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Hack SJ, Petereit J, Tseng KAS. Temporal Transcriptomic Profiling of the Developing Xenopus laevis Eye. Cells 2024; 13:1390. [PMID: 39195278 PMCID: PMC11352439 DOI: 10.3390/cells13161390] [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: 07/10/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024] Open
Abstract
Retinal progenitor cells (RPCs) are a multipotent and highly proliferative population that give rise to all retinal cell types during organogenesis. Defining their molecular signature is a key step towards identifying suitable approaches to treat visual impairments. Here, we performed RNA sequencing of whole eyes from Xenopus at three embryonic stages and used differential expression analysis to define the transcriptomic profiles of optic tissues containing proliferating and differentiating RPCs during retinogenesis. Gene Ontology and KEGG pathway analyses showed that genes associated with developmental pathways (including Wnt and Hedgehog signaling) were upregulated during the period of active RPC proliferation in early retinal development (Nieuwkoop Faber st. 24 and 27). Developing eyes had dynamic expression profiles and shifted to enrichment for metabolic processes and phototransduction during RPC progeny specification and differentiation (st. 35). Furthermore, conserved adult eye regeneration genes were also expressed during early retinal development, including sox2, pax6, nrl, and Notch signaling components. The eye transcriptomic profiles presented here span RPC proliferation to retinogenesis and include regrowth-competent stages. Thus, our dataset provides a rich resource to uncover molecular regulators of RPC activity and will allow future studies to address regulators of RPC proliferation during eye repair and regrowth.
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Affiliation(s)
- Samantha J. Hack
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA
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2
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Hack SJ, Petereit J, Tseng KAS. Temporal Transcriptomic Profiling of the Developing Xenopus laevis Eye. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.603187. [PMID: 39091861 PMCID: PMC11291033 DOI: 10.1101/2024.07.20.603187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Retinal progenitor cells (RPCs) are a multipotent and highly proliferative population that give rise to all retinal cell types during organogenesis. Defining their molecular signature is a key step towards identifying suitable approaches to treat visual impairments. Here, we performed RNA-sequencing of whole eyes from Xenopus at three embryonic stages and used differential expression analysis to define the transcriptomic profiles of optic tissues containing proliferating and differentiating RPCs during retinogenesis. Gene Ontology and KEGG pathway analyses showed that genes associated with developmental pathways (including Wnt and Hedgehog signaling) were upregulated during the period of active RPC proliferation in early retinal development (Nieuwkoop Faber st. 24 and 27). Developing eyes had dynamic expression profiles and shifted to enrichment for metabolic processes and phototransduction during RPC progeny specification and differentiation (st. 35). Furthermore, conserved adult eye regeneration genes were also expressed during early retinal development including sox2, pax6, nrl, and Notch signaling components. The eye transcriptomic profiles presented here span RPC proliferation to retinogenesis and included regrowth-competent stages. Thus, our dataset provides a rich resource to uncover molecular regulators of RPC activity and will allow future studies to address regulators of RPC proliferation during eye repair and regrowth.
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Affiliation(s)
- Samantha J. Hack
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno
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3
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Baxi AB, Li J, Quach VM, Pade LR, Moody SA, Nemes P. Cell lineage-guided mass spectrometry reveals increased energy metabolism and reactive oxygen species in the vertebrate organizer. Proc Natl Acad Sci U S A 2024; 121:e2311625121. [PMID: 38300871 PMCID: PMC10861879 DOI: 10.1073/pnas.2311625121] [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: 07/13/2023] [Accepted: 12/12/2023] [Indexed: 02/03/2024] Open
Abstract
Molecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been mostly limited to transcripts and a few proteins, the latter due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog (X. laevis), a popular model of development, has long been known to be the origin of signals that pattern the mesoderm and central nervous system. Molecular screens of the SMO have identified several genes responsible for the ability of the SMO to establish the body axis. Nonetheless, a comprehensive study of proteins and metabolites produced specifically in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the remainder of the embryo using high-resolution mass spectrometry (HRMS). Quantification of ~4,600 proteins and a panel of targeted metabolites documented differential expression for 460 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the SMO. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO. Chemical perturbation of the redox gradient perturbed mesoderm involution during early gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.
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Affiliation(s)
- Aparna B. Baxi
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
- Department of Anatomy and Cell Biology,School of Medical and Health Sciences,The George Washington University, Washington, DC20037
| | - Jie Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
| | - Vi M. Quach
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
| | - Leena R. Pade
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
| | - Sally A. Moody
- Department of Anatomy and Cell Biology,School of Medical and Health Sciences,The George Washington University, Washington, DC20037
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD20742
- Department of Anatomy and Cell Biology,School of Medical and Health Sciences,The George Washington University, Washington, DC20037
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4
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Colozza G, Lee H, Merenda A, Wu SHS, Català-Bordes A, Radaszkiewicz TW, Jordens I, Lee JH, Bamford AD, Farnhammer F, Low TY, Maurice MM, Bryja V, Kim J, Koo BK. Intestinal Paneth cell differentiation relies on asymmetric regulation of Wnt signaling by Daam1/2. SCIENCE ADVANCES 2023; 9:eadh9673. [PMID: 38000028 PMCID: PMC10672176 DOI: 10.1126/sciadv.adh9673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023]
Abstract
The mammalian intestine is one of the most rapidly self-renewing tissues, driven by stem cells residing at the crypt bottom. Paneth cells form a major element of the niche microenvironment providing various growth factors to orchestrate intestinal stem cell homeostasis, such as Wnt3. Different Wnt ligands can selectively activate β-catenin-dependent (canonical) or -independent (noncanonical) signaling. Here, we report that the Dishevelled-associated activator of morphogenesis 1 (Daam1) and its paralogue Daam2 asymmetrically regulate canonical and noncanonical Wnt (Wnt/PCP) signaling. Daam1/2 interacts with the Wnt inhibitor RNF43, and Daam1/2 double knockout stimulates canonical Wnt signaling by preventing RNF43-dependent degradation of the Wnt receptor, Frizzled (Fzd). Single-cell RNA sequencing analysis revealed that Paneth cell differentiation is impaired by Daam1/2 depletion because of defective Wnt/PCP signaling. Together, we identified Daam1/2 as an unexpected hub molecule coordinating both canonical and noncanonical Wnt, which is fundamental for specifying an adequate number of Paneth cells.
