Periodic Reporting for period 4 - SelforganisingEmbryo (Self-organisation across the scales in early mammalian development)
Okres sprawozdawczy: 2021-06-01 do 2023-02-28
A defining feature of living systems is the ability to self-organise form and pattern with function. This project aims to understand the design principle of this multi-cellular self-organisation using early mouse embryos as a model system. In mammals eggs lack polarity and symmetry is broken during early embryogenesis. This results in segregation of the first three cell lineages in the blastocyst. While gene expression changes are extensively studied, how molecular and physical signals are dynamically coupled for self-organised morphogenesis and patterning remains poorly understood. We aim to identify the mechanisms of feedback between cell polarity, mechanics and gene expression across sub-cellular to whole organismal scales that underlie tissue self-organisation. To this end we adopt an interdisciplinary approach that combines biology, physics and mathematics to measure molecular and physical parameters, build a model integrating them in a reduced system, and quantitatively manipulate the parameters to verify the model. We build up complexities from the single-cell level to patterning of three cell types with fluid-filled cavities in the mouse blastocyst. This study sets a paradigm for studying multi-cellular self-organisation.
Overall, the project successfully completed all four scheduled Projects. In addition, we developed new ex vivo systems to study peri-implantation mouse development following the blastocyst formation. The results of the four scheduled Projects are published in a total of 4 research papers and 2 more manuscripts are currently under review and deposited in bioRxiv. In addition, the extended-part of the project was published as one research paper (Ichikawa et al. 2022) and another is in press at EMBO J (Bondarenko et al. 2022 bioRxiv). Furthermore, new techniques developed in Projects, such as measurement of the fluid pressure, have been widely exploited by other scientists, part of which were published in 2 research papers as a result of collaboration (Yang et al. 2021; Stokkermans et al. 2022). These publications – all open access and accompanied by press release at the host institute – as well as numerous presentations we have made during this period at conferences, lectures and seminars effectively disseminated the results of our Projects not only to scientific communities and trainee but also to the broader public.
Specifically, for Project 1 (Apical domain assembly – self-organisation at the single-cell level), we developed an experimental system in which we can study the mechanisms underlying apical domain assembly and the possible role of cortical contractility. For Project 2 (Inside-outside patterning – self-organisation at the two-cell level), we developed a new reduced experimental system in which to study the role of cell adhesion, contractility and the apical domain in the inside – outside fate specification and patterning. We then combined the outcome of WP1 and WP2 for publication. In this research paper (Kim et al. 2022), we discovered a key role of integrin-extra-cellular-matrix (ECM) adhesion in specification of the inner cell fates (the inner cell mass, ICM, and epiblast, EPI) in pre-implantation mouse embryos.
For Project 3 (Blastocyst patterning – multi-cellular self-organisation with fluid cavities), we discovered new roles of fluid cavities in the mouse blastocyst: controlling embryo size and facilitating cell fate specification and sorting. First, we showed that interplay between luminal pressure and cell and tissue mechanics controls blastocyst size and call fate (Chan et al. 2019). We also showed that lumen expansion facilitates cell fate specification and cell sorting in the blastocyst. (Ryan et al. 2019). Furthermore, we discovered that cell shape and the apical domain compete to determine cell division orientation and this ensures robust cell allocation and patterning (Niwayama et al. 2019). In this study we developed automatic image processing pipeline, which formed a basis for many image analyses for the following studies in my group. Finally, we have recently completed another study investigating the mechanisms of ICM patterning in the blastocyst that involves sorting of salt-and-pepper EPI and primitive endoderm (PrE) cells. Combined with biophysical measurements and simulation, we present a comprehensive mechanism underlying the sorting driven by the apical polarization, guided through a gradient of ECM deposition by PrE cells, which is optimized for the ICM size and geometry across mammals (Moghe et al. 2023 bioRxiv).
For Project 4 (in silico reconstitution and design engineering of the blastocyst), we developed an AI-based image processing pipeline to automatically track cell lineage and segment cell membrane, in collaboration with the Kreshuk lab (EMBL), to establish the basis for computational analysis and theoretical modeling. Using this tool, we studied the role of spatial and temporal variabilities in robust development of early mouse embryos. Mammalian embryos exhibit intrinsic stochasticity during the complex morphogenetic events establishing form and function. Yet, they are remarkably robust. Due to technical and conceptual challenges, our understanding of the nature and role of spatio-temporal variabilities is limited. In this study (Fabreges et al. 2023 bioRxiv), we show how stochasticity has a counterintuitive role in granting robustness in early embryogenesis.
