Pro-inflammatory cytokines mediate the epithelial-to-mesenchymal-like transition of pediatric posterior fossa ependymoma

Abstract

Pediatric ependymoma is a devastating brain cancer marked by its relapsing pattern and lack of effective chemotherapies. This shortage of treatments is due to limited knowledge about ependymoma tumorigenic mechanisms. By means of single-nucleus chromatin accessibility and gene expression profiling of posterior fossa primary tumors and distal metastases, we reveal key transcription factors and enhancers associated with the differentiation of ependymoma tumor cells into tumor-derived cell lineages and their transition into a mesenchymal-like state. We identify NFκB, AP-1, and MYC as mediators of this transition, and show that the gene expression profiles of tumor cells and infiltrating microglia are consistent with abundant pro-inflammatory signaling between these populations. In line with these results, both TGF-β1 and TNF-α induce the expression of mesenchymal genes on a patient-derived cell model, and TGF-β1 leads to an invasive phenotype. Altogether, these data suggest that tumor gliosis induced by inflammatory cytokines and oxidative stress underlies the mesenchymal phenotype of posterior fossa ependymoma.

Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data

“…To investigate this process, we used ConDecon to study the changes in the gene expression profile of tumor-infiltrating microglia during the mesenchymal transformation of tumor cells. We considered a cohort of 42 ependymal tumors profiled with RNA-seq at the bulk-level and a reference single-nucleus RNA-seq atlas of primary and metastatic ependymoma 21 . Our analysis revealed that the abundance of mesenchymal-like tumor cells and microglia in each sample are positively correlated (Pearson’s r = 0.70, p -value = 3 × 10 -7 ), in agreement with previous results using clustering-based deconvolution methods 21 .…”

“…We considered a cohort of 42 ependymal tumors profiled with RNA-seq at the bulk-level and a reference single-nucleus RNA-seq atlas of primary and metastatic ependymoma 21 . Our analysis revealed that the abundance of mesenchymal-like tumor cells and microglia in each sample are positively correlated (Pearson’s r = 0.70, p -value = 3 × 10 -7 ), in agreement with previous results using clustering-based deconvolution methods 21 . However, it also showed that tumor infiltrating microglia describe a previously unnoticed trajectory in the gene expression space across samples (Figure S5), which suggests a change in the expression profile of these cells during the mesenchymal transformation of ependymoma.…”

“…Pediatric ependymoma is a brain cancer that is particularly aggressive in young children due to its very relapsing pattern and lack of effective chemotherapies [36][37][38] . Recent single-cell RNA-seq studies of ependymal tumors have identified a subpopulation of tumor cells with a mesenchymal-like gene expression profile that is associated with abundant microglia infiltration and poor prognosis 21,[39][40][41] . Mesenchymal-like tumor cells in ependymoma are thought to derive from neuroepithelial-like tumor cells by activation of brain injury repair and neuroinflammation pathways in response to microglia-secreted cytokines 21,41 .…”

“…Recent single-cell RNA-seq studies of ependymal tumors have identified a subpopulation of tumor cells with a mesenchymal-like gene expression profile that is associated with abundant microglia infiltration and poor prognosis 21,[39][40][41] . Mesenchymal-like tumor cells in ependymoma are thought to derive from neuroepithelial-like tumor cells by activation of brain injury repair and neuroinflammation pathways in response to microglia-secreted cytokines 21,41 . To investigate this process, we used ConDecon to study the changes in the gene expression profile of tumor-infiltrating microglia during the mesenchymal transformation of tumor cells.…”

“…We demonstrate the utility of ConDecon with three applications. First, by using it with single-cell and bulk gene expression data of pediatric ependymal tumors 21 , we uncover continuous changes in tumor infiltrating microglia related to the mesenchymal transformation of tumor stem cells. These results, which we confirm by immunohistochemistry, show that microglia surrounding mesenchymal tumor regions acquire an activation phenotype similar to that of microglia in neurodegenerative disease lessions [22][23][24] .…”