1
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Shi YB, Fu L, Tanizaki Y. Intestinal remodeling during Xenopus metamorphosis as a model for studying thyroid hormone signaling and adult organogenesis. Mol Cell Endocrinol 2024; 586:112193. [PMID: 38401883 PMCID: PMC10999354 DOI: 10.1016/j.mce.2024.112193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024]
Abstract
Intestinal development takes places in two phases, the initial formation of neonatal (mammals)/larval (anurans) intestine and its subsequent maturation into the adult form. This maturation occurs during postembryonic development when plasma thyroid hormone (T3) level peaks. In anurans such as the highly related Xenopus laevis and Xenopus tropicalis, the larval/tadpole intestine is drastically remodeled from a simple tubular structure to a complex, multi-folded adult organ during T3-dependent metamorphosis. This involved complete degeneration of larval epithelium via programmed cell death and de novo formation of adult epithelium, with concurrent maturation of the muscles and connective tissue. Here, we will summarize our current understanding of the underlying molecular mechanisms, with a focus on more recent genetic and genome-wide studies.
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Affiliation(s)
- Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Liezhen Fu
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Yuta Tanizaki
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
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2
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Chaudhry FN, Michki NS, Shirmer DL, McGrath-Morrow S, Young LR, Frank DB, Zepp JA. Dynamic Hippo pathway activity underlies mesenchymal differentiation during lung alveolar morphogenesis. Development 2024; 151:dev202430. [PMID: 38602485 DOI: 10.1242/dev.202430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024]
Abstract
Alveologenesis, the final stage in lung development, substantially remodels the distal lung, expanding the alveolar surface area for efficient gas exchange. Secondary crest myofibroblasts (SCMF) exist transiently in the neonatal distal lung and are crucial for alveologenesis. However, the pathways that regulate SCMF function, proliferation and temporal identity remain poorly understood. To address this, we purified SCMFs from reporter mice, performed bulk RNA-seq and found dynamic changes in Hippo-signaling components during alveologenesis. We deleted the Hippo effectors Yap/Taz from Acta2-expressing cells at the onset of alveologenesis, causing a significant arrest in alveolar development. Using single cell RNA-seq, we identified a distinct cluster of cells in mutant lungs with altered expression of marker genes associated with proximal mesenchymal cell types, airway smooth muscle and alveolar duct myofibroblasts. In vitro studies confirmed that Yap/Taz regulates myofibroblast-associated gene signature and contractility. Together, our findings show that Yap/Taz is essential for maintaining functional myofibroblast identity during postnatal alveologenesis.
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Affiliation(s)
- Fatima N Chaudhry
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nigel S Michki
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Cardiology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dain L Shirmer
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon McGrath-Morrow
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa R Young
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David B Frank
- Division of Cardiology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jarod A Zepp
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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3
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Abstract
Kidney disease is a devastating condition affecting millions of people worldwide, where over 100,000 patients in the United States alone remain waiting for a lifesaving organ transplant. Concomitant with a surge in personalized medicine, single-gene mutations, and polygenic risk alleles have been brought to the forefront as core causes of a spectrum of renal disorders. With the increasing prevalence of kidney disease, it is imperative to make substantial strides in the field of kidney genetics. Nephrons, the core functional units of the kidney, are epithelial tubules that act as gatekeepers of body homeostasis by absorbing and secreting ions, water, and small molecules to filter the blood. Each nephron contains a series of proximal and distal segments with explicit metabolic functions. The embryonic zebrafish provides an ideal platform to systematically dissect the genetic cues governing kidney development. Here, we review the use of zebrafish to discover nephrogenesis genes.
