Micro-Environment Causes Reversible Changes in DNA Methylation and mRNA Expression Profiles in Patient-Derived Glioma Stem Cells

In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient\u27s tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding xenografts, which were actually more similar to their original parental tumors. This points to the potentially critical role of the brain microenvironment in influencing methylation and transcriptional patterns of GSCs. Consistent with this possibility, ex vivo cultured GSCs isolated from xenografts showed a tendency to return to their initial in vitro states even after a short time in culture, supporting a rapid dynamic adaptation to the in vitro microenvironment. These results show that methylation and transcriptome profiles are highly dependent on the microenvironment and growth in orthotopic sites partially reverse the changes caused by in vitro culturing

Histone demethylase Jumonji D3 (JMJD3) as a tumor suppressor by regulating p53 protein nuclear stabilization.

Histone methylation regulates normal stem cell fate decisions through a coordinated interplay between histone methyltransferases and demethylases at lineage specific genes. Malignant transformation is associated with aberrant accumulation of repressive histone modifications, such as polycomb mediated histone 3 lysine 27 (H3K27me3) resulting in a histone methylation mediated block to differentiation. The relevance, however, of histone demethylases in cancer remains less clear. We report that JMJD3, a H3K27me3 demethylase, is induced during differentiation of glioblastoma stem cells (GSCs), where it promotes a differentiation-like phenotype via chromatin dependent (INK4A/ARF locus activation) and chromatin independent (nuclear p53 protein stabilization) mechanisms. Our findings indicate that deregulation of JMJD3 may contribute to gliomagenesis via inhibition of the p53 pathway resulting in a block to terminal differentiation

DNA methylation profiles of patient tumors and <i>in vitro</i>, <i>in vivo</i>, <i>ex vivo</i> GSCs for two cell lines.

<p>(A,B) HC and PCA for PT, <i>in vitro</i>, <i>in vivo</i> and <i>ex vivo</i> samples for early and late passages (ep, lp). 6825 sites with standard deviation greater than 0.15 are presented. These sites are not differentially methylated between 827 and 923 (Mann-Whitney p-value more than 0.5). (C) Median methylation values for each sample based on selected 6825 sites.</p

Fold changes (x-axis) and mean methylation differences (y-axis) between paired <i>in vitro</i>-PT pairs for both differentially expressed and differentially methylated genes.

<p>Differentially expressed genes determined with paired t-test. Genes with false discovery rate less than 0.05 (Benjamini-Hochberg) and absolute fold change greater than three are used. Differentially methylated sites determined with paired non-parametric Quade test and sites with false discovery rate less than 0.05 (Benjamini-Hochberg) and absolute methylation difference greater than 0.3 are used.</p

DNA methylation profiles for patient tumors and <i>in vitro</i> GSCs.

<p>(A) Principle Component Analyses (PCA) of 3847 methylation sites with standard deviation more than 0.35. PT represents patient tumor and in vitro represents the corresponding <i>in vitro</i> GSCs. Matched PT-<i>in vitro</i> pairs are connected with lines. (B) Median methylation values for each sample based on selected 3847 sites.</p