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Affiliation(s)
- Gabriele Colozza
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Heetak Lee
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon 34126, Republic of Korea
| | | | - Szu-Hsien Sam Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Andrea Català-Bordes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Tomasz W. Radaszkiewicz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ingrid Jordens
- Oncode Institute and Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Ji-Hyun Lee
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon 34126, Republic of Korea
| | - Aileen-Diane Bamford
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Fiona Farnhammer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Division of Metabolism and Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), University Kebangsaan Malaysia (UKM), Jalan Yaacob Latiff, Bandar Tun Razak, 56000 Kuala Lumpur, Malaysia
| | - Madelon M. Maurice
- Oncode Institute and Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Cytokinetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Jihoon Kim
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Center for Genome Engineering, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon 34126, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
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5
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Baxi AB, Li J, Quach VM, Nemes P. Cell Lineage-Guided Microanalytical Mass Spectrometry Reveals Increased Energy Metabolism and Reactive Oxygen Species in the Vertebrate Organizer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548174. [PMID: 37461553 PMCID: PMC10350060 DOI: 10.1101/2023.07.07.548174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2024]
Abstract
Molecular understanding of the vertebrate Organizer, a tissue center critical for inductive signaling during gastrulation, has so far been limited to transcripts and some proteins due to limitations in detection and sensitivity. The Spemann-Mangold Organizer (SMO) in the South African Clawed Frog ( X. laevis ), a popular model of development, has long been discovered to induce the patterning of the central nervous system. Molecular screens on the tissue have identified several genes, such as goosecoid, chordin, and noggin, with independent ability to establish a body axis. A comprehensive study of proteins and metabolites produced in the SMO and their functional roles has been lacking. Here, we pioneer a deep discovery proteomic and targeted metabolomic screen of the SMO in comparison to the rest of the embryo using liquid chromatography high-resolution mass spectrometry (HRMS). Quantification of ∼4,600 proteins and a panel of metabolites documented differential expression for ∼450 proteins and multiple intermediates of energy metabolism in the SMO. Upregulation of oxidative phosphorylation (OXPHOS) and redox regulatory proteins gave rise to elevated oxidative stress and an accumulation of reactive oxygen species in the Organizer. Imaging experiments corroborated these findings, discovering enrichment of hydrogen peroxide in the SMO tissue. Chemical perturbation of the redox gradient affected mesoderm involution during early tissue movements of gastrulation. HRMS expands the bioanalytical toolbox of cell and developmental biology, providing previously unavailable information on molecular classes to challenge and refine our classical understanding of the Organizer and its function during early patterning of the embryo.
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6
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Cheng C, Yan C, Qi CT, Zhao XL, Liu LX, Guo Y, Leng P, Sun J, Ahmtijiang, Liu J, Liu YG. Metabolome and transcriptome analysis of postharvest peach fruit in response to fungal pathogen Monilinia fructicola infection. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Johnson K, Freedman S, Braun R, LaBonne C. Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions. BMC Genomics 2022; 23:723. [PMID: 36273135 PMCID: PMC9588240 DOI: 10.1186/s12864-022-08953-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Background During embryogenesis, the developmental potential of initially pluripotent cells becomes progressively restricted as they transit to lineage restricted states. The pluripotent cells of Xenopus blastula-stage embryos are an ideal system in which to study cell state transitions during developmental decision-making, as gene expression dynamics can be followed at high temporal resolution. Results Here we use transcriptomics to interrogate the process by which pluripotent cells transit to four different lineage-restricted states: neural progenitors, epidermis, endoderm and ventral mesoderm, providing quantitative insights into the dynamics of Waddington’s landscape. Our findings provide novel insights into why the neural progenitor state is the default lineage state for pluripotent cells and uncover novel components of lineage-specific gene regulation. These data reveal an unexpected overlap in the transcriptional responses to BMP4/7 and Activin signaling and provide mechanistic insight into how the timing of signaling inputs such as BMP are temporally controlled to ensure correct lineage decisions. Conclusions Together these analyses provide quantitative insights into the logic and dynamics of developmental decision making in early embryos. They also provide valuable lineage-specific time series data following the acquisition of specific lineage states during development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08953-3.
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Affiliation(s)
- Kristin Johnson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Simon Freedman
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA.,Department of Engineering Sciences and Applied Math, Northwestern University, Evanston, IL, USA
| | - Rosemary Braun
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA.,Department of Engineering Sciences and Applied Math, Northwestern University, Evanston, IL, USA.,Northwestern Institute On Complex Systems, Northwestern University, Evanston, IL, USA
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA.
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8
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Evo-Devo of Urbilateria and its larval forms. Dev Biol 2022; 487:10-20. [DOI: 10.1016/j.ydbio.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/28/2022] [Accepted: 04/08/2022] [Indexed: 12/14/2022]
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9
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Yoon J, Kumar V, Goutam RS, Kim SC, Park S, Lee U, Kim J. Bmp Signal Gradient Modulates Convergent Cell Movement via Xarhgef3.2 during Gastrulation of Xenopus Embryos. Cells 2021; 11:44. [PMID: 35011606 PMCID: PMC8750265 DOI: 10.3390/cells11010044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 01/31/2023] Open
Abstract
Gastrulation is a critical step in the establishment of a basic body plan during development. Convergence and extension (CE) cell movements organize germ layers during gastrulation. Noncanonical Wnt signaling has been known as major signaling that regulates CE cell movement by activating Rho and Rac. In addition, Bmp molecules are expressed in the ventral side of a developing embryo, and the ventral mesoderm region undergoes minimal CE cell movement while the dorsal mesoderm undergoes dynamic cell movements. This suggests that Bmp signal gradient may affect CE cell movement. To investigate whether Bmp signaling negatively regulates CE cell movements, we performed microarray-based screening and found that the transcription of Xenopus Arhgef3.2 (Rho guanine nucleotide exchange factor) was negatively regulated by Bmp signaling. We also showed that overexpression or knockdown of Xarhgef3.2 caused gastrulation defects. Interestingly, Xarhgef3.2 controlled gastrulation cell movements through interacting with Disheveled (Dsh2) and Dsh2-associated activator of morphogenesis 1 (Daam1). Our results suggest that Bmp gradient affects gastrulation cell movement (CE) via negative regulation of Xarhgef3.2 expression.
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Affiliation(s)
- Jaeho Yoon
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
- National Cancer Institute, Frederick, MD 21702, USA
| | - Vijay Kumar
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
| | - Ravi Shankar Goutam
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
| | - Sung-Chan Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
| | - Soochul Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310, Korea;
| | - Unjoo Lee
- Department of Electrical Engineering, Hallym University, Chuncheon 24252, Korea;
| | - Jaebong Kim
- Department of Biochemistry, Institute of Cell Differentiation and Aging, College of Medicine, Hallym University, Chuncheon 24252, Korea; (J.Y.); (V.K.); (R.S.G.); (S.-C.K.)