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Affiliation(s)
- Brooke E Chambers
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
| | - Nicole E Weaver
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
| | - Caroline M Lara
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, Center for Stem Cells and Regenerative Medicine, Center for Zebrafish Research, Boler-Parseghian Center for Rare and Neglected Diseases, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (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, Warren Center for Drug Discovery, University of Notre Dame, Notre Dame, Indiana (IN), USA
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4
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Sun N, Shao H, Zhang Y, Ci B, Yao H, Bai B, Tan T. Establishing a 3D culture system for early organogenesis of monkey embryos ex vivo and single-cell transcriptome analysis of cultured embryos. STAR Protoc 2024; 5:102835. [PMID: 38224493 PMCID: PMC10826423 DOI: 10.1016/j.xpro.2023.102835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024] Open
Abstract
Creating in vitro culture platforms for monkey embryos is crucial for understanding the initial 4 weeks of early primate embryogenesis. Here, we present a protocol to culture cynomolgus monkey embryos in vitro for 25 days post-fertilization and to delineate the key developmental events of gastrulation and early organogenesis. We describe steps for culturing with a 3D system, immunofluorescence analysis, single-cell RNA sequencing, and bioinformatic analysis. For complete details on the use and execution of this protocol, please refer to Gong et al. (2023).1.
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Affiliation(s)
- Nianqin Sun
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Honglian Shao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Youyue Zhang
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Baiquan Ci
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Hui Yao
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China
| | - Bing Bai
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Tao Tan
- State Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
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5
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Lu P, Xu J, Shen X, Sun J, Liu M, Niu N, Wang Q, Xue J. Spatiotemporal role of SETD2-H3K36me3 in murine pancreatic organogenesis. Cell Rep 2024; 43:113703. [PMID: 38265933 DOI: 10.1016/j.celrep.2024.113703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/11/2023] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Pancreas development is tightly controlled by multilayer mechanisms. Despite years of effort, large gaps remain in understanding how histone modifications coordinate pancreas development. SETD2, a predominant histone methyltransferase of H3K36me3, plays a key role in embryonic stem cell differentiation, whose role in organogenesis remains elusive. Here, by combination of cleavage under targets and tagmentation (CUT&Tag), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing, we show a dramatic increase in the H3K36me3 level from the secondary transition phase and decipher the related transcriptional alteration. Using single-cell RNA sequencing, we define that pancreatic deletion of Setd2 results in abnormalities in both exocrine and endocrine lineages: hyperproliferative tip progenitor cells lead to abnormal differentiation; Ngn3+ endocrine progenitors decline due to the downregulation of Nkx2.2, leading to insufficient endocrine development. Thus, these data identify SETD2 as a crucial player in embryonic pancreas development, providing a clue to understanding the dysregulation of histone modifications in pancreatic disorders.
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Affiliation(s)
- Ping Lu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Junyi Xu
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuqing Shen
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiajun Sun
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingzhu Liu
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ningning Niu
- Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qidi Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jing Xue
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Stem Cell Research Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Imaz-Rosshandler I, Rode C, Guibentif C, Harland LTG, Ton MLN, Dhapola P, Keitley D, Argelaguet R, Calero-Nieto FJ, Nichols J, Marioni JC, de Bruijn MFTR, Göttgens B. Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale. Development 2024; 151:dev201867. [PMID: 37982461 PMCID: PMC10906099 DOI: 10.1242/dev.201867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023]
Abstract
Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled timecourse of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-seq to transcriptionally determine cell fates of grafted primitive streak regions after 24 h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.
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Affiliation(s)
- Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Carolina Guibentif
- Department of Microbiology and Immunology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Luke T. G. Harland
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Mai-Linh N. Ton
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 00 Lund, Sweden
| | - Daniel Keitley
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Ricard Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Altos Labs Cambridge Institute, Granta Park, Cambridge CB21 6GP, UK
| | - Fernando J. Calero-Nieto
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jennifer Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - John C. Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Saffron Walden CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Saffron Walden CB10 1SA, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Marella F. T. R. de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
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8
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Rodríguez-Montes L, Ovchinnikova S, Yuan X, Studer T, Sarropoulos I, Anders S, Kaessmann H, Cardoso-Moreira M. Sex-biased gene expression across mammalian organ development and evolution. Science 2023; 382:eadf1046. [PMID: 37917687 PMCID: PMC7615307 DOI: 10.1126/science.adf1046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
Abstract
Sexually dimorphic traits are common among mammals and are specified during development through the deployment of sex-specific genetic programs. Because little is known about these programs, we investigated them using a resource of gene expression profiles in males and females throughout the development of five organs in five mammals (human, mouse, rat, rabbit, and opossum) and a bird (chicken). We found that sex-biased gene expression varied considerably across organs and species and was often cell-type specific. Sex differences increased abruptly around sexual maturity instead of increasing gradually during organ development. Finally, sex-biased gene expression evolved rapidly at the gene level, with differences between organs in the evolutionary mechanisms used, but more slowly at the cellular level, with the same cell types being sexually dimorphic across species.
