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Menezes NA, Peterson KJ, Guo X, Castiglioni V, Kalvisa A, Filimonow K, Schachter K, Schuh CM, Pasias A, Mariani L, Brickman JM, Sedzinski J, Ferretti E. Cell-context response to germ layer differentiation signals is predetermined by the epigenome in regionalized epiblast populations. Nat Commun 2025; 16:5000. [PMID: 40442089 PMCID: PMC12122723 DOI: 10.1038/s41467-025-60348-6] [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: 06/21/2023] [Accepted: 05/21/2025] [Indexed: 06/02/2025] Open
Abstract
Stem cells hold promise in regenerative medicine as they have the potential to differentiate into a variety of specialized cell types. However, mechanisms underlying stem cell potency and lineage acquisition remain elusive. Epigenetic modifications and genome accessibility prime cellular feedback to signalling cues, influencing lineage differentiation outcomes. Deciphering how this epigenetic code influences the context-dependent response of pluripotent cells to differentiation cues will elucidate how mammalian tissue diversity is established. Using in vitro and in vivo models, we show that lineage-specific epigenetic signatures precede transcriptional activation of germ layer differentiation programs. We provide evidence that while distinct chromatin accessibility and methylome states prime extraembryonic mesodermal fate decisions, it is DNA methylation, and not chromatin accessibility that predetermines the fates of neuroectoderm, definitive endoderm and neuromesodermal lineages. This study establishes that epigenetic machinery fine-tunes epiblast potency, allowing context-specific spatiotemporal responses to promiscuously used signalling cues controlling organogenesis.
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Affiliation(s)
- Niels Alvaro Menezes
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kathryn Johanna Peterson
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Xiaogang Guo
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Veronica Castiglioni
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Adrija Kalvisa
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Katarzyna Filimonow
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552, Jastrzę biec, Poland
| | - Karen Schachter
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Christina Maria Schuh
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Athanasios Pasias
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Luca Mariani
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Joshua Mark Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jakub Sedzinski
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200, Copenhagen N, Denmark
- Department of Biomedical Sciences, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Elisabetta Ferretti
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200, Copenhagen N, Denmark.
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen N, Denmark.
- dawn-bio GmbH, Vienna BioCenter, 1030, Vienna, Austria.
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Anderson MJ, Lewandoski M. Response to Wu et al. Differentiation 2025; 143:100865. [PMID: 40349482 DOI: 10.1016/j.diff.2025.100865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2025] [Accepted: 04/26/2025] [Indexed: 05/14/2025]
Affiliation(s)
- Matthew J Anderson
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Mark Lewandoski
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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Chung E, Nosrati F, Adam M, Potter A, Sayed M, Ahn C, Humphreys BD, Lim HW, Hu YC, Potter SS, Park JS. Proximal tubule cells contribute to the thin descending limb of the loop of Henle during mouse kidney development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.14.633065. [PMID: 39868227 PMCID: PMC11761803 DOI: 10.1101/2025.01.14.633065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Background The thin descending limb of the loop of Henle is crucial for urine concentration, as it facilitates passive water reabsorption. Despite its importance, little is known about how this nephron segment forms during kidney development. Methods We assembled a large single-cell RNA sequencing (scRNA-seq) dataset by integrating multiple datasets of non-mutant developing mouse kidneys to identify developing thin descending limb cells. To test whether those cells originate from proximal tubule cells, we generated a proximal tubule-specific Cre line, Slc34a1eGFPCre, and conducted lineage tracing. Additionally, given that the transcription factor Hnf4a directly binds to the Aqp1 gene, we examined whether the loss of Hnf4a affects Aqp1 expression in thin descending limb cells. Results From our scRNA-seq dataset, we identified a small cluster of cells distinct from both the proximal tubule and the thick ascending limb of the loop of Henle. Those cells exhibited high expression of thin descending limb marker genes, including Aqp1 and Bst1. Notably, a subset of proximal tubule cells also expressed thin descending limb marker genes, suggesting that proximal tubule cells may give rise to thin descending limb cells. Using lineage tracing with the Slc34a1eGFPCre line, we found that, at least, a subset of thin descending limb cells are descendants of proximal tubule cells. Furthermore, the loss of Hnf4a, a transcription factor essential for mature proximal tubule cell formation, disrupted proper Aqp1 expression in thin descending limb cells, providing additional evidence of a developmental link between proximal tubule cells and thin descending limb cells. Conclusion Our findings shed new light on the developmental origin of thin descending limb cells and highlight the importance of Hnf4a in regulating their formation.
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Affiliation(s)
- Eunah Chung
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Feinberg Cardiovascular and Renal Research Institute, Chicago, IL, USA
| | - Fariba Nosrati
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Feinberg Cardiovascular and Renal Research Institute, Chicago, IL, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Andrew Potter
- Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Mohammed Sayed
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Christopher Ahn
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University, St. Louis, MO, USA
- Department of Developmental Biology, Washington University, St. Louis, MO, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - S. Steven Potter
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Joo-Seop Park
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Feinberg Cardiovascular and Renal Research Institute, Chicago, IL, USA
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4
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Isomura A, Kageyama R. Progress in understanding the vertebrate segmentation clock. Nat Rev Genet 2025:10.1038/s41576-025-00813-6. [PMID: 40038453 DOI: 10.1038/s41576-025-00813-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2025] [Indexed: 03/06/2025]
Abstract
The segmentation clock is a molecular oscillator that regulates the periodic formation of somites from the presomitic mesoderm during vertebrate embryogenesis. Synchronous oscillatory expression of a Hairy homologue or Hairy-related basic helix-loop-helix (bHLH) transcriptional repressor in presomitic mesoderm cells regulates periodic expression of downstream factors that control somite segmentation with a periodicity that varies across species. Although many of the key components of the clock have been identified and characterized, less is known about how the clock is synchronized across cells and how species-specific periodicity is achieved. Advances in live imaging, stem cell and organoid technologies, and synthetic approaches have started to uncover the detailed mechanisms underlying these aspects of somitogenesis, providing insight into how morphogenesis is coordinated in space and time during embryonic development.
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Affiliation(s)
- Akihiro Isomura
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences (KUIAS-iCeMS), Kyoto University, Kyoto, Japan.
- Japan Science and Technology Agency, PRESTO, Saitama, Japan.
- RIKEN Center for Brain Science, Wako, Japan.
| | - Ryoichiro Kageyama
- Institute for Integrated Cell-Material Sciences (KUIAS-iCeMS), Kyoto University, Kyoto, Japan.
- RIKEN Center for Brain Science, Wako, Japan.
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Iber D, Mederacke M, Vetter R. Coordination of nephrogenesis with branching of the urinary collecting system, the vasculature and the nervous system. Curr Top Dev Biol 2025; 163:45-82. [PMID: 40254350 DOI: 10.1016/bs.ctdb.2024.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2025]
Affiliation(s)
- Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Malte Mederacke
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Roman Vetter
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
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Edirisinghe O, Ternier G, Alraawi Z, Suresh Kumar TK. Decoding FGF/FGFR Signaling: Insights into Biological Functions and Disease Relevance. Biomolecules 2024; 14:1622. [PMID: 39766329 PMCID: PMC11726770 DOI: 10.3390/biom14121622] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2024] [Revised: 12/06/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
Fibroblast Growth Factors (FGFs) and their cognate receptors, FGFRs, play pivotal roles in a plethora of biological processes, including cell proliferation, differentiation, tissue repair, and metabolic homeostasis. This review provides a comprehensive overview of FGF-FGFR signaling pathways while highlighting their complex regulatory mechanisms and interconnections with other signaling networks. Further, we briefly discuss the FGFs involvement in developmental, metabolic, and housekeeping functions. By complementing current knowledge and emerging research, this review aims to enhance the understanding of FGF-FGFR-mediated signaling and its implications for health and disease, which will be crucial for therapeutic development against FGF-related pathological conditions.
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Affiliation(s)
- Oshadi Edirisinghe
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Gaëtane Ternier
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; (G.T.); (Z.A.)
| | - Zeina Alraawi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; (G.T.); (Z.A.)
| | - Thallapuranam Krishnaswamy Suresh Kumar
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA;
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; (G.T.); (Z.A.)
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7
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Hisler V, Bardot P, Detilleux D, Bernardini A, Stierle M, Sanchez EG, Richard C, Arab LH, Ehrhard C, Morlet B, Hadzhiev Y, Jung M, Le Gras S, Négroni L, Müller F, Tora L, Vincent SD. RNA polymerase II transcription initiation in holo-TFIID-depleted mouse embryonic stem cells. Cell Rep 2024; 43:114791. [PMID: 39352809 PMCID: PMC11551524 DOI: 10.1016/j.celrep.2024.114791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/09/2024] [Accepted: 09/07/2024] [Indexed: 10/04/2024] Open
Abstract
The recognition of core promoter sequences by TFIID is the first step in RNA polymerase II (Pol II) transcription initiation. Metazoan holo-TFIID is a trilobular complex, composed of the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs). Why and how TAFs are necessary for the formation of TFIID domains and how they contribute to transcription initiation remain unclear. Inducible TAF7 or TAF10 depletion, followed by comprehensive analysis of TFIID subcomplex formation, chromatin binding, and nascent transcription in mouse embryonic stem cells, result in the formation of a TAF7-lacking TFIID or a minimal core-TFIID complex, respectively. These partial complexes support TBP recruitment at promoters and nascent Pol II transcription at most genes early after depletion, but importantly, TAF10 is necessary for efficient Pol II pausing. We show that partially assembled TFIID complexes can sustain Pol II transcription initiation but cannot replace holo-TFIID over several cell divisions and/or development.
