1
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Farag N, Sacharen C, Avni L, Nachman I. Coordination between endoderm progression and mouse gastruloid elongation controls endodermal morphotype choice. Dev Cell 2024:S1534-5807(24)00335-6. [PMID: 38838673 DOI: 10.1016/j.devcel.2024.05.017] [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: 03/24/2023] [Revised: 09/11/2023] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Embryonic development is highly robust. Morphogenetic variability between embryos (under ideal conditions) is largely quantitative. This robustness stands in contrast to in vitro embryo-like models, which, like most organoids, can display a high degree of tissue morphogenetic variability. The source of this difference is not fully understood. We use the mouse gastruloid model to study the morphogenetic progression of definitive endoderm (DE) and its divergence. We first catalog the different morphologies and characterize their statistics. We then learn predictive models for DE morphotype based on earlier expression and morphology measurements. Finally, we analyze these models to identify key drivers of morphotype variability and devise gastruloid-specific and global interventions that can lower this variability and steer morphotype choice. In the process, we identify two types of coordination lacking in the in vitro model but required for robust gut-tube formation. This approach can help improve the quality and usability of 3D embryo-like models.
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Affiliation(s)
- Naama Farag
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Chen Sacharen
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Lara Avni
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Iftach Nachman
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel.
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2
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Hewitt MN, Cruz IA, Raible DW. Spherical harmonics analysis reveals cell shape-fate relationships in zebrafish lateral line neuromasts. Development 2024; 151:dev202251. [PMID: 38276966 PMCID: PMC10905750 DOI: 10.1242/dev.202251] [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: 08/11/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
Cell shape is a powerful readout of cell state, fate and function. We describe a custom workflow to perform semi-automated, 3D cell and nucleus segmentation, and spherical harmonics and principal components analysis to distill cell and nuclear shape variation into discrete biologically meaningful parameters. We apply these methods to analyze shape in the neuromast cells of the zebrafish lateral line system, finding that shapes vary with cell location and identity. The distinction between hair cells and support cells accounted for much of the variation, which allowed us to train classifiers to predict cell identity from shape features. Using transgenic markers for support cell subpopulations, we found that subtypes had different shapes from each other. To investigate how loss of a neuromast cell type altered cell shape distributions, we examined atoh1a mutants that lack hair cells. We found that mutant neuromasts lacked the cell shape phenotype associated with hair cells, but did not exhibit a mutant-specific cell shape. Our results demonstrate the utility of using 3D cell shape features to characterize, compare and classify cells in a living developing organism.
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Affiliation(s)
- Madeleine N. Hewitt
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Otolaryngology-HNS, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Iván A. Cruz
- Department of Biological Structure, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - David W. Raible
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Otolaryngology-HNS, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Biological Structure, University of Washington School of Medicine, Seattle, WA 98195, USA
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3
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Cochella L, Chaker Z. Development, regeneration and aging: a bizarre love triangle. Development 2023; 150:dev202086. [PMID: 37791585 DOI: 10.1242/dev.202086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Jacques Monod Conference on 'Growth and regeneration during development and aging' was organized by Claude Desplan and Allison Bardin in May 2023. The conference took place in Roscoff, France, where participants shared recent conceptual advances under the general motto that developmental processes do not end with embryogenesis. The meeting covered various aspects of how development relates to fitness, regeneration and aging across a refreshing diversity of evolutionarily distant organisms.