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Affiliation(s)
- Leticia Rodríguez-Montes
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | | | - Xuefei Yuan
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Tania Studer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Simon Anders
- BioQuant, Heidelberg University, D-69120 Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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9
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Sampath Kumar A, Tian L, Bolondi A, Hernández AA, Stickels R, Kretzmer H, Murray E, Wittler L, Walther M, Barakat G, Haut L, Elkabetz Y, Macosko EZ, Guignard L, Chen F, Meissner A. Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis. Nat Genet 2023; 55:1176-1185. [PMID: 37414952 PMCID: PMC10335937 DOI: 10.1038/s41588-023-01435-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/25/2023] [Indexed: 07/08/2023]
Abstract
Spatiotemporal orchestration of gene expression is required for proper embryonic development. The use of single-cell technologies has begun to provide improved resolution of early regulatory dynamics, including detailed molecular definitions of most cell states during mouse embryogenesis. Here we used Slide-seq to build spatial transcriptomic maps of complete embryonic day (E) 8.5 and E9.0, and partial E9.5 embryos. To support their utility, we developed sc3D, a tool for reconstructing and exploring three-dimensional 'virtual embryos', which enables the quantitative investigation of regionalized gene expression patterns. Our measurements along the main embryonic axes of the developing neural tube revealed several previously unannotated genes with distinct spatial patterns. We also characterized the conflicting transcriptional identity of 'ectopic' neural tubes that emerge in Tbx6 mutant embryos. Taken together, we present an experimental and computational framework for the spatiotemporal investigation of whole embryonic structures and mutant phenotypes.
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Affiliation(s)
- Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Luyi Tian
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Amèlia Aragonés Hernández
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Robert Stickels
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maria Walther
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gabriel Barakat
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Leah Haut
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Yechiel Elkabetz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Evan Z Macosko
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Léo Guignard
- Aix Marseille University, Toulon University, Centre National de la Recherche Scientifique, Laboratoire d'Informatique et Systèmes 7020, Turing Centre for Living Systems, Marseille, France
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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10
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Ton MLN, Keitley D, Theeuwes B, Guibentif C, Ahnfelt-Rønne J, Andreassen TK, Calero-Nieto FJ, Imaz-Rosshandler I, Pijuan-Sala B, Nichols J, Benito-Gutiérrez È, Marioni JC, Göttgens B. An atlas of rabbit development as a model for single-cell comparative genomics. Nat Cell Biol 2023; 25:1061-1072. [PMID: 37322291 DOI: 10.1038/s41556-023-01174-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Traditionally, the mouse has been the favoured vertebrate model for biomedical research, due to its experimental and genetic tractability. However, non-rodent embryological studies highlight that many aspects of early mouse development, such as its egg-cylinder gastrulation and method of implantation, diverge from other mammals, thus complicating inferences about human development. Like the human embryo, rabbits develop as a flat-bilaminar disc. Here we constructed a morphological and molecular atlas of rabbit development. We report transcriptional and chromatin accessibility profiles for over 180,000 single cells and high-resolution histology sections from embryos spanning gastrulation, implantation, amniogenesis and early organogenesis. Using a neighbourhood comparison pipeline, we compare the transcriptional landscape of rabbit and mouse at the scale of the entire organism. We characterize the gene regulatory programmes underlying trophoblast differentiation and identify signalling interactions involving the yolk sac mesothelium during haematopoiesis. We demonstrate how the combination of both rabbit and mouse atlases can be leveraged to extract new biological insights from sparse macaque and human data. The datasets and computational pipelines reported here set a framework for a broader cross-species approach to decipher early mammalian development, and are readily adaptable to deploy single-cell comparative genomics more broadly across biomedical research.
