1
|
Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron 2024; 112:2091-2111. [PMID: 38754415 DOI: 10.1016/j.neuron.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.
Collapse
Affiliation(s)
- Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Nuria Domínguez-Iturza
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Juliana R Brown
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
2
|
Manser CL, Perez-Carrasco R. A mathematical framework for measuring and tuning tempo in developmental gene regulatory networks. Development 2024; 151:dev202950. [PMID: 38780527 DOI: 10.1242/dev.202950] [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: 04/12/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Embryo development is a dynamic process governed by the regulation of timing and sequences of gene expression, which control the proper growth of the organism. Although many genetic programmes coordinating these sequences are common across species, the timescales of gene expression can vary significantly among different organisms. Currently, substantial experimental efforts are focused on identifying molecular mechanisms that control these temporal aspects. In contrast, the capacity of established mathematical models to incorporate tempo control while maintaining the same dynamical landscape remains less understood. Here, we address this gap by developing a mathematical framework that links the functionality of developmental programmes to the corresponding gene expression orbits (or landscapes). This unlocks the ability to find tempo differences as perturbations in the dynamical system that preserve its orbits. We demonstrate that this framework allows for the prediction of molecular mechanisms governing tempo, through both numerical and analytical methods. Our exploration includes two case studies: a generic network featuring coupled production and degradation, with a particular application to neural progenitor differentiation; and the repressilator. In the latter, we illustrate how altering the dimerisation rates of transcription factors can decouple the tempo from the shape of the resulting orbits. We conclude by highlighting how the identification of orthogonal molecular mechanisms for tempo control can inform the design of circuits with specific orbits and tempos.
Collapse
Affiliation(s)
- Charlotte L Manser
- Department of Life Sciences, Imperial College London, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Ruben Perez-Carrasco
- Department of Life Sciences, Imperial College London, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
3
|
Liberali P, Schier AF. The evolution of developmental biology through conceptual and technological revolutions. Cell 2024:S0092-8674(24)00632-9. [PMID: 38906136 DOI: 10.1016/j.cell.2024.05.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Developmental biology-the study of the processes by which cells, tissues, and organisms develop and change over time-has entered a new golden age. After the molecular genetics revolution in the 80s and 90s and the diversification of the field in the early 21st century, we have entered a phase when powerful technologies provide new approaches and open unexplored avenues. Progress in the field has been accelerated by advances in genomics, imaging, engineering, and computational biology and by emerging model systems ranging from tardigrades to organoids. We summarize how revolutionary technologies have led to remarkable progress in understanding animal development. We describe how classic questions in gene regulation, pattern formation, morphogenesis, organogenesis, and stem cell biology are being revisited. We discuss the connections of development with evolution, self-organization, metabolism, time, and ecology. We speculate how developmental biology might evolve in an era of synthetic biology, artificial intelligence, and human engineering.
Collapse
Affiliation(s)
- Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | | |
Collapse
|
4
|
Iwata R, Vanderhaeghen P. Metabolic mechanisms of species-specific developmental tempo. Dev Cell 2024:S1534-5807(24)00361-7. [PMID: 38906137 DOI: 10.1016/j.devcel.2024.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/27/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024]
Abstract
Development consists of a highly ordered suite of steps and transitions, like choreography. Although these sequences are often evolutionarily conserved, they can display species variations in duration and speed, thereby modifying final organ size or function. Despite their evolutionary significance, the mechanisms underlying species-specific scaling of developmental tempo have remained unclear. Here, we will review recent findings that implicate global cellular mechanisms, particularly intermediary and protein metabolism, as species-specific modifiers of developmental tempo. In various systems, from somitic cell oscillations to neuronal development, metabolic pathways display species differences. These have been linked to mitochondrial metabolism, which can influence the species-specific speed of developmental transitions. Thus, intermediary metabolic pathways regulate developmental tempo together with other global processes, including proteostasis and chromatin remodeling. By linking metabolism and the evolution of developmental trajectories, these findings provide opportunities to decipher how species-specific cellular timing can influence organism fitness.
Collapse
Affiliation(s)
- Ryohei Iwata
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium.
| |
Collapse
|
5
|
Diaz-Cuadros M. Mitochondrial metabolism and the continuing search for ultimate regulators of developmental rate. Curr Opin Genet Dev 2024; 86:102178. [PMID: 38461774 DOI: 10.1016/j.gde.2024.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The rate of embryonic development is a species-specific trait that depends on the properties of the intracellular environment, namely, the rate at which gene products flow through the central dogma of molecular biology. Although any given step in the production and degradation of gene products could theoretically be co-opted by evolution to modulate developmental speed, species are observed to accelerate or slow down all steps simultaneously. This suggests the rate of these molecular processes is jointly regulated by an upstream, ultimate factor. Mitochondrial metabolism was recently proposed to act as an ultimate regulator by controlling the pace of protein synthesis upstream of developmental tempo. Alternative candidates for ultimate regulators include species-specific gene expression levels of factors involved in the central dogma, as well as species-specific cell size. Overall, much work remains to be done before we can confidently identify the ultimate causes of species-specific developmental rates.
Collapse
Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Azzi C, Rayon T. Timing mechanisms: insights from comparative neural differentiation systems. Curr Opin Genet Dev 2024; 86:102197. [PMID: 38648722 DOI: 10.1016/j.gde.2024.102197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024]
Abstract
Temporal control is central to deploy and coordinate genetic programs during development. At present, there is limited understanding of the molecular mechanisms that govern the duration and speed of developmental processes. Timing mechanisms may run in parallel and/or interact with each other to integrate temporal signals throughout the organism. In this piece, we consider findings on the extrinsic control of developmental tempo and discuss the intrinsic roles of cell cycle, metabolic rates, protein turnover, and post-transcriptional mechanisms in the regulation of tempo during neural development.
Collapse
Affiliation(s)
- Chiara Azzi
- Epigenetics & Signalling Programmes, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK. https://twitter.com/@azziChiA
| | - Teresa Rayon
- Epigenetics & Signalling Programmes, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
| |
Collapse
|
7
|
Ecochard R, Stanford JB, Fehring RJ, Schneider M, Najmabadi S, Gronfier C. Evidence that the woman's ovarian cycle is driven by an internal circamonthly timing system. SCIENCE ADVANCES 2024; 10:eadg9646. [PMID: 38598621 PMCID: PMC11006216 DOI: 10.1126/sciadv.adg9646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
The ovarian cycle has a well-established circa-monthly rhythm, but the mechanisms involved in its regularity are unknown. Is the rhythmicity driven by an endogenous clock-like timer or by other internal or external processes? Here, using two large epidemiological datasets (26,912 cycles from 2303 European women and 4786 cycles from 721 North American women), analyzed with time series and circular statistics, we find evidence that the rhythmic characteristics of the menstrual cycle are more likely to be explained by an endogenous clock-like driving mechanism than by any other internal or external process. We also show that the menstrual cycle is weakly but significantly influenced by the 29.5-day lunar cycle and that the phase alignment between the two cycles differs between the European and the North American populations. Given the need to find efficient treatments of subfertility in women, our results should be confirmed in larger populations, and chronobiological approaches to optimize the ovulatory cycle should be evaluated.
Collapse
Affiliation(s)
- René Ecochard
- Pôle de Santé Publique, Service de Biostatistique, Hospices Civils de Lyon, Lyon 69424 Cedex 03, France
- Laboratoire Biostatistique Santé, Université Claude Bernard Lyon I, UMR CNRS 5558 UCBL, Lyon 69000, France
| | - John B. Stanford
- Office of Cooperative Reproductive Health, Division of Public Health, Department of Family and Preventive Medicine, University of Utah, Salt Lake City, 84108 UT, USA
| | - Richard J. Fehring
- College of Nursing, Marquette University, Milwaukee, P.O. Box 1881 WI, USA
| | - Marie Schneider
- College of Nursing, Marquette University, Milwaukee, P.O. Box 1881 WI, USA
- Institute for Natural Family Planning, Milwaukee, P.O. Box 1881 WI, USA
| | - Sam Najmabadi
- Office of Cooperative Reproductive Health, Division of Public Health, Department of Family and Preventive Medicine, University of Utah, Salt Lake City, 84108 UT, USA
| | - Claude Gronfier
- Centre de Recherche en Neurosciences de Lyon (CRNL), Neurocampus, Inserm U1028, CNRS UMR5292, Université de Lyon, Lyon 69500, France
| |
Collapse
|
8
|
Dermady APC, DeFazio DL, Hensley EM, Ruiz DL, Chavez AD, Iannone SA, Dermady NM, Grandel LV, Hill AS. Neuronal excitability modulates developmental time of Drosophila melanogaster. Dev Biol 2024; 508:38-45. [PMID: 38224932 DOI: 10.1016/j.ydbio.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Developmental time is a fundamental life history trait that affects the reproductive success of animals. Developmental time is known to be regulated by many genes and environmental conditions, yet mechanistic understandings of how various cellular processes influence the developmental timing of an organism are lacking. The nervous system is known to control key processes that affect developmental time, including the release of hormones that signal transitions between developmental stages. Here we show that the excitability of neurons plays a crucial role in modulating developmental time. Genetic manipulation of neuronal excitability in Drosophila melanogaster alters developmental time, which is faster in animals with increased neuronal excitability. We find that selectively modulating the excitability of peptidergic neurons is sufficient to alter developmental time, suggesting the intriguing hypothesis that the impact of neuronal excitability on DT may be at least partially mediated by peptidergic regulation of hormone release. This effect of neuronal excitability on developmental time is seen during embryogenesis and later developmental stages. Observed phenotypic plasticity in the effect of genetically increasing neuronal excitability at different temperatures, a condition also known to modulate excitability, suggests there is an optimal level of neuronal excitability, in terms of shortening DT. Together, our data highlight a novel connection between neuronal excitability and developmental time, with broad implications related to organismal physiology and evolution.
