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Stem cell modulation in neural development and regeneration

Stem cell modulation in neural development and regeneration

Jürgen A. Knoblich (ORCID: 0000-0002-6751-3404)
  • Grant DOI 10.55776/F78
  • Funding program Special Research Areas
  • Status ongoing
  • Start March 1, 2020
  • End February 29, 2028
  • Funding amount € 9,565,889
  • E-mail

Disciplines

Biology (100%)

Keywords

    Tissue Growth, Neural Tube, Pattern Formation, Morphogen

Abstract

Organs in our body are kept alive by so-called stem cells. Stem cells are unique because they can self renew, a property that allows them to create identical copies of themselves but at the same time also generate more specialized cells that fulfil important tasks in the various organs. By doing so, they keep alive for a long time and constantly replace dying or damaged cells. In our brain and spinal chord, however, the situation is slightly different. Here, huge numbers of highly specialized nerve cells fulfil very specific tasks, sometimes activating, sometimes inhibiting the neural circuits in our central nervous system. How do the stem cells know what type of neuron to generate at which position and at what point in time? How do they change in space and time so they can create the correct types of neurons? Understanding the mechanisms that regulate neural stem cells in space and time, finding out how the stem cell state is modulated despite the need for constant self-renewal is the key goal of our SFB. Our consortium combines numerous approaches centered around a few key enabling technologies to address this problem from a variety of different angles. We employ a number of different models ranging from sea-worms all the way to human 3D cell cultures. We focus on single-cell technologies that allow us to precisely follow stem cells in space and time. Our consortium is grouped around a central bio-informatics hub that allows us to maximise the interpretation and correlation of the various datasets. Together, we intend to build a central hub for neural stem cell biology in Austria that addresses a unique unifying biological question using cutting edge technologies at the forefront of what is technologically possible.

Consortium
  • Anna Kicheva, Institute of Science and Technology Austria - ISTA
    consortium member (01.03.2020 -)
  • Arndt Von Haeseler, Universität Wien
    consortium member (01.03.2020 -)
  • Elly Margaret Tanaka, Institut für Molekulare Pathologie - IMP
    consortium member (01.03.2020 -)
  • Florian Raible, Universität Wien
    consortium member (01.03.2020 -)
  • Frank Oliver Stefan Edenhofer, Universität Innsbruck
    consortium member (01.03.2020 -)
  • Gaia Novarino, Institute of Science and Technology Austria - ISTA
    consortium member (01.03.2020 -)
  • Igor Igorevich Adameyko, Medizinische Universität Wien
    consortium member (01.03.2024 -)
  • Jürgen A. Knoblich, IMBA – Institut für Molekulare Biotechnologie GmbH
    consortium member (01.03.2020 -)
  • Kristin Tessmar-Raible, Universität Wien
    consortium member (01.03.2020 -)
  • Lora Sweeney, Institute of Science and Technology Austria - ISTA
    consortium member (01.03.2024 -)
  • Noelia Urban Avellaneda, IMBA – Institut für Molekulare Biotechnologie GmbH
    consortium member (01.03.2020 -)
  • Simon Hippenmeyer, Institute of Science and Technology Austria - ISTA
    consortium member (01.03.2020 -)
  • Sofia Cristina Soares De Morais Grade, IMBA – Institut für Molekulare Biotechnologie GmbH
    consortium member (01.03.2024 -)
Research institution(s)
  • IMBA – Institut für Molekulare Biotechnologie GmbH
Project participants
  • Daniela D. Pollak-Monje Quiroga, Medizinische Universität Wien , national collaboration partner
International project participants
  • Guillaume Balavoine, Université Paris Diderot - Paris 7 - France
  • Ana Martin-Villalba, Deutsches Krebsforschungszentrum - Germany
  • Andreas Trumpp, Deutsches Krebsforschungszentrum Heidelberg - Germany
  • Florian Heyd, Freie Universität Berlin - Germany
  • Wolfgang Enard, Ludwig-Maximilians-Universität München - Germany
  • Barbara Treutlein, Max-Planck-Gesellschaft - Germany
  • Kent Duncan, Universität Hamburg - Germany
  • Cesare Indiveri, Università di Calabria - Italy
  • Jens C. Schwamborn, Université du Luxembourg - Luxembourg
  • Andras Simon, Karolinska Institute - Sweden
  • Rolf Zeller, University of Bern - Switzerland
  • Matthias Lütolf, École polytechnique fédérale de Lausanne - Switzerland
  • Ahmet Okay Caglayan, Istanbul Bilim University - Turkey
  • Fritz J. Sedlazeck, Baylor College of Medicine - USA
  • Molly M. Stevens, Imperial College of London - United Kingdom
  • Stefano Pluchino, University of Cambridge - United Kingdom

