Project description:Microglia, brain-resident macrophages, have been proposed to play an active role in synaptic refinement and maturation, influencing plasticity and circuit-level connectivity. Using a genetically modified mouse which lacks microglia (Csf1r ∆FIRE/∆FIRE), we investigate the effect on gene expression in particular cell types of the presence or absence of microglia in the developing mouse brain.
Project description:A fundamental interest in developmental neuroscience is to map the complete single-cell lineages within the brain. We developed a CRISPR editing-based lineage specific tracing (CREST) method for clonal tracing in Cre mice. We combined two complementary strategies to map the comprehensive single-cell lineage landscape in developing mouse brain. Applying snapCREST (snapshotting CREST) in mouse ventral midbrain (vMB), we constructed a spatiotemporal lineage landscape spanning the major developmental stage of vMB. Specifically, we identified six progenitor archetypes that could represent principal clonal fate of individual vMB progenitors, whose progenies showed restricted and graded distribution along the dorsal-ventral axis. We uncovered subregion-specific relationship between glutamatergic and GABAergic neurons and identified three distinct clonal lineages in the floor plate that specified glutamatergic neurons, dopaminergic neurons, or both neuronal types. We further created pandaCREST (progenitor and derivative associating CREST) by combining CREST, ex vivo organoid culture, and clonal splitting strategy to associate the transcriptome of progenitor cells in vivo with their differentiation potentials. Using pandaCREST, we identified multiple developmental origins of dopaminergic neurons and demonstrated that the fate potential of a transcriptome-defined progenitor type reflects the composite potentials of individual progenitors, each with distinct clonal fate and molecular signatures. Thus, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.
Project description:Gene expression is finely regulated during development, and deregulation can lead to disease. In pediatric brain tumors (PBT), disruption of neurodevelopmental gene regulation programs are suspected to drive oncogenesis. However, the transcriptional landscape and genetic regulation processes of the healthy developing brain are not fully characterized, limiting our investigation of these tumors. We used single-cell RNA-sequencing to generate a transcriptomic atlas of >65,000 cells in the developing forebrain and pons in human and mouse, two regions where PBT commonly arise. We projected bulk RNA-seq profiles for a cohort of 198 PBT onto these cell types, followed by focused analysis of three PBT subtypes by single-cell profiling: WNT medulloblastoma, embryonal tumors with multilayered rosettes (ETMR), and atypical teratoid/rhabdoid tumors (ATRT). Altogether, we pinpoint stalled differentiation during developmental programs as a common etiological mechanism of PBT, providing a valuable resource to aid modeling and therapeutics.
Project description:Here, we derive human brain organoids with innately developing microglia to investigate the cellular responses to SARS-CoV-2 infection on a single cell level. We find evidence of limited tropism to SARS-CoV-2 for all major cell types and observe extensive neuronal cell death that also include non-infected cells. Single cell transcriptome profiling reveals distinct responses in microglia and astrocytes that share features with cellular states observed in neurodegenerative diseases
Project description:Microglia, brain-resident macrophages, have been proposed to play an active role in synaptic refinement and maturation, influencing plasticity and circuit-level connectivity. Using a genetically modified mouse which lacks microglia (Csf1r ∆FIRE/∆FIRE), we investigate the effect on gene expression of the presence or absence of microglia in the developing mouse brain.
Project description:Gene expression is finely regulated during development, and deregulation can lead to disease. In pediatric brain tumors (PBT), disruption of neurodevelopmental gene regulation programs are suspected to drive oncogenesis. However, the transcriptional landscape and genetic regulation processes of the healthy developing brain are not fully characterized, limiting our investigation of these tumors. We used single-cell RNA-sequencing to generate a transcriptomic atlas of the developing forebrain and pons in human and mouse, two regions where PBT commonly arise. We projected bulk RNA-seq profiles for a cohort of 200 PBT onto these cell types, followed by focused analysis of three PBT subtypes by single-cell profiling: WNT medulloblastoma, embryonal tumors with multilayered rosettes (ETMR), and atypical teratoid/rhabdoid tumors (ATRT). In diffuse intrinsic pontine glioma (DIPG), we investigated the effect of removal of the driver H3K27M mutation on differentiation potential using primary tumor-derived cell lines. Altogether, for WNT medulloblastoma, ETMR, and DIPG, we pinpoint stalled differentiation during developmental programs as a common etiological mechanism of these tumors, providing a valuable resource to aid modeling and therapeutics.