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Küchenhoff L, Lukas P, Metz-Zumaran C, Rothhaar P, Ruggieri A, Lohmann V, Höfer T, Stanifer ML, Boulant S, Talemi SR, Graw F. Extended methods for spatial cell classification with DBSCAN-CellX. Sci Rep 2023; 13:18868. [PMID: 37914751 PMCID: PMC10620226 DOI: 10.1038/s41598-023-45190-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Local cell densities and positioning within cellular monolayers and stratified epithelia have important implications for cell interactions and the functionality of various biological processes. To analyze the relationship between cell localization and tissue physiology, density-based clustering algorithms, such as DBSCAN, allow for a detailed characterization of the spatial distribution and positioning of individual cells. However, these methods rely on predefined parameters that influence the outcome of the analysis. With varying cell densities in cell cultures or tissues impacting cell sizes and, thus, cellular proximities, these parameters need to be carefully chosen. In addition, standard DBSCAN approaches generally come short in appropriately identifying individual cell positions. We therefore developed three extensions to the standard DBSCAN-algorithm that provide: (i) an automated parameter identification to reliably identify cell clusters, (ii) an improved identification of cluster edges; and (iii) an improved characterization of the relative positioning of cells within clusters. We apply our novel methods, which are provided as a user-friendly OpenSource-software package (DBSCAN-CellX), to cellular monolayers of different cell lines. Thereby, we show the importance of the developed extensions for the appropriate analysis of cell culture experiments to determine the relationship between cell localization and tissue physiology.
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Affiliation(s)
- Leonie Küchenhoff
- BioQuant-Center for Quantitative Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Pascal Lukas
- BioQuant-Center for Quantitative Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Camila Metz-Zumaran
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
- Department of Infectious Diseases, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Paul Rothhaar
- Department of Infectious Diseases, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Megan L Stanifer
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
- Department of Infectious Diseases, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Steeve Boulant
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL, USA
- Department of Infectious Diseases, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
| | - Soheil Rastgou Talemi
- Department of Infectious Diseases, Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, 69120, Heidelberg, Germany
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frederik Graw
- BioQuant-Center for Quantitative Biology, Heidelberg University, 69120, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing, Heidelberg University, 69120, Heidelberg, Germany.
- Department of Medicine 5, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 12, 91054, Erlangen, Germany.
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2
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Virtual cells in a virtual microenvironment recapitulate early development-like patterns in human pluripotent stem cell colonies. Stem Cell Reports 2022; 18:377-393. [PMID: 36332630 PMCID: PMC9859929 DOI: 10.1016/j.stemcr.2022.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
The mechanism by which morphogenetic signals engage the regulatory networks responsible for early embryonic tissue patterning is incompletely understood. Here, we developed a minimal gene regulatory network (GRN) model of human pluripotent stem cell (hPSC) lineage commitment and embedded it into "cellular" agents that respond to a dynamic morphogenetic signaling microenvironment. Simulations demonstrated that GRN wiring had significant non-intuitive effects on tissue pattern order, composition, and dynamics. Experimental perturbation of GRN connectivities supported model predictions and demonstrated the role of OCT4 as a master regulator of peri-gastrulation fates. Our so-called GARMEN strategy provides a multiscale computational platform to understand how single-cell-based regulatory interactions scale to tissue domains. This foundation provides new opportunities to simulate the impact of network motifs on normal and aberrant tissue development.
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3
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Prochazka L, Michaels YS, Lau C, Jones RD, Siu M, Yin T, Wu D, Jang E, Vázquez‐Cantú M, Gilbert PM, Kaul H, Benenson Y, Zandstra PW. Synthetic gene circuits for cell state detection and protein tuning in human pluripotent stem cells. Mol Syst Biol 2022; 18:e10886. [PMID: 36366891 PMCID: PMC9650275 DOI: 10.15252/msb.202110886] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
During development, cell state transitions are coordinated through changes in the identity of molecular regulators in a cell type‐ and dose‐specific manner. The ability to rationally engineer such transitions in human pluripotent stem cells (hPSC) will enable numerous applications in regenerative medicine. Herein, we report the generation of synthetic gene circuits that can detect a desired cell state using AND‐like logic integration of endogenous miRNAs (classifiers) and, upon detection, produce fine‐tuned levels of output proteins using an miRNA‐mediated output fine‐tuning technology (miSFITs). Specifically, we created an “hPSC ON” circuit using a model‐guided miRNA selection and circuit optimization approach. The circuit demonstrates robust PSC‐specific detection and graded output protein production. Next, we used an empirical approach to create an “hPSC‐Off” circuit. This circuit was applied to regulate the secretion of endogenous BMP4 in a state‐specific and fine‐tuned manner to control the composition of differentiating hPSCs. Our work provides a platform for customized cell state‐specific control of desired physiological factors in hPSC, laying the foundation for programming cell compositions in hPSC‐derived tissues and beyond.
