Subgroup-specific immune and stromal microenvironment in medulloblastoma

Abstract

Knowledge on immune and stromal cells in medulloblastoma microenvironment is still limited as previous work was frequently restricted by low sample size and the lack of molecular subgroup information. We characterized 10 microenvironment cell populations as well as PD-L1 from gene expression in 1422 brain tumors and 763 medulloblastomas. All in all, medulloblastomas showed low expression of immune markers. Still, there were substantial differences with a clustering of medulloblastoma subgroups according to their microenvironment profile. Specifically, SHH medulloblastomas displayed strong signatures of fibroblasts, T cells and macrophages, while markers of cytotoxic lymphocytes were enriched in Group 4 tumors. PD-L1 gene expression appeared to be relatively high in single SHH and WNT cases but was undetectable by immunohistochemistry. In addition, two diverse immuno-stromal patterns were identified, indicating distinct types of local tumor immunosuppression, which were primarily controlled by either macrophage and regulatory T cell-mediated mechanisms or immunosuppressive cytokines and checkpoints, respectively. None of the immune cell signatures had an independent prognostic value in the present dataset after multiple testing correction. These results suggest a mild, but subgroup-specific infiltration of immune cells in medulloblastoma.

Keywords: PD-L1, stroma; gene expression; immune system; medulloblastoma; microenvironment.

Figure 1.

Association of the expression scores for 10 microenvironment cell populations and PD-L1 in 8 brain tumors. A: Heatmap representing the median expression score for each cell population and each tumor type. Medulloblastoma has rather low levels of immune and stromal cells and the expression patterns are most similar to AT/RT and ependymoma. B: Each dot corresponds to one tumor in the beeswarm plots. The bands indicate the median, the lower and the upper quartile. Medulloblastoma shows rather low expression scores for most cell types and PD-L1 compared to other brain tumors but the variance is large.

Figure 2.

Association of the microenvironment populations and PD-L1 with molecular subgroups of medulloblastoma. A: Heatmap representing the expression scores for each individual tumor. Only very few tumors express higher levels of PD-L1, belonging mostly to the WNT and SHH subgroup. B: Beeswarm plots reveal strongly subgroup-specific expression patterns for most of the considered microenvironment cell populations. The bands indicate the median, the lower and the upper quartile. Depicted p-values are computed with the Kruskal-Wallis test.

Figure 3.

Immuno-stromal classification of medulloblastoma. A: Two-dimensional embedding using t-SNE of medulloblastomas according to the expression of 98 MCP marker genes reveals subgroup-specific clustering. B: Definition of five distinct immuno-stromal subgroups using k-means clustering. C: Expression values of the 10 MCPcounter populations and 4 immunosuppressive signatures. There are two major patterns (type I + II) potentially associated with immunosuppression in medulloblastoma. Endothelial-, B-, NK- and myeloid dendritic cells did not group into these two patterns.

Figure 4.

Association of the microenvironment populations and PD-L1 with survival in molecular subgroups of medulloblastoma. Hazard ratios (HR) with 95% confidence interval (CI) are shown for univariate survival analysis. *significant after correction for multiple testing (Benjamini-Hochberg method).