Collapse
Affiliation(s)
- Aidan P C Dermady
- College of the Holy Cross, Department of Biology, Worcester, MA, USA
| | - Dionna L DeFazio
- College of the Holy Cross, Department of Biology, Worcester, MA, USA
| | - Emily M Hensley
- College of the Holy Cross, Department of Biology, Worcester, MA, USA
| | - Daniel L Ruiz
- College of the Holy Cross, Department of Biology, Worcester, MA, USA
| | | | - Sarah A Iannone
- College of the Holy Cross, Department of Biology, Worcester, MA, USA
| | - Niall M Dermady
- College of the Holy Cross, Department of Biology, Worcester, MA, USA
| | - Lexis V Grandel
- College of the Holy Cross, Department of Biology, Worcester, MA, USA
| | - Alexis S Hill
- College of the Holy Cross, Department of Biology, Worcester, MA, USA.
| |
Collapse
|
9
|
Rekaik H, Duboule D. A CTCF-dependent mechanism underlies the Hox timer: relation to a segmented body plan. Curr Opin Genet Dev 2024; 85:102160. [PMID: 38377879 DOI: 10.1016/j.gde.2024.102160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/27/2024] [Accepted: 01/28/2024] [Indexed: 02/22/2024]
Abstract
During gastrulation, Hox genes are activated in a time-sequence that follows the order of the genes along their clusters. This property, which is observed in all animals that develop following a progressive rostral-to-caudal morphogenesis, is associated with changes in the chromatin structure and epigenetic profiles of Hox clusters, suggesting a process at least partly based on sequential gene accessibility. Here, we discuss recent work on this issue, as well as a possible mechanism based on the surprising conservation in both the distribution and orientation of CTCF sites inside vertebrate Hox clusters.
Collapse
Affiliation(s)
- Hocine Rekaik
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France. https://twitter.com/@hocine_Rekaik
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France.
| |
Collapse
|
10
|
Li XM, Jenke H, Strauss S, Bazakos C, Mosca G, Lymbouridou R, Kierzkowski D, Neumann U, Naik P, Huijser P, Laurent S, Smith RS, Runions A, Tsiantis M. Cell-cycle-linked growth reprogramming encodes developmental time into leaf morphogenesis. Curr Biol 2024; 34:541-556.e15. [PMID: 38244542 DOI: 10.1016/j.cub.2023.12.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
How is time encoded into organ growth and morphogenesis? We address this question by investigating heteroblasty, where leaf development and form are modified with progressing plant age. By combining morphometric analyses, fate-mapping through live-imaging, computational analyses, and genetics, we identify age-dependent changes in cell-cycle-associated growth and histogenesis that underpin leaf heteroblasty. We show that in juvenile leaves, cell proliferation competence is rapidly released in a "proliferation burst" coupled with fast growth, whereas in adult leaves, proliferative growth is sustained for longer and at a slower rate. These effects are mediated by the SPL9 transcription factor in response to inputs from both shoot age and individual leaf maturation along the proximodistal axis. SPL9 acts by activating CyclinD3 family genes, which are sufficient to bypass the requirement for SPL9 in the control of leaf shape and in heteroblastic reprogramming of cellular growth. In conclusion, we have identified a mechanism that bridges across cell, tissue, and whole-organism scales by linking cell-cycle-associated growth control to age-dependent changes in organ geometry.
Collapse
Affiliation(s)
- Xin-Min Li
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Hannah Jenke
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Gabriella Mosca
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Rena Lymbouridou
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Daniel Kierzkowski
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Ulla Neumann
- Central Microscopy (CeMic), Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Purva Naik
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Peter Huijser
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Adam Runions
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany.
| |
Collapse
|
11
|
Ciceri G, Baggiolini A, Cho HS, Kshirsagar M, Benito-Kwiecinski S, Walsh RM, Aromolaran KA, Gonzalez-Hernandez AJ, Munguba H, Koo SY, Xu N, Sevilla KJ, Goldstein PA, Levitz J, Leslie CS, Koche RP, Studer L. An epigenetic barrier sets the timing of human neuronal maturation. Nature 2024; 626:881-890. [PMID: 38297124 PMCID: PMC10881400 DOI: 10.1038/s41586-023-06984-8] [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: 05/17/2022] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
The pace of human brain development is highly protracted compared with most other species1-7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3-5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.
Collapse
Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arianna Baggiolini
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Hyein S Cho
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meghana Kshirsagar
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Microsoft AI for Good Research, Redmond, WA, USA
| | - Silvia Benito-Kwiecinski
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan M Walsh
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - So Yeon Koo
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Nan Xu
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaylin J Sevilla
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Goldstein
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
12
|
Filippopoulou K, Konstantinides N. Evolution of patterning. FEBS J 2024; 291:663-671. [PMID: 37943156 DOI: 10.1111/febs.16995] [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: 06/19/2023] [Revised: 09/28/2023] [Accepted: 11/07/2023] [Indexed: 11/10/2023]
Abstract
Developing tissues are patterned in space and time; this enables them to differentiate their cell types and form complex structures to support different body plans. Although space and time are two independent entities, there are many examples of spatial patterns that originate from temporal ones. The most prominent example is the expression of the genes hunchback, Krüppel, pdm, and castor, which are expressed temporally in the neural stem cells of the Drosophila ventral nerve cord and spatially along the anteroposterior axis of the blastoderm stage embryo. In this Viewpoint, we investigate the relationship between space and time in specific examples of spatial and temporal patterns with the aim of gaining insight into the evolutionary history of patterning.
Collapse
|
13
|
Busby L, Serrano Nájera G, Steventon BJ. Intrinsic and extrinsic cues time somite progenitor contribution to the vertebrate primary body axis. eLife 2024; 13:e90499. [PMID: 38193440 PMCID: PMC10834026 DOI: 10.7554/elife.90499] [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: 06/26/2023] [Accepted: 01/08/2024] [Indexed: 01/10/2024] Open
Abstract
During embryonic development, the timing of events at the cellular level must be coordinated across multiple length scales to ensure the formation of a well-proportioned body plan. This is clear during somitogenesis, where progenitors must be allocated to the axis over time whilst maintaining a progenitor population for continued elaboration of the body plan. However, the relative importance of intrinsic and extrinsic signals in timing progenitor addition at the single-cell level is not yet understood. Heterochronic grafts from older to younger embryos have suggested a level of intrinsic timing whereby later staged cells contribute to more posterior portions of the axis. To determine the precise step at which cells are delayed, we performed single-cell transcriptomic analysis on heterochronic grafts of somite progenitors in the chicken embryo. This revealed a previously undescribed cell state within which heterochronic grafted cells are stalled. The delayed exit of older cells from this state correlates with expression of posterior Hox genes. Using grafting and explant culture, we find that both Hox gene expression and the migratory capabilities of progenitor populations are intrinsically regulated at the population level. However, by grafting varied sizes of tissue, we find that small heterochronic grafts disperse more readily and contribute to more anterior portions of the body axis while still maintaining Hox gene expression. This enhanced dispersion is not replicated in explant culture, suggesting that it is a consequence of interaction between host and donor tissue and thus extrinsic to the donor tissue. Therefore, we demonstrate that the timing of cell dispersion and resulting axis contribution is impacted by a combination of both intrinsic and extrinsic cues.
Collapse
Affiliation(s)
- Lara Busby
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | | | | |
Collapse
|
14
|
Qiao S, Bernasek S, Gallagher KD, O'Connell J, Yamada S, Bagheri N, Amaral LAN, Carthew RW. Energy metabolism modulates the regulatory impact of activators on gene expression. Development 2024; 151:dev201986. [PMID: 38063847 PMCID: PMC10820824 DOI: 10.1242/dev.201986] [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: 05/15/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023]
Abstract
Gene expression is a regulated process fueled by ATP consumption. Therefore, regulation must be coupled to constraints imposed by the level of energy metabolism. Here, we explore this relationship both theoretically and experimentally. A stylized mathematical model predicts that activators of gene expression have variable impact depending on metabolic rate. Activators become less essential when metabolic rate is reduced and more essential when metabolic rate is enhanced. We find that, in the Drosophila eye, expression dynamics of the yan gene are less affected by loss of EGFR-mediated activation when metabolism is reduced, and the opposite effect is seen when metabolism is enhanced. The effects are also seen at the level of pattern regularity in the adult eye, where loss of EGFR-mediated activation is mitigated by lower metabolism. We propose that gene activation is tuned by energy metabolism to allow for faithful expression dynamics in the face of variable metabolic conditions.