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Affiliation(s)
- Vincent Hisler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Paul Bardot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Dylane Detilleux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Emmanuel Garcia Sanchez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Claire Richard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Lynda Hadj Arab
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Cynthia Ehrhard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; Proteomics Platform (IGBMC), 67400 Illkirch, France
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Matthieu Jung
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; GenomEast (IGBMC), 67400 Illkirch, France
| | - Stéphanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; GenomEast (IGBMC), 67400 Illkirch, France
| | - Luc Négroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France; Proteomics Platform (IGBMC), 67400 Illkirch, France
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France
| | - Stéphane D Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; CNRS, UMR7104, 67400 Illkirch, France; INSERM, U1258, 67400 Illkirch, France; Université de Strasbourg, 67400 Illkirch, France.
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8
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Zhu M, Gu B, Thomas EC, Huang Y, Kim YK, Tao H, Yung TM, Chen X, Zhang K, Woolaver EK, Nevin MR, Huang X, Winklbauer R, Rossant J, Sun Y, Hopyan S. A fibronectin gradient remodels mixed-phase mesoderm. SCIENCE ADVANCES 2024; 10:eadl6366. [PMID: 39028807 PMCID: PMC11259159 DOI: 10.1126/sciadv.adl6366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
Physical processes ultimately shape tissue during development. Two emerging proposals are that cells migrate toward stiffer tissue (durotaxis) and that the extent of cell rearrangements reflects tissue phase, but it is unclear whether and how these concepts are related. Here, we identify fibronectin-dependent tissue stiffness as a control variable that underlies and unifies these phenomena in vivo. In murine limb bud mesoderm, cells are either caged, move directionally, or intercalate as a function of their location along a stiffness gradient. A modified Landau phase equation that incorporates tissue stiffness accurately predicts cell diffusivity upon loss or gain of fibronectin. Fibronectin is regulated by WNT5A-YAP feedback that controls cell movements, tissue shape, and skeletal pattern. The results identify a key determinant of phase transition and show how fibronectin-dependent directional cell movement emerges in a mixed-phase environment in vivo.
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Affiliation(s)
- Min Zhu
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Bin Gu
- Department of Obstetrics Gynecology and Reproductive Biology, and Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Evan C. Thomas
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Yunyun Huang
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Yun-Kyo Kim
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Hirotaka Tao
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Theodora M. Yung
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xin Chen
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Kaiwen Zhang
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Elizabeth K. Woolaver
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mikaela R. Nevin
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xi Huang
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Rudolph Winklbauer
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yu Sun
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Sevan Hopyan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Orthopaedic Surgery, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada
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9
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Chen KQ, Kawakami H, Anderson A, Corcoran D, Soni A, Nishinakamura R, Kawakami Y. Sall genes regulate hindlimb initiation in mouse embryos. Genetics 2024; 227:iyae029. [PMID: 38386912 PMCID: PMC11075541 DOI: 10.1093/genetics/iyae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 01/15/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
Vertebrate limbs start to develop as paired protrusions from the lateral plate mesoderm at specific locations of the body with forelimb buds developing anteriorly and hindlimb buds posteriorly. During the initiation process, limb progenitor cells maintain active proliferation to form protrusions and start to express Fgf10, which triggers molecular processes for outgrowth and patterning. Although both processes occur in both types of limbs, forelimbs (Tbx5), and hindlimbs (Isl1) utilize distinct transcriptional systems to trigger their development. Here, we report that Sall1 and Sall4, zinc finger transcription factor genes, regulate hindlimb initiation in mouse embryos. Compared to the 100% frequency loss of hindlimb buds in TCre; Isl1 conditional knockouts, Hoxb6Cre; Isl1 conditional knockout causes a hypomorphic phenotype with only approximately 5% of mutants lacking the hindlimb. Our previous study of SALL4 ChIP-seq showed SALL4 enrichment in an Isl1 enhancer, suggesting that SALL4 acts upstream of Isl1. Removing 1 allele of Sall4 from the hypomorphic Hoxb6Cre; Isl1 mutant background caused loss of hindlimbs, but removing both alleles caused an even higher frequency of loss of hindlimbs, suggesting a genetic interaction between Sall4 and Isl1. Furthermore, TCre-mediated conditional double knockouts of Sall1 and Sall4 displayed a loss of expression of hindlimb progenitor markers (Isl1, Pitx1, Tbx4) and failed to develop hindlimbs, demonstrating functional redundancy between Sall1 and Sall4. Our data provides genetic evidence that Sall1 and Sall4 act as master regulators of hindlimb initiation.
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Affiliation(s)
- Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aaron Anderson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aditi Soni
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
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10
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Ortiz-Salazar MA, Camacho-Aguilar E, Warmflash A. Endogenous Nodal switches Wnt interpretation from posteriorization to germ layer differentiation in geometrically constrained human pluripotent cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584912. [PMID: 38559061 PMCID: PMC10979992 DOI: 10.1101/2024.03.13.584912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The Wnt pathway is essential for inducing the primitive streak, the precursor of the mesendoderm, as well as setting anterior-posterior coordinates. How Wnt coordinates these diverse activities remains incompletely understood. Here, we show that in Wnt-treated human pluripotent cells, endogenous Nodal signaling is a crucial switch between posteriorizing and primitive streak-including activities. While treatment with Wnt posteriorizes cells in standard culture, in micropatterned colonies, higher levels of endogenously induced Nodal signaling combine with exogenous Wnt to drive endoderm differentiation. Inhibition of Nodal signaling restores dose-dependent posteriorization by Wnt. In the absence of Nodal inhibition, micropatterned colonies undergo spontaneous, elaborate morphogenesis concomitant with endoderm differentiation even in the absence of added extracellular matrix proteins like Matrigel. Our study shows how Wnt and Nodal combinatorially coordinate germ layer differentiation with AP patterning and establishes a system to study a natural self-organizing morphogenetic event in in vitro culture.
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Affiliation(s)
| | - Elena Camacho-Aguilar
- Department of Biosciences, Rice University, Houston, TX, USA 77005
- Present address: Department of Gene Regulation and Morphogenesis, Andalusian Center for Developmental Biology (CSIC-UPO-JA), Seville, Spain, 41013
| | - Aryeh Warmflash
- Department of Biosciences, Rice University, Houston, TX, USA 77005
- Department of Bioengineering, Rice University, Houston, TX, USA 77005
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11
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Pappas MP, Kawakami H, Corcoran D, Chen KQ, Scott EP, Wong J, Gearhart MD, Nishinakamura R, Nakagawa Y, Kawakami Y. Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm. Development 2024; 151:dev202649. [PMID: 38345319 PMCID: PMC10946440 DOI: 10.1242/dev.202649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024]
Abstract
The trunk axial skeleton develops from paraxial mesoderm cells. Our recent study demonstrated that conditional knockout of the stem cell factor Sall4 in mice by TCre caused tail truncation and a disorganized axial skeleton posterior to the lumbar level. Based on this phenotype, we hypothesized that, in addition to the previously reported role of Sall4 in neuromesodermal progenitors, Sall4 is involved in the development of the paraxial mesoderm tissue. Analysis of gene expression and SALL4 binding suggests that Sall4 directly or indirectly regulates genes involved in presomitic mesoderm differentiation, somite formation and somite differentiation. Furthermore, ATAC-seq in TCre; Sall4 mutant posterior trunk mesoderm shows that Sall4 knockout reduces chromatin accessibility. We found that Sall4-dependent open chromatin status drives activation and repression of WNT signaling activators and repressors, respectively, to promote WNT signaling. Moreover, footprinting analysis of ATAC-seq data suggests that Sall4-dependent chromatin accessibility facilitates CTCF binding, which contributes to the repression of neural genes within the mesoderm. This study unveils multiple mechanisms by which Sall4 regulates paraxial mesoderm development by directing activation of mesodermal genes and repression of neural genes.
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Affiliation(s)
- Matthew P. Pappas
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Katherine Q. Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Earl Parker Scott
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Julia Wong
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Micah D. Gearhart
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yasushi Nakagawa
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
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12
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Clark JF, Soriano P. Diverse Fgfr1 signaling pathways and endocytic trafficking regulate early mesoderm development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580629. [PMID: 38405698 PMCID: PMC10888970 DOI: 10.1101/2024.02.16.580629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The Fibroblast growth factor (FGF) pathway is a conserved signaling pathway required for embryonic development. Activated FGF receptor 1 (FGFR1) drives multiple intracellular signaling cascade pathways, including ERK/MAPK and PI3K/AKT, collectively termed canonical signaling. However, unlike Fgfr1 null embryos, embryos containing hypomorphic mutations in Fgfr1 lacking the ability to activate canonical downstream signals are still able to develop to birth, but exhibit severe defects in all mesodermal-derived tissues. The introduction of an additional signaling mutation further reduces the activity of Fgfr1, leading to earlier lethality, reduced somitogenesis, and more severe changes in transcriptional outputs. Genes involved in migration, ECM-interaction, and phosphoinositol signaling were significantly downregulated, proteomic analysis identified changes in interactions with endocytic pathway components, and cells expressing mutant receptors show changes in endocytic trafficking. Together, we identify processes regulating early mesoderm development by mechanisms involving both canonical and non-canonical Fgfr1 pathways, including direct interaction with cell adhesion components and endocytic regulation.
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Affiliation(s)
- James F. Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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13
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Wang SX, Streit A. Shared features in ear and kidney development - implications for oto-renal syndromes. Dis Model Mech 2024; 17:dmm050447. [PMID: 38353121 PMCID: PMC10886756 DOI: 10.1242/dmm.050447] [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] [Indexed: 02/16/2024] Open
Abstract
The association between ear and kidney anomalies has long been recognized. However, little is known about the underlying mechanisms. In the last two decades, embryonic development of the inner ear and kidney has been studied extensively. Here, we describe the developmental pathways shared between both organs with particular emphasis on the genes that regulate signalling cross talk and the specification of progenitor cells and specialised cell types. We relate this to the clinical features of oto-renal syndromes and explore links to developmental mechanisms.
