Project description:WHO classification for tumors of the central nervous system strongly endorses molecular tests for the precise diagnosis of diffuse gliomas. While alterations in the DNA methylation status of gliomas are already well documented and used in specialised clinical centers to distinguish between brain tumor entities, changes to the epigenetic layer at the level of histone modifications are only poorly characterised. Here, we applied a recently developed data-independent acquisition (DIA) - mass spectrometry method to generate a comprehensive histone epi-proteomic map that documents the abundance of almost all characterized and many uncharacterized histone modifications to a series of IDH-mutant oligodendroglioma and astrocytoma samples. Our analysis documented significant abundance differences in almost one-third of the 144 quantified histone peptides. Among them are lower abundance levels of the polycomb repressive mark H3K27me3 in oligodendroglioma samples compared to astrocytomas. We validated this finding by immunohistochemistry using the C36B11 antibody. Surprisingly, we observed inconsistencies with another widely applied H3K27me3 antibody (07-449), providing a warning flag for immunohistochemistry of brain cancers. An unbiased unsupervised clustering analysis of the proteomic dataset separated the two IDH-mutant glioma subtypes in full accordance to the EPIC DNA methylation classifier and the 1p/19q status. The clustering also revealed at least two histone epi-proteomic subgroups of oligodendroglioma, a feature not observable in the DNA methylation dataset. Our results indicate that histone epi-proteomic profiling at the depth of the current method has the capacity to identify clinically-relevant glioma sub-groups. In addition to being of use for diagnostic purposes, this could also provide novel insights in glioma biology and may identify new therapeutic targets.

2020-01-17 | PXD015151 | Pride

c7323295-9332-40ab-97dd-2b5a5a7375dc - samples

Project description:SF10619 snATAC Oligodendroglioma (WHO gr. 2).Tumor Location: Parietal. Age: 52. Sex: Male

| EGAD00001006316 | EGA

af727b32-3e89-4bd8-b2c9-2cdb131a0dc6 - samples

Project description:SF4007 snATAC Seq. Oligodendroglioma (WHO gr. 2) Tumor Location: Left frontotemporal. Age:33. Sex: Female.

| EGAD00001006317 | EGA

b66b3472-05b3-423d-be5b-44d292d16290 - samples

Project description:SF10679 snATAC Seq. Oligodendroglioma, Anaplastic (WHO gr. 3). Tumor Location: Frontal Age: 43. Sex: Male.

| EGAD00001006312 | EGA