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10
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Bou-Rouphael J, Durand BC. T-Cell Factors as Transcriptional Inhibitors: Activities and Regulations in Vertebrate Head Development. Front Cell Dev Biol 2021; 9:784998. [PMID: 34901027 PMCID: PMC8651982 DOI: 10.3389/fcell.2021.784998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
Since its first discovery in the late 90s, Wnt canonical signaling has been demonstrated to affect a large variety of neural developmental processes, including, but not limited to, embryonic axis formation, neural proliferation, fate determination, and maintenance of neural stem cells. For decades, studies have focused on the mechanisms controlling the activity of β-catenin, the sole mediator of Wnt transcriptional response. More recently, the spotlight of research is directed towards the last cascade component, the T-cell factor (TCF)/Lymphoid-Enhancer binding Factor (LEF), and more specifically, the TCF/LEF-mediated switch from transcriptional activation to repression, which in both embryonic blastomeres and mouse embryonic stem cells pushes the balance from pluri/multipotency towards differentiation. It has been long known that Groucho/Transducin-Like Enhancer of split (Gro/TLE) is the main co-repressor partner of TCF/LEF. More recently, other TCF/LEF-interacting partners have been identified, including the pro-neural BarH-Like 2 (BARHL2), which belongs to the evolutionary highly conserved family of homeodomain-containing transcription factors. This review describes the activities and regulatory modes of TCF/LEF as transcriptional repressors, with a specific focus on the functions of Barhl2 in vertebrate brain development. Specific attention is given to the transcriptional events leading to formation of the Organizer, as well as the roles and regulations of Wnt/β-catenin pathway in growth of the caudal forebrain. We present TCF/LEF activities in both embryonic and neural stem cells and discuss how alterations of this pathway could lead to tumors.
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Affiliation(s)
| | - Béatrice C. Durand
- Sorbonne Université, CNRS UMR7622, IBPS Developmental Biology Laboratory, Campus Pierre et Marie Curie, Paris, France
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11
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Abraham SP, Nita A, Krejci P, Bosakova M. Cilia kinases in skeletal development and homeostasis. Dev Dyn 2021; 251:577-608. [PMID: 34582081 DOI: 10.1002/dvdy.426] [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: 07/07/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 11/08/2022] Open
Abstract
Primary cilia are dynamic compartments that regulate multiple aspects of cellular signaling. The production, maintenance, and function of cilia involve more than 1000 genes in mammals, and their mutations disrupt the ciliary signaling which manifests in a plethora of pathological conditions-the ciliopathies. Skeletal ciliopathies are genetic disorders affecting the development and homeostasis of the skeleton, and encompass a broad spectrum of pathologies ranging from isolated polydactyly to lethal syndromic dysplasias. The recent advances in forward genetics allowed for the identification of novel regulators of skeletogenesis, and revealed a growing list of ciliary proteins that are critical for signaling pathways implicated in bone physiology. Among these, a group of protein kinases involved in cilia assembly, maintenance, signaling, and disassembly has emerged. In this review, we summarize the functions of cilia kinases in skeletal development and disease, and discuss the available and upcoming treatment options.
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Affiliation(s)
- Sara P Abraham
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Alexandru Nita
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Institute of Animal Physiology and Genetics of the CAS, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Michaela Bosakova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Institute of Animal Physiology and Genetics of the CAS, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
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12
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Satou-Kobayashi Y, Kim JD, Fukamizu A, Asashima M. Temporal transcriptomic profiling reveals dynamic changes in gene expression of Xenopus animal cap upon activin treatment. Sci Rep 2021; 11:14537. [PMID: 34267234 PMCID: PMC8282838 DOI: 10.1038/s41598-021-93524-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
Activin, a member of the transforming growth factor-β (TGF-β) superfamily of proteins, induces various tissues from the amphibian presumptive ectoderm, called animal cap explants (ACs) in vitro. However, it remains unclear how and to what extent the resulting cells recapitulate in vivo development. To comprehensively understand whether the molecular dynamics during activin-induced ACs differentiation reflect the normal development, we performed time-course transcriptome profiling of Xenopus ACs treated with 50 ng/mL of activin A, which predominantly induced dorsal mesoderm. The number of differentially expressed genes (DEGs) in response to activin A increased over time, and totally 9857 upregulated and 6663 downregulated DEGs were detected. 1861 common upregulated DEGs among all Post_activin samples included several Spemann's organizer genes. In addition, the temporal transcriptomes were clearly classified into four distinct groups in correspondence with specific features, reflecting stepwise differentiation into mesoderm derivatives, and a decline in the regulation of nuclear envelop and golgi. From the set of early responsive genes, we also identified the suppressor of cytokine signaling 3 (socs3) as a novel activin A-inducible gene. Our transcriptome data provide a framework to elucidate the transcriptional dynamics of activin-driven AC differentiation, reflecting the molecular characteristics of early normal embryogenesis.
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Affiliation(s)
- Yumeko Satou-Kobayashi
- grid.264706.10000 0000 9239 9995Strategic Innovation and Research Center, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.264706.10000 0000 9239 9995Advanced Comprehensive Research Organization, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan
| | - Jun-Dal Kim
- grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan ,grid.267346.20000 0001 2171 836XDivision of Complex Bioscience Research, Department of Research and Development, Institute of National Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194 Japan
| | - Akiyoshi Fukamizu
- grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan
| | - Makoto Asashima
- grid.264706.10000 0000 9239 9995Strategic Innovation and Research Center, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.264706.10000 0000 9239 9995Advanced Comprehensive Research Organization, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605 Japan ,grid.20515.330000 0001 2369 4728Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1, Tsukuba, Tennoudai Ibaraki 305-8577 Japan
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13
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Plöger R, Viebahn C. Expression patterns of signalling molecules and transcription factors in the early rabbit embryo and their significance for modelling amniote axis formation. Dev Genes Evol 2021; 231:73-83. [PMID: 34100128 PMCID: PMC8213660 DOI: 10.1007/s00427-021-00677-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 11/25/2022]
Abstract
The anterior-posterior axis is a central element of the body plan and, during amniote gastrulation, forms through several transient domains with specific morphogenetic activities. In the chick, experimentally proven activity of signalling molecules and transcription factors lead to the concept of a 'global positioning system' for initial axis formation whereas in the (mammotypical) rabbit embryo, a series of morphological or molecular domains are part of a putative 'three-anchor-point model'. Because circular expression patterns of genes involved in axis formation exist in both amniote groups prior to, and during, gastrulation and may thus be suited to reconcile these models, the expression patterns of selected genes known in the chick, namely the ones coding for the transcription factors eomes and tbx6, the signalling molecule wnt3 and the wnt inhibitor pkdcc, were analysed in the rabbit embryonic disc using in situ hybridisation and placing emphasis on their germ layer location. Peripheral wnt3 and eomes expression in all layers is found initially to be complementary to central pkdcc expression in the hypoblast during early axis formation. Pkdcc then appears - together with a posterior-anterior gradient in wnt3 and eomes domains - in the epiblast posteriorly before the emerging primitive streak is marked by pkdcc and tbx6 at its anterior and posterior extremities, respectively. Conserved circular expression patterns deduced from some of this data may point to shared mechanisms in amniote axis formation while the reshaping of localised gene expression patterns is discussed as part of the 'three-anchor-point model' for establishing the mammalian body plan.