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Affiliation(s)
- Scarlet Xiaoyan Wang
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
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14
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Mederacke M, Conrad L, Doumpas N, Vetter R, Iber D. Geometric effects position renal vesicles during kidney development. Cell Rep 2023; 42:113526. [PMID: 38060445 DOI: 10.1016/j.celrep.2023.113526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 07/25/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
During kidney development, reciprocal signaling between the epithelium and the mesenchyme coordinates nephrogenesis with branching morphogenesis of the collecting ducts. The mechanism that positions the renal vesicles, and thus the nephrons, relative to the branching ureteric buds has remained elusive. By combining computational modeling and experiments, we show that geometric effects concentrate the key regulator, WNT9b, at the junctions between parent and daughter branches where renal vesicles emerge, even when uniformly expressed in the ureteric epithelium. This curvature effect might be a general paradigm to create non-uniform signaling in development.
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Affiliation(s)
- Malte Mederacke
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Lisa Conrad
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland; Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Nikolaos Doumpas
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Roman Vetter
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland.
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15
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Hisler V, Bardot P, Detilleux D, Stierle M, Sanchez EG, Richard C, Arab LH, Ehrhard C, Morlet B, Hadzhiev Y, Jung M, Gras SL, Négroni L, Müller F, Tora L, Vincent SD. RNA polymerase II transcription with partially assembled TFIID complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.567046. [PMID: 38076793 PMCID: PMC10705246 DOI: 10.1101/2023.11.27.567046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The recognition of core promoter sequences by the general transcription factor TFIID is the first step in the process of RNA polymerase II (Pol II) transcription initiation. Metazoan holo-TFIID is composed of the TATA binding protein (TBP) and of 13 TBP associated factors (TAFs). Inducible Taf7 knock out (KO) results in the formation of a Taf7-less TFIID complex, while Taf10 KO leads to serious defects within the TFIID assembly pathway. Either TAF7 or TAF10 depletions correlate with the detected TAF occupancy changes at promoters, and with the distinct phenotype severities observed in mouse embryonic stem cells or mouse embryos. Surprisingly however, under either Taf7 or Taf10 deletion conditions, TBP is still associated to the chromatin, and no major changes are observed in nascent Pol II transcription. Thus, partially assembled TFIID complexes can sustain Pol II transcription initiation, but cannot replace holo-TFIID over several cell divisions and/or development.
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Affiliation(s)
- Vincent Hisler
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Paul Bardot
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Dylane Detilleux
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Matthieu Stierle
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Emmanuel Garcia Sanchez
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Claire Richard
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Lynda Hadj Arab
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Cynthia Ehrhard
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Bastien Morlet
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- Proteomics platform
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Matthieu Jung
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- GenomEast
| | - Stéphanie Le Gras
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- GenomEast
| | - Luc Négroni
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- Proteomics platform
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - László Tora
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Stéphane D. Vincent
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
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16
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Schüle KM, Weckerle J, Probst S, Wehmeyer AE, Zissel L, Schröder CM, Tekman M, Kim GJ, Schlägl IM, Sagar, Arnold SJ. Eomes restricts Brachyury functions at the onset of mouse gastrulation. Dev Cell 2023; 58:1627-1642.e7. [PMID: 37633271 DOI: 10.1016/j.devcel.2023.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/12/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
Mammalian specification of mesoderm and definitive endoderm (DE) is instructed by the two related Tbx transcription factors (TFs) Eomesodermin (Eomes) and Brachyury sharing partially redundant functions. Gross differences in mutant embryonic phenotypes suggest specific functions of each TF. To date, the molecular details of separated lineage-specific gene regulation by Eomes and Brachyury remain poorly understood. Here, we combine mouse embryonic and stem-cell-based analyses to delineate the non-overlapping, lineage-specific transcriptional activities. On a genome-wide scale, binding of both TFs overlaps at promoters of target genes but shows specificity for distal enhancer regions that is conferred by differences in Tbx DNA-binding motifs. The unique binding to enhancer sites instructs the specification of anterior mesoderm (AM) and DE by Eomes and caudal mesoderm by Brachyury. Remarkably, EOMES antagonizes BRACHYURY gene regulatory functions in coexpressing cells during early gastrulation to ensure the proper sequence of early AM and DE lineage specification followed by posterior mesoderm derivatives.
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Affiliation(s)
- Katrin M Schüle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
| | - Jelena Weckerle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Simone Probst
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Alexandra E Wehmeyer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Lea Zissel
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Chiara M Schröder
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, 79104 Freiburg, Germany
| | - Mehmet Tekman
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Gwang-Jin Kim
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Inga-Marie Schlägl
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Sagar
- Department of Medicine II, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, 79104 Freiburg, Germany.
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17
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Kawakami H, Chen KQ, Zhang R, Pappas MP, Bailey A, Reisz JA, Corcoran D, Nishinakamura R, D'Alessandro A, Kawakami Y. Sall4 restricts glycolytic metabolism in limb buds through transcriptional regulation of glycolytic enzyme genes. Dev Biol 2023; 501:28-38. [PMID: 37301463 PMCID: PMC10330914 DOI: 10.1016/j.ydbio.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/09/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Recent studies illustrate the importance of regulation of cellular metabolism, especially glycolysis and pathways branching from glycolysis, during vertebrate embryo development. For example, glycolysis generates cellular energy ATP. Glucose carbons are also directed to the pentose phosphate pathway, which is needed to sustain anabolic processes in the rapidly growing embryos. However, our understanding of the exact status of glycolytic metabolism as well as genes that regulate glycolytic metabolism are still incomplete. Sall4 is a zinc finger transcription factor that is highly expressed in undifferentiated cells in developing mouse embryos, such as blastocysts and the post-implantation epiblast. TCre; Sall4 conditional knockout mouse embryos exhibit various defects in the posterior part of the body, including hindlimbs. Using transcriptomics approaches, we found that many genes encoding glycolytic enzymes are upregulated in the posterior trunk, including the hindlimb-forming region, of Sall4 conditional knockout mouse embryos. In situ hybridization and qRT-PCR also confirmed upregulation of expression of several glycolytic genes in hindlimb buds. A fraction of those genes are bound by SALL4 at the promoters, gene bodies or distantly-located regions, suggesting that Sall4 directly regulates expression of several glycolytic enzyme genes in hindlimb buds. To further gain insight into the metabolic status associated with the observed changes at the transcriptional level, we performed a comprehensive analysis of metabolite levels in limb buds in wild type and Sall4 conditional knockout embryos by high-resolution mass spectrometry. We found that the levels of metabolic intermediates of glycolysis are lower, but glycolytic end-products pyruvate and lactate did not exhibit differences in Sall4 conditional knockout hindlimb buds. The increased expression of glycolytic genes would have caused accelerated glycolytic flow, resulting in low levels of intermediates. This condition may have prevented intermediates from being re-directed to other pathways, such as the pentose phosphate pathway. Indeed, the change in glycolytic metabolite levels is associated with reduced levels of ATP and metabolites of the pentose phosphate pathway. To further test whether glycolysis regulates limb patterning downstream of Sall4, we conditionally inactivated Hk2, which encodes a rate-limiting enzyme gene in glycolysis and is regulated by Sall4. The TCre; Hk2 conditional knockout hindlimb exhibited a short femur, and a lack of tibia and anterior digits in hindlimbs, which are defects similarly found in the TCre; Sall4 conditional knockout. The similarity of skeletal defects in Sall4 mutants and Hk2 mutants suggests that regulation of glycolysis plays a role in hindlimb patterning. These data suggest that Sall4 restricts glycolysis in limb buds and contributes to patterning and regulation of glucose carbon flow during development of limb buds.
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Affiliation(s)
- Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ruizhi Zhang
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Matthew P Pappas
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Abigail Bailey
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN, USA.
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18
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Crossen MJ, Wilbourne J, Fogarty A, Zhao F. Epithelial and mesenchymal fate decisions in Wolffian duct development. Trends Endocrinol Metab 2023; 34:462-473. [PMID: 37330364 PMCID: PMC10524679 DOI: 10.1016/j.tem.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
Wolffian ducts (WDs) are the paired embryonic structures that give rise to internal male reproductive tract organs. WDs are initially formed in both sexes but have sex-specific fates during sexual differentiation. Understanding WD differentiation requires insights into the process of fate decisions of epithelial and mesenchymal cells, which are tightly coordinated by endocrine, paracrine, and autocrine signals. In this review, we discuss current advances in understanding the fate-decision process of WD epithelial and mesenchymal lineages from their initial formation at the embryonic stage to postnatal differentiation. Finally, we discuss aberrant cell differentiation in WD abnormalities and pathologies and identify opportunities for future investigations.
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Affiliation(s)
- McKenna J Crossen
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jillian Wilbourne
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Allyssa Fogarty
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; Comparative Biomedical Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fei Zhao
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA; Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Comparative Biomedical Sciences Program, University of Wisconsin-Madison, Madison, WI 53706, USA.
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19
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Anderson MJ, Misaghian S, Sharma N, Perantoni AO, Lewandoski M. Fgf8 promotes survival of nephron progenitors by regulating BAX/BAK-mediated apoptosis. Differentiation 2023; 130:7-15. [PMID: 36527791 PMCID: PMC10718080 DOI: 10.1016/j.diff.2022.12.001] [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: 08/23/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Fibroblast growth factors (Fgfs) have long been implicated in processes critical to embryonic development, such as cell survival, migration, and differentiation. Several mouse models of organ development ascribe a prosurvival requirement specifically to FGF8. Here, we explore the potential role of prosurvival FGF8 signaling in kidney development. We have previously demonstrated that conditional deletion of Fgf8 in the mesodermal progenitors that give rise to the kidney leads to renal aplasia in the mutant neonate. Deleterious consequences caused by loss of FGF8 begin to manifest by E14.5 when massive aberrant cell death occurs in the cortical nephrogenic zone in the rudimentary kidney as well as in the renal vesicles that give rise to the nephrons. To rescue cell death in the Fgf8 mutant kidney, we inactivate the genes encoding the pro-apoptotic factors BAK and BAX. In a wild-type background, the loss of Bak and Bax abrogates normal cell death and has minimal effect on renal development. However, in Fgf8 mutants, the combined loss of Bak and Bax rescues aberrant cell death in the kidneys and restores some measure of kidney development: 1) the nephron progenitor population is greatly increased; 2) some glomeruli form, which are rarely observed in Fgf8 mutants; and 3) kidney size is rescued by about 50% at E18.5. The development of functional nephrons, however, is not rescued. Thus, FGF8 signaling is required for nephron progenitor survival by regulating BAK/BAX and for subsequent steps involving, as yet, undefined roles in kidney development.
