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Brückner DB, Tkačik G. Information content and optimization of self-organized developmental systems. Proc Natl Acad Sci U S A 2024; 121:e2322326121. [PMID: 38819997 PMCID: PMC11161761 DOI: 10.1073/pnas.2322326121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/27/2024] [Indexed: 06/02/2024] Open
Abstract
A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction-diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes.
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Affiliation(s)
- David B. Brückner
- Institute of Science and Technology Austria, AT-3400Klosterneuburg, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, AT-3400Klosterneuburg, Austria
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2
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Lee HC, Oliveira NMM, Hastings C, Baillie-Benson P, Moverley AA, Lu HC, Zheng Y, Wilby EL, Weil TT, Page KM, Fu J, Moris N, Stern CD. Regulation of long-range BMP gradients and embryonic polarity by propagation of local calcium-firing activity. Nat Commun 2024; 15:1463. [PMID: 38368410 PMCID: PMC10874436 DOI: 10.1038/s41467-024-45772-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/02/2024] [Indexed: 02/19/2024] Open
Abstract
Many amniote vertebrate species including humans can form identical twins from a single embryo, but this only occurs rarely. It has been suggested that the primitive-streak-forming embryonic region emits signals that inhibit streak formation elsewhere but the signals involved, how they are transmitted and how they act has not been elucidated. Here we show that short tracks of calcium firing activity propagate through extraembryonic tissue via gap junctions and prevent ectopic primitive streak formation in chick embryos. Cross-regulation of calcium activity and an inhibitor of primitive streak formation (Bone Morphogenetic Protein, BMP) via NF-κB and NFAT establishes a long-range BMP gradient spanning the embryo. This mechanism explains how embryos of widely different sizes can maintain positional information that determines embryo polarity. We provide evidence for similar mechanisms in two different human embryo models and in Drosophila, suggesting an ancient evolutionary origin.
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Affiliation(s)
- Hyung Chul Lee
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
- School of Biological Sciences and Technology, College of Natural Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju, 61186, Korea.
| | - Nidia M M Oliveira
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- College of Professional Services, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Cato Hastings
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Adam A Moverley
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui-Chun Lu
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, Guy's Tower, London, SE1 9RT, UK
| | - Yi Zheng
- Departments of Mechanical Engineering, Biomedical Engineering, and Cell & Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA
- BioInspired Syracuse Institute for Materials and Living Systems, Syracuse University, Syracuse, NY, USA
| | - Elise L Wilby
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Karen M Page
- Department of Mathematics, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jianping Fu
- Departments of Mechanical Engineering, Biomedical Engineering, and Cell & Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Naomi Moris
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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Emig AA, Hansen M, Grimm S, Coarfa C, Lord ND, Williams MK. Temporal dynamics of BMP/Nodal ratio drive tissue-specific gastrulation morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579243. [PMID: 38370754 PMCID: PMC10871350 DOI: 10.1101/2024.02.06.579243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Anteroposterior (AP) elongation of the vertebrate body plan is driven by convergence and extension (C&E) gastrulation movements in both the mesoderm and neuroectoderm, but how or whether molecular regulation of C&E differs between tissues remains an open question. Using a zebrafish explant model of AP axis extension, we show that C&E of the neuroectoderm and mesoderm can be uncoupled ex vivo, and that morphogenesis of individual tissues results from distinct morphogen signaling dynamics. Using precise temporal manipulation of BMP and Nodal signaling, we identify a critical developmental window during which high or low BMP/Nodal ratios induce neuroectoderm- or mesoderm-driven C&E, respectively. Increased BMP activity similarly enhances C&E specifically in the ectoderm of intact zebrafish gastrulae, highlighting the in vivo relevance of our findings. Together, these results demonstrate that temporal dynamics of BMP and Nodal morphogen signaling activate distinct morphogenetic programs governing C&E gastrulation movements within individual tissues.
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Affiliation(s)
- Alyssa A Emig
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Megan Hansen
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Sandra Grimm
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Cristian Coarfa
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Nathan D Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA
| | - Margot Kossmann Williams
- Center for Precision Environmental Health and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Previous address: Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO
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4
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Abdel Fattah AR, Grebenyuk S, de Rooij LPMH, Salmon I, Ranga A. Neuroepithelial organoid patterning is mediated by a neighborhood watch mechanism. Cell Rep 2023; 42:113334. [PMID: 38511989 DOI: 10.1016/j.celrep.2023.113334] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/29/2023] [Accepted: 10/10/2023] [Indexed: 03/22/2024] Open
Abstract
During epithelial tissue patterning, morphogens operate across multiple length scales to instruct cell identities. However, how cell fate changes are coordinated over these scales to establish spatial organization remains poorly understood. Here, we use human neural tube organoids as models of epithelial patterning and develop an in silico approach to define conditions permissive to patterning. By systematically varying morphogen position, diffusivity, and fate-inducing concentration levels, we show that cells follow a "neighborhood watch" (NW) mechanism that is deterministically dictated by initial morphogen source positions, reflecting scale-invariant in vitro phenotypes. We define how the frequency and local bias of morphogen sources stabilize pattern orientation. The model predicts enhanced patterning through floor plate inhibition, and receptor-ligand interaction analysis of single-cell RNA sequencing (scRNA-seq) data identifies wingless-related integration site (WNT) and bone morphogenic protein (BMP) as inhibition modulators, which we validate in vitro. These results suggest that developing neuroepithelia employ NW-based mechanisms to organize morphogen sources, define cellular identity, and establish patterns.
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Affiliation(s)
- Abdel Rahman Abdel Fattah
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Sergei Grebenyuk
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Laura P M H de Rooij
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Idris Salmon
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium
| | - Adrian Ranga
- Laboratory of Bioengineering and Morphogenesis, Biomechanics Section, Department of Mechanical Engineering, KU Leuven, Leuven, Belgium.
