ABSTRACT: To understand the diversity of expression states within oligodendroglioma tumors, we obtained six freshly resected samples, profiled ~1000 cells from each tumor and examined their diversity.
Project description:Six freshly resected recurrent glioma samples were obatined to analyze the diversity of expression states of human gliomas. About 3000 cells from each sample were profiled.
Project description:To understand the diversity of expression states within human gliomas, we obtained eleven freshly resected glioma-related samples, profiled ~3000 cells from each sample and examined their diversity.
Project description:To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq.
Project description:To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq. Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2. *Raw data files absent for samples GSM1851356 and GSM1851494.* **Submitter declares reads will be made available through dbGaP.**
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.
Project description:In the past decades, ample evidence has shown that combined radio-chemotherapy is superior to either radiotherapy or chemotherapy alone in oligodendroglioma. However, the survival benefit comes at the cost of immediate and long-term toxicities. Therefore, deferring postoperative therapy until progression may be a valid option to delay treatment-related side effects. Still, systematic data and reliable predictive biomarkers are limited. In this large retrospective series of oligodendroglioma cases, we could show that early postoperative treatment is not associated with improved PFS and OS while correcting for baseline differences between both groups. In addition, we performed whole-genome DNA methylation analyses and observed a predictive role of certain methylation patterns independent from MGMT promoter methylation status, extent of resection and CNS WHO grade. The results of this real-life study may serve as a benchmark for future trial planning in oligodendroglioma, and further studies should evaluate the predictive value of DNA methylation profiles.
Project description:Fresh resected lung tissues were obtained from six tuberculosis patients with elevated pulmonary 18F-FDG avidity. Lung tissues with 18F-FDG avidity and nearby uninvolved tissues were profiled with single-cell RNA sequencing.
Project description:Here we have stimulated human fetal microglia HMC3 cells and human oligodendroglioma HOG cells with LPS for 24 hours and subsequently with a combination of TNFα and IL-1β for 24 hours , and analyzed their transcriptome-wide response to compare the responsivity of the two cell lines to the pro-inflammatory stimuli.