Specifically, for Project 1 (Apical domain assembly – self-organisation at the single-cell level), we developed an experimental system in which we can study the mechanisms underlying apical domain assembly and the possible role of cortical contractility. For Project 2 (Inside-outside patterning – self-organisation at the two-cell level), we developed a new reduced experimental system in which to study the role of cell adhesion, contractility and the apical domain in the inside – outside fate specification and patterning. We then combined the outcome of WP1 and WP2 for publication. In this research paper (Kim et al. 2022), we discovered a key role of integrin-extra-cellular-matrix (ECM) adhesion in specification of the inner cell fates (the inner cell mass, ICM, and epiblast, EPI) in pre-implantation mouse embryos.
For Project 3 (Blastocyst patterning – multi-cellular self-organisation with fluid cavities), we discovered new roles of fluid cavities in the mouse blastocyst: controlling embryo size and facilitating cell fate specification and sorting. First, we showed that interplay between luminal pressure and cell and tissue mechanics controls blastocyst size and call fate (Chan et al. 2019). We also showed that lumen expansion facilitates cell fate specification and cell sorting in the blastocyst. (Ryan et al. 2019). Furthermore, we discovered that cell shape and the apical domain compete to determine cell division orientation and this ensures robust cell allocation and patterning (Niwayama et al. 2019). In this study we developed automatic image processing pipeline, which formed a basis for many image analyses for the following studies in my group. Finally, we have recently completed another study investigating the mechanisms of ICM patterning in the blastocyst that involves sorting of salt-and-pepper EPI and primitive endoderm (PrE) cells. Combined with biophysical measurements and simulation, we present a comprehensive mechanism underlying the sorting driven by the apical polarization, guided through a gradient of ECM deposition by PrE cells, which is optimized for the ICM size and geometry across mammals (Moghe et al. 2023 bioRxiv).
For Project 4 (in silico reconstitution and design engineering of the blastocyst), we developed an AI-based image processing pipeline to automatically track cell lineage and segment cell membrane, in collaboration with the Kreshuk lab (EMBL), to establish the basis for computational analysis and theoretical modeling. Using this tool, we studied the role of spatial and temporal variabilities in robust development of early mouse embryos. Mammalian embryos exhibit intrinsic stochasticity during the complex morphogenetic events establishing form and function. Yet, they are remarkably robust. Due to technical and conceptual challenges, our understanding of the nature and role of spatio-temporal variabilities is limited. In this study (Fabreges et al. 2023 bioRxiv), we show how stochasticity has a counterintuitive role in granting robustness in early embryogenesis.
Our model of blastocyst size control (Chan et al. 2019) introduced a new parameter to the mechanistic model of tissue size control and morphogenesis: luminal pressure. This has a fundamental impact on understanding of development and regeneration in various systems, and resulted in a number of collaborations in which we measured luminal pressure in other tissues and organisms (Yang et al. 2021; Stokkermans et al. 2022).
Furthermore, we have developed new ex vivo systems to culture, live-image, measure and perturb biophysics of peri-implantation mouse development. Our study using the first method, 3D-geec, discovered a key role of biochemical and mechanical interactions between embryonic and extra-embryonic tissues during peri-implantation development (Ichikawa et al. 2022). The second method, 3E-uterus, revealed an essential role of dynamic embryo-uterus interaction in peri-implantation development (Bondarenko et al. 2022 in press and bioRxiv). These two methods and studies opened a new field to study molecular, cellular and biophysical mechanisms underlying peri-implantation mouse development, and their findings and new questions formed a basis for the next ERC AdG project, COORDINATION, to start from 2023.
Furthermore, we have developed new ex vivo systems to culture, live-image, measure and perturb biophysics of peri-implantation mouse development. Our study using the first method, 3D-geec, discovered a key role of biochemical and mechanical interactions between embryonic and extra-embryonic tissues during peri-implantation development (Ichikawa et al. 2022). The second method, 3E-uterus, revealed an essential role of dynamic embryo-uterus interaction in peri-implantation development (Bondarenko et al. 2022 in press and bioRxiv). These two methods and studies opened a new field to study molecular, cellular and biophysical mechanisms underlying peri-implantation mouse development, and their findings and new questions formed a basis for the next ERC AdG project, COORDINATION, to start from 2023.