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Affiliation(s)
- Mai-Linh Nu Ton
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Daniel Keitley
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Bart Theeuwes
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carolina Guibentif
- Inst. Biomedicine, Dept. Microbiology and Immunology, Sahlgrenska Center for Cancer Research, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Fernando J Calero-Nieto
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Blanca Pijuan-Sala
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jennifer Nichols
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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11
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Boezio GLM, Zhao S, Gollin J, Priya R, Mansingh S, Guenther S, Fukuda N, Gunawan F, Stainier DYR. The developing epicardium regulates cardiac chamber morphogenesis by promoting cardiomyocyte growth. Dis Model Mech 2023; 16:dmm049571. [PMID: 36172839 PMCID: PMC9612869 DOI: 10.1242/dmm.049571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/13/2022] [Indexed: 11/20/2022] Open
Abstract
The epicardium, the outermost layer of the heart, is an important regulator of cardiac regeneration. However, a detailed understanding of the crosstalk between the epicardium and myocardium during development requires further investigation. Here, we generated three models of epicardial impairment in zebrafish by mutating the transcription factor genes tcf21 and wt1a, and ablating tcf21+ epicardial cells. Notably, all three epicardial impairment models exhibited smaller ventricles. We identified the initial cause of this phenotype as defective cardiomyocyte growth, resulting in reduced cell surface and volume. This failure of cardiomyocyte growth was followed by decreased proliferation and increased abluminal extrusion. By temporally manipulating its ablation, we show that the epicardium is required to support cardiomyocyte growth mainly during early cardiac morphogenesis. By transcriptomic profiling of sorted epicardial cells, we identified reduced expression of FGF and VEGF ligand genes in tcf21-/- hearts, and pharmacological inhibition of these signaling pathways in wild type partially recapitulated the ventricular growth defects. Taken together, these data reveal distinct roles of the epicardium during cardiac morphogenesis and signaling pathways underlying epicardial-myocardial crosstalk.
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Affiliation(s)
- Giulia L. M. Boezio
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Shengnan Zhao
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Josephine Gollin
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Rashmi Priya
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Shivani Mansingh
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Stefan Guenther
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Nana Fukuda
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Felix Gunawan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, 61231 Bad Nauheim, Germany
- Cardio-Pulmonary Institute, Aulweg 130, 35392 Giessen, Germany
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12
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Danopoulos S, Belgacemi R, Hein RFC, Miller AJ, Deutsch GH, Glass I, Spence JR, Al Alam D. FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells. Am J Physiol Lung Cell Mol Physiol 2023; 324:L433-L444. [PMID: 36791060 PMCID: PMC10027085 DOI: 10.1152/ajplung.00316.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Fibroblast growth factor (FGF) signaling is known to play an important role in lung organogenesis. However, we recently demonstrated that FGF10 fails to induce branching in human fetal lungs as is observed in mouse. Our previous human fetal lung RNA sequencing data exhibited increased FGF18 during the pseudoglandular stage of development, suggestive of its importance in human lung branching morphogenesis. Whereas it has been previously reported that FGF18 is critical during alveologenesis, few studies have described its implication in lung branching, specifically in human. Therefore, we aimed to determine the role of FGF18 in human lung branching morphogenesis. Human fetal lung explants within the pseudoglandular stage of development were treated with recombinant human FGF18 in air-liquid interface culture. Explants were analyzed grossly to assess differences in branching pattern, as well as at the cellular and molecular levels. FGF18 treatment promoted branching in explant cultures and demonstrated increased epithelial proliferation as well as maintenance of the double positive SOX2/SOX9 distal bud progenitor cells, confirming its role in human lung branching morphogenesis. In addition, FGF18 treated explants displayed increased expression of SOX9, FN1, and COL2A1 within the mesenchyme, all factors that are important to chondrocyte differentiation. In humans, cartilaginous airways extend deep into the lung up to the 12th generation of branching whereas in mouse these are restricted to the trachea and main bronchi. Therefore, our data suggest that FGF18 promotes human lung branching morphogenesis through regulating mesenchymal progenitor cells.
