A5070799693- Single-cell and spatial transcriptomics
- Pluripotent Stem Cells Research
- Cancer Cells and Metastasis
- Renal and related cancers
- CRISPR and Genetic Engineering
- Cell Image Analysis Techniques
- Gene Regulatory Network Analysis
- Neurogenesis and neuroplasticity mechanisms
- RNA Research and Splicing
- Cancer Genomics and Diagnostics
- Digestive system and related health
- Gene expression and cancer classification
- Liver physiology and pathology
- Neuroinflammation and Neurodegeneration Mechanisms
- 3D Printing in Biomedical Research
- Epigenetics and DNA Methylation
- Protist diversity and phylogeny
- Gut microbiota and health
- Neonatal Respiratory Health Research
- Genomics and Chromatin Dynamics
- Neuroscience and Neuropharmacology Research
- Retinal Development and Disorders
- MicroRNA in disease regulation
- Cellular Mechanics and Interactions
- Slime Mold and Myxomycetes Research
University of Basel
2019-2025
Roche (Switzerland)
2021-2025
Institute of Molecular and Clinical Ophthalmology Basel
2019-2023
Max Planck Institute for Evolutionary Anthropology
2015-2022
Roche (Bosnia-Herzegovina)
2022
Bioengineering (Switzerland)
2022
ETH Zurich
2019
Stanford University
2014-2017
University of North Carolina at Chapel Hill
2009-2017
University of Colorado Health
1998
Cerebral organoids-3D cultures of human cerebral tissue derived from pluripotent stem cells-have emerged as models cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) dissect compare composition progenitor-to-neuron lineage relationships organoids fetal neocortex. Covariation network analysis using...
The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic FACS-based single-cell RNA sequencing of mouse provides a well-resolved classification striatal type diversity. Transcriptome analysis revealed ten differentiated, distinct types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, vascular cells, enabled the discovery numerous marker genes. Furthermore, we identified two discrete...
How the axolotl makes a new limb Unlike most vertebrate limbs, regenerates skeleton after amputation. Dermal and interstitial fibroblasts have been thought to provide sources for skeletal regeneration, but it has unclear whether preexisting stem cells or dedifferentiation of formed blastema. Gerber et al. developed transgenic reporter animals compare periskeletal cell fibroblast contributions regeneration. Callus-forming extended existing bone, built segments. Single-cell transcriptomics...
Human neocortex expansion likely contributed to the remarkable cognitive abilities of humans. This is thought primarily reflect differences in proliferation versus differentiation neural progenitors during cortical development. Here, we have searched for such by analysing cerebral organoids from human and chimpanzees using immunohistofluorescence, live imaging, single-cell transcriptomics. We find that cytoarchitecture, cell type composition, neurogenic gene expression programs humans are...
Self-organizing neural organoids grown from pluripotent stem cells
Abstract Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enable highly resolved descriptions of states within these systems; however, approaches are needed directly measure lineage relationships. Here we establish iTracer, a recorder that combines reporter barcodes with inducible CRISPR–Cas9 scarring and is compatible single-cell spatial transcriptomics. We apply iTracer explore clonality dynamics during...
Organs are composed of diverse cell types that traverse transient states during organogenesis. To interrogate this diversity human development, we generate a single-cell transcriptome atlas from multiple developing endodermal organs the respiratory and gastrointestinal tract. We illuminate states, transcription factors, organ-specific epithelial stem mesenchyme interactions across lineages. implement as high-dimensional search space to benchmark pluripotent (hPSC)-derived intestinal...
Salamanders are tetrapod models to study brain organization and regeneration; however, the identity evolutionary conservation of cell types largely unknown. We delineated populations in axolotl telencephalon during homeostasis regeneration using single-cell genomic profiling. identified glutamatergic neurons with similarities amniote hippocampus, dorsal lateral cortex, conserved γ-aminobutyric acid-releasing (GABAergic) neuron classes. inferred transcriptional dynamics gene regulatory...
Abstract Organoids generated from human pluripotent stem cells provide experimental systems to study development and disease, but quantitative measurements across different spatial scales molecular modalities are lacking. In this study, we multiplexed protein maps over a retinal organoid time course primary adult tissue. We developed toolkit visualize progenitor neuron location, the arrangements of extracellular subcellular components global patterning in each addition, single-cell...
The intimate relationship between the epithelium and immune system is crucial for maintaining tissue homeostasis, with perturbations therein linked to autoimmune disease cancer
Human neural organoids, generated from pluripotent stem cells in vitro, are useful tools to study human brain development, evolution and disease. However, it is unclear which parts of the covered by existing protocols, has been difficult quantitatively assess organoid variation fidelity. Here we integrate 36 single-cell transcriptomic datasets spanning 26 protocols into one integrated cell atlas totalling more than 1.7 million cells1–26. Mapping developing references27–30 shows primary types...
Organoids and organs-on-a-chip have emerged as powerful tools for modeling human gut physiology disease in vitro. Although physiologically relevant, these systems often lack the environmental milieu, spatial organization, cell type diversity, maturity necessary mimicking intestinal mucosa. To instead generate models closely resembling vivo tissue, we herein integrated organoid organ-on-a-chip technology to develop an advanced model, called "mini-colons." By employing asymmetric stimulation...
Microbiota regulate intestinal physiology by modifying host gene expression along the length of intestine, but underlying regulatory mechanisms remain unresolved. Transcriptional specificity occurs through interactions between transcription factors (TFs) and cis -regulatory regions (CRRs) characterized nucleosome-depleted accessible chromatin. We profiled transcriptome chromatin landscapes in epithelial cells (IECs) from mice reared presence or absence microbiota. show that regional...
Identification of gene expression traits unique to the human brain sheds light on molecular mechanisms underlying evolution. Here, we searched for uniquely by analyzing 422 samples from humans, chimpanzees, bonobos, and macaques representing 33 anatomical regions, as well 88,047 cell nuclei composing three these regions. Among cerebral cortex areas, hypothalamus, cerebellar gray white matter evolved rapidly in humans. At cellular level, astrocytes oligodendrocyte progenitors displayed more...