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Affiliation(s)
- Ruben Plöger
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
| | - Christoph Viebahn
- Institute of Anatomy and Embryology, University Medical Center Göttingen, Göttingen, Germany
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14
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Artinger KB, Monsoro-Burq AH. Neural crest multipotency and specification: power and limits of single cell transcriptomic approaches. Fac Rev 2021; 10:38. [PMID: 34046642 PMCID: PMC8130411 DOI: 10.12703/r/10-38] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The neural crest is a unique population of multipotent cells forming in vertebrate embryos. Their vast cell fate potential enables the generation of a diverse array of differentiated cell types in vivo. These include, among others, connective tissue, cartilage and bone of the face and skull, neurons and glia of the peripheral nervous system (including enteric nervous system), and melanocytes. Following migration, these derivatives extensively populate multiple germ layers. Within the competent neural border ectoderm, an area located at the junction between the neural and non-neural ectoderm during embryonic development, neural crest cells form in response to a series of inductive secreted cues including BMP, Wnt, and FGF signals. As cells become progressively specified, they express transcriptional modules conducive with their stage of fate determination or cell state. Those sequential states include the neural border state, the premigratory neural crest state, the epithelium-to-mesenchyme transitional state, and the migratory state to end with post-migratory and differentiation states. However, despite the extensive knowledge accumulated over 150 years of neural crest biology, many key questions remain open, in particular the timing of neural crest lineage determination, the control of potency during early developmental stages, and the lineage relationships between different subpopulations of neural crest cells. In this review, we discuss the recent advances in understanding early neural crest formation using cutting-edge high-throughput single cell sequencing approaches. We will discuss how this new transcriptomic data, from 2017 to 2021, has advanced our knowledge of the steps in neural crest cell lineage commitment and specification, the mechanisms driving multipotency, and diversification. We will then discuss the questions that remain to be resolved and how these approaches may continue to unveil the biology of these fascinating cells.
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Affiliation(s)
- Kristin B Artinger
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, USA
| | - Anne H Monsoro-Burq
- Université Paris-Saclay, Faculté des Sciences d'Orsay, France
- Institut Curie, INSERM U1021, CNRS UMR3347, Orsay, France
- Institut Universitaire de France, Paris, France
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15
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Kakebeen AD, Huebner RJ, Shindo A, Kwon K, Kwon T, Wills AE, Wallingford JB. A temporally resolved transcriptome for developing "Keller" explants of the Xenopus laevis dorsal marginal zone. Dev Dyn 2021; 250:717-731. [PMID: 33368695 DOI: 10.1002/dvdy.289] [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] [Received: 09/22/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Explanted tissues from vertebrate embryos reliably develop in culture and have provided essential paradigms for understanding embryogenesis, from early embryological investigations of induction, to the extensive study of Xenopus animal caps, to the current studies of mammalian gastruloids. Cultured explants of the Xenopus dorsal marginal zone ("Keller" explants) serve as a central paradigm for studies of convergent extension cell movements, yet we know little about the global patterns of gene expression in these explants. RESULTS In an effort to more thoroughly develop this important model system, we provide here a time-resolved bulk transcriptome for developing Keller explants. CONCLUSIONS The dataset reported here provides a useful resource for those using Keller explants for studies of morphogenesis and provide genome-scale insights into the temporal patterns of gene expression in an important tissue when explanted and grown in culture.
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Affiliation(s)
- Anneke D Kakebeen
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Robert J Huebner
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
| | - Asako Shindo
- Division of Biological Science, Nagoya University, Nagoya, Japan
| | - Kujin Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, (UNIST), Ulsan, Republic of Korea
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, (UNIST), Ulsan, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Republic of Korea
| | - Andrea E Wills
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
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16
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Colozza G. Purified Bighead protein efficiently promotes head development in the South African clawed frog, Xenopus laevis. MICROPUBLICATION BIOLOGY 2021; 2021. [PMID: 33426508 PMCID: PMC7786221 DOI: 10.17912/micropub.biology.000347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Vertebrate embryonic development is regulated by a few families of extracellular signaling molecules. Xenopus laevis embryos offer an excellent system to study the cell-cell communication signals that govern embryonic patterning. In the frog embryos, Wnt/β-catenin plays a pivotal role in regulating embryonic axis development, and modulation of the Wnt pathway is required for proper antero-posterior patterning. Recently, a novel secreted, organizer-specific Wnt inhibitor, Bighead, was identified that acts by downregulating Lrp6 plasma membrane levels. Here, I describe a method to purify biologically active Bighead protein and confirm that Bighead promotes Xenopus head development.
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17
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Colozza G, De Robertis EM. Dact-4 is a Xenopus laevis Spemann organizer gene related to the Dapper/Frodo antagonist of β-catenin family of proteins. Gene Expr Patterns 2020; 38:119153. [PMID: 33186756 DOI: 10.1016/j.gep.2020.119153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/07/2020] [Accepted: 11/07/2020] [Indexed: 12/27/2022]
Abstract
Dact/Dapper/Frodo members belong to an evolutionarily conserved family of Dishevelled-binding proteins present in mammals, birds, amphibians and fishes that are involved in the regulation of Wnt and TGF-β signaling. In addition to the three established genes (Dact1-3) that compose the Dact family, a fourth paralogue group of related proteins has been recently identified and named Dact-4. Interestingly, Dact-4 is the most rapidly evolving gene of the entire family, as it displays very low homology with other Dact proteins and has lost key conserved domains. Dact-4 is not present in mammals, but weakly conserved homologs were found in reptiles and fishes. Recent RNAseq from our group identified new genes specifically expressed in the Xenopus laevis Spemann organizer. Among these, LOC100170590 mRNA encoded a protein sharing weak homology with a coelacanth Dact-like protein member. Here, by analyzing protein phylogeny and synteny, we show that this organizer gene corresponds to Dact-4. We report that Dact-4 is expressed in the Xenopus blastula pre-organizer region in addition to the gastrula organizer, as well as in placodes, eyes, neural tube, presomitic mesoderm and pronephros. Dact-4-Flag microinjection experiments suggest it is a nucleocytoplasmic protein, as are the other Dact paralogues.
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Affiliation(s)
- Gabriele Colozza
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095-1662, USA.
| | - Edward M De Robertis
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095-1662, USA
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18
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Shigeoka T, Koppers M, Wong HHW, Lin JQ, Cagnetta R, Dwivedy A, de Freitas Nascimento J, van Tartwijk FW, Ströhl F, Cioni JM, Schaeffer J, Carrington M, Kaminski CF, Jung H, Harris WA, Holt CE. On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons. Cell Rep 2020; 29:3605-3619.e10. [PMID: 31825839 PMCID: PMC6915326 DOI: 10.1016/j.celrep.2019.11.025] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 09/30/2019] [Accepted: 11/06/2019] [Indexed: 01/19/2023] Open
Abstract
Ribosome assembly occurs mainly in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation decreases local translation activity and reduces axon branching in the developing brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.