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Affiliation(s)
- Soula Danopoulos
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
- Division of Neonatology, Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, California, United States
| | - Randa Belgacemi
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
| | - Renee F C Hein
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Alyssa J Miller
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Gail H Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine and Seattle Children's Research Institute, Seattle, Washington, United States
| | - Ian Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States
| | - Jason R Spence
- Department of Cell and Developmental biology, University of Michigan Medical School, Ann Arbor, Michigan, United States
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, California, United States
- Division of Neonatology, Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, California, United States
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13
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Li MH, Kuetemeyer JM, Yallowitz AR, Wellik DM. Characterization of a novel Hoxa5eGFP mouse line. Dev Dyn 2023; 252:536-546. [PMID: 36577717 PMCID: PMC10066829 DOI: 10.1002/dvdy.563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Hox genes encode transcription factors that are important for establishing the body plan. Hoxa5 is a member of the mammalian Hox5 paralogous group that regulates the patterning and morphology of the cervical-thoracic region of the axial skeleton. Hoxa5 also plays crucial functions in lung morphogenesis. RESULTS We generated a Hoxa5eGFP reporter mouse line using CRISPR technology, allowing real-time visualization of Hoxa5 expression. Hoxa5eGFP recapitulates reported embryonic Hoxa5 mRNA expression patterns. Specifically, Hoxa5eGFP can be visualized in the developing mouse neural tube, somites, lung, diaphragm, foregut, and midgut, among other organs. In the stomach, posteriorly biased Hoxa5eGFP expression correlates with a drastic morphological reduction of the corpus in Hox5 paralogous mutants. Expression of Hoxa5eGFP in the lung continues in all lung fibroblast populations through postnatal and adult stages. CONCLUSIONS We identified cell types that express Hoxa5 in postnatal and adult mouse lungs, including various fibroblasts and vascular endothelial cells. This reporter line will be a powerful tool for studies of the function of Hoxa5 during mouse development, homeostasis, and disease processes.
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Affiliation(s)
- Mu-Hang Li
- Genetics Training Program, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
| | - Julia M. Kuetemeyer
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
| | - Alisha R. Yallowitz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
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14
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Nojiri T, Werneburg I, Tu VT, Fukui D, Takechi M, Iseki S, Furutera T, Koyabu D. Timing of organogenesis underscores the evolution of neonatal life histories and powered flight in bats. Proc Biol Sci 2023; 290:20221928. [PMID: 36629110 PMCID: PMC9832570 DOI: 10.1098/rspb.2022.1928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/09/2022] [Indexed: 01/12/2023] Open
Abstract
Bats have undergone one of the most drastic limb innovations in vertebrate history, associated with the evolution of powered flight. Knowledge of the genetic basis of limb organogenesis in bats has increased but little has been documented regarding the differences between limb organogenesis in bats and that of other vertebrates. We conducted embryological comparisons of the timelines of limb organogenesis in 24 bat species and 72 non-bat amniotes. In bats, the time invested for forelimb organogenesis has been considerably extended and the appearance timing of the forelimb ridge has been significantly accelerated, whereas the timing of the finger and first appearance of the claw development has been delayed, facilitating the enlargement of the manus. Furthermore, we discovered that bats initiate the development of their hindlimbs earlier than their forelimbs compared with other placentals. Bat neonates are known to be able to cling continuously with their well-developed foot to the maternal bodies or habitat substrates soon after birth. We suggest that this unique life history of neonates, which possibly coevolved with powered flight, has driven the accelerated development of the hindlimb and precocious foot.
