DNA Methylation Profiles Are Stable in H3 K27M-Mutant Diffuse Midline Glioma Neurosphere Cell Lines

TL;DR

This study shows that DNA methylation profiles remain stable in cultured H3 K27M-mutant glioma cells, indicating they closely resemble the original tumors.

Contribution

The study confirms the fidelity of neurosphere cell cultures to their source tumors despite chromosomal changes.

Findings

DNA methylation profiles in cultured glioma cells remained highly similar to the original tumors.

All cell lines showed a gain of 1q, with two cell lines developing it during culture.

Classifier scores and clustering analysis confirmed the consistency with H3 K27M-mutant gliomas.

Abstract

Diffuse midline gliomas are among the deadliest human cancers and have had little progress in treatment in the last 50 years. Cell cultures of these tumors have been developed recently, but the degree to which such cultures retain the characteristics of the source tumors is unknown. DNA methylation profiling offers a powerful tool to look at genome-wide epigenetic changes that are biologically meaningful and can help assess the similarity of cultured tumor cells to their in vivo progenitors. Paraffinized diagnostic tissue from three diffuse intrinsic pontine gliomas with H3 K27M mutations was compared with subsequent passages of neurosphere cell cultures from those tumors. Each cell line was passaged 3–4 times and analyzed with DNA methylation arrays and standard algorithms that provided a comparison of diagnostic classification and cluster analysis. All samples tested maintained high classifier scores and clustered within the reference group of H3 K27M-mutant diffuse midline gliomas. There was a gain of 1q in all cell lines, with two cell lines initially manifesting the gain of 1q only during culture. In vitro cell cultures of H3 K27M-mutant gliomas maintain high degrees of similarity in DNA methylation profiles to their source tumor, confirming their fidelity even with some chromosomal changes.

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