Research Output

  • 407 Citations
  • 47 Publications
Publications
  • 2025
    Title Adeno-associated viruses for efficient gene expression in the axolotl nervous system
    DOI 10.1073/pnas.2421373122
    Type Journal Article
    Author Lust K
    Journal Proceedings of the National Academy of Sciences
    Link Publication
  • 2025
    Title ß-catenin-driven endomesoderm specification is a Bilateria-specific novelty
    DOI 10.1038/s41467-025-57109-w
    Type Journal Article
    Author Lebedeva T
    Journal Nature Communications
    Pages 2476
    Link Publication
  • 2024
    Title Molecular circadian rhythms are robust in marine annelids lacking rhythmic behavior
    DOI 10.1371/journal.pbio.3002572
    Type Journal Article
    Author Häfker N
    Journal PLOS Biology
    Link Publication
  • 2025
    Title SOX2+ sustentacular cells are stem cells of the postnatal adrenal medulla
    DOI 10.1038/s41467-024-55289-5
    Type Journal Article
    Author Kemkem Y
    Journal Nature Communications
  • 2025
    Title Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).
    DOI 10.1007/978-1-0716-4310-5_7
    Type Journal Article
    Author Cheung G
    Journal Methods in molecular biology (Clifton, N.J.)
    Pages 139-151
  • 2025
    Title Guiding Light: Mechanisms and Adjustments of Environmental Light Interpretation with Insights from Platynereis dumerilii and Other Selected Examples
    DOI 10.2108/zs240099
    Type Journal Article
    Author Wulf P
    Journal Zoological Science
  • 2025
    Title A cost- and time-efficient method for high-throughput cryoprocessing and tissue analysis using multiplexed tissue molds
    DOI 10.1016/j.crmeth.2025.101023
    Type Journal Article
    Author Reumann D
    Journal Cell Reports Methods
    Pages 101023
    Link Publication
  • 2025
    Title Advancing autism research: Insights from brain organoid modeling
    DOI 10.1016/j.conb.2025.103030
    Type Journal Article
    Author Li C
    Journal Current Opinion in Neurobiology
    Pages 103030
    Link Publication
  • 2025
    Title The role of microheterogeneity in cell fate decisions in neural progenitors and neural crest
    DOI 10.1016/j.conb.2025.103031
    Type Journal Article
    Author Kamenev D
    Journal Current Opinion in Neurobiology
    Pages 103031
    Link Publication
  • 2025
    Title How radial glia progenitor lineages generate cell-type diversity in the developing cerebral cortex
    DOI 10.1016/j.conb.2025.103046
    Type Journal Article
    Author Pipicelli F
    Journal Current Opinion in Neurobiology
    Pages 103046
    Link Publication
  • 2023
    Title Odontodes: The Developmental and Evolutionary Building Blocks of Dentitions
    Type Book
    Author Chen Donglei
    Publisher Taylor & Francis Ltd
  • 2023
    Title The promise of genetic screens in human in vitro brain models
    DOI 10.1515/hsz-2023-0174
    Type Journal Article
    Author Beirute-Herrera J
    Journal Biological Chemistry
    Pages 13-24
    Link Publication
  • 2024
    Title Single-cell Profiling of Reprogrammed Human Neural Stem Cells Unveils High Similarity to Neural Progenitors in the Developing Central Nervous System
    DOI 10.1007/s12015-024-10698-3
    Type Journal Article
    Author Spathopoulou A
    Journal Stem Cell Reviews and Reports
    Pages 1325-1339
    Link Publication
  • 2024
    Title Assessing the precision of morphogen gradients in neural tube development
    DOI 10.1038/s41467-024-45148-8
    Type Journal Article
    Author Zagorski M
    Journal Nature Communications
    Pages 929
    Link Publication
  • 2024
    Title Adeno-associated viral tools to trace neural development and connectivity across amphibians
    DOI 10.1016/j.devcel.2024.10.025
    Type Journal Article
    Author Jaeger E
    Journal Developmental Cell
    Link Publication
  • 2024
