. (L) Inferred phylogenetic tree (8) of individual subclones detected for BCH869. Circle sizes indicate relative number of cells in subclone. Genetic events are indicated at the inferred point of their first detection. (M) Relative number of malignant cells classified into OPC-, AC-, or OC-like states for BCH869 subclone 1 or the combination of subclones 2 and 3.

  • Fig. 4 Single-cell comparisons of matched H3K27M-glioma patient sample, PDX, and culture models for tumor BCH869.

    (A) Cells ordered by sample type and within each sample by means of hierarchical clustering (fig. S19). (B) Heatmap shows expression of the top 30 genes of the cell cycle and lineage programs (P1 to P4) described in Fig. 2 and in (8), for cells ordered as in (A). (C) (Left) Mouse brain magnetic resonance images (MRIs) with three-dimensional reconstruction at 22 weeks after injection of 200,000 BCH869 cells. (Right) MRI tumor volume (8). **P < 0.01 by paired, two-tailed Student’s t test. Error bars indicate SEM. (D) Heatmap shows expression of differentially expressed genes between sample types, for each pairwise comparison. Cells are ordered as in (A). (Right) Average expression in each sample type. (E) Model of H3K27M-glioma cellular architecture (right) compared with normal development (left).

Supplementary Materials

  • Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

    Mariella G. Filbin, Itay Tirosh, Volker Hovestadt, McKenzie L. Shaw, Leah E. Escalante, Nathan D. Mathewson, Cyril Neftel, Nelli Frank, Kristine Pelton, Christine M. Hebert, Christine Haberler, Keren Yizhak, Johannes Gojo, Kristof Egervari, Christopher Mount, Peter van Galen, Dennis M. Bonal, Quang-De Nguyen, Alexander Beck, Claire Sinai, Thomas Czech, Christian Dorfer, Liliana Goumnerova, Cinzia Lavarino, Angel M. Carcaboso, Jaume Mora, Ravindra Mylvaganam, Christina C. Luo, Andreas Peyrl, Mara Popović, Amedeo Azizi, Tracy. T. Batchelor, Matthew P. Frosch, Maria Martinez-Lage, Mark W. Kieran, Pratiti Bandopadhayay, Rameen Beroukhim, Gerhard Fritsch, Gad Getz, Orit Rozenblatt-Rosen, Kai W. Wucherpfennig, David N. Louis, Michelle Monje, Irene Slavc, Keith L. Ligon, Todd R. Golub, Aviv Regev, Bradley E. Bernstein,* Mario L. Suvà

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S19
    • References
    Table S1
    Clinical and molecular characteristics of H3K27M-glioma samples profiled by scRNA-seq
    Table S2
    Single-cell cohort characteristics
    Table S3
    Differentially expressed genes between glioma types
    Table S4
    Supplementary patient annotations
    Table S5
    Gene expression signatures in H3K27M-glioma
    Table S6
    Differentially expressed genes in H3K27M-gliomas vs normal cell types
    Table S7
    Subclones based on haplotype and copy number state in BCH836 and BCH869
    Table S8
    Differentially expressed genes between each pair of sample types

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