Collapse
Affiliation(s)
- Sha Qiao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sebastian Bernasek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Kevin D. Gallagher
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Jessica O'Connell
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Shigehiro Yamada
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Neda Bagheri
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
| | - Luis A. N. Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - 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
| |
Collapse
|
15
|
Zhang K, Aung T, Yao E, Chuang PT. Lung patterning: Is a distal-to-proximal gradient of cell allocation and fate decision a general paradigm?: A gradient of distal-to-proximal distribution and differentiation of tip progenitors produces distinct compartments in the lung. Bioessays 2024; 46:e2300083. [PMID: 38010492 DOI: 10.1002/bies.202300083] [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: 05/13/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/29/2023]
Abstract
Recent studies support a model in which the progeny of SOX9+ epithelial progenitors at the distal tip of lung branches undergo cell allocation and differentiation sequentially along the distal-to-proximal axis. Concomitant with the elongation and ramification of lung branches, the descendants of the distal SOX9+ progenitors are distributed proximally, express SOX2, and differentiate into cell types in the conducting airways. Amid subsequent sacculation, the distal SOX9+ progenitors generate alveolar epithelial cells to form alveoli. Sequential cell allocation and differentiation are integrated with the branching process to generate a functional branching organ. This review focuses on the roles of SOX9+ cells as precursors for new branches, as the source of various cell types in the conducting airways, and as progenitors of the alveolar epithelium. All of these processes are controlled by multiple signaling pathways. Many mouse mutants with defective lung branching contain underlying defects in one or more steps of cell allocation and differentiation of SOX9+ progenitors. This model provides a framework to understand the molecular basis of lung phenotypes and to elucidate the molecular mechanisms of lung patterning. It builds a foundation on which comparing and contrasting the mechanisms employed by different branching organs in diverse species can be made.
Collapse
Affiliation(s)
- Kuan Zhang
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - Thin Aung
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - Erica Yao
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| | - Pao-Tien Chuang
- Cardiovascular Research Institute, University of California, San Francisco, California, USA
| |
Collapse
|
16
|
Chen CC, Tran W, Song K, Sugimoto T, Obusan MB, Wang L, Sheu KM, Cheng D, Ta L, Varuzhanyan G, Huang A, Xu R, Zeng Y, Borujerdpur A, Bayley NA, Noguchi M, Mao Z, Morrissey C, Corey E, Nelson PS, Zhao Y, Huang J, Park JW, Witte ON, Graeber TG. Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation. Cancer Cell 2023; 41:2066-2082.e9. [PMID: 37995683 PMCID: PMC10878415 DOI: 10.1016/j.ccell.2023.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Trans-differentiation from an adenocarcinoma to a small cell neuroendocrine state is associated with therapy resistance in multiple cancer types. To gain insight into the underlying molecular events of the trans-differentiation, we perform a multi-omics time course analysis of a pan-small cell neuroendocrine cancer model (termed PARCB), a forward genetic transformation using human prostate basal cells and identify a shared developmental, arc-like, and entropy-high trajectory among all transformation model replicates. Further mapping with single cell resolution reveals two distinct lineages defined by mutually exclusive expression of ASCL1 or ASCL2. Temporal regulation by groups of transcription factors across developmental stages reveals that cellular reprogramming precedes the induction of neuronal programs. TFAP4 and ASCL1/2 feedback are identified as potential regulators of ASCL1 and ASCL2 expression. Our study provides temporal transcriptional patterns and uncovers pan-tissue parallels between prostate and lung cancers, as well as connections to normal neuroendocrine cell states.
Collapse
Affiliation(s)
- Chia-Chun Chen
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Wendy Tran
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Kai Song
- Department of Bioengineering, UCLA, Los Angeles, CA, USA
| | - Tyler Sugimoto
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Matthew B Obusan
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Liang Wang
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Katherine M Sheu
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Donghui Cheng
- Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA
| | - Lisa Ta
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Grigor Varuzhanyan
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Arthur Huang
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Runzhe Xu
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
| | - Yuanhong Zeng
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Amirreza Borujerdpur
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Nicholas A Bayley
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Miyako Noguchi
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Yue Zhao
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA; Department of Pathology, College of Basic Medical Sciences and the First Hospital, China Medical University, Shenyang, China
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jung Wook Park
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Owen N Witte
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA; Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA; Molecular Biology Institute, UCLA, Los Angeles, CA, USA; Parker Institute for Cancer Immunotherapy, UCLA, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA, USA; California NanoSystems Institute, UCLA, Los Angeles, CA, USA; Metabolomics Center, UCLA, Los Angeles, CA, USA.
| |
Collapse
|
17
|
Kinney B, Sahu S, Stec N, Hills-Muckey K, Adams DW, Wang J, Jaremko M, Joshua-Tor L, Keil W, Hammell CM. A circadian-like gene network programs the timing and dosage of heterochronic miRNA transcription during C. elegans development. Dev Cell 2023; 58:2563-2579.e8. [PMID: 37643611 PMCID: PMC10840721 DOI: 10.1016/j.devcel.2023.08.006] [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: 04/14/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023]
Abstract
Development relies on the exquisite control of both the timing and the levels of gene expression to achieve robust developmental transitions. How cis- and trans-acting factors control both aspects simultaneously is unclear. We show that transcriptional pulses of the temporal patterning microRNA (miRNA) lin-4 are generated by two nuclear hormone receptors (NHRs) in C. elegans, NHR-85 and NHR-23, whose mammalian orthologs, Rev-Erb and ROR, function in the circadian clock. Although Rev-Erb and ROR antagonize each other to control once-daily transcription in mammals, NHR-85/NHR-23 heterodimers bind cooperatively to lin-4 regulatory elements to induce a single pulse of expression during each larval stage. Each pulse's timing, amplitude, and duration are dictated by the phased expression of these NHRs and the C. elegans Period ortholog, LIN-42, that binds to and represses NHR-85. Therefore, during nematode temporal patterning, an evolutionary rewiring of circadian clock components couples the timing of gene expression to the control of transcriptional dosage.
Collapse
Affiliation(s)
- Brian Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shubham Sahu
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168 Laboratoire Physico Chimie Curie, Paris 75005, France
| | - Natalia Stec
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Dexter W Adams
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jing Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Matt Jaremko
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Wolfgang Keil
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168 Laboratoire Physico Chimie Curie, Paris 75005, France.
| | | |
Collapse
|
18
|
Sedas Perez S, McQueen C, Stainton H, Pickering J, Chinnaiya K, Saiz-Lopez P, Placzek M, Ros MA, Towers M. Fgf signalling triggers an intrinsic mesodermal timer that determines the duration of limb patterning. Nat Commun 2023; 14:5841. [PMID: 37730682 PMCID: PMC10511490 DOI: 10.1038/s41467-023-41457-6] [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: 02/22/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023] Open
Abstract
Complex signalling between the apical ectodermal ridge (AER - a thickening of the distal epithelium) and the mesoderm controls limb patterning along the proximo-distal axis (humerus to digits). However, the essential in vivo requirement for AER-Fgf signalling makes it difficult to understand the exact roles that it fulfils. To overcome this barrier, we developed an amenable ex vivo chick wing tissue explant system that faithfully replicates in vivo parameters. Using inhibition experiments and RNA-sequencing, we identify a transient role for Fgfs in triggering the distal patterning phase. Fgfs are then dispensable for the maintenance of an intrinsic mesodermal transcriptome, which controls proliferation/differentiation timing and the duration of patterning. We also uncover additional roles for Fgf signalling in maintaining AER-related gene expression and in suppressing myogenesis. We describe a simple logic for limb patterning duration, which is potentially applicable to other systems, including the main body axis.
Collapse
Affiliation(s)
- Sofia Sedas Perez
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Caitlin McQueen
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Chester Medical School, Chester, CH2 1BR, UK
| | - Holly Stainton
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Joseph Pickering
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Kavitha Chinnaiya
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Patricia Saiz-Lopez
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria), 39011, Santander, Spain
- Departamento de Anatomía y Biología Celular Facultad de Medicina, Universidad de Cantabria, 39011, Santander, Spain
| | - Marysia Placzek
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Maria A Ros
- Instituto de Biomedicina y Biotecnología de Cantabria, IBBTEC (CSIC-Universidad de Cantabria), 39011, Santander, Spain
- Departamento de Anatomía y Biología Celular Facultad de Medicina, Universidad de Cantabria, 39011, Santander, Spain
| | - Matthew Towers
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| |
Collapse
|
19
|
Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, Petkov S, Behr R, Trivedi V, Matsuda M, Ebisuya M. A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals. Cell Stem Cell 2023; 30:938-949.e7. [PMID: 37343565 PMCID: PMC10321541 DOI: 10.1016/j.stem.2023.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Differential speeds in biochemical reactions have been proposed to be responsible for the differences in developmental tempo between mice and humans. However, the underlying mechanism controlling the species-specific kinetics remains to be determined. Using in vitro differentiation of pluripotent stem cells, we recapitulated the segmentation clocks of diverse mammalian species varying in body weight and taxa: marmoset, rabbit, cattle, and rhinoceros. Together with mouse and human, the segmentation clock periods of the six species did not scale with the animal body weight, but with the embryogenesis length. The biochemical kinetics of the core clock gene HES7 displayed clear scaling with the species-specific segmentation clock period. However, the cellular metabolic rates did not show an evident correlation. Instead, genes involving biochemical reactions showed an expression pattern that scales with the segmentation clock period. Altogether, our stem cell zoo uncovered general scaling laws governing species-specific developmental tempo.