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Affiliation(s)
- Luisa Cochella
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zayna Chaker
- Biozentrum, University of Basel, 4056 Basel, Switzerland
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4
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Guo JL, Januszyk M, Longaker MT. Machine Learning in Tissue Engineering. Tissue Eng Part A 2023; 29:2-19. [PMID: 35943870 PMCID: PMC9885550 DOI: 10.1089/ten.tea.2022.0128] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/02/2022] [Indexed: 02/03/2023] Open
Abstract
Machine learning (ML) and artificial intelligence have accelerated scientific discovery, augmented clinical practice, and deepened fundamental understanding of many biological phenomena. ML technologies have now been applied to diverse areas of tissue engineering research, including biomaterial design, scaffold fabrication, and cell/tissue modeling. Emerging ML-empowered strategies include machine-optimized polymer synthesis, predictive modeling of scaffold fabrication processes, complex analyses of structure-function relationships, and deep learning of spatialized cell phenotypes and tissue composition. The emergence of ML in tissue engineering, while relatively recent, has already enabled increasingly complex and multivariate analyses of the relationships between biological, chemical, and physical factors in driving tissue regenerative outcomes. This review highlights the novel methodologies, emerging strategies, and areas of potential growth within this rapidly evolving area of research. Impact statement Machine learning (ML) has accelerated scientific discovery and augmented clinical practice across multiple fields. Now, ML has driven exciting new paradigms in tissue engineering research, including machine-optimized biomaterial design, predictive modeling of scaffold fabrication, and spatiotemporal analysis of cell and tissue systems. The emergence of ML in tissue engineering, while relatively recent, has already enabled increasingly complex analyses of the relationships between biological, chemical, and physical factors in driving tissue regenerative outcomes. This review highlights the novel methodologies, emerging strategies, and areas of potential growth within this rapidly evolving area of research.
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Affiliation(s)
- Jason L. Guo
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Michael Januszyk
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Michael T. Longaker
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
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5
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Single-cell transcriptome analysis reveals three sequential phases of gene expression during zebrafish sensory hair cell regeneration. Dev Cell 2022; 57:799-819.e6. [PMID: 35316618 PMCID: PMC9188816 DOI: 10.1016/j.devcel.2022.03.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/19/2021] [Accepted: 02/28/2022] [Indexed: 12/20/2022]
Abstract
Loss of sensory hair cells (HCs) in the mammalian inner ear leads to permanent hearing and vestibular defects, whereas loss of HCs in zebrafish results in their regeneration. We used single-cell RNA sequencing (scRNA-seq) to characterize the transcriptional dynamics of HC regeneration in zebrafish at unprecedented spatiotemporal resolution. We uncovered three sequentially activated modules: first, an injury/inflammatory response and downregulation of progenitor cell maintenance genes within minutes after HC loss; second, the transient activation of regeneration-specific genes; and third, a robust re-activation of developmental gene programs, including HC specification, cell-cycle activation, ribosome biogenesis, and a metabolic switch to oxidative phosphorylation. The results are relevant not only for our understanding of HC regeneration and how we might be able to trigger it in mammals but also for regenerative processes in general. The data are searchable and publicly accessible via a web-based interface.
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6
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Udagawa T, Atkinson PJ, Milon B, Abitbol JM, Song Y, Sperber M, Huarcaya Najarro E, Scheibinger M, Elkon R, Hertzano R, Cheng AG. Lineage-tracing and translatomic analysis of damage-inducible mitotic cochlear progenitors identifies candidate genes regulating regeneration. PLoS Biol 2021; 19:e3001445. [PMID: 34758021 PMCID: PMC8608324 DOI: 10.1371/journal.pbio.3001445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 11/22/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
Cochlear supporting cells (SCs) are glia-like cells critical for hearing function. In the neonatal cochlea, the greater epithelial ridge (GER) is a mitotically quiescent and transient organ, which has been shown to nonmitotically regenerate SCs. Here, we ablated Lgr5+ SCs using Lgr5-DTR mice and found mitotic regeneration of SCs by GER cells in vivo. With lineage tracing, we show that the GER houses progenitor cells that robustly divide and migrate into the organ of Corti to replenish ablated SCs. Regenerated SCs display coordinated calcium transients, markers of the SC subtype inner phalangeal cells, and survive in the mature cochlea. Via RiboTag, RNA-sequencing, and gene clustering algorithms, we reveal 11 distinct gene clusters comprising markers of the quiescent and damaged GER, and damage-responsive genes driving cell migration and mitotic regeneration. Together, our study characterizes GER cells as mitotic progenitors with regenerative potential and unveils their quiescent and damaged translatomes.