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Affiliation(s)
- Matthew J Anderson
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Salvia Misaghian
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Nirmala Sharma
- Renal Differentiation and Neoplasia Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Alan O Perantoni
- Renal Differentiation and Neoplasia Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Mark Lewandoski
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA.
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20
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Shi M, McCracken KW, Patel AB, Zhang W, Ester L, Valerius MT, Bonventre JV. Human ureteric bud organoids recapitulate branching morphogenesis and differentiate into functional collecting duct cell types. Nat Biotechnol 2023; 41:252-261. [PMID: 36038632 PMCID: PMC9957856 DOI: 10.1038/s41587-022-01429-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/13/2022] [Indexed: 12/29/2022]
Abstract
Directed differentiation of human pluripotent stem cells (hPSCs) into functional ureteric and collecting duct (CD) epithelia is essential to kidney regenerative medicine. Here we describe highly efficient, serum-free differentiation of hPSCs into ureteric bud (UB) organoids and functional CD cells. The hPSCs are first induced into pronephric progenitor cells at 90% efficiency and then aggregated into spheres with a molecular signature similar to the nephric duct. In a three-dimensional matrix, the spheres form UB organoids that exhibit branching morphogenesis similar to the fetal UB and correct distal tip localization of RET expression. Organoid-derived cells incorporate into the UB tips of the progenitor niche in chimeric fetal kidney explant culture. At later stages, the UB organoids differentiate into CD organoids, which contain >95% CD cell types as estimated by single-cell RNA sequencing. The CD epithelia demonstrate renal electrophysiologic functions, with ENaC-mediated vectorial sodium transport by principal cells and V-type ATPase proton pump activity by FOXI1-induced intercalated cells.
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Affiliation(s)
- Min Shi
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu, China
| | - Kyle W McCracken
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Nephrology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, USA.
| | - Ankit B Patel
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Weitao Zhang
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lioba Ester
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department II of Internal Medicine, University of Cologne, Faculty of Medicine, and University Hospital Cologne, Cologne, Germany
| | - M Todd Valerius
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge and Boston, Boston, MA, USA
| | - Joseph V Bonventre
- Division of Renal Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge and Boston, Boston, MA, USA.
- Division of Engineering in Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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21
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Chang YC, Manent J, Schroeder J, Wong SFL, Hauswirth GM, Shylo NA, Moore EL, Achilleos A, Garside V, Polo JM, Trainor P, McGlinn E. Nr6a1 controls Hox expression dynamics and is a master regulator of vertebrate trunk development. Nat Commun 2022; 13:7766. [PMID: 36522318 PMCID: PMC9755267 DOI: 10.1038/s41467-022-35303-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
The vertebrate main-body axis is laid down during embryonic stages in an anterior-to-posterior (head-to-tail) direction, driven and supplied by posteriorly located progenitors. Whilst posterior expansion and segmentation appears broadly uniform along the axis, there is developmental and evolutionary support for at least two discrete modules controlling processes within different axial regions: a trunk and a tail module. Here, we identify Nuclear receptor subfamily 6 group A member 1 (Nr6a1) as a master regulator of trunk development in the mouse. Specifically, Nr6a1 was found to control vertebral number and segmentation of the trunk region, autonomously from other axial regions. Moreover, Nr6a1 was essential for the timely progression of Hox signatures, and neural versus mesodermal cell fate choice, within axial progenitors. Collectively, Nr6a1 has an axially-restricted role in all major cellular and tissue-level events required for vertebral column formation, supporting the view that changes in Nr6a1 levels may underlie evolutionary changes in axial formulae.
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Affiliation(s)
- Yi-Cheng Chang
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Jan Manent
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Jan Schroeder
- grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC Australia
| | - Siew Fen Lisa Wong
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Gabriel M. Hauswirth
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Natalia A. Shylo
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA
| | - Emma L. Moore
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA
| | - Annita Achilleos
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA ,grid.413056.50000 0004 0383 4764University of Nicosia, Nicosia, Cyprus
| | - Victoria Garside
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Jose M. Polo
- grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC Australia
| | - Paul Trainor
- grid.250820.d0000 0000 9420 1591Stowers Institute for Medical Research, Kansas City, Missouri USA ,grid.412016.00000 0001 2177 6375Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas USA
| | - Edwina McGlinn
- grid.1002.30000 0004 1936 7857EMBL Australia, Monash University, Clayton, Victoria 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
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22
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Sharma A, Meer M, Dapkunas A, Ihermann-Hella A, Kuure S, Vainio SJ, Iber D, Naillat F. FGF8 induces chemokinesis and regulates condensation of mouse nephron progenitor cells. Development 2022; 149:277149. [DOI: 10.1242/dev.201012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Kidneys develop via iterative branching of the ureteric epithelial tree and subsequent nephrogenesis at the branch points. Nephrons form in the cap mesenchyme as the metanephric mesenchyme (MM) condenses around the epithelial ureteric buds (UBs). Previous work has demonstrated that FGF8 is important for the survival of nephron progenitor cells (NPCs), and early deletion of Fgf8 leads to the cessation of nephron formation, which results in post-natal lethality. We now reveal a previously unreported function of FGF8. By combining transgenic mouse models, quantitative imaging assays and data-driven computational modelling, we show that FGF8 has a strong chemokinetic effect and that this chemokinetic effect is important for the condensation of NPCs to the UB. The computational model shows that the motility must be lower close to the UB to achieve NPC attachment. We conclude that the FGF8 signalling pathway is crucial for the coordination of NPC condensation at the UB. Chemokinetic effects have also been described for other FGFs and may be generally important for the formation of mesenchymal condensates.
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Affiliation(s)
- Abhishek Sharma
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
| | - Marco Meer
- ETH Zürich 3 Department of Biosystems, Science and Engineering , , Zürich 04058, Switzerland
- Swiss Institute of Bioinformatics 4 , Lausanne 1015 , Switzerland
| | - Arvydas Dapkunas
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
| | - Anneliis Ihermann-Hella
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
| | - Satu Kuure
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
- LAC/HiLIFE, and Medicum, University of Helsinki 6 GM-Unit , , Helsinki 00014, Finland
| | - Seppo J. Vainio
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
- Infotech Oulu 7 , Oulu 90200, Finland
- Borealis Biobank 8 , Oulu 90200, Finland
- Kvantum Institute, University of Oulu 9 , Oulu 90200, Finland
| | - Dagmar Iber
- ETH Zürich 3 Department of Biosystems, Science and Engineering , , Zürich 04058, Switzerland
- Swiss Institute of Bioinformatics 4 , Lausanne 1015 , Switzerland
| | - Florence Naillat
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
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23
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Genuth NR, Shi Z, Kunimoto K, Hung V, Xu AF, Kerr CH, Tiu GC, Oses-Prieto JA, Salomon-Shulman REA, Axelrod JD, Burlingame AL, Loh KM, Barna M. A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production. Nat Commun 2022; 13:5491. [PMID: 36123354 PMCID: PMC9485161 DOI: 10.1038/s41467-022-33263-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/09/2022] [Indexed: 02/05/2023] Open
Abstract
Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.
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Affiliation(s)
- Naomi R Genuth
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Zhen Shi
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Genentech Inc, South San Francisco, CA, 94080, USA
| | - Koshi Kunimoto
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Victoria Hung
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Adele F Xu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gerald C Tiu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | | | - Jeffrey D Axelrod
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Kyle M Loh
- Department of Developmental Biology, Stanford University, Stanford, CA, 94305, USA
| | - Maria Barna
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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24
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Ornitz DM, Itoh N. New developments in the biology of fibroblast growth factors. WIREs Mech Dis 2022; 14:e1549. [PMID: 35142107 PMCID: PMC10115509 DOI: 10.1002/wsbm.1549] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/28/2023]
Abstract
The fibroblast growth factor (FGF) family is composed of 18 secreted signaling proteins consisting of canonical FGFs and endocrine FGFs that activate four receptor tyrosine kinases (FGFRs 1-4) and four intracellular proteins (intracellular FGFs or iFGFs) that primarily function to regulate the activity of voltage-gated sodium channels and other molecules. The canonical FGFs, endocrine FGFs, and iFGFs have been reviewed extensively by us and others. In this review, we briefly summarize past reviews and then focus on new developments in the FGF field since our last review in 2015. Some of the highlights in the past 6 years include the use of optogenetic tools, viral vectors, and inducible transgenes to experimentally modulate FGF signaling, the clinical use of small molecule FGFR inhibitors, an expanded understanding of endocrine FGF signaling, functions for FGF signaling in stem cell pluripotency and differentiation, roles for FGF signaling in tissue homeostasis and regeneration, a continuing elaboration of mechanisms of FGF signaling in development, and an expanding appreciation of roles for FGF signaling in neuropsychiatric diseases. This article is categorized under: Cardiovascular Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology Congenital Diseases > Stem Cells and Development Cancer > Stem Cells and Development.