Collapse
Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Maria Costanzo
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marina Sanaki-Matsumiya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Masafumi Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Katsuhiko Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Sebastian Diecke
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | | | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Stoyan Petkov
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Vikas Trivedi
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Mitsuhiro Matsuda
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
| |
Collapse
|
20
|
Koo B, Lee KH, Ming GL, Yoon KJ, Song H. Setting the clock of neural progenitor cells during mammalian corticogenesis. Semin Cell Dev Biol 2023; 142:43-53. [PMID: 35644876 PMCID: PMC9699901 DOI: 10.1016/j.semcdb.2022.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/06/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
Abstract
Radial glial cells (RGCs) as primary neural stem cells in the developing mammalian cortex give rise to diverse types of neurons and glial cells according to sophisticated developmental programs with remarkable spatiotemporal precision. Recent studies suggest that regulation of the temporal competence of RGCs is a key mechanism for the highly conserved and predictable development of the cerebral cortex. Various types of epigenetic regulations, such as DNA methylation, histone modifications, and 3D chromatin architecture, play a key role in shaping the gene expression pattern of RGCs. In addition, epitranscriptomic modifications regulate temporal pre-patterning of RGCs by affecting the turnover rate and function of cell-type-specific transcripts. In this review, we summarize epigenetic and epitranscriptomic regulatory mechanisms that control the temporal competence of RGCs during mammalian corticogenesis. Furthermore, we discuss various developmental elements that also dynamically regulate the temporal competence of RGCs, including biochemical reaction speed, local environmental changes, and subcellular organelle remodeling. Finally, we discuss the underlying mechanisms that regulate the interspecies developmental tempo contributing to human-specific features of brain development.
Collapse
Affiliation(s)
- Bonsang Koo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki-Heon Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ki-Jun Yoon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
21
|
Klingler E. Temporal controls over cortical projection neuron fate diversity. Curr Opin Neurobiol 2023; 79:102677. [PMID: 36736108 DOI: 10.1016/j.conb.2023.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023]
Abstract
During neocortex development, cortical projection neurons (PN) are sequentially produced and assemble into circuits underlying our interactions with the environment. Cortical PN are heterogeneous in terms of birthdate, layer position, molecular identity, connectivity, and function. This diversity increases in evolutionarily most recent species, but when and how it emerges during corticogenesis is still debated. While time-locked expression of determinant genes and early stochasticity allow the production of different types of PN, temporal differences in unfolding similar transcriptional programs, rather than fundamental differences in these programs, further account for anatomical variability between PN subtypes and across species. Altogether, these mechanisms, which will be discussed here, participate in increasing cortical PN diversity.
Collapse
Affiliation(s)
- Esther Klingler
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211, Geneva, Switzerland.
| |
Collapse
|
22
|
Liu YJ, Auwerx J. Mitochondria: A "pacemaker" for species-specific development. Mol Cell 2023; 83:824-826. [PMID: 36931252 DOI: 10.1016/j.molcel.2023.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
We highlight papers by Diaz-Cuadros et al.1 and Iwata et al.2 that demonstrate the role of mitochondrial metabolism in setting developmental pace through their control over cellular bioenergetics and redox homeostasis in mice and humans.
Collapse
Affiliation(s)
- Yasmine J Liu
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| |
Collapse
|
23
|
Iwata R, Casimir P, Erkol E, Boubakar L, Planque M, Gallego López IM, Ditkowska M, Gaspariunaite V, Beckers S, Remans D, Vints K, Vandekeere A, Poovathingal S, Bird M, Vlaeminck I, Creemers E, Wierda K, Corthout N, Vermeersch P, Carpentier S, Davie K, Mazzone M, Gounko NV, Aerts S, Ghesquière B, Fendt SM, Vanderhaeghen P. Mitochondria metabolism sets the species-specific tempo of neuronal development. Science 2023; 379:eabn4705. [PMID: 36705539 DOI: 10.1126/science.abn4705] [Citation(s) in RCA: 76] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Neuronal development in the human cerebral cortex is considerably prolonged compared with that of other mammals. We explored whether mitochondria influence the species-specific timing of cortical neuron maturation. By comparing human and mouse cortical neuronal maturation at high temporal and cell resolution, we found a slower mitochondria development in human cortical neurons compared with that in the mouse, together with lower mitochondria metabolic activity, particularly that of oxidative phosphorylation. Stimulation of mitochondria metabolism in human neurons resulted in accelerated development in vitro and in vivo, leading to maturation of cells weeks ahead of time, whereas its inhibition in mouse neurons led to decreased rates of maturation. Mitochondria are thus important regulators of the pace of neuronal development underlying human-specific brain neoteny.
Collapse
Affiliation(s)
- Ryohei Iwata
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium.,Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium
| | - Pierre Casimir
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium.,Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium
| | - Emir Erkol
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Leïla Boubakar
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium.,Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium
| | - Mélanie Planque
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), 3000 Leuven, Belgium
| | - Isabel M Gallego López
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Martyna Ditkowska
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Vaiva Gaspariunaite
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Sofie Beckers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Daan Remans
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Katlijn Vints
- KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, 3000 Leuven, Belgium
| | - Anke Vandekeere
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), 3000 Leuven, Belgium
| | | | - Matthew Bird
- Clinical Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Ine Vlaeminck
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,Electrophysiology Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Eline Creemers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,Electrophysiology Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,Electrophysiology Unit, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Nikky Corthout
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,VIB Bio Imaging Core, 3000 Leuven, Belgium
| | - Pieter Vermeersch
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium, and Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Sébastien Carpentier
- SYBIOMA, KU Leuven Center for SYstems BIOlogy based MAss spectrometry, 3000 Leuven, Belgium
| | - Kristofer Davie
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, 3000 Leuven, Belgium.,Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Natalia V Gounko
- KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, 3000 Leuven, Belgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium
| | - Bart Ghesquière
- Metabolomics Expertise Center, Center for Cancer Biology, VIB, KU Leuven, 3000 Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, 3000 Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), 3000 Leuven, Belgium
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences & Leuven Brain Institute, 3000 Leuven, Belgium.,Université Libre de Bruxelles (ULB), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium
| |
Collapse
|
24
|
Gómez de la Torre Canny S, Nordgård CT, Mathisen AJH, Degré Lorentsen E, Vadstein O, Bakke I. A novel gnotobiotic experimental system for Atlantic salmon ( Salmo salar L.) reveals a microbial influence on mucosal barrier function and adipose tissue accumulation during the yolk sac stage. Front Cell Infect Microbiol 2023; 12:1068302. [PMID: 36817693 PMCID: PMC9929952 DOI: 10.3389/fcimb.2022.1068302] [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: 10/12/2022] [Accepted: 12/05/2022] [Indexed: 02/04/2023] Open
Abstract
Gnotobiotic models have had a crucial role in studying the effect that commensal microbiota has on the health of their animal hosts. Despite their physiological and ecological diversity, teleost fishes are still underrepresented in gnotobiotic research. Moreover, a better understanding of host-microbe interactions in farmed fish has the potential to contribute to sustainable global food supply. We have developed a novel gnotobiotic experimental system that includes the derivation of fertilized eggs of farmed and wild Atlantic salmon, and gnotobiotic husbandry of fry during the yolk sac stage. We used a microscopy-based approach to estimate the barrier function of the skin mucus layer and used this measurement to select the derivation procedure that minimized adverse effects on the skin mucosa. We also used this method to demonstrate that the mucus barrier was reduced in germ-free fry when compared to fry colonized with two different bacterial communities. This alteration in the mucus barrier was preceded by an increase in the number of cells containing neutral mucosubstances in the anterior segment of the body, but without changes in the number of cells containing acidic substances in any of the other segments studied along the body axis. In addition, we showed how the microbial status of the fry temporarily affected body size and the utilization of internal yolk stores during the yolk sac stage. Finally, we showed that the presence of bacterial communities associated with the fry, as well as their composition, affected the size of adipose tissue. Fry colonized with water from a lake had a larger visceral adipose tissue depot than both conventionally raised and germ-free fry. Together, our results show that this novel gnotobiotic experimental system is a useful tool for the study of host-microbe interactions in this species of aquacultural importance.
Collapse
Affiliation(s)
| | - Catherine Taylor Nordgård
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Amalie Johanne Horn Mathisen
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eirik Degré Lorentsen
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingrid Bakke
- *Correspondence: Sol Gómez de la Torre Canny, ; Ingrid Bakke,
| |
Collapse
|
25
|
Saunders TE, Monteiro A. Colour patterns: Predicting patterns without knowing the details. Curr Biol 2022; 32:R1306-R1308. [PMID: 36473439 DOI: 10.1016/j.cub.2022.10.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A bewildering array of colour patterns occurs across animals. New work studying five lizard species reveals that reaction-diffusion models can be remarkably predictive of future adult skin patterning, even though molecular details are unknown. This has implications for understanding how complex patterns evolve.
Collapse
Affiliation(s)
- Timothy E Saunders
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK; Department of Biological Sciences, National University of Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore.
