EMBL Seminars

Abstract
How do human cells collectively generate a body plan and build tissues and organs with remarkable spatial and temporal precision? Despite major advances in developmental biology, the cellular and molecular principles governing human and primate post-gastrulation development remain difficult to interrogate experimentally. Stem cell-based embryo models now provide an opportunity not only to reconstruct these processes in vitro, but also to perturb, control, and ultimately understand the underlying principles of developmental self-organization. Our laboratory develops human and non-human primate stem cell models spanning developmental dynamics, axial patterning, morphogenesis, and early organogenesis. We initially reconstructed the human segmentation clock in vitro, revealing species-specific properties of this conserved developmental oscillator (Matsuda, Yamanaka et al., Nature 2020; Matsuda et al., Science 2020). We subsequently developed human “axioloids,” self-organizing 3D systems that couple segmentation clock oscillations with axial elongation, periodic somite formation, epithelialization, and rostrocaudal patterning (Yamanaka et al., Nature 2023). Building on these systems, we are now moving toward increasingly complex models of primate development that integrate multiple embryonic lineages and reproduce aspects of symmetry breaking, body-axis formation, tissue morphogenesis, and early organogenesis. Comparative models generated from diverse primate pluripotent stem cells further provide an experimental framework for identifying conserved and species-specific developmental programs. I will discuss how these emerging systems can be used to dissect the principles by which signaling dynamics, cell state, tissue interactions, and morphogenesis are coordinated during primate development, and how combining developmental biology with synthetic and quantitative approaches may allow us to move from observing embryogenesis toward experimentally reconstructing and controlling it in vitro.

About the speaker
Prof. Cantas Alev is a Principal Investigator and tenured Professor at the Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University. His laboratory develops stem cell-based models to uncover fundamental principles of human and primate embryonic development and organogenesis. Prof. Alev earned his MD and PhD degrees from Ruhr University Bochum, Germany, and conducted postdoctoral research at the RIKEN Center for Developmental Biology in Kobe. He subsequently joined Kyoto University’s Center for iPS Cell Research and Application (CiRA), where he pioneered pluripotent stem cell-based models of human mesoderm development, including systems for studying the segmentation clock and somitogenesis. At ASHBi, his team aims to reconstitute key aspects of human and primate development in vitro to advance our understanding of development, disease, and evolution.

Abstract
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About the speaker
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Connection details
Zoom*: https://embl-org.zoom.us/j/91702795470?pwd=LmPdfEmO4LFcXf6ZIBmMXt9sZal5cP.1&jst=2  (Meeting ID: 91702795470 , Password: 529151)

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Global views of development

The interplay between transcription factors and chromatin accessibility regulates spatiotemporal gene expression and cell type diversification. However, comprehensive atlases and gene regulatory networks underlying these processes have remained elusive. I will present our recent efforts in single-cell multiomics and spatial transcriptomics to address this challenge. We generated a single-cell multiomics atlas of RNA expression and chromatin accessibility during zebrafish embryogenesis and developed DeepDanio, a deep learning model to dissect cis-regulatory interactions. In parallel, we developed a whole-embryo imaging platform to quantify the expression of hundreds of genes at subcellular resolution. Integration with the single-cell multiomics data generated an atlas detailing the expression of ~25,000 genes and the accessibility of ~300,00 chromatin regions, as well as the online browser MERFISHEYES. I will discuss how exploration of the atlas and the gene regulatory network identified instant differentiation as a novel mode of cell differentiation and how changes in gene expression generate sharp boundaries during gastrulation. 

Abstract
Animals have evolved within the framework of microbes and are constantly exposed to diverse microbiota. Eukaryotic organisms are therefore metaorganisms: consortia of zygote-derived host cells and associated microorganisms, including bacteria, archaea, fungi, protists, and viruses. Hosts and microbes are deeply interconnected, often co-evolving and shaping one another’s fitness.

Over the past decades, microbiome research has shown that microbial communities are essential for normal animal development, physiology, and reproduction. Microbial signals also become integrated into neural circuits, influencing behaviour across evolution—from simple reflexes in Hydra to associative learning in honey bees and emotional regulation in mammals. Yet how animals perceive, transmit, and integrate these signals remains largely unknown.

Using the ancestral metazoan Hydra as a model, I will argue that animal development and behaviour are not autonomous processes, but emerge through transient and persistent interactions with the microbial world. Symbiotic microbes provide developmental and behavioural signals that contribute directly to phenotype formation. Integrating the microbiome into our understanding of development and evolution therefore reveals a more complete picture of how organisms function, adapt, and evolve—and of the very fabric of life itself.

About the speaker
Thomas is a leading researcher in host–microbe interactions and the biology of metaorganisms. Using the freshwater polyp Hydra as a model, his group has transformed our understanding of how microbial communities shape animal development, nervous-system function, and behaviour. His seminar will offer a fascinating perspective on animals as deeply integrated partnerships between hosts and microbes, with broad implications for development, behaviour, and evolution.