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Affiliation(s)
- Tomokatsu Udagawa
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Otorhinolaryngology, The Jikei University School of Medicine, Tokyo, Japan
| | - Patrick J. Atkinson
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Beatrice Milon
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Julia M. Abitbol
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Michal Sperber
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Elvis Huarcaya Najarro
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mirko Scheibinger
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronna Hertzano
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alan G. Cheng
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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7
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Raina D, Bahadori A, Stanoev A, Protzek M, Koseska A, Schröter C. Cell-cell communication through FGF4 generates and maintains robust proportions of differentiated cell types in embryonic stem cells. Development 2021; 148:dev199926. [PMID: 34651174 PMCID: PMC8602943 DOI: 10.1242/dev.199926] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/04/2021] [Indexed: 01/20/2023]
Abstract
During embryonic development and tissue homeostasis, reproducible proportions of differentiated cell types are specified from populations of multipotent precursor cells. Molecular mechanisms that enable both robust cell-type proportioning despite variable initial conditions in the precursor cells, and the re-establishment of these proportions upon perturbations in a developing tissue remain to be characterized. Here, we report that the differentiation of robust proportions of epiblast-like and primitive endoderm-like cells in mouse embryonic stem cell cultures emerges at the population level through cell-cell communication via a short-range fibroblast growth factor 4 (FGF4) signal. We characterize the molecular and dynamical properties of the communication mechanism and show how it controls both robust cell-type proportioning from a wide range of experimentally controlled initial conditions, as well as the autonomous re-establishment of these proportions following the isolation of one cell type. The generation and maintenance of reproducible proportions of discrete cell types is a new function for FGF signaling that might operate in a range of developing tissues.
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Affiliation(s)
| | | | | | | | | | - Christian Schröter
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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8
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Betjes MA, Zheng X, Kok RNU, van Zon JS, Tans SJ. Cell Tracking for Organoids: Lessons From Developmental Biology. Front Cell Dev Biol 2021; 9:675013. [PMID: 34150770 PMCID: PMC8209328 DOI: 10.3389/fcell.2021.675013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022] Open
Abstract
Organoids have emerged as powerful model systems to study organ development and regeneration at the cellular level. Recently developed microscopy techniques that track individual cells through space and time hold great promise to elucidate the organizational principles of organs and organoids. Applied extensively in the past decade to embryo development and 2D cell cultures, cell tracking can reveal the cellular lineage trees, proliferation rates, and their spatial distributions, while fluorescent markers indicate differentiation events and other cellular processes. Here, we review a number of recent studies that exemplify the power of this approach, and illustrate its potential to organoid research. We will discuss promising future routes, and the key technical challenges that need to be overcome to apply cell tracking techniques to organoid biology.
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Affiliation(s)
| | | | | | | | - Sander J Tans
- AMOLF, Amsterdam, Netherlands.,Bionanoscience Department, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
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9
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Dual recombinases-based genetic lineage tracing for stem cell research with enhanced precision. SCIENCE CHINA-LIFE SCIENCES 2021; 64:2060-2072. [PMID: 33847909 DOI: 10.1007/s11427-020-1889-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Stem cell research has become a hot topic in biology, as the understanding of stem cell biology can provide new insights for both regenerative medicine and clinical treatment of diseases. Accurately deciphering the fate of stem cells is the basis for understanding the mechanism and function of stem cells during tissue repair and regeneration. Cre-loxP-mediated recombination has been widely applied in fate mapping of stem cells for many years. However, nonspecific labeling by conventional cell lineage tracing strategies has led to discrepancies or even controversies in multiple fields. Recently, dual recombinase-mediated lineage tracing strategies have been developed to improve both the resolution and precision of stem cell fate mapping. These new genetic strategies also expand the application of lineage tracing in studying cell origin and fate. Here, we review cell lineage tracing methods, especially dual genetic approaches, and then provide examples to describe how they are used to study stem cell fate plasticity and function in vivo.