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore
| |
Collapse
|
26
|
Fang W, Bell CM, Sapirstein A, Asami S, Leeper K, Zack DJ, Ji H, Kalhor R. Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. Cell 2022; 185:4604-4620.e32. [PMID: 36423582 PMCID: PMC9708097 DOI: 10.1016/j.cell.2022.10.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/23/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022]
Abstract
Natural and induced somatic mutations that accumulate in the genome during development record the phylogenetic relationships of cells; whether these lineage barcodes capture the complex dynamics of progenitor states remains unclear. We introduce quantitative fate mapping, an approach to reconstruct the hierarchy, commitment times, population sizes, and commitment biases of intermediate progenitor states during development based on a time-scaled phylogeny of their descendants. To reconstruct time-scaled phylogenies from lineage barcodes, we introduce Phylotime, a scalable maximum likelihood clustering approach based on a general barcoding mutagenesis model. We validate these approaches using realistic in silico and in vitro barcoding experiments. We further establish criteria for the number of cells that must be analyzed for robust quantitative fate mapping and a progenitor state coverage statistic to assess the robustness. This work demonstrates how lineage barcodes, natural or synthetic, enable analyzing progenitor fate and dynamics long after embryonic development in any organism.
Collapse
Affiliation(s)
- Weixiang Fang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Claire M Bell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Abel Sapirstein
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Soichiro Asami
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen Leeper
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Donald J Zack
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Reza Kalhor
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
27
|
Hosoya M, Kitama T, Iwabu K, Nishiyama T, Oishi N, Okano H, Ozawa H. Development of the stria vascularis in the common marmoset, a primate model. Sci Rep 2022; 12:19811. [PMID: 36396805 PMCID: PMC9672111 DOI: 10.1038/s41598-022-24380-6] [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: 08/24/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Stria vascularis is a structure that generates potassium gradients in the cochlea, which is vital for hair cells to convert mechanical sound waves into electrical pulses. The precise development of the stria vascularis and subsequent generation of endocochlear potential are thus essential for hearing. Understanding the development of the stria vascularis is valuable for studying hearing loss caused by aging or genetics and designing regenerative therapy. Although inter-species differences have been reported between rodents and humans, most of our current knowledge regarding cochlear development has been obtained from rodent models because of the difficulty in using human fetal samples in this field of research. Therefore, we investigated the development of the cochlear stria vascularis in the common marmoset (Callithrix jacchus), a small monkey species native to the New World. Our study confirms that stria vascularis development in the common marmoset is similar to that in humans and is suitable for furthering our understanding of human cochlear development. The time course established in this report will aid in studying the primate-specific developmental biology of the inner ear, which could eventually lead to new treatment strategies for hearing loss in humans.
Collapse
Affiliation(s)
- Makoto Hosoya
- grid.26091.3c0000 0004 1936 9959Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Tsubasa Kitama
- grid.26091.3c0000 0004 1936 9959Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Kaho Iwabu
- grid.26091.3c0000 0004 1936 9959Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Takanori Nishiyama
- grid.26091.3c0000 0004 1936 9959Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Naoki Oishi
- grid.26091.3c0000 0004 1936 9959Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Hideyuki Okano
- grid.26091.3c0000 0004 1936 9959Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan ,grid.7597.c0000000094465255Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0193 Japan
| | - Hiroyuki Ozawa
- grid.26091.3c0000 0004 1936 9959Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582 Japan
| |
Collapse
|
28
|
Medina-Cano D, Corrigan EK, Glenn RA, Islam MT, Lin Y, Kim J, Cho H, Vierbuchen T. Rapid and robust directed differentiation of mouse epiblast stem cells into definitive endoderm and forebrain organoids. Development 2022; 149:dev200561. [PMID: 35899604 PMCID: PMC10655922 DOI: 10.1242/dev.200561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/04/2022] [Indexed: 11/20/2022]
Abstract
Directed differentiation of pluripotent stem cells (PSCs) is a powerful model system for deconstructing embryonic development. Although mice are the most advanced mammalian model system for genetic studies of embryonic development, state-of-the-art protocols for directed differentiation of mouse PSCs into defined lineages require additional steps and generates target cell types with lower purity than analogous protocols for human PSCs, limiting their application as models for mechanistic studies of development. Here, we examine the potential of mouse epiblast stem cells cultured in media containing Wnt pathway inhibitors as a starting point for directed differentiation. As a proof of concept, we focused our efforts on two specific cell/tissue types that have proven difficult to generate efficiently and reproducibly from mouse embryonic stem cells: definitive endoderm and neural organoids. We present new protocols for rapid generation of nearly pure definitive endoderm and forebrain-patterned neural organoids that model the development of prethalamic and hippocampal neurons. These differentiation models present new possibilities for combining mouse genetic tools with in vitro differentiation to characterize molecular and cellular mechanisms of embryonic development.
Collapse
Affiliation(s)
- Daniel Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Emily K. Corrigan
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Rachel A. Glenn
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Mohammed T. Islam
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Yuan Lin
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Juliet Kim
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Hyunwoo Cho
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
- Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| |
Collapse
|
29
|
Conti E, Harschnitz O. Human stem cell models to study placode development, function and pathology. Development 2022; 149:276462. [DOI: 10.1242/dev.200831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Placodes are embryonic structures originating from the rostral ectoderm that give rise to highly diverse organs and tissues, comprising the anterior pituitary gland, paired sense organs and cranial sensory ganglia. Their development, including the underlying gene regulatory networks and signalling pathways, have been for the most part characterised in animal models. In this Review, we describe how placode development can be recapitulated by the differentiation of human pluripotent stem cells towards placode progenitors and their derivatives, highlighting the value of this highly scalable platform as an optimal in vitro tool to study the development of human placodes, and identify human-specific mechanisms in their development, function and pathology.
Collapse
Affiliation(s)
- Eleonora Conti
- Neurogenomics Research Centre, Human Technopole , Viale Rita Levi-Montalcini, 1, 20157 Milan , Italy
| | - Oliver Harschnitz
- Neurogenomics Research Centre, Human Technopole , Viale Rita Levi-Montalcini, 1, 20157 Milan , Italy
| |
Collapse
|
30
|
Rowton M, Perez-Cervantes C, Hur S, Jacobs-Li J, Lu E, Deng N, Guzzetta A, Hoffmann AD, Stocker M, Steimle JD, Lazarevic S, Oubaha S, Yang XH, Kim C, Yu S, Eckart H, Koska M, Hanson E, Chan SSK, Garry DJ, Kyba M, Basu A, Ikegami K, Pott S, Moskowitz IP. Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. Dev Cell 2022; 57:2181-2203.e9. [PMID: 36108627 PMCID: PMC10506397 DOI: 10.1016/j.devcel.2022.08.009] [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: 01/14/2022] [Revised: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 11/18/2022]
Abstract
Many developmental signaling pathways have been implicated in lineage-specific differentiation; however, mechanisms that explicitly control differentiation timing remain poorly defined in mammals. We report that murine Hedgehog signaling is a heterochronic pathway that determines the timing of progenitor differentiation. Hedgehog activity was necessary to prevent premature differentiation of second heart field (SHF) cardiac progenitors in mouse embryos, and the Hedgehog transcription factor GLI1 was sufficient to delay differentiation of cardiac progenitors in vitro. GLI1 directly activated a de novo progenitor-specific network in vitro, akin to that of SHF progenitors in vivo, which prevented the onset of the cardiac differentiation program. A Hedgehog signaling-dependent active-to-repressive GLI transition functioned as a differentiation timer, restricting the progenitor network to the SHF. GLI1 expression was associated with progenitor status across germ layers, and it delayed the differentiation of neural progenitors in vitro, suggesting a broad role for Hedgehog signaling as a heterochronic pathway.
Collapse
Affiliation(s)
- Megan Rowton
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Suzy Hur
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Jessica Jacobs-Li
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Emery Lu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Nikita Deng
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Alexander Guzzetta
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Andrew D Hoffmann
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Matthew Stocker
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sonja Lazarevic
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sophie Oubaha
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Xinan H Yang
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Chul Kim
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Shuhan Yu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Heather Eckart
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Mervenaz Koska
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Erika Hanson
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sunny S K Chan
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel J Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anindita Basu
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Kohta Ikegami
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Sebastian Pott
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, Human Genetics, and Genetic Medicine, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
31
|
Chou FS, Chen CY, Lee AC, Wang PS. Impaired Cell Cycle Progression and Self-Renewal of Fetal Neural Stem and Progenitor Cells in a Murine Model of Intrauterine Growth Restriction. Front Cell Dev Biol 2022; 10:821848. [PMID: 35903551 PMCID: PMC9314876 DOI: 10.3389/fcell.2022.821848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
Individuals with intrauterine growth restriction (IUGR) are at an increased risk for neurodevelopmental impairment. Fetal cortical neurogenesis is a time-sensitive process in which fetal neural stem cells (NSCs) follow a distinct pattern of layer-specific neuron generation to populate the cerebral cortex. Here, we used a murine maternal hypoxia-induced IUGR model to study the impact of IUGR on fetal NSC development. In this model, timed-pregnant mice were exposed to hypoxia during the active stage of neurogenesis, followed by fetal brain collection and analysis. In the IUGR fetal brains, we found a significant reduction in cerebral cortical thickness accompanied by decreases in layer-specific neurons. Using EdU labeling, we demonstrated that cell cycle progression of fetal NSCs was delayed, primarily observed in the G2/M phase during inward interkinetic nuclear migration. Following relief from maternal hypoxia exposure, the remaining fetal NSCs re-established their neurogenic ability and resumed production of layer-specific neurons. Surprisingly, the newly generated neurons matched their control counterparts in layer-specific marker expression, suggesting preservation of the fetal NSC temporal identity despite IUGR effects. As expected, the absolute number of neurons generated in the IUGR group remained lower compared to that in the control group due to a reduced fetal NSC pool size as a result of cell cycle defect. Transcriptome analysis identified genes related to energy expenditure and G2/M cell cycle progression being affected by maternal hypoxia-induced IUGR. Taken together, maternal hypoxia-induced IUGR is associated with a defect in cell cycle progression of fetal NSCs, and has a long-term impact on offspring cognitive development.