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Affiliation(s)
- Toshiaki Shigeoka
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
| | - Max Koppers
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Hovy Ho-Wai Wong
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Julie Qiaojin Lin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Roberta Cagnetta
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Asha Dwivedy
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | | | - Francesca W van Tartwijk
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Florian Ströhl
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Jean-Michel Cioni
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Julia Schaeffer
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, UK
| | - Hosung Jung
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - William A Harris
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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19
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Abstract
As the crucial non-cellular component of tissues, the extracellular matrix (ECM) provides both physical support and signaling regulation to cells. Some ECM molecules provide a fibrillar environment around cells, while others provide a sheet-like basement membrane scaffold beneath epithelial cells. In this Review, we focus on recent studies investigating the mechanical, biophysical and signaling cues provided to developing tissues by different types of ECM in a variety of developing organisms. In addition, we discuss how the ECM helps to regulate tissue morphology during embryonic development by governing key elements of cell shape, adhesion, migration and differentiation. Summary: This Review discusses our current understanding of how the extracellular matrix helps guide developing tissues by influencing cell adhesion, migration, shape and differentiation, emphasizing the biophysical cues it provides.
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Affiliation(s)
- David A Cruz Walma
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892-4370, USA
| | - Kenneth M Yamada
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892-4370, USA
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20
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Gilchrist MJ, Veenstra GJC, Cho KWY. Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues. Cold Spring Harb Protoc 2020; 2020:098350. [PMID: 31772075 DOI: 10.1101/pdb.top098350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The general field of quantitative biology has advanced significantly on the back of recent improvements in both sequencing technology and proteomics methods. The development of high-throughput, short-read sequencing has revolutionized RNA-based expression studies, while improvements in proteomics methods have enabled quantitative studies to attain better resolution. Here we introduce methods to undertake global analyses of gene expression through RNA and protein quantification in Xenopus embryos and tissues.
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Affiliation(s)
- Michael J Gilchrist
- The Francis Crick Institute, London NW1 1AT, United Kingdom; .,Department of Molecular Developmental Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- The Francis Crick Institute, London NW1 1AT, United Kingdom; .,Department of Molecular Developmental Biology, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, California 92697
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21
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Chang LS, Kim M, Glinka A, Reinhard C, Niehrs C. The tumor suppressor PTPRK promotes ZNRF3 internalization and is required for Wnt inhibition in the Spemann organizer. eLife 2020; 9:51248. [PMID: 31934854 PMCID: PMC6996932 DOI: 10.7554/elife.51248] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/12/2020] [Indexed: 12/12/2022] Open
Abstract
A hallmark of Spemann organizer function is its expression of Wnt antagonists that regulate axial embryonic patterning. Here we identify the tumor suppressor Protein tyrosine phosphatase receptor-type kappa (PTPRK), as a Wnt inhibitor in human cancer cells and in the Spemann organizer of Xenopus embryos. We show that PTPRK acts via the transmembrane E3 ubiquitin ligase ZNRF3, a negative regulator of Wnt signaling promoting Wnt receptor degradation, which is also expressed in the organizer. Deficiency of Xenopus Ptprk increases Wnt signaling, leading to reduced expression of Spemann organizer effector genes and inducing head and axial defects. We identify a '4Y' endocytic signal in ZNRF3, which PTPRK maintains unphosphorylated to promote Wnt receptor depletion. Our discovery of PTPRK as a negative regulator of Wnt receptor turnover provides a rationale for its tumor suppressive function and reveals that in PTPRK-RSPO3 recurrent cancer fusions both fusion partners, in fact, encode ZNRF3 regulators. How human and other animals form distinct head- and tail-ends as embryos is a fundamental question in biology. The fertilized eggs of the African clawed frog (also known as Xenopus) become embryos and grow into tadpoles within two days. This rapid growth makes Xenopus particularly suitable as a model to study how animals with backbones form their body plans. In Xenopus embryos, a small group of cells known as the Spemann organizer plays a pivotal role in forming the body plan. It produces several enzymes known as Wnt inhibitors that repress a signal pathway known as Wnt signaling to determine the head- and tail-ends of the embryo. Chang, Kim et al. searched for new Wnt inhibitors in the Spemann organizer of Xenopus embryos. The experiments revealed that the Spemann organizer produced an enzyme known as PTPRK that was essential to permit the head-to-tail patterning of the brain. PTPRK inhibited Wnt signaling by activating another enzyme known as ZNRF3. Previous studies have shown that defects in Wnt signaling and in the activities of PTPRK and ZNRF3 are involved in colon cancer in mammals. Thus, these findings may help to develop new approaches for treating cancer in the future.
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Affiliation(s)
- Ling-Shih Chang
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Minseong Kim
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Andrey Glinka
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Carmen Reinhard
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
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22
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Abstract
Background The study of the mechanisms controlling wound healing is an attractive area within the field of biology, with it having a potentially significant impact on the health sector given the current medical burden associated with healing in the elderly population. Healing is a complex process and includes many steps that are regulated by coding and noncoding RNAs, proteins and other molecules. Nitric oxide (NO) is one of these small molecule regulators and its function has already been associated with inflammation and angiogenesis during adult healing. Results Our results showed that NO is also an essential component during embryonic scarless healing and acts via a previously unknown mechanism. NO is mainly produced during the early phase of healing and it is crucial for the expression of genes associated with healing. However, we also observed a late phase of healing, which occurs for several hours after wound closure and takes place under the epidermis and includes tissue remodelling that is dependent on NO. We also found that the NO is associated with multiple cellular metabolic pathways, in particularly the glucose metabolism pathway. This is particular noteworthy as the use of NO donors have already been found to be beneficial for the treatment of chronic healing defects (including those associated with diabetes) and it is possible that its mechanism of action follows those observed during embryonic wound healing. Conclusions Our study describes a new role of NO during healing, which may potentially translate to improved therapeutic treatments, especially for individual suffering with problematic healing.
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23
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Harada H, Farhani N, Wang XF, Sugita S, Charish J, Attisano L, Moran M, Cloutier JF, Reber M, Bremner R, Monnier PP. Extracellular phosphorylation drives the formation of neuronal circuitry. Nat Chem Biol 2019; 15:1035-1042. [PMID: 31451763 DOI: 10.1038/s41589-019-0345-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/14/2019] [Indexed: 12/29/2022]
Abstract
Until recently, the existence of extracellular kinase activity was questioned. Many proteins of the central nervous system are targeted, but it remains unknown whether, or how, extracellular phosphorylation influences brain development. Here we show that the tyrosine kinase vertebrate lonesome kinase (VLK), which is secreted by projecting retinal ganglion cells, phosphorylates the extracellular protein repulsive guidance molecule b (RGMb) in a dorsal-ventral descending gradient. Silencing of VLK or RGMb causes aberrant axonal branching and severe axon misguidance in the chick optic tectum. Mice harboring RGMb with a point mutation in the phosphorylation site also display aberrant axonal pathfinding. Mechanistic analyses show that VLK-mediated RGMb phosphorylation modulates Wnt3a activity by regulating LRP5 protein gradients. Thus, the secretion of VLK by projecting neurons provides crucial signals for the accurate formation of nervous system circuitry. The dramatic effect of VLK on RGMb and Wnt3a signaling implies that extracellular phosphorylation likely has broad and profound effects on brain development, function and disease.
