Project description:RNA-seq analysis on a human neuronal cell line derived from fetal mesencephalon (LUHMES) wild type and RFX2 knockout from day 0 to day 6.
Project description:RNA-seq analysis on neurospheres derived from wt and Cstb-knockout mouse embryo brains before differentiation and during differentiation at days 1, 5, and 12.
Project description:RNA-seq samples from 3 species across a differentiation from induced pluripotent stem cells to neural progenitor cells were generated to study gene expression evolution. Briefly, previously generated urinary stem cell derived iPSCs of 3 human (Homo sapiens) individuals (3 clones), 1 gorilla (Gorilla gorilla) individual and fibroblast derived cynomolgus macaque (Macaca fascicularis) iPSCs of 2 individuals (4 clones) (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). Bulk RNA-seq libraries of iPSCs and NPCs were generated using prime-seq protocol (Janjic et al. 2022).
Project description:Neurodegenerative disorders are an increasingly common and irreversible burden on society, often affecting the ageing population, but their aetiology and disease mechanisms are poorly understood. Studying monogenic neurodegenerative diseases, with known genetic cause, provides an opportunity to understand cellular mechanisms also affected in more complex disorders. We recently reported that loss-of-function mutations in the autophagy adaptor protein, SQSTM1/p62, lead to a slowly progressive neurodegenerative disease presenting in childhood. To further elucidate the neuronal involvement, we studied the cellular consequences of loss of p62 in a neuroepithelial stem (NES) cell model and differentiated neurones, derived from reprogrammed p62 patient cells, or by CRISPR/Cas9-directed gene editing in NES cells. Transcriptomic and proteomic analyses suggest that p62 is essential for neuronal differentiation by controlling the metabolic shift from aerobic glycolysis to oxidative phosphorylation required for neuronal maturation. This shift is blocked by the failure to sufficiently downregulate lactate dehydrogenase expression due to the loss of p62, possibly through impaired Hif-1α downregulation and increased sensitivity to oxidative stress. The findings implicate an important role for p62 in neuronal energy metabolism and particularly in the regulation of the shift between glycolysis and oxidative phosphorylation, required for normal neurodifferentiation.
Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.
Project description:To investigate the effects of ZIKV infection or ZIKV-NS4B-transduction on the global proteome scale at early stages of hNPC differentiation into neurons, hNPC cells were infected with ZIKV (Asian strain: H/PF/2013; MOI=0.01) or transduced with ZIKV-NS4B or HCV-NS4B and one day later cells were either left under proliferative conditions or neuronal differentiation was induced with ROCK inhibitors treatment and growth factors withdrawals. Five days later samples were harvested and processed for quantitative label-free proteomics.
Project description:Sphere-forming progenitor cells can be isolated from the fetal and adult mammalian inner ear and give rise to inner ear specific cell types in vitro. Here, we provide phenotypical and functional characterization of a new pool of auditory progenitors as sustainable source for sphere-derived auditory neurons. The so-called phoenix auditory neuroprogenitors, isolated from the A/J mouse spiral ganglion, exhibit nearly unlimited intrinsic self-renewal properties (beyond 40 passages). At any passage, phoenix spheres can be efficiently differentiated by withdrawing growth factors into mature spiral ganglion cells, expressing both neurons and glial cells phenotypic markers and exhibiting similar functional properties as mouse spiral ganglion explants and human sphere-derived spiral ganglion cells. The present dataset includes RNAseq-based transcriptome analysis of phoenix auditory neurons following 7 days of differentiation. mRNA levels in differentiated cells are expressed relatively to neuroprogenitor spheres of equivalent passage (paired samples at passage 12, 21 and 36)
Project description:The adult mammalian heart has been traditionally regarded as a post-mitotic organ with no regenerative capacity. However, this dogma has been refuted by some recent landmark studies. Both cardiac progenitor cells (CPCs) and epicardial progenitor cells (EPDCs) are activated after myocardium infarction and they may influence each other through paracrine mechanisms or direct interactions. Currently, efforts are being made to discover and develop therapeutic molecules to increase the number of CPCs and EPDCs in an infarcted heart. To better understand the characteristics and therapeutic potential of CPCs and EPDCs, as well as the regulatory mechanisms, we performed transcriptomic analysis of human iPSC-derived CPCs and human primary EPDCs and discovered unique gene expression profiles for each cell type. To make sure that the biological and pharmacological findings in cell assays under ambient oxygen conditions are relevant to the in vivo situation, it is important to understand the effect of hypoxia on the behavior, gene expression, and paracrine profiles of the cells. <br>Comparative transcriptomic analysis of human epicardial progenitor cells and hiPSC-derived cardiac progenitor cells was conducted. We performed global transcriptional analysis of two sources of cardiac progenitors, i.e., patient epicardium-derived cells (EPDCs) and cardiac progenitor cells (CPCs) derived from human induced pluripotent stem cells. In addition, we also compared the gene expression profiles of these cells when they were cultured under normoxic- and hypoxic conditions.
Project description:we performed lentiviral CRISPR interference (CRISPRi) by recruiting dCas9 fused with the KRAB domain to the CSMD1 enhancer (fam3) in the neuronal precursor cell line – Lund human mesencephalic (LUHMES). Given that the expression of CSMD1 was not detectable in LUHMES cells we differentiated these cells into neurons. Differentiated neurons with CRISPRi of CSMD1 enhancer showed significantly higher expression of CSMD1 than control.
Project description:The Notch signaling pathway is a cell-cell communication system with fundamental roles in embryonic development and the nervous system, including neural stem cell proliferation and differentiation. To investigate the multivalency effect of ligands on the activation of the Notch receptor, we treated iPSc-derived neuroepithelial stem-like (lt-NES) cells with different Jag1 nanopatterns on DNA origami nanostructures.