Collapse
Affiliation(s)
- Fu-Sheng Chou
- Department of Pediatrics, The University of Kansas Medical Center, Kansas City, KS, United States
- Division of Neonatology, Children’s Mercy-Kansas City, Kansas City, MO, United States
- *Correspondence: Fu-Sheng Chou, ; Pei-Shan Wang,
| | - Chu-Yen Chen
- Department of Pediatrics, The University of Kansas Medical Center, Kansas City, KS, United States
| | - An-Chun Lee
- Department of Pediatrics, The University of Kansas Medical Center, Kansas City, KS, United States
| | - Pei-Shan Wang
- Department of Pediatrics, The University of Kansas Medical Center, Kansas City, KS, United States
- *Correspondence: Fu-Sheng Chou, ; Pei-Shan Wang,
| |
Collapse
|
32
|
Bond AM, Ming GL, Song H. What Is the Relationship Between Hippocampal Neurogenesis Across Different Stages of the Lifespan? Front Neurosci 2022; 16:891713. [PMID: 35685774 PMCID: PMC9173723 DOI: 10.3389/fnins.2022.891713] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
Hippocampal neurogenesis has typically been studied during embryonic development or in adulthood, promoting the perception of two distinct phenomena. We propose a perspective that hippocampal neurogenesis in the mammalian brain is one continuous, lifelong developmental process. We summarize the common features of hippocampal neurogenesis that are maintained across the lifespan, as well as dynamic age-dependent properties. We highlight that while the progression of hippocampal neurogenesis across the lifespan is conserved between mammalian species, the timing of this progression is species-dependent. Finally, we discuss some current challenges in the hippocampus neurogenesis field, and future research directions to address them, such as time course analysis across the lifespan, mechanisms regulating neurogenesis progression, and interspecies comparisons. We hope that this new perspective of hippocampal neurogenesis will prompt fresh insight into previous research and inspire new directions to advance the field to identify biologically significant ways to harness the endogenous capacity for neurogenesis in the hippocampus.
Collapse
Affiliation(s)
- Allison M. Bond
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Guo-li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States,*Correspondence: Hongjun Song,
| |
Collapse
|
33
|
Hosoya M, Fujioka M, Okahara J, Yoshimatsu S, Okano H, Ozawa H. Early development of the cochlea of the common marmoset, a non-human primate model. Neural Dev 2022; 17:6. [PMID: 35524278 PMCID: PMC9077934 DOI: 10.1186/s13064-022-00162-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/13/2022] [Indexed: 11/12/2022] Open
Abstract
Background Fine-tuned cochlear development is essential for hearing. Owing to the difficulty in using early human fetal samples, most of our knowledge regarding cochlear development has been obtained from rodents. However, several inter-species differences in cochlear development between rodents and humans have been reported. To bridge these differences, we investigated early otic development of a non-human primate model animal, the common marmoset (Callithrix jacchus). Methods We examined 20 genes involved in early cochlear development and described the critical developmental steps for morphogenesis, which have been reported to vary between rodents and marmosets. Results The results revealed that several critical genes involved in prosensory epithelium specifications showed higher inter-species differences, suggesting that the molecular process for hair cell lineage acquisition in primates differs considerably from that of rodents. We also observed that the tempo of cochlear development was three times slower in the primate than in rodents. Conclusions Our data provide new insights into early cochlear development in primates and humans and imply that the procedures used for manipulating rodent cochlear sensory cells cannot be directly used for the research of primate cells due to the intrinsic inter-species differences in the cell fate determination program.
Collapse
Affiliation(s)
- Makoto Hosoya
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Masato Fujioka
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan. .,Department of Molecular Genetics, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan.
| | - Junko Okahara
- Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0193, Japan.,Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, 3-25-12 Tonomachi Kawasaki-ku Kawasaki, Kanagawa, 210-0821, Japan
| | - Sho Yoshimatsu
- Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0193, Japan.,Department of Physiology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Laboratory for Marmoset Neural Architecture, Center for Brain Science, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0193, Japan.,Department of Physiology, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroyuki Ozawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, 35 Shinanomachi Shinjuku-ku, Tokyo, 160-8582, Japan
| |
Collapse
|
34
|
Sanaki-Matsumiya M, Matsuda M, Gritti N, Nakaki F, Sharpe J, Trivedi V, Ebisuya M. Periodic formation of epithelial somites from human pluripotent stem cells. Nat Commun 2022; 13:2325. [PMID: 35484123 PMCID: PMC9050736 DOI: 10.1038/s41467-022-29967-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/11/2022] [Indexed: 12/19/2022] Open
Abstract
During embryonic development, epithelial cell blocks called somites are periodically formed according to the segmentation clock, becoming the foundation for the segmental pattern of the vertebral column. The process of somitogenesis has recently been recapitulated with murine and human pluripotent stem cells. However, an in vitro model for human somitogenesis coupled with the segmentation clock and epithelialization is still missing. Here, we report the generation of human somitoids, organoids that periodically form pairs of epithelial somite-like structures. Somitoids display clear oscillations of the segmentation clock that coincide with the segmentation of the presomitic mesoderm. The resulting somites show anterior-posterior and apical-basal polarities. Matrigel is essential for epithelialization but dispensable for the differentiation into somite cells. The size of somites is rather constant, irrespective of the initial cell number. The amount of WNT signaling instructs the proportion of mesodermal lineages in somitoids. Somitoids provide a novel platform to study human somitogenesis. Somitogenesis has been well characterized in model organisms, resulting in detailed description of the somite segmentation clock. Here they generate somitogenic organoids from human pluripotent stem cells that recapitulate somitogenesis, periodic segmentation, and proper polarity.
Collapse
Affiliation(s)
| | - Mitsuhiro Matsuda
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Nicola Gritti
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Fumio Nakaki
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - James Sharpe
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Vikas Trivedi
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain.,EMBL Heidelberg, Developmental Biology Unit, Heidelberg, Germany
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain.
| |
Collapse
|
35
|
Hidalgo Aguilar A, Smith L, Owens D, Quelch R, Przyborski S. Recreating Tissue Structures Representative of Teratomas In Vitro Using a Combination of 3D Cell Culture Technology and Human Embryonic Stem Cells. Bioengineering (Basel) 2022; 9:bioengineering9050185. [PMID: 35621463 PMCID: PMC9138123 DOI: 10.3390/bioengineering9050185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/22/2022] Open
Abstract
In vitro studies using human embryonic stem cells (hESCs) are a valuable method to study aspects of embryogenesis, avoiding ethical issues when using embryonic materials and species dissimilarities. The xenograft teratoma assay is often traditionally used to establish pluripotency in putative PSC populations, but also has additional applications, including the study of tissue differentiation. The stem cell field has long sought an alternative due to various well-established issues with the in vivo technique, including significant protocol variability and animal usage. We have established a two-step culture method which combines PSC-derived embryoid bodies (EBs) with porous scaffolds to enhance their viability, prolonging the time these structures can be maintained, and therefore, permitting more complex, mature differentiation. Here, we have utilised human embryonic stem cell-derived EBs, demonstrating the formation of tissue rudiments of increasing complexity over time and the ability to manipulate their differentiation through the application of exogenous morphogens to achieve specific lineages. Crucially, these EB-derived tissues are highly reminiscent of xenograft teratoma samples derived from the same cell line. We believe this in vitro approach represents a reproducible, animal-free alternative to the teratoma assay, which can be used to study human tissue development.
Collapse
Affiliation(s)
| | - Lucy Smith
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (A.H.A.); (L.S.); (D.O.); (R.Q.)
| | - Dominic Owens
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (A.H.A.); (L.S.); (D.O.); (R.Q.)
| | - Rebecca Quelch
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (A.H.A.); (L.S.); (D.O.); (R.Q.)
| | - Stefan Przyborski
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (A.H.A.); (L.S.); (D.O.); (R.Q.)