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Affiliation(s)
- Hidekiyo Harada
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada
| | - Nahal Farhani
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada
| | - Xue-Fan Wang
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada
| | - Shuzo Sugita
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada
| | - Jason Charish
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada.,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Liliana Attisano
- Department of Biochemistry, Donnelly Center, University of Toronto, Toronto, Ontario, Canada
| | - Michael Moran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Michael Reber
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Ontario, Toronto, Canada.,CNRS UPR3212, University of Strasbourg, Strasbourg, France
| | - Rod Bremner
- Lunenfeld Tannenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Philippe P Monnier
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada. .,Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada. .,Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Ontario, Toronto, Canada.
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24
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Sosa EA, Moriyama Y, Ding Y, Tejeda-Muñoz N, Colozza G, De Robertis EM. Transcriptome analysis of regeneration during Xenopus laevis experimental twinning. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2019; 63:301-309. [PMID: 31250914 DOI: 10.1387/ijdb.190006ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Animal embryos have the remarkable property of self-organization. Over 125 years ago, Hans Driesch separated the two blastomeres of sea urchin embryos and obtained twins, in what was the foundation of experimental embryology. Since then, embryonic twinning has been obtained experimentally in many animals. In a recent study, we developed bisection methods that generate identical twins reliably from Xenopus blastula embryos. In the present study, we have investigated the transcriptome of regenerating half-embryos after sagittal and dorsal-ventral (D-V) bisections. Individual embryos were operated at midblastula (stage 8) with an eyelash hair and cultured until early gastrula (stage 10.5) or late gastrula (stage 12) and the transcriptome of both halves were analyzed by RNA-seq. Since many genes are activated by wound healing in Xenopus embryos, we resorted to stringent sequence analyses and identified genes up-regulated in identical twins but not in either dorsal or ventral fragments. At early gastrula, cell division-related transcripts such as histones were elevated, whereas at late gastrula, pluripotency genes (such as sox2) and germ layer determination genes (such as eomesodermin, ripply2 and activin receptor ACVRI) were identified. Among the down-regulated transcripts, sizzled, a regulator of Chordin stability, was prominent. These findings are consistent with a model in which cell division is required to heal damage, while maintaining pluripotency to allow formation of the organizer with a displacement of 90 0 from its original site. The extensive transcriptomic data presented here provides a valuable resource for data mining of gene expression during early vertebrate development.
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Affiliation(s)
- Eric A Sosa
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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25
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Jalvy S, Veschambre P, Fédou S, Rezvani HR, Thézé N, Thiébaud P. Leukemia inhibitory factor signaling in Xenopus embryo: Insights from gain of function analysis and dominant negative mutant of the receptor. Dev Biol 2019; 447:200-213. [DOI: 10.1016/j.ydbio.2018.12.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 01/19/2023]
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26
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Bighead is a Wnt antagonist secreted by the Xenopus Spemann organizer that promotes Lrp6 endocytosis. Proc Natl Acad Sci U S A 2018; 115:E9135-E9144. [PMID: 30209221 PMCID: PMC6166843 DOI: 10.1073/pnas.1812117115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Xenopus laevis embryo has been subjected to almost saturating screens for molecules specifically expressed in dorsal Spemann organizer tissue. In this study, we performed high-throughput RNA sequencing of ectodermal explants, called animal caps, which normally give rise to epidermis. We analyzed dissociated animal cap cells that, through sustained activation of MAPK, differentiate into neural tissue. We also microinjected mRNAs for Cerberus, Chordin, FGF8, BMP4, Wnt8, and Xnr2, which induce neural or other germ layer differentiations. The searchable database provided here represents a valuable resource for the early vertebrate cell differentiation. These analyses resulted in the identification of a gene present in frog and fish, which we call Bighead. Surprisingly, at gastrula, it was expressed in the Spemann organizer and endoderm, rather than in ectoderm as we expected. Despite the plethora of genes already mined from Spemann organizer tissue, Bighead encodes a secreted protein that proved to be a potent inhibitor of Wnt signaling in a number of embryological and cultured cell signaling assays. Overexpression of Bighead resulted in large head structures very similar to those of the well-known Wnt antagonists Dkk1 and Frzb-1. Knockdown of Bighead with specific antisense morpholinos resulted in embryos with reduced head structures, due to increased Wnt signaling. Bighead protein bound specifically to the Wnt coreceptor lipoprotein receptor-related protein 6 (Lrp6), leading to its removal from the cell surface. Bighead joins two other Wnt antagonists, Dkk1 and Angptl4, which function as Lrp6 endocytosis regulators. These results suggest that endocytosis plays a crucial role in Wnt signaling.
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27
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Baxi AB, Lombard-Banek C, Moody SA, Nemes P. Proteomic Characterization of the Neural Ectoderm Fated Cell Clones in the Xenopus laevis Embryo by High-Resolution Mass Spectrometry. ACS Chem Neurosci 2018; 9:2064-2073. [PMID: 29578674 DOI: 10.1021/acschemneuro.7b00525] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The molecular program by which embryonic ectoderm is induced to form neural tissue is essential to understanding normal and impaired development of the central nervous system. Xenopus has been a powerful vertebrate model in which to elucidate this process. However, abundant vitellogenin (yolk) proteins in cells of the early Xenopus embryo interfere with protein detection by high-resolution mass spectrometry (HRMS), the technology of choice for identifying these gene products. Here, we systematically evaluated strategies of bottom-up proteomics to enhance proteomic detection from the neural ectoderm (NE) of X. laevis using nanoflow high-performance liquid chromatography (nanoLC) HRMS. From whole embryos, high-pH fractionation prior to nanoLC-HRMS yielded 1319 protein groups vs 762 proteins without fractionation (control). Compared to 702 proteins from dorsal halves of embryos (control), 1881 proteins were identified after yolk platelets were depleted via sucrose-gradient centrifugation. We combined these approaches to characterize protein expression in the NE of the early embryo. To guide microdissection of the NE tissues from the gastrula (stage 10), their precursor (midline dorsal-animal, or D111) cells were fate-mapped from the 32-cell embryo using a fluorescent lineage tracer. HRMS of the cell clones identified 2363 proteins, including 147 phosphoproteins (without phosphoprotein enrichment), transcription factors, and members from pathways of cellular signaling. In reference to transcriptomic maps of the developing X. laevis, 76 proteins involved in signaling pathways were gene matched to transcripts with known enrichment in the neural plate. Besides a protocol, this work provides qualitative proteomic data on the early developing NE.