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Affiliation(s)
- David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nobuyuki Itoh
- Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo, Kyoto, Japan
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25
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Normal embryonic development and neonatal digit regeneration in mice overexpressing a stem cell factor, Sall4. PLoS One 2022; 17:e0267273. [PMID: 35482646 PMCID: PMC9049339 DOI: 10.1371/journal.pone.0267273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/05/2022] [Indexed: 01/29/2023] Open
Abstract
Sall4 encodes a transcription factor and is known to participate in the pluripotency network of embryonic stem cells. Sall4 expression is known to be high in early stage post-implantation mouse embryos. During early post-gastrulation stages, Sall4 is highly expressed in the tail bud and distal limb buds, where progenitor cells are maintained in an undifferentiated status. The expression of Sall4 is rapidly downregulated during embryonic development. We previously demonstrated that Sall4 is required for limb and posterior axial skeleton development by conditional deletion of Sall4 in the T (Brachyury) lineage. To gain insight into Sall4 functions in embryonic development and postnatal digit regeneration, we genetically overexpressed Sall4 in the mesodermal lineage by the TCre transgene and a novel knockin allele of Rosa26-loxP-stop-loxP-Sall4. In significant contrast to severe defects by Sall4 loss of function reported in previous studies, overexpression of Sall4 resulted in normal morphology and pattern in embryos and neonates. The length of limb long bones showed subtle reduction in Sall4-overexpression mice. It is known that the digit tip of neonatal mice has level-specific regenerative ability after experimental amputation. We observed Sall4 expression in the digit tip by using a sensitive Sall4-LacZ knock-in reporter expression. Sall4 overexpression did not alter the regenerative ability of the terminal phalange that normally regenerates after amputation. Moreover, Sall4 overexpression did not confer regenerative ability to the second phalange that normally does not regenerate after amputation. These genetic experiments show that overexpression of Sall4 does not alter the development of the appendicular and axial skeleton, or neonatal digit regeneration. The results suggest that Sall4 acts as a permissive factor rather than playing an instructive role.
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26
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Cooper F, Tsakiridis A. Shaping axial identity during human pluripotent stem cell differentiation to neural crest cells. Biochem Soc Trans 2022; 50:499-511. [PMID: 35015077 PMCID: PMC9022984 DOI: 10.1042/bst20211152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022]
Abstract
The neural crest (NC) is a multipotent cell population which can give rise to a vast array of derivatives including neurons and glia of the peripheral nervous system, cartilage, cardiac smooth muscle, melanocytes and sympathoadrenal cells. An attractive strategy to model human NC development and associated birth defects as well as produce clinically relevant cell populations for regenerative medicine applications involves the in vitro generation of NC from human pluripotent stem cells (hPSCs). However, in vivo, the potential of NC cells to generate distinct cell types is determined by their position along the anteroposterior (A-P) axis and, therefore the axial identity of hPSC-derived NC cells is an important aspect to consider. Recent advances in understanding the developmental origins of NC and the signalling pathways involved in its specification have aided the in vitro generation of human NC cells which are representative of various A-P positions. Here, we explore recent advances in methodologies of in vitro NC specification and axis patterning using hPSCs.
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Affiliation(s)
- Fay Cooper
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K
- Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K
- Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield S10 2TN, U.K
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27
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Miyazawa H, Snaebjornsson MT, Prior N, Kafkia E, Hammarén HM, Tsuchida-Straeten N, Patil KR, Beck M, Aulehla A. Glycolytic flux-signaling controls mouse embryo mesoderm development. eLife 2022; 11:83299. [PMID: 36469462 PMCID: PMC9771359 DOI: 10.7554/elife.83299] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/06/2022] [Indexed: 12/12/2022] Open
Abstract
How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here, we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic PFKFB3 (cytoPFKFB3). Overexpression of cytoPFKFB3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPFKFB3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization.
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Affiliation(s)
- Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Nicole Prior
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Eleni Kafkia
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Henrik M Hammarén
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Kiran R Patil
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
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28
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Bai Y, Wei C, Li P, Sun X, Cai G, Chen X, Hong Q. Primary cilium in kidney development, function and disease. Front Endocrinol (Lausanne) 2022; 13:952055. [PMID: 36072924 PMCID: PMC9441790 DOI: 10.3389/fendo.2022.952055] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
The primary cilium is a hair-like, microtubule-based organelle that is covered by the cell membrane and extends from the surface of most vertebrate cells. It detects and translates extracellular signals to direct various cellular signaling pathways to maintain homeostasis. It is mainly distributed in the proximal and distal tubules and collecting ducts in the kidney. Specific signaling transduction proteins localize to primary cilia. Defects in cilia structure and function lead to a class of diseases termed ciliopathies. The proper functioning of primary cilia is essential to kidney organogenesis and the maintenance of epithelial cell differentiation and proliferation. Persistent cilia dysfunction has a role in the early stages and progression of renal diseases, such as cystogenesis and acute tubular necrosis (ATN). In this review, we focus on the central role of cilia in kidney development and illustrate how defects in cilia are associated with renal disease progression.
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Affiliation(s)
- Yunfeng Bai
- Department of Nephrology, First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Cuiting Wei
- Department of Nephrology, First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ping Li
- Department of Nephrology, First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Xuefeng Sun
- Department of Nephrology, First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Guangyan Cai
- Department of Nephrology, First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
| | - Xiangmei Chen
- Department of Nephrology, First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- *Correspondence: Xiangmei Chen, ; Quan Hong,
| | - Quan Hong
- Department of Nephrology, First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, Nephrology Institute of the Chinese People's Liberation Army, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Disease Research, Beijing, China
- *Correspondence: Xiangmei Chen, ; Quan Hong,
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29
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Tikka P, Mercker M, Skovorodkin I, Saarela U, Vainio S, Ronkainen VP, Sluka JP, Glazier JA, Marciniak-Czochra A, Schaefer F. Computational modelling of nephron progenitor cell movement and aggregation during kidney organogenesis. Math Biosci 2021; 344:108759. [PMID: 34883105 DOI: 10.1016/j.mbs.2021.108759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
During early kidney organogenesis, nephron progenitor (NP) cells move from the tip to the corner region of the ureteric bud (UB) branches in order to form the pretubular aggregate, the early structure giving rise to nephron formation. NP cells derive from metanephric mesenchymal cells and physically interact with them during the movement. Chemotaxis and cell-cell adhesion differences are believed to drive the cell patterning during this critical period of organogenesis. However, the effect of these forces to the cell patterns and their respective movements are known in limited details. We applied a Cellular Potts Model to explore how these forces and organizations contribute to directed cell movement and aggregation. Model parameters were estimated based on fitting to experimental data obtained in ex vivo kidney explant and dissociation-reaggregation organoid culture studies. Our simulations indicated that optimal enrichment and aggregation of NP cells in the UB corner niche requires chemoattractant secretion from both the UB epithelial cells and the NP cells themselves, as well as differences in cell-cell adhesion energies. Furthermore, NP cells were observed, both experimentally and by modelling, to move at higher speed in the UB corner as compared to the tip region where they originated. The existence of different cell speed domains along the UB was confirmed using self-organizing map analysis. In summary, we saw faster NP cell movements near aggregation. The applicability of Cellular Potts Model approach to simulate cell movement and patterning was found to be good during for this early nephrogenesis process. Further refinement of the model should allow us to recapitulate the effects of developmental changes of cell phenotypes and molecular crosstalk during further organ development.
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Affiliation(s)
- Pauli Tikka
- Division of Pediatric Nephrology. Heidelberg University Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany.
| | - Moritz Mercker
- Institute of Applied Mathematics (IAM) and Interdisciplinary Center of Scientific Computing (IWR), Mathematikon, Heidelberg University, Germany
| | - Ilya Skovorodkin
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ulla Saarela
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Seppo Vainio
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Veli-Pekka Ronkainen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - James P Sluka
- Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, Indiana, USA
| | - James A Glazier
- Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University, Bloomington, Indiana, USA
| | - Anna Marciniak-Czochra
- Institute of Applied Mathematics (IAM) and Interdisciplinary Center of Scientific Computing (IWR), Mathematikon, Heidelberg University, Germany
| | - Franz Schaefer
- Division of Pediatric Nephrology. Heidelberg University Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany
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30
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Schifferl D, Scholze-Wittler M, Wittler L, Veenvliet JV, Koch F, Herrmann BG. A 37 kb region upstream of brachyury comprising a notochord enhancer is essential for notochord and tail development. Development 2021; 148:273520. [PMID: 34822716 PMCID: PMC8722351 DOI: 10.1242/dev.200059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
The node-streak border region comprising notochord progenitor cells (NPCs) at the posterior node and neuro-mesodermal progenitor cells (NMPs) in the adjacent epiblast is the prime organizing center for axial elongation in mouse embryos. The T-box transcription factor brachyury (T) is essential for both formation of the notochord and maintenance of NMPs, and thus is a key regulator of trunk and tail development. The T promoter controlling T expression in NMPs and nascent mesoderm has been characterized in detail; however, control elements for T expression in the notochord have not been identified yet. We have generated a series of deletion alleles by CRISPR/Cas9 genome editing in mESCs, and analyzed their effects in mutant mouse embryos. We identified a 37 kb region upstream of T that is essential for notochord function and tailbud outgrowth. Within that region, we discovered a T-binding enhancer required for notochord cell specification and differentiation. Our data reveal a complex regulatory landscape controlling cell type-specific expression and function of T in NMP/nascent mesoderm and node/notochord, allowing proper trunk and tail development. Summary: Genetic dissection of the mouse brachyury locus identifies a notochord enhancer and predicts additional control elements essential for trunk and tail development of the mouse embryo.
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Affiliation(s)
- Dennis Schifferl
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.,Institute of Biology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 1-3, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Frederic Koch
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
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31
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Chioni AM, Grose RP. Biological Significance and Targeting of the FGFR Axis in Cancer. Cancers (Basel) 2021; 13:5681. [PMID: 34830836 PMCID: PMC8616401 DOI: 10.3390/cancers13225681] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022] Open
Abstract
The pleiotropic effects of fibroblast growth factors (FGFs), the widespread expression of all seven signalling FGF receptors (FGFRs) throughout the body, and the dramatic phenotypes shown by many FGF/R knockout mice, highlight the diversity, complexity and functional importance of FGFR signalling. The FGF/R axis is critical during normal tissue development, homeostasis and repair. Therefore, it is not surprising that substantial evidence also pinpoints the involvement of aberrant FGFR signalling in disease, including tumourigenesis. FGFR aberrations in cancer include mutations, gene fusions, and amplifications as well as corrupted autocrine/paracrine loops. Indeed, many clinical trials on cancer are focusing on targeting the FGF/FGFR axis, using selective FGFR inhibitors, nonselective FGFR tyrosine kinase inhibitors, ligand traps, and monoclonal antibodies and some have already been approved for the treatment of cancer patients. The heterogeneous tumour microenvironment and complexity of FGFR signalling may be some of the factors responsible for the resistance or poor response to therapy with FGFR axis-directed therapeutic agents. In the present review we will focus on the structure and function of FGF(R)s, their common irregularities in cancer and the therapeutic value of targeting their function in cancer.
