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Villaronga-Luque A, Savill RG, López-Anguita N, Bolondi A, Garai S, Gassaloglu SI, Rouatbi R, Schmeisser K, Poddar A, Bauer L, Alves T, Traikov S, Rodenfels J, Chavakis T, Bulut-Karslioglu A, Veenvliet JV. Integrated molecular-phenotypic profiling reveals metabolic control of morphological variation in a stem-cell-based embryo model. Cell Stem Cell 2025; 32:759-777.e13. [PMID: 40245869 DOI: 10.1016/j.stem.2025.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 11/27/2024] [Accepted: 03/21/2025] [Indexed: 04/19/2025]
Abstract
Considerable phenotypic variation under identical culture conditions limits the potential of stem-cell-based embryo models (SEMs) in basic and applied research. The biological processes causing this seemingly stochastic variation remain unclear. Here, we investigated the roots of phenotypic variation by parallel recording of transcriptomic states and morphological history in individual structures modeling embryonic trunk formation. Machine learning and integration of time-resolved single-cell RNA sequencing with imaging-based phenotypic profiling identified early features predictive of phenotypic end states. Leveraging this predictive power revealed that early imbalance of oxidative phosphorylation and glycolysis results in aberrant morphology and a neural lineage bias, which we confirmed by metabolic measurements. Accordingly, metabolic interventions improved phenotypic end states. Collectively, our work establishes divergent metabolic states as drivers of phenotypic variation and offers a broadly applicable framework to chart and predict phenotypic variation in organoids and SEMs. The strategy can be used to identify and control underlying biological processes, ultimately increasing reproducibility.
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Affiliation(s)
- Alba Villaronga-Luque
- Stembryogenesis Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Faculty of Biology, Technische Universität Dresden, 01307 Dresden, Germany
| | - Ryan G Savill
- Stembryogenesis Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Faculty of Biology, Technische Universität Dresden, 01307 Dresden, Germany
| | | | - Adriano Bolondi
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Sumit Garai
- Stembryogenesis Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Seher Ipek Gassaloglu
- Stembryogenesis Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Roua Rouatbi
- MOSAIC Group, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany; Faculty of Computer Science, Technische Universität Dresden, 01062 Dresden, Germany; Center for Scalable Data Analytics and Artificial Intelligence Dresden/Leipzig, 01062 Dresden, Germany
| | - Kathrin Schmeisser
- Energetics of Biological Systems Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Aayush Poddar
- Stembryogenesis Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Lisa Bauer
- Stembryogenesis Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tiago Alves
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Sofia Traikov
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Jonathan Rodenfels
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany; Energetics of Biological Systems Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Triantafyllos Chavakis
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | | | - Jesse V Veenvliet
- Stembryogenesis Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany.
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The people behind the papers - Julia Grzymkowski and Nanette Nascone-Yoder. Development 2024; 151:dev202745. [PMID: 38369734 DOI: 10.1242/dev.202745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
As the digestive system develops, the gut tube lengthens and convolutes to correctly package the intestine. Intestinal malrotation is a prevalent birth anomaly, but its underlying causes are not well understood. In this new study, Nanette Nascone-Yoder and colleagues show that exposure of Xenopus embryos to atrazine, a widely-used herbicide, can disrupt cellular metabolism in the developing gut tube and lead to intestinal malrotation. We caught up with first author Julia Grzymkowski and corresponding author Nanette Nascone-Yoder, Professor at North Carolina State University, to hear more about the story.
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