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Affiliation(s)
- Laura Prochazka
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Yale S Michaels
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Charles Lau
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Ross D Jones
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Mona Siu
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
| | - Ting Yin
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Diana Wu
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Esther Jang
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
| | - Mercedes Vázquez‐Cantú
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biosystems Science and Engineering (D‐BSSE) Basel Switzerland
| | - Penney M Gilbert
- Institute of Biomedical Engineering (BME) University of Toronto Toronto ON Canada
- Donnelly Centre for Cellular & Biomolecular Research University of Toronto Toronto ON Canada
- Department of Cell and Systems Biology University of Toronto Toronto ON Canada
| | - Himanshu Kaul
- School of Engineering University of Leicester Leicester UK
- Department of Respiratory Sciences University of Leicester Leicester UK
| | - Yaakov Benenson
- Swiss Federal Institute of Technology (ETH) Zürich, Department of Biosystems Science and Engineering (D‐BSSE) Basel Switzerland
| | - Peter W Zandstra
- Michael Smith Laboratories University of British Columbia Vancouver BC Canada
- School of Biomedical Engineering University of British Columbia Vancouver BC Canada
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4
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Heydari T, A. Langley M, Fisher CL, Aguilar-Hidalgo D, Shukla S, Yachie-Kinoshita A, Hughes M, M. McNagny K, Zandstra PW. IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data. PLoS Comput Biol 2022; 18:e1009907. [PMID: 35213533 PMCID: PMC8906617 DOI: 10.1371/journal.pcbi.1009907] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 03/09/2022] [Accepted: 02/08/2022] [Indexed: 01/03/2023] Open
Abstract
The increasing availability of single-cell RNA-sequencing (scRNA-seq) data from various developmental systems provides the opportunity to infer gene regulatory networks (GRNs) directly from data. Herein we describe IQCELL, a platform to infer, simulate, and study executable logical GRNs directly from scRNA-seq data. Such executable GRNs allow simulation of fundamental hypotheses governing developmental programs and help accelerate the design of strategies to control stem cell fate. We first describe the architecture of IQCELL. Next, we apply IQCELL to scRNA-seq datasets from early mouse T-cell and red blood cell development, and show that the platform can infer overall over 74% of causal gene interactions previously reported from decades of research. We will also show that dynamic simulations of the generated GRN qualitatively recapitulate the effects of known gene perturbations. Finally, we implement an IQCELL gene selection pipeline that allows us to identify candidate genes, without prior knowledge. We demonstrate that GRN simulations based on the inferred set yield results similar to the original curated lists. In summary, the IQCELL platform offers a versatile tool to infer, simulate, and study executable GRNs in dynamic biological systems.
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Affiliation(s)
- Tiam Heydari
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew A. Langley
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Cynthia L. Fisher
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Aguilar-Hidalgo
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shreya Shukla
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
- Notch Therapeutics, Vancouver, British Columbia, Canada
| | - Ayako Yachie-Kinoshita
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Michael Hughes
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Kelly M. McNagny
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
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5
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Abstract
Micropatterning encompasses a set of methods aimed at precisely controlling the spatial distribution of molecules onto the surface of materials. Biologists have borrowed the idea and adapted these methods, originally developed for electronics, to impose physical constraints on biological systems with the aim of addressing fundamental questions across biological scales from molecules to multicellular systems. Here, I approach this topic from a developmental biologist's perspective focusing specifically on how and why micropatterning has gained in popularity within the developmental biology community in recent years. Overall, this Primer provides a concise overview of how micropatterns are used to study developmental processes and emphasises how micropatterns are a useful addition to the developmental biologist's toolbox.
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Affiliation(s)
- Guillaume Blin
- Institute for Regeneration and Repair, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, 5 Little France Drive, Edinburgh BioQuarter, Edinburgh EH16 4UU, UK
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6
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Dziedzicka D, Tewary M, Keller A, Tilleman L, Prochazka L, Östblom J, Couvreu De Deckersberg E, Markouli C, Franck S, Van Nieuwerburgh F, Spits C, Zandstra PW, Sermon K, Geens M. Endogenous suppression of WNT signalling in human embryonic stem cells leads to low differentiation propensity towards definitive endoderm. Sci Rep 2021; 11:6137. [PMID: 33731744 PMCID: PMC7969605 DOI: 10.1038/s41598-021-85447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
Low differentiation propensity towards a targeted lineage can significantly hamper the utility of individual human pluripotent stem cell (hPSC) lines in biomedical applications. Here, we use monolayer and micropatterned cell cultures, as well as transcriptomic profiling, to investigate how variability in signalling pathway activity between human embryonic stem cell lines affects their differentiation efficiency towards definitive endoderm (DE). We show that endogenous suppression of WNT signalling in hPSCs at the onset of differentiation prevents the switch from self-renewal to DE specification. Gene expression profiling reveals that this inefficient switch is reflected in NANOG expression dynamics. Importantly, we demonstrate that higher WNT stimulation or inhibition of the PI3K/AKT signalling can overcome the DE commitment blockage. Our findings highlight that redirection of the activity of Activin/NODAL pathway by WNT signalling towards mediating DE fate specification is a vulnerable spot, as disruption of this process can result in poor hPSC specification towards DE.
