Abstract
BackgroundDiffuse midline gliomas with histone H3 K27M (H3K27M) mutations occur in early childhood and are marked by an invasive phenotype and global decrease in H3K27me3, an epigenetic mark that regulates differentiation and development. H3K27M mutation timing and effect on early embryonic brain development are not fully characterized.ResultsWe analyzed multiple publicly available RNA sequencing datasets to identify differentially expressed genes between H3K27M and non-K27M pediatric gliomas. We found that genes involved in the epithelial-mesenchymal transition (EMT) were significantly overrepresented among differentially expressed genes. Overall, the expression of pre-EMT genes was increased in the H3K27M tumors as compared to non-K27M tumors, while the expression of post-EMT genes was decreased. We hypothesized that H3K27M may contribute to gliomagenesis by stalling an EMT required for early brain development, and evaluated this hypothesis by using another publicly available dataset of single-cell and bulk RNA sequencing data from developing cerebral organoids. This analysis revealed similarities between H3K27M tumors and pre-EMT normal brain cells. Finally, a previously published single-cell RNA sequencing dataset of H3K27M and non-K27M gliomas revealed subgroups of cells at different stages of EMT. In particular, H3.1K27M tumors resemble a later EMT stage compared to H3.3K27M tumors.ConclusionsOur data analyses indicate that this mutation may be associated with a differentiation stall evident from the failure to proceed through the EMT-like developmental processes, and that H3K27M cells preferentially exist in a pre-EMT cell phenotype. This study demonstrates how novel biological insights could be derived from combined analysis of several previously published datasets, highlighting the importance of making genomic data available to the community in a timely manner.
Highlights
Diffuse midline gliomas with histone H3 K27M (H3K27M) mutations occur in early childhood and are marked by an invasive phenotype and global decrease in H3K27me3, an epigenetic mark that regulates differentiation and development
Using Gene Set Enrichment Analysis (GSEA) and the Molecular Signatures Database (MSigDB) [44], we found 23 biological signaling pathways with significant enrichment in protein-coding genes overexpressed in the H3K27M cohort (Supplementary Table S2)
We identified genes with outlier expression only in non-K27M pediatric high-grade glioma (pHGG) samples as compared to a background glioma cohort and noted that 4 of the top 10 enriched pathways were related to epithelial-mesenchymal transition (EMT), including “TGF-Beta regulation of the extracellular matrix” and “Extracellular matrix organization” (Supplementary Fig. S1, Supplementary Table S2)
Summary
Pediatric high-grade gliomas (pHGGs) are aggressive brain tumors occurring at a median age of 6 years [1]. This shows that our assay contains distinct populations of pre- and post-EMT cerebral cells and is consistent with the levels of SNAI1, CDH2, CDH11, FN1, and TWIST1 in the bulk weeks 1–6 organoid data This dataset enables us to investigate transcriptional similarities between H3K27M-mutant gliomas and normal pre-EMT cell types during neural development. In keeping with our previous analysis, we noted that Cluster A, which is composed mainly of H3WT glioma cells, strongly resembles post-EMT cells and most highly expresses canonical post-EMT markers including CDH2, CDH6, and VIM [65, 66] This is consistent with our observation that non-K27M gliomas transcriptionally resemble a post-EMT state as compared to H3K27M in the bulk RNA-seq pHGG cohort. These data suggest that the histone H3K27M mutation is associated with a preferentially early or pre-EMT cell state as compared with non-K27M cells but that H3.1K27M cells may represent a somewhat later or intermediate-EMT cell state as compared with H3.3K27M cells
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