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Affiliation(s)
- Aparna B. Baxi
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC 20052, United States
| | - Camille Lombard-Banek
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Sally A. Moody
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC 20052, United States
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Department of Anatomy and Regenerative Biology, The George Washington University, Washington, DC 20052, United States
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28
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Monteiro RS, Gentsch GE, Smith JC. Transcriptomics of dorso-ventral axis determination in Xenopus tropicalis. Dev Biol 2018; 439:69-79. [PMID: 29709598 PMCID: PMC5971218 DOI: 10.1016/j.ydbio.2018.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/08/2018] [Accepted: 04/24/2018] [Indexed: 11/26/2022]
Abstract
Amphibian embryos provide a powerful system to study early cell fate determination because their eggs are externally fertilised, large, and easy to manipulate. Ultraviolet (UV) or lithium chloride (LiCl) treatment are classic embryonic manipulations frequently used to perturb specification of the dorso-ventral (DV) axis by affecting the stability of the maternal Wnt mediator β-catenin. Such treatments result in the formation of so-called ventralised or dorsalised embryos. Although these phenotypes have been well described with respect to their morphology and some aspects of gene expression, their whole transcriptomes have never been systematically characterised and compared. Here we show that at the early gastrula stage UV-treated embryos are transcriptionally more closely related to untreated embryos than to LiCl-treated embryos. Transcriptional comparisons with dissected ventral and dorsal regions of unperturbed gastrula embryos indicate that UV and LiCl treatments indeed enrich for ventral and dorsal cells, respectively. However, these treatments also affect the balance of neural induction in the ectodermal germ layer, with LiCl stimulating pro-neural BMP inhibition and UV preferentially generating epidermis because of elevated BMP levels. Thus the transcriptomes of UV- and LiCl-treated embryos can best be described as ventro-epidermalised and dorso-neuralised. These descriptions notwithstanding, our profiling reveals several hitherto uncharacterized genes with differential expression along the DV axis. At least one of these genes, a RNF220-like ubiquitin ligase, is activated dorsally by β-catenin. Our analysis of UV/LiCl-mediated axis perturbation will enhance the mechanistic understanding of DV axis determination in vertebrates.
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Affiliation(s)
- Rita S Monteiro
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London NW1 1AT, United Kingdom.
| | - George E Gentsch
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London NW1 1AT, United Kingdom
| | - James C Smith
- The Francis Crick Institute, Developmental Biology Laboratory, 1 Midland Road, London NW1 1AT, United Kingdom.
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29
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Collins MM, Maischein HM, Dufourcq P, Charpentier M, Blader P, Stainier DY. Pitx2c orchestrates embryonic axis extension via mesendodermal cell migration. eLife 2018; 7:34880. [PMID: 29952749 PMCID: PMC6023614 DOI: 10.7554/elife.34880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/14/2018] [Indexed: 12/13/2022] Open
Abstract
Pitx2c, a homeodomain transcription factor, is classically known for its left-right patterning role. However, an early wave of pitx2 expression occurs at the onset of gastrulation in several species, indicating a possible earlier role that remains relatively unexplored. Here we show that in zebrafish, maternal-zygotic (MZ) pitx2c mutants exhibit a shortened body axis indicative of convergence and extension (CE) defects. Live imaging reveals that MZpitx2c mutants display less persistent mesendodermal migration during late stages of gastrulation. Transplant data indicate that Pitx2c functions cell non-autonomously to regulate this cell behavior by modulating cell shape and protrusive activity. Using transcriptomic analyses and candidate gene approaches, we identify transcriptional changes in components of the chemokine-ECM-integrin dependent mesendodermal migration network. Together, our results define pathways downstream of Pitx2c that are required during early embryogenesis and reveal novel functions for Pitx2c as a regulator of morphogenesis.
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Affiliation(s)
- Michelle M Collins
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hans-Martin Maischein
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Pascale Dufourcq
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université Toulouse III - Paul Sabatier, CNRS, Toulouse, France
| | | | - Patrick Blader
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université Toulouse III - Paul Sabatier, CNRS, Toulouse, France
| | - Didier Yr Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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30
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Skariah G, Perry KJ, Drnevich J, Henry JJ, Ceman S. RNA helicase Mov10 is essential for gastrulation and central nervous system development. Dev Dyn 2018; 247:660-671. [PMID: 29266590 DOI: 10.1002/dvdy.24615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 11/21/2017] [Accepted: 12/18/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Mov10 is an RNA helicase that modulates access of Argonaute 2 to microRNA recognition elements in mRNAs. We examined the role of Mov10 in Xenopus laevis development and show a critical role for Mov10 in gastrulation and in the development of the central nervous system (CNS). RESULTS Knockdown of maternal Mov10 in Xenopus embryos using a translation blocking morpholino led to defects in gastrulation and the development of notochord and paraxial mesoderm, and a failure to neurulate. RNA sequencing of the Mov10 knockdown embryos showed significant upregulation of many mRNAs when compared with controls at stage 10.5 (including those related to the cytoskeleton, adhesion, and extracellular matrix, which are involved in those morphogenetic processes). Additionally, the degradation of the miR-427 target mRNA, cyclin A1, was delayed in the Mov10 knockdowns. These defects suggest that Mov10's role in miRNA-mediated regulation of the maternal to zygotic transition could lead to pleiotropic effects that cause the gastrulation defects. Additionally, the knockdown of zygotic Mov10 showed that it was necessary for normal head, eye, and brain development in Xenopus consistent with a recent study in the mouse. CONCLUSIONS Mov10 is essential for gastrulation and normal CNS development. Developmental Dynamics 247:660-671, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Geena Skariah
- Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, Illinois
| | - Kimberly J Perry
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, Illinois
| | - Jenny Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, Illinois
| | - Jonathan J Henry
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, Illinois
| | - Stephanie Ceman
- Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, Illinois.,Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, Illinois.,College of Medicine, University of Illinois-Urbana Champaign, Urbana, Illinois
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31
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Angiopoietin-like 4 Is a Wnt Signaling Antagonist that Promotes LRP6 Turnover. Dev Cell 2017; 43:71-82.e6. [PMID: 29017031 DOI: 10.1016/j.devcel.2017.09.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 08/25/2017] [Accepted: 09/13/2017] [Indexed: 11/23/2022]
Abstract
Angiopoietin-like 4 (ANGPTL4) is a secreted signaling protein that is implicated in cardiovascular disease, metabolic disorder, and cancer. Outside of its role in lipid metabolism, ANGPTL4 signaling remains poorly understood. Here, we identify ANGPTL4 as a Wnt signaling antagonist that binds to syndecans and forms a ternary complex with the Wnt co-receptor Lipoprotein receptor-related protein 6 (LRP6). This protein complex is internalized via clathrin-mediated endocytosis and degraded in lysosomes, leading to attenuation of Wnt/β-catenin signaling. Angptl4 is expressed in the Spemann organizer of Xenopus embryos and acts as a Wnt antagonist to promote notochord formation and prevent muscle differentiation. This unexpected function of ANGPTL4 invites re-interpretation of its diverse physiological effects in light of Wnt signaling and may open therapeutic avenues for human disease.
