Project description:Tuberous Sclerosis Complex (TSC) is a genetic disorder characterized by benign growths called hamartomas that can be a significant cause of morbidity and mortality. Hamartomas are found along the neurocutaneous axis including along the brain’s ventricles near the boundaries of the striatum. They can be categorized by size and include small subependymal nodules (SENs) or larger subependymal giant cell astrocytomas (SEGAs). SEGAs are associated with changes in neurological presentation and are a substantial cause of hydrocephalus if left untreated. Immunohistochemistry, electron microscopy, and bulk RNA sequencing have been used to examine SEGA cellular composition. However, there remains considerable debate over the results because bulk techniques do not parcellate transcriptomic changes within individual cells and SEGAs contain cells with abnormal morphology that betray canonical classification. Here, we describe a quantitative analysis of SEGA cell identities based on single nuclei RNA sequencing.
Project description:These samples are part of a study investigating cancer cell plasticity in colorectal cancer metastasis. Tumour microenvironment cell types and cancer cell states were identified using 10x Genomics Multiome (paired snRNA-seq + snATAC-seq). snRNA-seq data is uploaded here.
Project description:EOMES is an essential transcription factor (TF) for murine trophoblast stem cell (TSC) maintenance. Despite that, the details of EOMES' function at the molecular level remain obscure. Here, we carried out rapid immunoprecipitation and mass spectrometry of endogenous protein (RIME) to identify TSC-specific protein interactors on EOMES. In addition to other established TFs involved in TSC maintenance, we found that EOMES interacts with several chromatin remodeller subunits, including BRG1. By exploiting an Eomes-degron system, we acutely depleted EOMES protein in TSCs and in parallel inhibited BRG1 function with small molecule BRM014. EOMES depletion and BRG1 inhibition resulted in reduced accessibility at largely overlapping genomic regions associated with TSC-related loci. Additionally, EOMES depletion results in misregulation of genes essential for TSC maintenance and function, as well as genes encoding cytoskeletal, cell-cell interaction and matricellular components.
Project description:We performed single-cell/nuclei RNA-sequencing (sc/snRNA-seq) of 22 treatment-naïve melanoma brain metastases (MBM; 5 samples using scRNA-seq and 17 snRNA-seq) from 21 patients and 10 treatment-naïve extracranial (peripheral) metastases (MPM; all snRNA-seq) from 10 patients . In total, we recovered 145,555 cell transcriptomes in 32 samples including 73,369 cells from MBM and 72,186 from MPM.
Project description:EOMES is an essential transcription factor (TF) for murine trophoblast stem cell (TSC) maintenance. Despite that, the details of EOMES' function at the molecular level remain obscure. Here, we carried out rapid immunoprecipitation and mass spectrometry of endogenous protein (RIME) to identify TSC-specific protein interactors on EOMES. In addition to other established TFs involved in TSC maintenance, we found that EOMES interacts with several chromatin remodeller subunits, including BRG1. By exploiting an Eomes-degron system, we acutely depleted EOMES protein in TSCs and in parallel inhibited BRG1 function with small molecule BRM014. EOMES depletion and BRG1 inhibition resulted in reduced accessibility at largely overlapping genomic regions associated with TSC-related loci. Additionally, EOMES depletion results in misregulation of genes essential for TSC maintenance and function, as well as genes encoding cytoskeletal, cell-cell interaction and matricellular components.
Project description:EOMES is an essential transcription factor (TF) for murine trophoblast stem cell (TSC) maintenance. Despite that, the details of EOMES' function at the molecular level remain obscure. Here, we carried out rapid immunoprecipitation and mass spectrometry of endogenous protein (RIME) to identify TSC-specific protein interactors on EOMES. In addition to other established TFs involved in TSC maintenance, we found that EOMES interacts with several chromatin remodeller subunits, including BRG1. By exploiting an Eomes-degron system, we acutely depleted EOMES protein in TSCs and in parallel inhibited BRG1 function with small molecule BRM014. EOMES depletion and BRG1 inhibition resulted in reduced accessibility at largely overlapping genomic regions associated with TSC-related loci. Additionally, EOMES depletion results in misregulation of genes essential for TSC maintenance and function, as well as genes encoding cytoskeletal, cell-cell interaction and matricellular components.