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10
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Liang Z, Zhang T, Zhan T, Cheng G, Zhang W, Jia H, Yang H. Metformin alleviates cisplatin-induced ototoxicity by autophagy induction possibly via the AMPK/FOXO3a pathway. J Neurophysiol 2021; 125:1202-1212. [PMID: 33625942 DOI: 10.1152/jn.00417.2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cisplatin is an antitumor drug that is widely used for the treatment of various solid tumors. Unfortunately, patients are often troubled by serious side effects, especially hearing loss. Up to now, there have been no clear and effective measures to prevent cisplatin-induced ototoxicity in clinical use. We explored the role of autophagy and the efficacy of metformin in cisplatin-induced ototoxicity in cells, zebrafish, and mice. Furthermore, the underlying molecular mechanism of how metformin affects cisplatin-induced ototoxicity was examined. In in vitro experiments, autophagy levels in HEI-OC1 cells were assessed using fluorescence and Western blot analyses. In in vivo experiments, whether metformin had a protective effect against cisplatin ototoxicity was validated in zebrafish and C57BL/6 mice. The results showed that cisplatin induced autophagy activation in HEI-OC1 cells. Metformin exerted antagonistic effects against cisplatin ototoxicity in HEI-OC1 cells, zebrafish, and mice. Notably, metformin activated autophagy and increased the expression levels of the adenosine monophosphate-activated protein kinase (AMPK) and the transcription factor Forkhead box protein O3 (FOXO3a), whereas cells with AMPK silencing displayed otherwise. Our findings indicate that metformin alleviates cisplatin-induced ototoxicity possibly through AMPK/FOXO3a-mediated autophagy machinery. This study underpins further researches on the prevention and treatment of cisplatin ototoxicity.NEW & NOTEWORTHY Cisplatin is an antitumor drug that is widely used for the treatment of various solid tumors. Up to now, there have been no clear and effective measures to prevent cisplatin-induced ototoxicity in clinical use. We investigated the protective effect of metformin on cisplatin ototoxicity in vitro and in vivo. Our findings indicate that metformin alleviates cisplatin-induced ototoxicity possibly through AMPK/FOXO3a-mediated autophagy machinery. This study underpins further researches on the prevention and treatment of cisplatin ototoxicity.
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Affiliation(s)
- Zhengrong Liang
- Department of Otolaryngology, The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
| | - Tao Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
| | - Ting Zhan
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Gui Cheng
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Weijian Zhang
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Haiying Jia
- Department of Otolaryngology, The First Affiliated Hospital of Jinan University, Guangzhou, People's Republic of China
| | - Haidi Yang
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.,Hearing and Speech Department, Xinhua College of Sun Yat-sen University, Guangzhou, People's Republic of China
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11
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Tissue-Nonspecific Alkaline Phosphatase-A Gatekeeper of Physiological Conditions in Health and a Modulator of Biological Environments in Disease. Biomolecules 2020; 10:biom10121648. [PMID: 33302551 PMCID: PMC7763311 DOI: 10.3390/biom10121648] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022] Open
Abstract
Tissue-nonspecific alkaline phosphatase (TNAP) is a ubiquitously expressed enzyme that is best known for its role during mineralization processes in bones and skeleton. The enzyme metabolizes phosphate compounds like inorganic pyrophosphate and pyridoxal-5′-phosphate to provide, among others, inorganic phosphate for the mineralization and transportable vitamin B6 molecules. Patients with inherited loss of function mutations in the ALPL gene and consequently altered TNAP activity are suffering from the rare metabolic disease hypophosphatasia (HPP). This systemic disease is mainly characterized by impaired bone and dental mineralization but may also be accompanied by neurological symptoms, like anxiety disorders, seizures, and depression. HPP characteristically affects all ages and shows a wide range of clinical symptoms and disease severity, which results in the classification into different clinical subtypes. This review describes the molecular function of TNAP during the mineralization of bones and teeth, further discusses the current knowledge on the enzyme’s role in the nervous system and in sensory perception. An additional focus is set on the molecular role of TNAP in health and on functional observations reported in common laboratory vertebrate disease models, like rodents and zebrafish.