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32
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Plouhinec JL, Medina-Ruiz S, Borday C, Bernard E, Vert JP, Eisen MB, Harland RM, Monsoro-Burq AH. A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates. PLoS Biol 2017; 15:e2004045. [PMID: 29049289 PMCID: PMC5663519 DOI: 10.1371/journal.pbio.2004045] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 10/31/2017] [Accepted: 09/29/2017] [Indexed: 12/18/2022] Open
Abstract
During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal component analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes directly from its transcriptome. In parallel, we use nonnegative matrix factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g., Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research. Vertebrate embryo germ layers become progressively regionalized by evolutionarily conserved molecular processes. Catching the early steps of this dynamic spatial cell diversification at the scale of the transcriptome was challenging, even with the advent of efficient RNA sequencing. We have microdissected complementary and defined areas of a single germ layer, the developing ectoderm, and explored how the transcriptome changes over time and space in the ectoderm during the differentiation of frog epidermis, neural plate, and neural crest. We have created EctoMap, a searchable interface using these regional transcriptomes, to predict the expression of the 31 thousand genes expressed in neurulae and their networks of co-expression, predictive of functional relationships. Through several examples, we illustrate how these data provide insights in development, cancer, evolution and stem cell biology.
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Affiliation(s)
- Jean-Louis Plouhinec
- Université Paris Sud, Université Paris Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
- Institut Curie Research Division, PSL Research University, CNRS UMR 3347, INSERM U1021, Orsay, France
- MINES ParisTech, PSL Research University, CBIO - Centre for Computational Biology, Paris, France
| | - Sofía Medina-Ruiz
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Caroline Borday
- Université Paris Sud, Université Paris Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
- Institut Curie Research Division, PSL Research University, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Elsa Bernard
- MINES ParisTech, PSL Research University, CBIO - Centre for Computational Biology, Paris, France
- Institut Curie, INSERM U900, Paris, France
- INSERM U900, Paris, France
| | - Jean-Philippe Vert
- MINES ParisTech, PSL Research University, CBIO - Centre for Computational Biology, Paris, France
- Institut Curie, INSERM U900, Paris, France
- INSERM U900, Paris, France
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development Biology, University of California, Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Richard M. Harland
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Anne H. Monsoro-Burq
- Université Paris Sud, Université Paris Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
- Institut Curie Research Division, PSL Research University, CNRS UMR 3347, INSERM U1021, Orsay, France
- Institut Universitaire de France, Paris, France
- * E-mail:
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33
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De Robertis EM, Moriyama Y, Colozza G. Generation of animal form by the Chordin/Tolloid/BMP gradient: 100 years after D'Arcy Thompson. Dev Growth Differ 2017; 59:580-592. [PMID: 28815565 DOI: 10.1111/dgd.12388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/03/2017] [Accepted: 07/03/2017] [Indexed: 12/30/2022]
Abstract
The classic book "On Growth and Form" by naturalist D'Arcy Thompson was published 100 years ago. To celebrate this landmark, we present experiments in the Xenopus embryo that provide a framework for understanding how simple, quantitative transformations of a morphogen gradient might have affected evolution and morphological diversity of organisms. D'Arcy Thompson proposed that different morphologies might be generated by modifying physical parameters in an underlying system of Cartesian coordinates that pre-existed in Nature and arose during evolutionary history. Chordin is a BMP antagonist secreted by the Spemann organizer located on the dorsal side of the gastrula. Chordin generates a morphogen gradient as first proposed by mathematician Alan Turing. The rate-limiting step of this dorsal-ventral (D-V) morphogen is the degradation of Chordin by the Tolloid metalloproteinase in the ventral side. Chordin is expressed at gastrula on the dorsal side where BMP signaling is low, while at the opposite side peak levels of BMP signaling are reached. In fishes, amphibians, reptiles and birds, high BMP signaling in the ventral region induces transcription of a secreted inhibitor of Tolloid called Sizzled. By depleting Sizzled exclusively in the ventral half of the embryo we were able to expand the ventro-posterior region in an otherwise normal embryo. Conversely, ventral depletion of Tolloid, which stabilizes Chordin, decreased ventral and tail structures, phenocopying the tolloid zebrafish mutation. We explain how historical constraints recorded in the language of DNA become subject to the universal laws of physics when an ancestral reaction-diffusion morphogen gradient dictates form.
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Affiliation(s)
- Edward M De Robertis
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1662, USA
| | - Yuki Moriyama
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1662, USA
| | - Gabriele Colozza
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1662, USA
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34
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Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis. Proc Natl Acad Sci U S A 2017; 114:E3081-E3090. [PMID: 28348214 DOI: 10.1073/pnas.1700766114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The earliest event in Xenopus development is the dorsal accumulation of nuclear β-catenin under the influence of cytoplasmic determinants displaced by fertilization. In this study, a genome-wide approach was used to examine transcription of the 43,673 genes annotated in the Xenopus laevis genome under a variety of conditions that inhibit or promote formation of the Spemann organizer signaling center. Loss of function of β-catenin with antisense morpholinos reproducibly reduced the expression of 247 mRNAs at gastrula stage. Interestingly, only 123 β-catenin targets were enriched on the dorsal side and defined an early dorsal β-catenin gene signature. These genes included several previously unrecognized Spemann organizer components. Surprisingly, only 3 of these 123 genes overlapped with the late Wnt signature recently defined by two other groups using inhibition by Dkk1 mRNA or Wnt8 morpholinos, which indicates that the effects of β-catenin/Wnt signaling in early development are exquisitely regulated by stage-dependent mechanisms. We analyzed transcriptome responses to a number of treatments in a total of 46 RNA-seq libraries. These treatments included, in addition to β-catenin depletion, regenerating dorsal and ventral half-embryos, lithium chloride treatment, and the overexpression of Wnt8, Siamois, and Cerberus mRNAs. Only some of the early dorsal β-catenin signature genes were activated at blastula whereas others required the induction of endomesoderm, as indicated by their inhibition by Cerberus overexpression. These comprehensive data provide a rich resource for analyzing how the dorsal and ventral regions of the embryo communicate with each other in a self-organizing vertebrate model embryo.
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35
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Charney RM, Paraiso KD, Blitz IL, Cho KWY. A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs. Semin Cell Dev Biol 2017; 66:12-24. [PMID: 28341363 DOI: 10.1016/j.semcdb.2017.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/12/2017] [Accepted: 03/20/2017] [Indexed: 02/08/2023]
Abstract
Germ layer formation is among the earliest differentiation events in metazoan embryos. In triploblasts, three germ layers are formed, among which the endoderm gives rise to the epithelial lining of the gut tube and associated organs including the liver, pancreas and lungs. In frogs (Xenopus), where early germ layer formation has been studied extensively, the process of endoderm specification involves the interplay of dozens of transcription factors. Here, we review the interactions between these factors, summarized in a transcriptional gene regulatory network (GRN). We highlight regulatory connections conserved between frog, fish, mouse, and human endodermal lineages. Especially prominent is the conserved role and regulatory targets of the Nodal signaling pathway and the T-box transcription factors, Vegt and Eomes. Additionally, we highlight network topologies and motifs, and speculate on their possible roles in development.
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Affiliation(s)
- Rebekah M Charney
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, CA 92697, USA.
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