- Reprocell Europe, NETPark, Sedgefield TS21 3FD, UK
- Correspondence:
| |
Collapse
|
36
|
|
37
|
Abstract
An enduring mystery of development is how its timing is controlled, particularly for development after birth, where timing is highly flexible and depends on environmental conditions, such as food availability and diet. We followed timing of cell- and organism-level events in individual Caenorhabditis elegans larvae developing from hatching to adulthood, uncovering widespread variations in event timing, both between isogenic individuals in the same environment and when changing conditions and genotypes. However, in almost all cases, we found that events occurred at the same time, when time was rescaled by the duration of development measured in each individual. This observation of “temporal scaling” poses strong constraints on models to explain timing of larval development. It is essential that correct temporal order of cellular events is maintained during animal development. During postembryonic development, the rate of development depends on external conditions, such as food availability, diet, and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism level is not known. We used a unique time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions, and cuticle shedding in individual Caenorhabditis elegans larvae, as they developed from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed “temporal scaling,” meaning that events occurred at the same time when measured relative to the total duration of development in each individual. We also observed pervasive changes in timing when temperature, diet, or genotype were varied, but with larval development divided in “epochs” that differed in how event timing was impacted. Yet, these variations in timing were still explained by temporal scaling when time was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lacking lin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing. However, shifting conditions middevelopment perturbed temporal scaling and changed event order in a highly condition-specific manner, indicating that a complex machinery is responsible for temporal scaling under constant conditions.
Collapse
|
38
|
Multi-scale Chimerism: An experimental window on the algorithms of anatomical control. Cells Dev 2022; 169:203764. [PMID: 34974205 DOI: 10.1016/j.cdev.2021.203764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/12/2021] [Accepted: 12/24/2021] [Indexed: 12/22/2022]
Abstract
Despite the immense progress in genetics and cell biology, major knowledge gaps remain with respect to prediction and control of the global morphologies that will result from the cooperation of cells with known genomes. The understanding of cooperativity, competition, and synergy across diverse biological scales has been obscured by a focus on standard model systems that exhibit invariant species-specific anatomies. Morphogenesis of chimeric biological material is an especially instructive window on the control of biological growth and form because it emphasizes the need for prediction without reliance on familiar, standard outcomes. Here, we review an important and fascinating body of data from experiments utilizing DNA transfer, cell transplantation, organ grafting, and parabiosis. We suggest that these are all instances (at different levels of organization) of one general phenomenon: chimerism. Multi-scale chimeras are a powerful conceptual and experimental tool with which to probe the mapping between properties of components and large-scale anatomy: the laws of morphogenesis. The existing data and future advances in this field will impact not only the understanding of cooperation and the evolution of body forms, but also the design of strategies for system-level outcomes in regenerative medicine and swarm robotics.
Collapse
|
39
|
Pourquié O. A brief history of the segmentation clock. Dev Biol 2022; 485:24-36. [DOI: 10.1016/j.ydbio.2022.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
|
40
|
Stainton H, Towers M. Retinoic acid influences the timing and scaling of avian wing development. Cell Rep 2022; 38:110288. [PMID: 35081337 PMCID: PMC8810399 DOI: 10.1016/j.celrep.2021.110288] [Citation(s) in RCA: 6] [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: 06/01/2021] [Revised: 11/08/2021] [Accepted: 12/29/2021] [Indexed: 12/23/2022] Open
Abstract
A fundamental question in biology is how embryonic development is timed between different species. To address this problem, we compared wing development in the quail and the larger chick. We reveal that pattern formation is faster in the quail as determined by the earlier activation of 5′Hox genes, termination of developmental organizers (Shh and Fgf8), and the laying down of the skeleton (Sox9). Using interspecies tissue grafts, we show that developmental timing can be reset during a critical window of retinoic acid signaling. Accordingly, extending the duration of retinoic acid signaling switches developmental timing between the quail and the chick and the chick and the larger turkey. However, the incremental growth rate is comparable between all three species, suggesting that the pace of development primarily governs differences in the expansion of the skeletal pattern. The widespread distribution of retinoic acid could coordinate developmental timing throughout the embryo. Quail wings develop faster than chick and turkey wings Retinoic acid can set the species timing of wing development Developmental timing is independent of growth and scales the skeletal pattern
Collapse
Affiliation(s)
- Holly Stainton
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Matthew Towers
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| |
Collapse
|
41
|
Malovichko YV, Shikov AE, Nizhnikov AA, Antonets KS. Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications. Int J Mol Sci 2021; 22:ijms22179252. [PMID: 34502157 PMCID: PMC8430901 DOI: 10.3390/ijms22179252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 12/21/2022] Open
Abstract
In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.
Collapse
Affiliation(s)
- Yury V. Malovichko
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (Y.V.M.); (A.E.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence:
| |
Collapse
|
42
|
Nguyen P, Pease NA, Kueh HY. Scalable control of developmental timetables by epigenetic switching networks. J R Soc Interface 2021; 18:20210109. [PMID: 34283940 DOI: 10.1098/rsif.2021.0109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
During development, progenitor cells follow timetables for differentiation that span many cell generations. These developmental timetables are robustly encoded by the embryo, yet scalably adjustable by evolution, facilitating variation in organism size and form. Epigenetic switches, involving rate-limiting activation steps at regulatory gene loci, control gene activation timing in diverse contexts, and could profoundly impact the dynamics of gene regulatory networks controlling developmental lineage specification. Here, we develop a mathematical framework to model regulatory networks with genes controlled by epigenetic switches. Using this framework, we show that such epigenetic switching networks uphold developmental timetables that robustly span many cell generations, and enable the generation of differentiated cells in precisely defined numbers and fractions. Changes to epigenetic switching networks can readily alter the timing of developmental events within a timetable, or alter the overall speed at which timetables unfold, enabling scalable control over differentiated population sizes. With their robust, yet flexibly adjustable nature, epigenetic switching networks could represent central targets on which evolution acts to manufacture diversity in organism size and form.
Collapse
Affiliation(s)
- Phuc Nguyen
- Molecular Engineering and Sciences Program, University of Washington, Seattle, WA, USA
| | - Nicholas A Pease
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA, USA.,Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| |
Collapse
|
43
|
Yadav V, Tolwinski N, Saunders TE. Spatiotemporal sensitivity of mesoderm specification to FGFR signalling in the Drosophila embryo. Sci Rep 2021; 11:14091. [PMID: 34238963 PMCID: PMC8266908 DOI: 10.1038/s41598-021-93512-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Development of the Drosophila embryonic mesoderm is controlled through both internal and external inputs to the mesoderm. One such factor is Heartless (Htl), a Fibroblast Growth Factor Receptor (FGFR) expressed in the mesoderm. Although Htl has been extensively studied, the dynamics of its action are poorly understood after the initial phases of mesoderm formation and spreading. To begin to address this challenge, we have developed an optogenetic version of the FGFR Heartless in Drosophila (Opto-htl). Opto-htl enables us to activate the FGFR pathway in selective spatial (~ 35 μm section from one of the lateral sides of the embryo) and temporal domains (ranging from 40 min to 14 h) during embryogenesis. Importantly, the effects can be tuned by the intensity of light-activation, making this approach significantly more flexible than other genetic approaches. We performed controlled perturbations to the FGFR pathway to define the contribution of Htl signalling to the formation of the developing embryonic heart and somatic muscles. We find a direct correlation between Htl signalling dosage and number of Tinman-positive heart cells specified. Opto-htl activation favours the specification of Tinman positive cardioblasts and eliminates Eve-positive DA1 muscles. This effect is seen to increase progressively with increasing light intensity. Therefore, fine tuning of phenotypic responses to varied Htl signalling dosage can be achieved more conveniently than with other genetic approaches. Overall, Opto-htl is a powerful new tool for dissecting the role of FGFR signalling during development.
Collapse
Affiliation(s)
- V. Yadav
- grid.4280.e0000 0001 2180 6431Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - N. Tolwinski
- grid.4280.e0000 0001 2180 6431Yale-NUS, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - T. E. Saunders
- grid.4280.e0000 0001 2180 6431Mechanobiology Institute, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore ,grid.185448.40000 0004 0637 0221Institute of Molecular and Cell Biology, A*Star, Singapore, Singapore ,grid.7372.10000 0000 8809 1613Warwick Medical School, University of Warwick, Coventry, UK
| |
Collapse
|
44
|
Faerberg DF, Gurarie V, Ruvinsky I. Inferring temporal organization of postembryonic development from high-content behavioral tracking. Dev Biol 2021; 475:54-64. [PMID: 33636188 PMCID: PMC8107144 DOI: 10.1016/j.ydbio.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/22/2022]
Abstract
Understanding temporal regulation of development remains an important challenge. Whereas average, species-typical timing of many developmental processes has been established, less is known about inter-individual variability and correlations in timing of specific events. We addressed these questions in the context of postembryonic development in Caenorhabditis elegans. Based on patterns of locomotor activity of freely moving animals, we inferred durations of four larval stages (L1-L4) in over 100 individuals. Analysis of these data supports several conclusions. Individuals have consistently faster or slower rates of development because durations of L1 through L3 stages are positively correlated. The last larval stage, the L4, is less variable than the earlier stages and its duration is largely independent of the rate of early larval development, implying existence of two distinct larval epochs. We describe characteristic patterns of variation and correlation, as well as the fact that stage durations tend to scale relative to total developmental time. This scaling relationship suggests that each larval stage is not limited by an absolute duration, but is instead terminated when a subset of events that must occur prior to adulthood have been completed. The approach described here offers a scalable platform that will facilitate the study of temporal regulation of postembryonic development.