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Abstract
Metazoan embryos develop from a single cell into three-dimensional structured organisms while groups of genetically identical cells attain specialized identities. Cells of the developing embryo both create and accurately interpret morphogen gradients to determine their positions and make specific decisions in response. Here, we first cover intellectual roots of morphogen and positional information concepts. Focusing on animal embryos, we then provide a review of current understanding on how morphogen gradients are established and how their spans are controlled. Lastly, we cover how gradients evolve in time and space during development, and how they encode information to control patterning. In sum, we provide a list of patterning principles for morphogen gradients and review recent advances in quantitative methodologies elucidating information provided by morphogens.
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Affiliation(s)
- M. Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ertuğrul M. Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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Giri R, Brady S, Papadopoulos DK, Carthew RW. Single-cell Senseless protein analysis reveals metastable states during the transition to a sensory organ fate. iScience 2022; 25:105097. [PMID: 36157584 PMCID: PMC9494244 DOI: 10.1016/j.isci.2022.105097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/02/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Cell fate decisions can be envisioned as bifurcating dynamical systems, and the decision that Drosophila cells make during sensory organ differentiation has been described as such. We extended these studies by focusing on the Senseless protein which orchestrates sensory cell fate transitions. Wing cells contain intermediate Senseless numbers before their fate transition, after which they express much greater numbers of Senseless molecules as they differentiate. However, the dynamics are inconsistent with it being a simple bistable system. Cells with intermediate Senseless are best modeled as residing in four discrete states, each with a distinct protein number and occupying a specific region of the tissue. Although the states are stable over time, the number of molecules in each state vary with time. The fold change in molecule number between adjacent states is invariant and robust to absolute protein number variation. Thus, cells transitioning to sensory fates exhibit metastability with relativistic properties.
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Affiliation(s)
- Ritika Giri
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Shannon Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Dimitrios K. Papadopoulos
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institute, 17176 Stockholm, Sweden,Department of Biology, University of Crete, Voutes University Campus, Heraklion, Crete 70013, Greece
| | - Richard W. Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA,Corresponding author
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Lee HC, Hastings C, Stern CD. The extra-embryonic area opaca plays a role in positioning the primitive streak of the early chick embryo. Development 2022; 149:275748. [PMID: 35723262 PMCID: PMC9270967 DOI: 10.1242/dev.200303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Abstract
Classical studies have established that the marginal zone, a ring of extra-embryonic epiblast immediately surrounding the embryonic epiblast (area pellucida) of the chick embryo, is important in setting embryonic polarity by positioning the primitive streak, the site of gastrulation. The more external extra-embryonic region (area opaca) was thought to have only nutritive and support functions. Using experimental embryology approaches, this study reveals three separable functions for this outer region. First, juxtaposition of the area opaca directly onto the area pellucida induces a new marginal zone from the latter; this induced domain is entirely posterior in character. Second, ablation and grafting experiments using an isolated anterior half of the blastoderm and pieces of area opaca suggest that the area opaca can influence the polarity of the adjacent marginal zone. Finally, we show that the loss of the ability of such isolated anterior half-embryos to regulate (re-establish polarity spontaneously) at the early primitive streak stage can be rescued by replacing the area opaca by one from a younger stage. These results uncover new roles of chick extra-embryonic tissues in early development. Summary: Two adjacent extra-embryonic tissues, the area opaca and the marginal zone, interact to influence the polarity of the early chick embryo.
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Affiliation(s)
- Hyung Chul Lee
- University College London Department of Cell and Developmental Biology , , Gower Street, London WC1E 6BT , UK
| | - Cato Hastings
- University College London Department of Cell and Developmental Biology , , Gower Street, London WC1E 6BT , UK
| | - Claudio D. Stern
- University College London Department of Cell and Developmental Biology , , Gower Street, London WC1E 6BT , UK
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Lee HC, Oliveira NMM, Stern CD. Exploring the roles of FGF/MAPK and cVG1/GDF signalling on mesendoderm induction and convergent extension during chick primitive streak formation. Dev Genes Evol 2022; 232:115-123. [PMID: 36149507 PMCID: PMC9691481 DOI: 10.1007/s00427-022-00696-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/13/2022] [Indexed: 01/30/2023]
Abstract
During primitive streak formation in the chick embryo, cells undergo mesendoderm specification and convergent extension at the same time and in the same cells. Previous work has implicated cVG1 (GDF3) as a key factor for induction of primitive streak identity and positioning the primitive streak, whereas FGF signalling was implicated in regulating cell intercalation via regulation of components of the WNT-planar cell polarity (PCP) pathway. FGF has also been reported to be able to induce a primitive streak (but lacking the most axial derivatives such as notochord/prechordal mesendoderm). These signals emanate from different cell populations in the embryo, so how do they interact to ensure that the same cells undergo both cell intercalation and acquire primitive streak identity? Here we begin to address this question by examining in more detail the ability of the two classes of signals in regulating the two developmental events. Using misexpression of inducers and/or exposure to inhibitors and in situ hybridisation, we study how these two signals regulate expression of Brachyury (TBXT) and PRICKLE1 as markers for the primitive streak and the PCP, respectively. We find that both signals can induce both properties, but while FGF seems to be required for induction of the streak by cVG1, it is not necessary for induction of PRICKLE1. The results are consistent with cVG1 being a common regulator for both primitive streak identity and the initiation of convergent extension that leads to streak elongation.
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Affiliation(s)
- Hyung Chul Lee
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Nidia M. M. Oliveira
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Claudio D. Stern
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT UK
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