About Us
Research groups
Symposium
Friends
Back to research groups
The Sonnen group investigates how signalling pathway dynamics encode information to control development and homeostasis of multicellular systems.
Cells in multicellular organisms don’t act alone – they must constantly coordinate processes such as growth, specialization, movement, and cell death. From development to adult life, this careful balance ensures proper tissue formation and maintenance, and helps prevent diseases such as cancer.
Communication between cells happens through signalling pathways. While these pathways have long been studied as key mediators of cellular control, only in recent years has it become possible to experimentally investigate the role of signalling dynamics — the changes in signalling activity over time. The timing and dynamics of signals are crucial for accurate and efficient coordination between cells.
Work in single cells has shown that biological information can be encoded in signal dynamics. Thanks to new technologies and advanced in vitro model systems, we can now study how this dynamic encoding operates at the multicellular level (reviewed in Sonnen and Aulehla 2014).
In our lab, we apply these approaches to investigate dynamic signal encoding during early embryonic development, using model systems such as gastruloids, blastoids, and blastocysts. We also study signalling dynamics in tissue homeostasis and regeneration, with a particular focus on the intestine, and explore how disruptions in these processes can drive cancer.
To find out more about the lab, also visit our Sonnen Lab website.
The Sonnen lab studies how biological information is transmitted through signalling dynamics in multicellular systems, from early embryonic development to adult tissue homeostasis and disease.
We use advanced model systems such as mouse somitogenesis, gastruloids, and blastoids to investigate how dynamic signalling coordinates early development and blastocyst formation. To study tissue maintenance and regeneration, we focus on the small intestine as a model of homeostasis and examine how disruptions in these processes contribute to cancer.
Our work combines developmental biology, biochemistry, and cell biology with quantitative approaches. We quantify signalling dynamics using real-time fluorescence imaging in gastruloids, blastoids, and organoids, and complement this with time-resolved proteomics (preprint) and single-cell tracking (preprint) to capture signalling dynamics across scales.
A central focus of the lab is the development of new methods to control signalling in space and time. We use microfluidics to precisely manipulate signalling dynamics (Sonnen et al. 2018, Sonnen and Merten 2019) and are establishing optogenetic approaches for targeted, reversible perturbations with high spatiotemporal precision.
Somitogenesis is the periodic formation of somites – the building blocks of vertebrae and axial muscles – during early embryonic development. This sequential segmentation of the presomitic mesoderm (PSM) is regulated by a combination of signalling gradients and oscillations. Oscillatory activity in the Notch, Wnt, and FGF pathways forms the so-called segmentation clock, which determines the timing of somite formation.
Our work has shown that critical information for periodic segmentation is encoded not simply in the oscillations themselves, but in the relative timing between Wnt and Notch signalling oscillations (Sonnen et al. 2018). Using single-cell tracking in growing mouse embryos, we also found that coupling of cell proliferation to these signalling oscillations ensure robust somite scaling (preprint).
To investigate these mechanisms, we use both in vivo models and advanced in vitro systems. For early development, we study blastocysts and blastoids to explore how signalling dynamics guide the earliest steps of embryogenesis, while gastruloids allow us to model complex processes such as somitogenesis.
Together, these approaches help us uncover how dynamic signalling controls tissue patterning and timing during embryonic development, and provide insights into how disruptions in these processes may contribute to disease.
In adult tissues, signalling pathways regulate cell turnover and differentiation to maintain homeostasis. A well-studied example is the small intestine, where key pathways controlling stem cell renewal and differentiation have been identified. Yet, the role of signalling dynamics in these processes is still largely unknown.
The development of organoid cultures now allows us to grow adult tissues ex vivo, providing a controlled system to study dynamic regulation. By combining organoids with dynamic signalling reporters, real-time imaging, and microfluidic-based perturbations, we can dissect how signalling dynamics govern tissue homeostasis and regeneration.
Our recent preprint demonstrates that these tools allow precise monitoring and manipulation of signalling pathways in organoid cultures, revealing how the timing and coordination of signals control tissue maintenance and how disruptions can contribute to cancer.
Signalling pathways regulate a wide range of processes in the body, from embryonic development to tissue regeneration and homeostasis. Mutations or misregulation of these pathways can lead to developmental disorders or diseases such as cancer.
In our lab, we study how changes in signalling dynamics contribute to cancer development and explore whether these dynamic properties can be targeted for therapy. With support from the KWF Dutch Cancer Society, we are investigating how alterations in signalling timing and coordination drive tumor formation and progression. By combining advanced imaging, organoid models, and precise pathway perturbations, we aim to uncover new strategies to intervene in cancer at the level of temporal and spatial signal control.