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12
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Erzberger A, Jacobo A, Dasgupta A, Hudspeth AJ. Mechanochemical symmetry breaking during morphogenesis of lateral-line sensory organs. NATURE PHYSICS 2020; 16:949-957. [PMID: 33790985 PMCID: PMC8009062 DOI: 10.1038/s41567-020-0894-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Actively regulated symmetry breaking, which is ubiquitous in biological cells, underlies phenomena such as directed cellular movement and morphological polarization. Here we investigate how an organ-level polarity pattern emerges through symmetry breaking at the cellular level during the formation of a mechanosensory organ. Combining theory, genetic perturbations, and in vivo imaging, we study the development and regeneration of the fluid-motion sensors in the zebrafish's lateral line. We find that two interacting symmetry-breaking events - one mediated by biochemical signaling and the other by cellular mechanics - give rise to precise rotations of cell pairs, which produce a mirror-symmetric polarity pattern in the receptor organ.
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Affiliation(s)
- A. Erzberger
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065 USA
- These authors contributed equally
- ;
| | - A. Jacobo
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065 USA
- These authors contributed equally
| | - A. Dasgupta
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065 USA
| | - A. J. Hudspeth
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065 USA
- ;
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13
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Hartmann J, Wong M, Gallo E, Gilmour D. An image-based data-driven analysis of cellular architecture in a developing tissue. eLife 2020; 9:e55913. [PMID: 32501214 PMCID: PMC7274788 DOI: 10.7554/elife.55913] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/24/2020] [Indexed: 12/22/2022] Open
Abstract
Quantitative microscopy is becoming increasingly crucial in efforts to disentangle the complexity of organogenesis, yet adoption of the potent new toolbox provided by modern data science has been slow, primarily because it is often not directly applicable to developmental imaging data. We tackle this issue with a newly developed algorithm that uses point cloud-based morphometry to unpack the rich information encoded in 3D image data into a straightforward numerical representation. This enabled us to employ data science tools, including machine learning, to analyze and integrate cell morphology, intracellular organization, gene expression and annotated contextual knowledge. We apply these techniques to construct and explore a quantitative atlas of cellular architecture for the zebrafish posterior lateral line primordium, an experimentally tractable model of complex self-organized organogenesis. In doing so, we are able to retrieve both previously established and novel biologically relevant patterns, demonstrating the potential of our data-driven approach.
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Affiliation(s)
- Jonas Hartmann
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mie Wong
- Institute of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
| | - Elisa Gallo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Institute of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Darren Gilmour
- Institute of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
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14
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Ye Z, Su Z, Xie S, Liu Y, Wang Y, Xu X, Zheng Y, Zhao M, Jiang L. Yap-lin28a axis targets let7-Wnt pathway to restore progenitors for initiating regeneration. eLife 2020; 9:55771. [PMID: 32352377 PMCID: PMC7250571 DOI: 10.7554/elife.55771] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
The sox2 expressing (sox2+) progenitors in adult mammalian inner ear lose the capacity to regenerate while progenitors in the zebrafish lateral line are able to proliferate and regenerate damaged HCs throughout lifetime. To mimic the HC damage in mammals, we have established a zebrafish severe injury model to eliminate both progenitors and HCs. The atoh1a expressing (atoh1a+) HC precursors were the main population that survived post severe injury, and gained sox2 expression to initiate progenitor regeneration. In response to severe injury, yap was activated to upregulate lin28a transcription. Severe-injury-induced progenitor regeneration was disabled in lin28a or yap mutants. In contrary, overexpression of lin28a initiated the recovery of sox2+ progenitors. Mechanistically, microRNA let7 acted downstream of lin28a to activate Wnt pathway for promoting regeneration. Our findings that lin28a is necessary and sufficient to regenerate the exhausted sox2+ progenitors shed light on restoration of progenitors to initiate HC regeneration in mammals.