    Title Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling
    DOI 10.1016/j.devcel.2024.10.024
    Type Journal Article
    Author Lehr S
    Journal Developmental Cell
    Link Publication
  • 2024
    Title Applying single-cell and single-nucleus genomics to studies of cellular heterogeneity and cell fate transitions in the nervous system
    DOI 10.1038/s41593-024-01827-9
    Type Journal Article
    Author Adameyko I
    Journal Nature Neuroscience
    Pages 2278-2291
  • 2024
    Title Protocol for fabricating elastomeric stencils for patterned stem cell differentiation
    DOI 10.1016/j.xpro.2024.103187
    Type Journal Article
    Author Lehr S
    Journal STAR Protocols
    Pages 103187
    Link Publication
  • 2024
    Title Modeling early phenotypes of Parkinson’s disease by age-induced midbrain-striatum assembloids
    DOI 10.1038/s42003-024-07273-4
    Type Journal Article
    Author Barmpa K
    Journal Communications Biology
    Pages 1561
    Link Publication
  • 2024
    Title Alternative lengthening of telomere-based immortalization renders H3G34R-mutant diffuse hemispheric glioma hypersensitive to PARP inhibitor combination regimens
    DOI 10.1093/neuonc/noae228
    Type Journal Article
    Author Laemmerer A
    Journal Neuro-Oncology
    Pages 811-827
    Link Publication
  • 2024
    Title Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols
    DOI 10.1101/2024.11.15.623576
    Type Preprint
    Author Naas J
    Pages 2024.11.15.623576
    Link Publication
  • 2024
    Title Molecular profiles, sources and lineage restrictions of stem cells in an annelid regeneration model
    DOI 10.1038/s41467-024-54041-3
    Type Journal Article
    Author Stockinger A
    Journal Nature Communications
    Pages 9882
    Link Publication
  • 2024
    Title Protocol for mapping cell lineage and cell-type identity of clonally-related cells in situ using MADM-CloneSeq
    DOI 10.1016/j.xpro.2024.103168
    Type Journal Article
    Author Cheung G
    Journal STAR Protocols
    Pages 103168
    Link Publication
  • 2024
    Title Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice
    DOI 10.1016/j.xpro.2024.103157
    Type Journal Article
    Author Cheung G
    Journal STAR Protocols
    Pages 103157
    Link Publication
  • 2024
    Title The chromatin regulator Ankrd11 controls cardiac neural crest cell-mediated outflow tract remodeling and heart function
    DOI 10.1038/s41467-024-48955-1
    Type Journal Article
    Author Kibalnyk Y
    Journal Nature Communications
    Pages 4632
    Link Publication
  • 2024
    Title Motor innervation directs the correct development of the mouse sympathetic nervous system
    DOI 10.1038/s41467-024-51290-0
    Type Journal Article
    Author Erickson A
    Journal Nature Communications
    Pages 7065
    Link Publication
  • 2024
    Title Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma
    DOI 10.1186/s12943-024-02091-y
    Type Journal Article
    Author Olsen T
    Journal Molecular Cancer
    Pages 180
    Link Publication
  • 2024
    Title Time me by the moon
    DOI 10.1038/s44319-024-00196-5
    Type Journal Article
    Author Ritter A
    Journal EMBO Reports
    Pages 3169-3176
    Link Publication
  • 2024
    Title Lineage tracing of Shh+ floor plate cells and dynamics of dorsal–ventral gene expression in the regenerating axolotl spinal cord
    DOI 10.1111/dgd.12945
    Type Journal Article
    Author Arbanas L
    Journal Development, Growth & Differentiation
    Pages 414-425
    Link Publication
  • 2024
    Title Dynamics of morphogen source formation in a growing tissue
    DOI 10.1371/journal.pcbi.1012508
    Type Journal Article
    Author Ho R
    Journal PLOS Computational Biology
    Link Publication
  • 2024
    Title Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis
    DOI 10.1101/2024.09.20.614050