Collapse
Affiliation(s)
- Denis F Faerberg
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Victor Gurarie
- Department of Physics, University of Colorado, Boulder, CO, 80309, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
| |
Collapse
|
45
|
Shark and ray genomics for disentangling their morphological diversity and vertebrate evolution. Dev Biol 2021; 477:262-272. [PMID: 34102168 DOI: 10.1016/j.ydbio.2021.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/24/2022]
Abstract
Developmental studies of sharks and rays (elasmobranchs) have provided much insight into the process of morphological evolution of vertebrates. Although those studies are supposedly fueled by large-scale molecular sequencing information, whole-genome sequences of sharks and rays were made available only recently. One compelling difficulty of elasmobranch developmental biology is the low accessibility to embryonic study materials and their slow development. Another limiting factor is the relatively large size of their genomes. Moreover, their large body sizes restrict sustainable captive breeding, while their high body fluid osmolarity prevents reproducible cell culturing for in vitro experimentation, which has also limited our knowledge of their chromosomal organization for validation of genome sequencing products. This article focuses on egg-laying elasmobranch species used in developmental biology and provides an overview of the characteristics of the shark and ray genomes revealed to date. Developmental studies performed on a gene-by-gene basis are also reviewed from a whole-genome perspective. Among the popular regulatory genes studied in developmental biology, I scrutinize shark homologs of Wnt genes that highlight vanishing repertoires in many other vertebrate lineages, as well as Hox genes that underwent an unexpected modification unique to the elasmobranch lineage. These topics are discussed together with insights into the reconstruction of developmental programs in the common ancestor of vertebrates and its subsequent evolutionary trajectories that mark the features that are unique to, and those characterizing the diversity among, cartilaginous fishes.
Collapse
|
46
|
Rayon T, Briscoe J. Cross-species comparisons and in vitro models to study tempo in development and homeostasis. Interface Focus 2021; 11:20200069. [PMID: 34055305 PMCID: PMC8086913 DOI: 10.1098/rsfs.2020.0069] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 12/14/2022] Open
Abstract
Time is inherent to biological processes. It determines the order of events and the speed at which they take place. However, we still need to refine approaches to measure the course of time in biological systems and understand what controls the pace of development. Here, we argue that the comparison of biological processes across species provides molecular insight into the timekeeping mechanisms in biology. We discuss recent findings and the open questions in the field and highlight the use of in vitro systems as tools to investigate cell-autonomous control as well as the coordination of temporal mechanisms within tissues. Further, we discuss the relevance of studying tempo for tissue transplantation, homeostasis and lifespan.
Collapse
|
47
|
Busby L, Steventon B. Tissue tectonics and the multi-scale regulation of developmental timing. Interface Focus 2021; 11:20200057. [PMID: 34055304 PMCID: PMC8086930 DOI: 10.1098/rsfs.2020.0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 12/17/2022] Open
Abstract
Development encompasses processes that occur at multiple length scales, including gene-regulatory interactions, cell movements and reorganization, cell signalling and growth. It is essential that the timing of events in all of these different processes is coordinated to generate well-patterned tissues and organs. However, how the timing of intrinsic cell state changes is coordinated with events occurring at the multi-tissue and whole-organism level is unknown. Here, we argue that an important mechanism that accounts for the integration of timing across levels of organization is provided by tissue tectonics, i.e. how morphogenetic events driving tissue shape changes result in the relative displacement of signalling and responding tissues and coordinate developmental timing across scales. In doing so, tissue tectonics provides a mechanism by which the cell specification events intrinsic to cells can be modulated by the temporal exposure to extracellular signals. This exposure is in turn regulated by higher-order properties of the embryo, such as their physical properties, rates of growth and the combination of dynamic cell behaviours, impacting tissue morphogenesis. Tissue tectonics creates a downward flow of information from higher to lower levels of biological organization, providing an instance of downward causation in development.
Collapse
Affiliation(s)
- Lara Busby
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | | |
Collapse
|
48
|
Actuation enhances patterning in human neural tube organoids. Nat Commun 2021; 12:3192. [PMID: 34045434 PMCID: PMC8159931 DOI: 10.1038/s41467-021-22952-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/03/2021] [Indexed: 12/20/2022] Open
Abstract
Tissues achieve their complex spatial organization through an interplay between gene regulatory networks, cell-cell communication, and physical interactions mediated by mechanical forces. Current strategies to generate in-vitro tissues have largely failed to implement such active, dynamically coordinated mechanical manipulations, relying instead on extracellular matrices which respond to, rather than impose mechanical forces. Here, we develop devices that enable the actuation of organoids. We show that active mechanical forces increase growth and lead to enhanced patterning in an organoid model of the neural tube derived from single human pluripotent stem cells (hPSC). Using a combination of single-cell transcriptomics and immunohistochemistry, we demonstrate that organoid mechanoregulation due to actuation operates in a temporally restricted competence window, and that organoid response to stretch is mediated extracellularly by matrix stiffness and intracellularly by cytoskeleton contractility and planar cell polarity. Exerting active mechanical forces on organoids using the approaches developed here is widely applicable and should enable the generation of more reproducible, programmable organoid shape, identity and patterns, opening avenues for the use of these tools in regenerative medicine and disease modelling applications. Mechanical forces, along with gene regulatory networks and cell-cell signalling, play an important role in the complex organization of tissues. Here the authors describe devices that actively apply mechanical force to developing neural tube, demonstrating that mechanical forces increase growth and enhance patterning.
Collapse
|
49
|
Carvalho JE, Lahaye F, Yong LW, Croce JC, Escrivá H, Yu JK, Schubert M. An Updated Staging System for Cephalochordate Development: One Table Suits Them All. Front Cell Dev Biol 2021; 9:668006. [PMID: 34095136 PMCID: PMC8174843 DOI: 10.3389/fcell.2021.668006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
Chordates are divided into three subphyla: Vertebrata, Tunicata, and Cephalochordata. Phylogenetically, the Cephalochordata, more commonly known as lancelets or amphioxus, constitute the sister group of Vertebrata and Tunicata. Lancelets are small, benthic, marine filter feeders, and their roughly three dozen described species are divided into three genera: Branchiostoma, Epigonichthys, and Asymmetron. Due to their phylogenetic position and their stereotypical chordate morphology and genome architecture, lancelets are key models for understanding the evolutionary history of chordates. Lancelets have thus been studied by generations of scientists, with the first descriptions of adult anatomy and developmental morphology dating back to the 19th century. Today, several different lancelet species are used as laboratory models, predominantly for developmental, molecular and genomic studies. Surprisingly, however, a universal staging system and an unambiguous nomenclature for developing lancelets have not yet been adopted by the scientific community. In this work, we characterized the development of the European lancelet (Branchiostoma lanceolatum) using confocal microscopy and compiled a streamlined developmental staging system, from fertilization through larval life, including an unambiguous stage nomenclature. By tracing growth curves of the European lancelet reared at different temperatures, we were able to show that our staging system permitted an easy conversion of any developmental time into a specific stage name. Furthermore, comparisons of embryos and larvae from the European lancelet (B. lanceolatum), the Florida lancelet (Branchiostoma floridae), two Asian lancelets (Branchiostoma belcheri and Branchiostoma japonicum), and the Bahamas lancelet (Asymmetron lucayanum) demonstrated that our staging system could readily be applied to other lancelet species. Although the detailed staging description was carried out on developing B. lanceolatum, the comparisons with other lancelet species thus strongly suggested that both staging and nomenclature are applicable to all extant lancelets. We conclude that this description of embryonic and larval development will be of great use for the scientific community and that it should be adopted as the new standard for defining and naming developing lancelets. More generally, we anticipate that this work will facilitate future studies comparing representatives from different chordate lineages.
Collapse
Affiliation(s)
- João E Carvalho
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - François Lahaye
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Luok Wen Yong
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jenifer C Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Hector Escrivá
- Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, CNRS, Banyuls-sur-Mer, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| |
Collapse
|
50
|
Running the full human developmental clock in interspecies chimeras using alternative human stem cells with expanded embryonic potential. NPJ Regen Med 2021; 6:25. [PMID: 34001907 PMCID: PMC8128894 DOI: 10.1038/s41536-021-00135-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/20/2021] [Indexed: 02/08/2023] Open
Abstract
Human pluripotent stem cells (hPSCs) can generate specialized cell lineages that have great potential for regenerative therapies and disease modeling. However, the developmental stage of the lineages generated from conventional hPSC cultures in vitro are embryonic in phenotype, and may not possess the cellular maturity necessary for corrective regenerative function in vivo in adult recipients. Here, we present the scientific evidence for how adult human tissues could generate human–animal interspecific chimeras to solve this problem. First, we review the phenotypes of the embryonic lineages differentiated from conventional hPSC in vitro and through organoid technologies and compare their functional relevance to the tissues generated during normal human in utero fetal and adult development. We hypothesize that the developmental incongruence of embryo-stage hPSC-differentiated cells transplanted into a recipient adult host niche is an important mechanism ultimately limiting their utility in cell therapies and adult disease modeling. We propose that this developmental obstacle can be overcome with optimized interspecies chimeras that permit the generation of adult-staged, patient-specific whole organs within animal hosts with human-compatible gestational time-frames. We suggest that achieving this goal may ultimately have to await the derivation of alternative, primitive totipotent-like stem cells with improved embryonic chimera capacities. We review the scientific challenges of deriving alternative human stem cell states with expanded embryonic potential, outline a path forward for conducting this emerging research with appropriate ethical and regulatory oversight, and defend the case of why current federal funding restrictions on this important category of biomedical research should be liberalized.
Collapse
|