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Affiliation(s)
- Athina-Myrto Chioni
- School of Life Sciences Pharmacy and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK;
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32
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Trivedi N, Kumar D. Fibroblast growth factor and kidney disease: Updates for emerging novel therapeutics. J Cell Physiol 2021; 236:7909-7925. [PMID: 34196395 DOI: 10.1002/jcp.30497] [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: 03/01/2021] [Revised: 05/04/2021] [Accepted: 05/28/2021] [Indexed: 01/01/2023]
Abstract
The discovery of fibroblast growth factors (FGFs) and fibroblast growth factor receptors (FGFRs) provided a profound new insight into physiological and metabolic functions. FGF has a large family by having divergent structural elements and enable functional divergence and specification. FGF and FGFRs are highly expressed during kidney development. Signals from the ureteric bud regulate morphogenesis, nephrogenesis, and nephron progenitor survival. Thus, FGF signaling plays an important role in kidney progenitor cell aggregation at the sites of new nephron formation. This review will summarize the current knowledge about functions of FGF signaling in kidney development and their ability to promote regeneration in injured kidneys and its use as a biomarker and therapeutic target in kidney diseases. Further studies are essential to determine the predictive significance of the various FGF/FGFR deviations and to integrate them into clinical algorithms.
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Affiliation(s)
- Neerja Trivedi
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Devendra Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska, USA
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33
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Little MH. Returning to kidney development to deliver synthetic kidneys. Dev Biol 2021; 474:22-36. [PMID: 33333068 PMCID: PMC8052282 DOI: 10.1016/j.ydbio.2020.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022]
Abstract
There is no doubt that the development of transplantable synthetic kidneys could improve the outcome for the many millions of people worldwide suffering from chronic kidney disease. Substantial progress has been made in the last 6 years in the generation of kidney tissue from stem cells. However, the limited scale, incomplete cellular complexity and functional immaturity of such structures suggests we are some way from this goal. While developmental biology has successfully guided advances to date, these human kidney models are limited in their capacity for ongoing nephrogenesis and lack corticomedullary definition, a unified vasculature and a coordinated exit path for urinary filtrate. This review will reassess our developmental understanding of how the mammalian embryo manages to create kidneys, how this has informed our progress to date and how both engineering and developmental biology can continue to guide us towards a synthetic kidney.
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Affiliation(s)
- Melissa H Little
- Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC, Australia; Department of Paediatrics, The University of Melbourne, VIC, Australia; Department of Anatomy and Neuroscience, The University of Melbourne, VIC, Australia.
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34
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Balendran V, Skidmore JM, Ritter KE, Gao J, Cimerman J, Beyer LA, Hurd EA, Raphael Y, Martin DM. Chromatin remodeler CHD7 is critical for cochlear morphogenesis and neurosensory patterning. Dev Biol 2021; 477:11-21. [PMID: 34004180 DOI: 10.1016/j.ydbio.2021.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/12/2021] [Accepted: 05/10/2021] [Indexed: 11/18/2022]
Abstract
Epigenetic regulation of gene transcription by chromatin remodeling proteins has recently emerged as an important contributing factor in inner ear development. Pathogenic variants in CHD7, the gene encoding Chromodomain Helicase DNA binding protein 7, cause CHARGE syndrome, which presents with malformations in the developing ear. Chd7 is broadly expressed in the developing mouse otocyst and mature auditory epithelium, yet the pathogenic effects of Chd7 loss in the cochlea are not well understood. Here we characterized cochlear epithelial phenotypes in mice with deletion of Chd7 throughout the otocyst (using Foxg1Cre/+ and Pax2Cre), in the otic mesenchyme (using TCre), in hair cells (using Atoh1Cre), in developing neuroblasts (using NgnCre), or in spiral ganglion neurons (using ShhCre/+). Pan-otic deletion of Chd7 resulted in shortened cochleae with aberrant projections and axonal looping, disorganized, supernumerary hair cells at the apical turn and a narrowed epithelium with missing hair cells in the middle region. Deletion of Chd7 in the otic mesenchyme had no effect on overall cochlear morphology. Loss of Chd7 in hair cells did not disrupt their formation or organization of the auditory epithelium. Similarly, absence of Chd7 in spiral ganglion neurons had no effect on axonal projections. In contrast, deletion of Chd7 in developing neuroblasts led to smaller spiral ganglia and disorganized cochlear neurites. Together, these observations reveal dosage-, tissue-, and time-sensitive cell autonomous roles for Chd7 in cochlear elongation and cochlear neuron organization, with minimal functions for Chd7 in hair cells. These studies provide novel information about roles for Chd7 in development of auditory neurons.
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Affiliation(s)
- Vinodh Balendran
- Departments of Pediatrics, The University of Michigan, Ann Arbor, MI, USA
| | | | - K Elaine Ritter
- Departments of Pediatrics, The University of Michigan, Ann Arbor, MI, USA
| | - Jingxia Gao
- Departments of Pediatrics, The University of Michigan, Ann Arbor, MI, USA
| | - Jelka Cimerman
- Departments of Pediatrics, The University of Michigan, Ann Arbor, MI, USA
| | - Lisa A Beyer
- Otolaryngology - Head and Neck Surgery, The University of Michigan, Ann Arbor, MI, USA
| | | | - Yehoash Raphael
- Otolaryngology - Head and Neck Surgery, The University of Michigan, Ann Arbor, MI, USA
| | - Donna M Martin
- Departments of Pediatrics, The University of Michigan, Ann Arbor, MI, USA; Otolaryngology - Head and Neck Surgery, The University of Michigan, Ann Arbor, MI, USA; Human Genetics, The University of Michigan, Ann Arbor, MI, USA.
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35
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Wymeersch FJ, Wilson V, Tsakiridis A. Understanding axial progenitor biology in vivo and in vitro. Development 2021; 148:148/4/dev180612. [PMID: 33593754 DOI: 10.1242/dev.180612] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The generation of the components that make up the embryonic body axis, such as the spinal cord and vertebral column, takes place in an anterior-to-posterior (head-to-tail) direction. This process is driven by the coordinated production of various cell types from a pool of posteriorly-located axial progenitors. Here, we review the key features of this process and the biology of axial progenitors, including neuromesodermal progenitors, the common precursors of the spinal cord and trunk musculature. We discuss recent developments in the in vitro production of axial progenitors and their potential implications in disease modelling and regenerative medicine.
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Affiliation(s)
- Filip J Wymeersch
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Valerie Wilson
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield S10 2TN UK .,Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN UK
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36
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Hawkins MB, Henke K, Harris MP. Latent developmental potential to form limb-like skeletal structures in zebrafish. Cell 2021; 184:899-911.e13. [PMID: 33545089 DOI: 10.1016/j.cell.2021.01.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/28/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Changes in appendage structure underlie key transitions in vertebrate evolution. Addition of skeletal elements along the proximal-distal axis facilitated critical transformations, including the fin-to-limb transition that permitted generation of diverse modes of locomotion. Here, we identify zebrafish mutants that form supernumerary long bones in their pectoral fins. These new bones integrate into musculature, form joints, and articulate with neighboring elements. This phenotype is caused by activating mutations in previously unrecognized regulators of appendage patterning, vav2 and waslb, that function in a common pathway. This pathway is required for appendage development across vertebrates, and loss of Wasl in mice causes defects similar to those seen in murine Hox mutants. Concordantly, formation of supernumerary bones requires Hox11 function, and mutations in the vav2/wasl pathway drive enhanced expression of hoxa11b, indicating developmental homology with the forearm. Our findings reveal a latent, limb-like pattern ability in fins that is activated by simple genetic perturbation.
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Affiliation(s)
- M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA; Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Katrin Henke
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA.
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37
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The Classification of VACTERL Association into 3 Groups According to the Limb Defect. PLASTIC AND RECONSTRUCTIVE SURGERY-GLOBAL OPEN 2021; 9:e3360. [PMID: 33680640 PMCID: PMC7929542 DOI: 10.1097/gox.0000000000003360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 11/26/2022]
Abstract
The VACTERL association (VA) is defined as the nonrandom co-occurrence of 6 anomalies: vertebral anomalies (V), Anal atresia (A), Cardiac defects (C), Tracheo-esophageal fistula (TE), Renal defects (R), and Limb anomalies (L). The current communication presents an argument that patients with VA should be classified into three district groups based on their limb defects: VACTERL1: patients with normal limbs; VACTERL2: patients with limb anomalies other than radial ray defects of the upper limbs; and VACTERL3: patients with radial ray defects of the upper limbs. The author will demonstrate that the rationale behind the L1-3 classification in patients in VA is based on the embryogenesis of the 6 affected anatomical areas in VA. The pathogenesis of VACTERL1 is secondary to perturbations of Sonic Hedgehog (SHH) interactions. SHH signaling is known to have a major role in the normal development of the vertebrae, ano-rectal area, heart, tracheo-esophageal area, and kidney. However, SHH is not involved in the development of the radial ray; hence, patients present with no limb defects. The pathogenesis of VACTERL2 is variable depending on the type of gene mutation. The pathogenesis of VACTERL3 is related to errors in a group of proteins (namely, the proteins of the TBX5-SALL4-SALL1 loop and the FGF8-FGF10 loop/ pathway). These proteins are essential for the normal development of the radial ray and they interact in the development of the other anatomical areas of VA including the heart and kidney. Hence, VACTERL3 patients present with radial ray deficiency.