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Affiliation(s)
- Zhian Ye
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zhongwu Su
- Department of Otolaryngology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Siyu Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
| | - Yuye Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yongqiang Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xi Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
| | - Yiqing Zheng
- Department of Otolaryngology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Meng Zhao
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-Sen University, Ministry of Education, Guangzhou, China
| | - Linjia Jiang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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15
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Kozak EL, Palit S, Miranda-Rodríguez JR, Janjic A, Böttcher A, Lickert H, Enard W, Theis FJ, López-Schier H. Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2. Curr Biol 2020; 30:1142-1151.e6. [PMID: 32109392 DOI: 10.1016/j.cub.2020.01.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/28/2019] [Accepted: 01/08/2020] [Indexed: 12/24/2022]
Abstract
Most plane-polarized tissues are formed by identically oriented cells [1, 2]. A notable exception occurs in the vertebrate vestibular system and lateral-line neuromasts, where mechanosensory hair cells orient along a single axis but in opposite directions to generate bipolar epithelia [3-5]. In zebrafish neuromasts, pairs of hair cells arise from the division of a non-sensory progenitor [6, 7] and acquire opposing planar polarity via the asymmetric expression of the polarity-determinant transcription factor Emx2 [8-11]. Here, we reveal the initial symmetry-breaking step by decrypting the developmental trajectory of hair cells using single-cell RNA sequencing (scRNA-seq), diffusion pseudotime analysis, lineage tracing, and mutagenesis. We show that Emx2 is absent in non-sensory epithelial cells, begins expression in hair-cell progenitors, and is downregulated in one of the sibling hair cells via signaling through the Notch1a receptor. Analysis of Emx2-deficient specimens, in which every hair cell adopts an identical direction, indicates that Emx2 asymmetry does not result from auto-regulatory feedback. These data reveal a two-tiered mechanism by which the symmetric monodirectional ground state of the epithelium is inverted by deterministic initiation of Emx2 expression in hair-cell progenitors and a subsequent stochastic repression of Emx2 in one of the sibling hair cells breaks directional symmetry to establish planar bipolarity.
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Affiliation(s)
- Eva L Kozak
- Research Unit of Sensory Biology & Organogenesis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Subarna Palit
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jerónimo R Miranda-Rodríguez
- Research Unit of Sensory Biology & Organogenesis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Aleksandar Janjic
- Department Biology II, Anthropology and Human Genomics, Ludwig Maximilians University of Munich, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; German Center for Diabetes Research, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; German Center for Diabetes Research, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Stem Cell Research, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; School of Medicine, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany
| | - Wolfgang Enard
- Department Biology II, Anthropology and Human Genomics, Ludwig Maximilians University of Munich, Großhaderner Straße 2, 82152 Martinsried, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie, 85354 Freising, Germany; Department of Mathematics, Technical University of Munich, Boltzmannstraße 3, 85748 Garching, Germany
| | - Hernán López-Schier
- Research Unit of Sensory Biology & Organogenesis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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16
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Espinosa-Medina I, Garcia-Marques J, Cepko C, Lee T. High-throughput dense reconstruction of cell lineages. Open Biol 2019; 9:190229. [PMID: 31822210 PMCID: PMC6936253 DOI: 10.1098/rsob.190229] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/12/2019] [Indexed: 12/11/2022] Open
Abstract
The first meeting exclusively dedicated to the 'High-throughput dense reconstruction of cell lineages' took place at Janelia Research Campus (Howard Hughes Medical Institute) from 14 to 18 April 2019. Organized by Tzumin Lee, Connie Cepko, Jorge Garcia-Marques and Isabel Espinosa-Medina, this meeting echoed the recent eruption of new tools that allow the reconstruction of lineages based on the phylogenetic analysis of DNA mutations induced during development. Combined with single-cell RNA sequencing, these tools promise to solve the lineage of complex model organisms at single-cell resolution. Here, we compile the conference consensus on the technological and computational challenges emerging from the use of the new strategies, as well as potential solutions.
