<i>EGFR</i> promoter exhibits dynamic histone modifications and binding of ASH2L and P300 in human germinal matrix and gliomas

<div><p>Several signaling pathways important for the proliferation and growth of brain cells are pathologically dysregulated in gliomas, including the epidermal growth factor receptor (EGFR). Expression of EGFR is high in neural progenitors during development and in gliomas but decreases significantly in most adult brain regions. Here we show that EGFR expression is maintained in the astrocyte ribbon of the adult human subventricular zone. The transcriptional regulation of <i>EGFR</i> expression is poorly understood. To investigate the role of epigenetics on <i>EGFR</i> regulation in the contexts of neural development and gliomagenesis, we measured levels of DNA methylation and histone H3 modifications at the <i>EGFR</i> promoter in human brain tissues, glioma specimens, and EGFR-expressing neural cells, acutely isolated from their native niche. While DNA was constitutively hypomethylated in non-neoplastic and glioma samples, regardless of their EGFR-expression status, the activating histone modifications H3K27ac and H3K4me3 were enriched only when <i>EGFR</i> is highly expressed (developing germinal matrix and gliomas). Conversely, repressive H3K27me3 marks predominated in adult white matter where <i>EGFR</i> is repressed. Furthermore, the histone methyltransferase core enzyme ASH2L was bound at <i>EGFR</i> in the germinal matrix and in gliomas where levels of H3K4me3 are high, and the histone acetyltransferase P300 was bound in samples with H3K27ac enrichment. Our studies use human cells and tissues undisturbed by cell-culture artifact, and point to an important, locus-specific role for chromatin remodeling in <i>EGFR</i> expression in human neural development that may be dysregulated during gliomagenesis, unraveling potential novel targets for future drug therapy.</p></div

Additional file 7: Table S2. of Ligation-free ribosome profiling of cell type-specific translation in the brain

Table of genes altered following AZD-8055 treatment with p adj values <0.05 and fold change >2. (XLSX 11 kb

Additional file 5: Table S1. of Ligation-free ribosome profiling of cell type-specific translation in the brain

List of cell type-specific gene ontologies and their median TEs. (XLSX 13 kb

Additional file 1: Figure S1. of Ligation-free ribosome profiling of cell type-specific translation in the brain

Sensitivity of conventional and ligation-free strategies. Ligation-free and conventional libraries were generated from a serially diluted 34-base RNA oligonucleotide and analyzed via Bioanalyzer following an equal number of PCR cycles for each library. All ligation-free library preparations except for the 0.01 ng sample were loaded onto the Bioanalyzer at a 1:10 dilution to avoid saturating the detector at high concentrations. Detectable libraries were successfully generated for all concentrations using the ligation-free method but could only be generated using conventional methods for the 100- and 10-ng inputs. (PDF 665 kb

Scatter plot for the expression levels of CD44 vs. the mesenchymal transition metagene.

<p>Each dot in the scatter plot represents a glioma sample from the NCI Repository for Molecular Brain Neoplasia Data (Rembrandt) dataset. Dots are color coded red for glioblastomas and blue for lower grade gliomas. Expression levels are RNA normalized.</p

Kaplan-Meier curves comparing samples with high vs. low levels of the mesenchymal transition metagene.

<p>The 545 tumor samples were partitioned into two groups of equal size depending on their levels of the mesenchymal transition metagene. Shown are the Kaplan-Meier curves for the corresponding samples with entries in the “Days to Tumor Recurrence” field.</p

Top differentially expressed gene in glioblastomas vs. lower grade gliomas.

<p>Top differentially expressed gene in glioblastomas vs. lower grade gliomas.</p

Top genes in terms of the rank sum for the “Days to Tumor Recurrence” phenotype.

<p>Top genes in terms of the rank sum for the “Days to Tumor Recurrence” phenotype.</p

Multivariate Cox regression using GBM subtypes as covariates.

<p>Likelihood ratio test = 12.3, degrees of freedom = 4, <i>P</i> value = 0.0153.</p>*<p>The table shows all four linear contrasts between individual subtype mean log-hazard ratios and overall mean log-hazard ratio. In practice there are three contrasts in each Cox regression regardless of which contrast is chosen as the noncoding group. We used two separate Cox regressions to produce the results in the table.</p

Genes comprising the Slug-based EMT signature.

<p>Genes comprising the Slug-based EMT signature.</p