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Affiliation(s)
- Dominika Dziedzicka
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mukul Tewary
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada ,grid.13097.3c0000 0001 2322 6764Centre for Stem Cells and Regenerative Medicine, King’s College London, Guy’s Hospital, London, SE1 9RT UK
| | - Alexander Keller
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Laurentijn Tilleman
- grid.5342.00000 0001 2069 7798Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura Prochazka
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Joel Östblom
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada
| | - Edouard Couvreu De Deckersberg
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Christina Markouli
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Silvie Franck
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Filip Van Nieuwerburgh
- grid.5342.00000 0001 2069 7798Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Claudia Spits
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Peter W. Zandstra
- grid.17063.330000 0001 2157 2938Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON M5S 3E1 Canada ,grid.17091.3e0000 0001 2288 9830Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada ,grid.17091.3e0000 0001 2288 9830School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Karen Sermon
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mieke Geens
- grid.8767.e0000 0001 2290 8069Research Group Reproduction and Genetics, Vrije Universiteit Brussel, 1090 Brussels, Belgium
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7
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Morgani SM, Hadjantonakis AK. Signaling regulation during gastrulation: Insights from mouse embryos and in vitro systems. Curr Top Dev Biol 2019; 137:391-431. [PMID: 32143751 DOI: 10.1016/bs.ctdb.2019.11.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gastrulation is the process whereby cells exit pluripotency and concomitantly acquire and pattern distinct cell fates. This is driven by the convergence of WNT, BMP, Nodal and FGF signals, which are tightly spatially and temporally controlled, resulting in regional and stage-specific signaling environments. The combination, level and duration of signals that a cell is exposed to, according its position within the embryo and the developmental time window, dictates the fate it will adopt. The key pathways driving gastrulation exhibit complex interactions, which are difficult to disentangle in vivo due to the complexity of manipulating multiple signals in parallel with high spatiotemporal resolution. Thus, our current understanding of the signaling dynamics regulating gastrulation is limited. In vitro stem cell models have been established, which undergo organized cellular differentiation and patterning. These provide amenable, simplified, deconstructed and scalable models of gastrulation. While the foundation of our understanding of gastrulation stems from experiments in embryos, in vitro systems are now beginning to reveal the intricate details of signaling regulation. Here we discuss the current state of knowledge of the role, regulation and dynamic interaction of signaling pathways that drive mouse gastrulation.
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Affiliation(s)
- Sophie M Morgani
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge, United Kingdom.
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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8
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Tewary M, Dziedzicka D, Ostblom J, Prochazka L, Shakiba N, Heydari T, Aguilar-Hidalgo D, Woodford C, Piccinini E, Becerra-Alonso D, Vickers A, Louis B, Rahman N, Danovi D, Geens M, Watt FM, Zandstra PW. High-throughput micropatterning platform reveals Nodal-dependent bisection of peri-gastrulation-associated versus preneurulation-associated fate patterning. PLoS Biol 2019; 17:e3000081. [PMID: 31634368 PMCID: PMC6822778 DOI: 10.1371/journal.pbio.3000081] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/31/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
In vitro models of postimplantation human development are valuable to the fields of regenerative medicine and developmental biology. Here, we report characterization of a robust in vitro platform that enabled high-content screening of multiple human pluripotent stem cell (hPSC) lines for their ability to undergo peri-gastrulation-like fate patterning upon bone morphogenetic protein 4 (BMP4) treatment of geometrically confined colonies and observed significant heterogeneity in their differentiation propensities along a gastrulation associable and neuralization associable axis. This cell line-associated heterogeneity was found to be attributable to endogenous Nodal expression, with up-regulation of Nodal correlated with expression of a gastrulation-associated gene profile, and Nodal down-regulation correlated with a preneurulation-associated gene profile expression. We harness this knowledge to establish a platform of preneurulation-like fate patterning in geometrically confined hPSC colonies in which fates arise because of a BMPs signalling gradient conveying positional information. Our work identifies a Nodal signalling-dependent switch in peri-gastrulation versus preneurulation-associated fate patterning in hPSC cells, provides a technology to robustly assay hPSC differentiation outcomes, and suggests conserved mechanisms of organized fate specification in differentiating epiblast and ectodermal tissues.
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Affiliation(s)
- Mukul Tewary
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Dominika Dziedzicka
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joel Ostblom
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura Prochazka
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nika Shakiba
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Tiam Heydari
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Aguilar-Hidalgo
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis Woodford
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Elia Piccinini
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - David Becerra-Alonso
- Department of Quantitative Methods, Universidad Loyola Andalucia, Sevilla, Spain
| | - Alice Vickers
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Blaise Louis
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Nafees Rahman
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Davide Danovi
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Mieke Geens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fiona M. Watt
- Centre for Stem Cells & Regenerative Medicine, King's College London, London, United Kingdom
| | - Peter W. Zandstra
- Institute of Biomaterials and Biomedical Engineering (IBBME), University of Toronto, Toronto, Ontario, Canada
- Collaborative Program in Developmental Biology, University of Toronto, Toronto, Ontario, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
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