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Affiliation(s)
- Isabel Espinosa-Medina
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Jorge Garcia-Marques
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Connie Cepko
- Department of Genetics and Ophthalmology, Harvard Medical School, Boston, MA 02115, USA
| | - Tzumin Lee
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
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17
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Abstract
Deafness or hearing deficits are debilitating conditions. They are often caused by loss of sensory hair cells or defects in their function. In contrast to mammals, nonmammalian vertebrates robustly regenerate hair cells after injury. Studying the molecular and cellular basis of nonmammalian vertebrate hair cell regeneration provides valuable insights into developing cures for human deafness. In this review, we discuss the current literature on hair cell regeneration in the context of other models for sensory cell regeneration, such as the retina and the olfactory epithelium. This comparison reveals commonalities with, as well as differences between, the different regenerating systems, which begin to define a cellular and molecular blueprint of regeneration. In addition, we propose how new technical advances can address outstanding questions in the field.
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Affiliation(s)
- Nicolas Denans
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;
| | - Sungmin Baek
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;
| | - Tatjana Piotrowski
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;
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18
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Thomas ED, Raible DW. Distinct progenitor populations mediate regeneration in the zebrafish lateral line. eLife 2019; 8:43736. [PMID: 30834891 PMCID: PMC6433462 DOI: 10.7554/elife.43736] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 02/28/2019] [Indexed: 01/06/2023] Open
Abstract
Mechanosensory hair cells of the zebrafish lateral line regenerate rapidly following damage. These renewed hair cells arise from the proliferation of surrounding support cells, which undergo symmetric division to produce two hair cell daughters. Given the continued regenerative capacity of the lateral line, support cells presumably have the ability to replenish themselves. Utilizing novel transgenic lines, we identified support cell populations with distinct progenitor identities. These populations show differences in their ability to generate new hair cells during homeostasis and regeneration. Targeted ablation of support cells reduced the number of regenerated hair cells. Furthermore, progenitors regenerated after targeted support cell ablation in the absence of hair cell damage. We also determined that distinct support cell populations are independently regulated by Notch signaling. The existence of independent progenitor populations could provide flexibility for the continued generation of new hair cells under a variety of conditions throughout the life of the animal.
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Affiliation(s)
- Eric D Thomas
- Department of Biological Structure, University of Washington, Seattle, United States.,Graduate Program in Neuroscience, University of Washington, Seattle, United States
| | - David W Raible
- Department of Biological Structure, University of Washington, Seattle, United States.,Graduate Program in Neuroscience, University of Washington, Seattle, United States.,Virginia Merrill Bloedel Hearing Research Center, University of Washington, Seattle, United States
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19
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Hu F, Manghnani PN, Feng G, Wu W, Teh C, Liu B. Visualize Embryogenesis and Cell Fate Using Fluorescent Probes with Aggregation-Induced Emission. ACS APPLIED MATERIALS & INTERFACES 2019; 11:3737-3744. [PMID: 30656936 DOI: 10.1021/acsami.8b19391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Horseradish peroxidase (HRP) and fluorogen-dextran conjugate are tracers extensively used for injection-based lineage tracing. However, HRP is sensitive to proteolytic digestion, whereas the high-molecular-weight dextran may have antigenicity. Small molecular tracers can overcome these problems, but they usually diffuse from labeled cells, causing inaccurate information. Herein, we developed a small-molecular-weight fluorogen with aggregation-induced emission (AIEgen) for embryonic cell tracing with strong signals against tracer dilution caused by cell division. Once injected into the ancestor cells, the AIEgen can be entrapped in the cells without leakage because of the two hydrophilic and neutral arms. Consequently, it can specifically trace the progenies of the treated ancestor cells. More importantly, the operating concentration of AIEgen can be much higher than that of fluorogens with aggregation-caused quenching, which provides bright signals in daughter cells during embryonic cell tracing, thus overcoming the problem of fast signal degradation typically encountered with the use of traditional cell tracers.