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38
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Nedelec S, Martinez-Arias A. In vitro models of spinal motor circuit's development in mammals: achievements and challenges. Curr Opin Neurobiol 2021; 66:240-249. [PMID: 33677159 DOI: 10.1016/j.conb.2020.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/12/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022]
Abstract
The connectivity patterns of neurons sustaining the functionality of spinal locomotor circuits rely on the specification of hundreds of motor neuron and interneuron subtypes precisely arrayed within the embryonic spinal cord. Knowledge acquired by developmental biologists on the molecular mechanisms underpinning this process in vivo has supported the development of 2D and 3D differentiation strategies to generate spinal neuronal diversity from mouse and human pluripotent stem cells (PSCs). Here, we review recent breakthroughs in this field and the perspectives opened up by models of in vitro embryogenesis to approach the mechanisms underlying neuronal diversification and the formation of functional mouse and human locomotor circuits. Beyond serving fundamental investigations, these new approaches should help engineering neuronal circuits differentially impacted in neuromuscular disorders, such as amyotrophic lateral sclerosis or spinal muscular atrophies, and thus open new avenues for disease modeling and drug screenings.
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Affiliation(s)
- Stéphane Nedelec
- Institut du Fer à Moulin, 75005, Paris, France; Inserm, UMR-S 1270, 75005 Paris, France; Sorbonne Université, Science and Engineering Faculty, 75005 Paris, France.
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39
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Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive intra- and inter-enhancer redundancy. Nat Commun 2021; 12:439. [PMID: 33469032 PMCID: PMC7815712 DOI: 10.1038/s41467-020-20714-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
Developmental genes are often regulated by multiple elements with overlapping activity. Yet, in most cases, the relative function of those elements and their contribution to endogenous gene expression remain poorly characterized. An example of this phenomenon is that distinct sets of enhancers have been proposed to direct Fgf8 in the limb apical ectodermal ridge and the midbrain-hindbrain boundary. Using in vivo CRISPR/Cas9 genome engineering, we functionally dissect this complex regulatory ensemble and demonstrate two distinct regulatory logics. In the apical ectodermal ridge, the control of Fgf8 expression appears distributed between different enhancers. In contrast, we find that in the midbrain-hindbrain boundary, one of the three active enhancers is essential while the other two are dispensable. We further dissect the essential midbrain-hindbrain boundary enhancer to reveal that it is also composed by a mixture of essential and dispensable modules. Cross-species transgenic analysis of this enhancer suggests that its composition may have changed in the vertebrate lineage.
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40
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Probst S, Sagar, Tosic J, Schwan C, Grün D, Arnold SJ. Spatiotemporal sequence of mesoderm and endoderm lineage segregation during mouse gastrulation. Development 2021; 148:dev.193789. [PMID: 33199445 DOI: 10.1242/dev.193789] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/06/2020] [Indexed: 12/20/2022]
Abstract
Anterior mesoderm (AM) and definitive endoderm (DE) progenitors represent the earliest embryonic cell types that are specified during germ layer formation at the primitive streak (PS) of the mouse embryo. Genetic experiments indicate that both lineages segregate from Eomes-expressing progenitors in response to different Nodal signaling levels. However, the precise spatiotemporal pattern of the emergence of these cell types and molecular details of lineage segregation remain unexplored. We combined genetic fate labeling and imaging approaches with single-cell RNA sequencing (scRNA-seq) to follow the transcriptional identities and define lineage trajectories of Eomes-dependent cell types. Accordingly, all cells moving through the PS during the first day of gastrulation express Eomes AM and DE specification occurs before cells leave the PS from Eomes-positive progenitors in a distinct spatiotemporal pattern. ScRNA-seq analysis further suggested the immediate and complete separation of AM and DE lineages from Eomes-expressing cells as last common bipotential progenitor.
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Affiliation(s)
- Simone Probst
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany .,Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, D-79104 Freiburg, Germany
| | - Sagar
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Jelena Tosic
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, D-79104 Freiburg, Germany.,Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Carsten Schwan
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany
| | - Dominic Grün
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, D-79104 Freiburg, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, D-79104 Freiburg, Germany .,Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, D-79104 Freiburg, Germany
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41
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Anderson MJ, Magidson V, Kageyama R, Lewandoski M. Fgf4 maintains Hes7 levels critical for normal somite segmentation clock function. eLife 2020; 9:55608. [PMID: 33210601 PMCID: PMC7717904 DOI: 10.7554/elife.55608] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
During vertebrate development, the presomitic mesoderm (PSM) periodically segments into somites, which will form the segmented vertebral column and associated muscle, connective tissue, and dermis. The periodicity of somitogenesis is regulated by a segmentation clock of oscillating Notch activity. Here, we examined mouse mutants lacking only Fgf4 or Fgf8, which we previously demonstrated act redundantly to prevent PSM differentiation. Fgf8 is not required for somitogenesis, but Fgf4 mutants display a range of vertebral defects. We analyzed Fgf4 mutants by quantifying mRNAs fluorescently labeled by hybridization chain reaction within Imaris-based volumetric tissue subsets. These data indicate that FGF4 maintains Hes7 levels and normal oscillatory patterns. To support our hypothesis that FGF4 regulates somitogenesis through Hes7, we demonstrate genetic synergy between Hes7 and Fgf4, but not with Fgf8. Our data indicate that Fgf4 is potentially important in a spectrum of human Segmentation Defects of the Vertebrae caused by defective Notch oscillations.
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Affiliation(s)
- Matthew J Anderson
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, United States
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mark Lewandoski
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, United States
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42
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Boylan M, Anderson MJ, Ornitz DM, Lewandoski M. The Fgf8 subfamily (Fgf8, Fgf17 and Fgf18) is required for closure of the embryonic ventral body wall. Development 2020; 147:dev189506. [PMID: 32907848 PMCID: PMC7595690 DOI: 10.1242/dev.189506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 08/28/2020] [Indexed: 12/26/2022]
Abstract
The closure of the embryonic ventral body wall in amniotes is an important morphogenetic event and is essential for life. Defects in human ventral wall closure are a major class of birth defect and a significant health burden. Despite this, very little is understood about how the ventral body wall is formed. Here, we show that fibroblast growth factor (FGF) ligands FGF8, FGF17 and FGF18 are essential for this process. Conditional mouse mutants for these genes display subtle migratory defects in the abdominal muscles of the ventral body wall and an enlarged umbilical ring, through which the internal organs are extruded. By refining where and when these genes are required using different Cre lines, we show that Fgf8 and Fgf17 are required in the presomitic mesoderm, whereas Fgf18 is required in the somites. This study identifies complex and multifactorial origins of ventral wall defects and has important implications for understanding their origins during embryonic development.
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Affiliation(s)
- Michael Boylan
- Cancer and Developmental Biology Lab, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Matthew J Anderson
- Cancer and Developmental Biology Lab, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Mark Lewandoski
- Cancer and Developmental Biology Lab, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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Bernheim S, Meilhac SM. Mesoderm patterning by a dynamic gradient of retinoic acid signalling. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190556. [PMID: 32829679 PMCID: PMC7482219 DOI: 10.1098/rstb.2019.0556] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/15/2022] Open
Abstract
Retinoic acid (RA), derived from vitamin A, is a major teratogen, clinically recognized in 1983. Identification of its natural presence in the embryo and dissection of its molecular mechanism of action became possible in the animal model with the advent of molecular biology, starting with the cloning of its nuclear receptor. In normal development, the dose of RA is tightly controlled to regulate organ formation. Its production depends on enzymes, which have a dynamic expression profile during embryonic development. As a small molecule, it diffuses rapidly and acts as a morphogen. Here, we review advances in deciphering how endogenously produced RA provides positional information to cells. We compare three mesodermal tissues, the limb, the somites and the heart, and discuss how RA signalling regulates antero-posterior and left-right patterning. A common principle is the establishment of its spatio-temporal dynamics by positive and negative feedback mechanisms and by antagonistic signalling by FGF. However, the response is cell-specific, pointing to the existence of cofactors and effectors, which are as yet incompletely characterized. This article is part of a discussion meeting issue 'Contemporary morphogenesis'.
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Affiliation(s)
- Ségolène Bernheim
- Imagine-Institut Pasteur, Laboratory of Heart Morphogenesis, 75015 Paris, France
- INSERM UMR1163, 75015 Paris, France
- Université de Paris, Paris, France
| | - Sigolène M. Meilhac
- Imagine-Institut Pasteur, Laboratory of Heart Morphogenesis, 75015 Paris, France
- INSERM UMR1163, 75015 Paris, France
- Université de Paris, Paris, France
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44
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Chambers JM, Wingert RA. Advances in understanding vertebrate nephrogenesis. Tissue Barriers 2020; 8:1832844. [PMID: 33092489 PMCID: PMC7714473 DOI: 10.1080/21688370.2020.1832844] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
The kidney is a complex organ that performs essential functions such as blood filtration and fluid homeostasis, among others. Recent years have heralded significant advancements in our knowledge of the mechanisms that control kidney formation. Here, we provide an overview of vertebrate renal development with a focus on nephrogenesis, the process of generating the epithelialized functional units of the kidney. These steps begin with intermediate mesoderm specification and proceed all the way to the terminally differentiated nephron cell, with many detailed stages in between. The establishment of nephron architecture with proper cellular barriers is vital throughout these processes. Continuously striving to gain further insights into nephrogenesis can ultimately lead to a better understanding and potential treatments for developmental maladies such as Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
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Affiliation(s)
- Joseph M. Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN, USA
| | - Rebecca A. Wingert
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, IN, USA
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45
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Dissecting the Interaction of FGF8 with Receptor FGFRL1. Biomolecules 2020; 10:biom10101399. [PMID: 33019532 PMCID: PMC7600612 DOI: 10.3390/biom10101399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022] Open
Abstract
In mammals, the novel protein fibroblast growth factor receptor-like 1 (FGFRL1) is involved in the development of metanephric kidneys. It appears that this receptor controls a crucial transition of the induced metanephric mesenchyme to epithelial renal vesicles, which further develop into functional nephrons. FGFRL1 knockout mice lack metanephric kidneys and do not express any fibroblast growth factor (FGF) 8 in the metanephric mesenchyme, suggesting that FGFRL1 and FGF8 play a decisive role during kidney formation. FGFRL1 consists of three extracellular immunoglobulin (Ig) domains (Ig1-Ig2-Ig3), a transmembrane domain and a short intracellular domain. We have prepared the extracellular domain (Ig123), the three individual Ig domains (Ig1, Ig2, Ig3) as well as all combinations containing two Ig domains (Ig12, Ig23, Ig13) in recombinant form in human cells. All polypeptides that contain the Ig2 domain (Ig123, Ig12, Ig23, Ig2) were found to interact with FGF8 with very high affinity, whereas all constructs that lack the Ig2 domain (Ig1, Ig3, Ig13) poorly interacted with FGF8 as shown by ELISA and surface plasmon resonance. It is therefore likely that FGFRL1 represents a physiological receptor for FGF8 in the kidney and that the ligand primarily binds to the Ig2 domain of the receptor. With Biacore experiments, we also measured the affinity of FGF8 for the different constructs. All constructs containing the Ig2 domain showed a rapid association and a slow dissociation phase, from which a KD of 2–3 × 10−9 M was calculated. Our data support the hypothesis that binding of FGF8 to FGFRL1 could play an important role in driving the formation of nephrons in the developing kidney.