Tomas E. J. C. Noordzij*, Martina Celotti*, Ruben van Esch, Lisa Sackmann, Adriana Martìnez-Silgado, Franka de Jong, Hiromune Eto, Harry Begthel, Jeroen Korving, Theresa M. Sommer, Gaby S. Steba, Nicolas Rivron, Esther B. Baart, Johan H. van Es, Hans Clevers# and Katharina F. Sonnen#
2025
preprint
Wilke H. M. Meijer*, Virginia Andrade*, Suzan Stelloo*, Wouter M. Thomas, Marek J. van Oostrom, Eveline F. Ilcken, Kim T. J. Peters, Michiel Vermeulen# and Katharina F. Sonnen#
Marek J. van Oostrom, Yuting I. Li, Wilke H. M. Meijer, Tomas E. J. C. Noordzij, Charis Fountas, Erika Timmers, Jeroen Korving, Wouter M. Thomas, Benjamin D. Simons and Katharina F. Sonnen#
Weterings* SDC, Eto* H, de Leede J, Giladi A, Hoekstra ME, Beijk WF, Liefting EJM, van den Anker KB, van Rheenen J, van Oudenaarden A and Sonnen KF#
2024
Stelloo, S., Alejo-Vinogradova, M. T., van Gelder, C. A. G. H., Zijlmans, D. W., van Oostrom, M. J., Valverde, J. M., Lamers, L. A., Rus, T., Sobrevals Alcaraz, P., Schäfers, T., Furlan, C., Jansen, P. W. T. C., Baltissen, M. P. A., Sonnen, K. F., Burgering, B., Altelaar, M. A. F. M., Vos, H. R. & Vermeulen#, M.
El Azhar, Y., Schulthess, P., van Oostrom, M. J., Weterings, S. D. C., Meijer, W. H. M., Tsuchida-Straeten, N., Thomas, W. M., Bauer, M. & Sonnen#, K. F.
Sonnen, K. F. & Janda, C. Y.
2021
van Oostrom, M. J., Meijer, W. H. M. & Sonnen#, K. F.
Gupta, A., Lutolf#, M. P., Hughes#, A. J. & Sonnen#, K. F.
Weterings, S. D. C., van Oostrom, M. J. & Sonnen#, K. F.
15 J
SC v d Brink, A Alemany, V van Batenburg, N Moris, M Blotenburg, J Vivié, P Baillie-Johnson, J Nichols, KF Sonnen, A Martinez Arias, A v Oudenaarden
Download|2020
V v Batenburg, SC vd Brink, M Blotenburg, A Alemany, N Moris, P Baillie-Johnson, Y el Azhar, KF Sonnen, A Martinez Arias, A v Oudenaarden
Sonnen KF, Merten CA
Download|
Sonnen KF, Lauschke V, Uraji J, Falk H J, Petersen Y, Funk MC, Beaupeux M, François P, Merten CA and Aulehla A.
Download|2018
Bulusu V, Prior N, Snaebjornsson MT, Kuehne A, Sonnen KF, Kress J, Stein F, Schultz C, Sauer U and Aulehla A.
Download|2017
Sonnen KF and Aulehla A.
Download|2014
Sonnen KF, Gabryjonczyk AM, Anselm E, Stierhof YD and Nigg EA.
Download|2013
Sonnen KF, Schermelleh L, Leonhardt H, Nigg EA
Ina is senior group leader at the Hubrecht Institute. Her group studies how biological information is robustly transmitted via signalling pathway dynamics in multicellular systems. They focus on the role of signalling pathway dynamics (1) during development using mouse somitogenesis as model system and (2) during tissue homeostasis using intestinal organoids as model system. The Sonnen group uses techniques to perturb and quantitatively analyse the dynamics of signalling pathways. They have established a microfluidic system to dynamically modulate intercellular signalling in multicellular systems. In addition, they complement those tools with biochemical and cell biological techniques to unravel the mechanism of dynamic signal encoding at the molecular level.
Scientific training and positions
2025 ERC Consolidator Grant 2025 Senior group leader 2019 Recipient of an ERC Starting Grant 2018 Group leader at the Hubrecht Institute from September 2013-2018 Postdoc in the groups of Alexander Aulehla and Christoph Merten, European Molecular Biology Laboratory, Heidelberg, Germany 2007-2012 PhD in the group of Erich Nigg at the Max-Planck-Institute of Biochemistry, Martinsried, Germany and Biozentrum, University of Basel, Switzerland Studies of biochemistry and molecular biology
Read less
Grants and fellowships
Contact
Laboratory website
Bluesky
Group Leader
Technician
Postdoc
PhD Student
Student
Show all group members
We currently have projects available for PhD students and postdoctoral researchers. If you are interested in joining our group, please email Ina Sonnen with a cover letter, CV, academic transcripts, and the contact details of 2–3 references.
We are currently looking for a PhD student or postdoctoral researcher to join our team at the interface of experimental biology and theory, modelling, and data analysis. The ideal candidate is excited about integrating experiments with quantitative and computational approaches to understand complex biological systems.