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Affiliation(s)
- Fang Hu
- Department of Chemical and Biomolecular Engineering , National University of Singapore , 4 Engineering Drive 4 , Singapore 117585 , Singapore
| | - Purnima Naresh Manghnani
- Department of Chemical and Biomolecular Engineering , National University of Singapore , 4 Engineering Drive 4 , Singapore 117585 , Singapore
| | - Guangxue Feng
- Department of Chemical and Biomolecular Engineering , National University of Singapore , 4 Engineering Drive 4 , Singapore 117585 , Singapore
| | - Wenbo Wu
- Department of Chemical and Biomolecular Engineering , National University of Singapore , 4 Engineering Drive 4 , Singapore 117585 , Singapore
| | - Cathleen Teh
- Institute of Molecular and Cell Biology, Biopolis , Singapore 138673 , Singapore
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering , National University of Singapore , 4 Engineering Drive 4 , Singapore 117585 , Singapore
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20
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Lush ME, Diaz DC, Koenecke N, Baek S, Boldt H, St Peter MK, Gaitan-Escudero T, Romero-Carvajal A, Busch-Nentwich EM, Perera AG, Hall KE, Peak A, Haug JS, Piotrowski T. scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. eLife 2019; 8:e44431. [PMID: 30681411 PMCID: PMC6363392 DOI: 10.7554/elife.44431] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 01/24/2019] [Indexed: 12/25/2022] Open
Abstract
Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells, zebrafish ear and lateral line hair cells regenerate from poorly characterized support cells. Equally ill-defined is the gene regulatory network underlying the progression of support cells to differentiated hair cells. scRNA-Seq of lateral line organs uncovered five different support cell types, including quiescent and activated stem cells. Ordering of support cells along a developmental trajectory identified self-renewing cells and genes required for hair cell differentiation. scRNA-Seq analyses of fgf3 mutants, in which hair cell regeneration is increased, demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA-Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. The data is searchable and publicly accessible via a web-based interface.
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Affiliation(s)
- Mark E Lush
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Daniel C Diaz
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Nina Koenecke
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Sungmin Baek
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Helena Boldt
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | - Andres Romero-Carvajal
- Stowers Institute for Medical ResearchKansas CityUnited States
- Pontificia Universidad Catolica del EcuadorCiencias BiologicasQuitoEcuador
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Department of MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Anoja G Perera
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Kathryn E Hall
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Allison Peak
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jeffrey S Haug
- Stowers Institute for Medical ResearchKansas CityUnited States
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21
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Fuentes R, Letelier J, Tajer B, Valdivia LE, Mullins MC. Fishing forward and reverse: Advances in zebrafish phenomics. Mech Dev 2018; 154:296-308. [PMID: 30130581 PMCID: PMC6289646 DOI: 10.1016/j.mod.2018.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/06/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022]
Abstract
Understanding how the genome instructs the phenotypic characteristics of an organism is one of the major scientific endeavors of our time. Advances in genetics have progressively deciphered the inheritance, identity and biological relevance of genetically encoded information, contributing to the rise of several, complementary omic disciplines. One of them is phenomics, an emergent area of biology dedicated to the systematic multi-scale analysis of phenotypic traits. This discipline provides valuable gene function information to the rapidly evolving field of genetics. Current molecular tools enable genome-wide analyses that link gene sequence to function in multi-cellular organisms, illuminating the genome-phenome relationship. Among vertebrates, zebrafish has emerged as an outstanding model organism for high-throughput phenotyping and modeling of human disorders. Advances in both systematic mutagenesis and phenotypic analyses of embryonic and post-embryonic stages in zebrafish have revealed the function of a valuable collection of genes and the general structure of several complex traits. In this review, we summarize multiple large-scale genetic efforts addressing parental, embryonic, and adult phenotyping in the zebrafish. The genetic and quantitative tools available in the zebrafish model, coupled with the broad spectrum of phenotypes that can be assayed, make it a powerful model for phenomics, well suited for the dissection of genotype-phenotype associations in development, physiology, health and disease.
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Affiliation(s)
- Ricardo Fuentes
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joaquín Letelier
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Seville, Spain; Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Benjamin Tajer
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonardo E Valdivia
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
| | - Mary C Mullins
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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