    Type Preprint
    Author Vijatovic D
    Pages 2024.09.20.614050
    Link Publication
  • 2024
    Title A polarized FGF8 source specifies frontotemporal signatures in spatially oriented cell populations of cortical assembloids
    DOI 10.1038/s41592-024-02412-5
    Type Journal Article
    Author Bosone C
    Journal Nature Methods
    Pages 2147-2159
    Link Publication
  • 2020
    Title The Still Dark Side of the Moon: Molecular Mechanisms of Lunar-Controlled Rhythms and Clocks
    DOI 10.1016/j.jmb.2020.03.009
    Type Journal Article
    Author Andreatta G
    Journal Journal of Molecular Biology
    Pages 3525-3546
    Link Publication
  • 2020
    Title A human tissue screen identifies a regulator of ER secretion as a brain-size determinant
    DOI 10.1126/science.abb5390
    Type Journal Article
    Author Esk C
    Journal Science
    Pages 935-941
    Link Publication
  • 2024
    Title Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers; In: Neuronal Morphogenesis - Methods and Protocols
    DOI 10.1007/978-1-0716-3969-6_19
    Type Book Chapter
    Publisher Springer US
  • 2024
    Title A framework for neural organoids, assembloids and transplantation studies
    DOI 10.1038/s41586-024-08487-6
    Type Journal Article
    Author Arlotta P
    Journal Nature
  • 2024
    Title Dynamic microvilli sculpt bristles at nanometric scale
    DOI 10.1038/s41467-024-48044-3
    Type Journal Article
    Author Ikeda K
    Journal Nature Communications
    Pages 3733
    Link Publication
  • 2024
    Title Cerebral organoids display dynamic clonal growth and tunable tissue replenishment
    DOI 10.1038/s41556-024-01412-z
    Type Journal Article
    Author Lindenhofer D
    Journal Nature Cell Biology
    Pages 710-718
    Link Publication
  • 2024
    Title ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum
    DOI 10.1016/j.stem.2024.04.014
    Type Journal Article
    Author Martins-Costa C
    Journal Cell Stem Cell
    Link Publication
  • 2024
    Title Human enteric nervous system progenitor transplantation improves functional responses in Hirschsprung disease patient-derived tissue
    DOI 10.1136/gutjnl-2023-331532
    Type Journal Article
    Author Jevans B
    Journal Gut
    Pages 1441-1453
    Link Publication
  • 2024
    Title Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition
    DOI 10.1016/j.devcel.2024.04.021
    Type Journal Article
    Author Krammer T
    Journal Developmental Cell
    Link Publication
  • 2024
    Title Increased cholesterol synthesis drives neurotoxicity in patient stem cell-derived model of multiple sclerosis.
    DOI 10.1016/j.stem.2024.09.014
    Type Journal Article
    Author Ionescu Rb
    Journal Cell stem cell
  • 2024
    Title Neutral competition explains the clonal composition of neural organoids
    DOI 10.1371/journal.pcbi.1012054
    Type Journal Article
    Author Pflug F
    Journal PLOS Computational Biology
    Link Publication
  • 2023
    Title Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry
    DOI 10.1016/j.xpro.2023.102771
    Type Journal Article
    Author Amberg N
    Journal STAR Protocols
    Pages 102771
    Link Publication
  • 2023
    Title Multipotent progenitors instruct ontogeny of the superior colliculus
    DOI 10.1016/j.neuron.2023.11.009
    Type Journal Article
    Author Cheung G
    Journal Neuron
    Link Publication
  • 2021
    Title Autophagy in a-Synucleinopathies—An Overstrained System
    DOI 10.3390/cells10113143
    Type Journal Article
    Author Fellner L
    Journal Cells
    Pages 3143
    Link Publication
  • 2021
    Title Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration
    DOI 10.15252/embj.2021108714
    Type Journal Article
    Author Bajaj S
    Journal The EMBO Journal
    Link Publication

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