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Xie Y, Su N, Yang J, Tan Q, Huang S, Jin M, Ni Z, Zhang B, Zhang D, Luo F, Chen H, Sun X, Feng JQ, Qi H, Chen L. FGF/FGFR signaling in health and disease. Signal Transduct Target Ther 2020; 5:181. [PMID: 32879300 PMCID: PMC7468161 DOI: 10.1038/s41392-020-00222-7] [Citation(s) in RCA: 473] [Impact Index Per Article: 94.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/28/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Growing evidences suggest that the fibroblast growth factor/FGF receptor (FGF/FGFR) signaling has crucial roles in a multitude of processes during embryonic development and adult homeostasis by regulating cellular lineage commitment, differentiation, proliferation, and apoptosis of various types of cells. In this review, we provide a comprehensive overview of the current understanding of FGF signaling and its roles in organ development, injury repair, and the pathophysiology of spectrum of diseases, which is a consequence of FGF signaling dysregulation, including cancers and chronic kidney disease (CKD). In this context, the agonists and antagonists for FGF-FGFRs might have therapeutic benefits in multiple systems.
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Affiliation(s)
- Yangli Xie
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China.
| | - Nan Su
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Jing Yang
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Qiaoyan Tan
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Shuo Huang
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Min Jin
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Zhenhong Ni
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Bin Zhang
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Dali Zhang
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Fengtao Luo
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Hangang Chen
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Xianding Sun
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Jian Q Feng
- Department of Biomedical Sciences, Texas A&M University College of Dentistry, Dallas, TX, 75246, USA
| | - Huabing Qi
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China.
| | - Lin Chen
- Department of Wound Repair and Rehabilitation Medicine, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China.
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47
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Huh SH, Ha L, Jang HS. Nephron Progenitor Maintenance Is Controlled through Fibroblast Growth Factors and Sprouty1 Interaction. J Am Soc Nephrol 2020; 31:2559-2572. [PMID: 32753399 DOI: 10.1681/asn.2020040401] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/08/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Nephron progenitor cells (NPCs) give rise to all segments of functional nephrons and are of great interest due to their potential as a source for novel treatment strategies for kidney disease. Fibroblast growth factor (FGF) signaling plays pivotal roles in generating and maintaining NPCs during kidney development, but little is known about the molecule(s) regulating FGF signaling during nephron development. Sprouty 1 (SPRY1) is an antagonist of receptor tyrosine kinases. Although SPRY1 antagonizes Ret-GDNF signaling, which modulates renal branching, its role in NPCs is not known. METHODS Spry1, Fgf9, and Fgf20 compound mutant animals were used to evaluate kidney phenotypes in mice to understand whether SPRY1 modulates FGF signaling in NPCs and whether FGF8 functions with FGF9 and FGF20 in maintaining NPCs. RESULTS Loss of one copy of Spry1 counters effects of the loss of Fgf9 and Fgf20, rescuing bilateral renal agenesis premature NPC differentiation, NPC proliferation, and cell death defects. In the absence of SPRY1, FGF9, and FGF20, another FGF ligand, FGF8, promotes nephrogenesis. Deleting both Fgf8 and Fgf20 results in kidney agenesis, defects in NPC proliferation, and cell death. Deleting one copy of Fgf8 reversed the effect of deleting one copy of Spry1, which rescued the renal agenesis due to loss of Fgf9 and Fgf20. CONCLUSIONS SPRY1 expressed in NPCs modulates the activity of FGF signaling and regulates NPC stemness. These findings indicate the importance of the balance between positive and negative signals during NPC maintenance.
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Affiliation(s)
- Sung-Ho Huh
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska .,Holland Regenerative Medicine Program, University of Nebraska Medical Center, Omaha, Nebraska
| | - Ligyeom Ha
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hee-Seong Jang
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
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48
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Urness LD, Wang X, Li C, Quadros RM, Harms DW, Gurumurthy CB, Mansour SL. Slc26a9P2ACre : a new CRE driver to regulate gene expression in the otic placode lineage and other FGFR2b-dependent epithelia. Development 2020; 147:dev.191015. [PMID: 32541002 DOI: 10.1242/dev.191015] [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: 03/27/2020] [Accepted: 06/02/2020] [Indexed: 11/20/2022]
Abstract
Pan-otic CRE drivers enable gene regulation throughout the otic placode lineage, comprising the inner ear epithelium and neurons. However, intersection of extra-otic gene-of-interest expression with the CRE lineage can compromise viability and impede auditory analyses. Furthermore, extant pan-otic CREs recombine in auditory and vestibular brain nuclei, making it difficult to ascribe resulting phenotypes solely to the inner ear. We have previously identified Slc26a9 as an otic placode-specific target of the FGFR2b ligands FGF3 and FGF10. We show here that Slc26a9 is otic specific through E10.5, but is not required for hearing. We targeted P2ACre to the Slc26a9 stop codon, generating Slc26a9P2ACre mice, and observed CRE activity throughout the otic epithelium and neurons, with little activity evident in the brain. Notably, recombination was detected in many FGFR2b ligand-dependent epithelia. We generated Fgf10 and Fgf8 conditional mutants, and activated an FGFR2b ligand trap from E17.5 to P3. In contrast to analogous mice generated with other pan-otic CREs, these were viable. Auditory thresholds were elevated in mutants, and correlated with cochlear epithelial cell losses. Thus, Slc26a9P2ACre provides a useful complement to existing pan-otic CRE drivers, particularly for postnatal analyses.
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Affiliation(s)
- Lisa D Urness
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Xiaofen Wang
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Chaoying Li
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Suzanne L Mansour
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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49
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Lewis EMA, Sankar S, Tong C, Patterson ES, Waller LE, Gontarz P, Zhang B, Ornitz DM, Kroll KL. Geminin is required for Hox gene regulation to pattern the developing limb. Dev Biol 2020; 464:11-23. [PMID: 32450229 DOI: 10.1016/j.ydbio.2020.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/09/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023]
Abstract
Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5' Hox transcription factor expression is essential for proper limb bud patterning and elaboration of distinct limb skeletal elements. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5' Hox gene expression expanded into more proximal and anterior regions of the embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior SHH signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the HOXD13 target Shh, and the SHH target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of GLI3, a SHH pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.
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Affiliation(s)
- Emily M A Lewis
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Savita Sankar
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Caili Tong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ethan S Patterson
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura E Waller
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul Gontarz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kristen L Kroll
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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50
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Gerber SD, Beauchamp P, Zhuang L, Villiger PM, Trueb B. Functional domains of the FgfrL1 receptor. Dev Biol 2020; 461:43-54. [PMID: 31923383 DOI: 10.1016/j.ydbio.2020.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/27/2019] [Accepted: 01/03/2020] [Indexed: 10/25/2022]
Abstract
FgfrL1 is a novel growth factor receptor that is primarily expressed in musculoskeletal tissues and the kidney. FgfrL1-deficient mice have a malformed diaphragm and no kidneys. Such animals die immediately after birth because they are not able to inflate their lungs. The FgfrL1 molecule is composed of three extracellular Ig domains, a transmembrane helix and a short intracellular domain. To investigate the contribution of each of these domains to the function of the novel receptor, we generated mice with deletions of the individual domains. Mice lacking the intracellular domain are viable and phenotypically normal. Mice lacking the first (N-terminal) Ig domain are also viable and normal, but have a reduced life span. Mice lacking the Ig2 or the Ig3 domain are born alive, but die within 24 h after birth. Ig2-deficient animals exhibit substantially smaller kidneys than wild-type littermates and contain a lower number of glomeruli. Ig3-deficient mice completely lack metanephric kidneys. Interestingly, both the Ig2 and the Ig3-deficient animals show only minor alterations in the diaphragm, which still enables them to inflate their lungs after birth. Our results demonstrate that the principal function of the FgfrL1 receptor is to control the growth of the metanephric kidneys by regulating nephrogenesis. It appears that this function is primarily accomplished by the Ig3 domain with some contribution of the Ig2 domain. It is conceivable that the two domains interact with an Fgf ligand and another molecule from the surface of neighboring cells to induce condensation of the metanephric mesenchyme to renal epithelia and glomeruli.
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Affiliation(s)
- Simon D Gerber
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Philippe Beauchamp
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Lei Zhuang
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Peter M Villiger
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland; Department of Rheumatology, University Hospital, 3010, Bern, Switzerland
| | - Beat Trueb
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland; Department of Rheumatology, University Hospital, 3010, Bern, Switzerland.
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