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Affiliation(s)
- Taro Nojiri
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Graduate School of Environmental Science, Hokkaido University, North 11, West 10, Sapporo 060-0811, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Ingmar Werneburg
- Senckenberg Centre for Human Evolution and Palaeoenvironment an der Eberhard Karls Universität, Sigwartstraße 10, D-72076 Tübingen, Germany
- Fachbereich Geowissenschaften, Eberhard Karls Universität, Hölderlinstraße 12, 72074 Tübingen, Germany
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet road, Cau Giay district, Hanoi, Vietnam
- Vietnam Academy of Science and Technology, Graduate University of Science and Technology, No. 18, Hoang Quac Viet road, Cau Giay district, Hanoi, Vietnam
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 9-61, Yamabe-Higashimachi, Furano, Hokkaido 079-1563, Japan
| | - Masaki Takechi
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Sachiko Iseki
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Toshiko Furutera
- Graduate School of Medicine, Juntendo University, 2-1-1, Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
| | - Daisuke Koyabu
- Molecular Craniofacial Embryology, Graduate School of Medicine and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
- Research and Development Center for Precision Medicine, University of Tsukuba, 1-2 Kasuga, Tsukuba-shi, Ibaraki 305-8550, Japan
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15
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Xu J, Liu H, Lan Y, Jiang R. The transcription factors Foxf1 and Foxf2 integrate the SHH, HGF and TGFβ signaling pathways to drive tongue organogenesis. Development 2022; 149:dev200667. [PMID: 36227576 PMCID: PMC10655918 DOI: 10.1242/dev.200667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 09/26/2022] [Indexed: 11/19/2023]
Abstract
The tongue is a highly specialized muscular organ with diverse cellular origins, which provides an excellent model for understanding mechanisms controlling tissue-tissue interactions during organogenesis. Previous studies showed that SHH signaling is required for tongue morphogenesis and tongue muscle organization, but little is known about the underlying mechanisms. Here we demonstrate that the Foxf1/Foxf2 transcription factors act in the cranial neural crest cell (CNCC)-derived mandibular mesenchyme to control myoblast migration into the tongue primordium during tongue initiation, and thereafter continue to regulate intrinsic tongue muscle assembly and lingual tendon formation. We performed chromatin immunoprecipitation sequencing analysis and identified Hgf, Tgfb2 and Tgfb3 among the target genes of Foxf2 in the embryonic tongue. Through genetic analyses of mice with CNCC-specific inactivation of Smo or both Foxf1 and Foxf2, we show that Foxf1 and Foxf2 mediate hedgehog signaling-mediated regulation of myoblast migration during tongue initiation and intrinsic tongue muscle formation by regulating the activation of the HGF and TGFβ signaling pathways. These data uncover the molecular network integrating the SHH, HGF and TGFβ signaling pathways in regulating tongue organogenesis.
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Affiliation(s)
- Jingyue Xu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Han Liu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yu Lan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Departments of Pediatrics and Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Rulang Jiang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Departments of Pediatrics and Surgery, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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16
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Abstract
The mechanisms underlying kidney development in mice and humans is an area of intense study. Insights into kidney organogenesis have the potential to guide our understanding of the origin of congenital anomalies and enable the assembly of genetic diagnostic tools. A number of studies have delineated signalling nodes that regulate positional identities and cell fates of nephron progenitor and precursor cells, whereas cross-species comparisons have markedly enhanced our understanding of conserved and divergent features of mammalian kidney organogenesis. Greater insights into the complex cellular movements that occur as the proximal-distal axis is established have challenged our understanding of nephron patterning and provided important clues to the elaborate developmental context in which human kidney diseases can arise. Studies of kidney development in vivo have also facilitated efforts to recapitulate nephrogenesis in kidney organoids in vitro, by providing a detailed blueprint of signalling events, cell movements and patterning mechanisms that are required for the formation of correctly patterned nephrons and maturation of physiologically functional apparatus that are responsible for maintaining human health.
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Affiliation(s)
- Jack Schnell
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at University of Southern California, Los Angeles, CA, USA
| | - MaryAnne Achieng
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at University of Southern California, Los Angeles, CA, USA
| | - Nils Olof Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at University of Southern California, Los Angeles, CA, USA.
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17
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Guan N, Kobayashi H, Ishii K, Davidoff O, Sha F, Ikizler TA, Hao CM, Chandel NS, Haase VH. Disruption of mitochondrial complex III in cap mesenchyme but not in ureteric progenitors results in defective nephrogenesis associated with amino acid deficiency. Kidney Int 2022; 102:108-120. [PMID: 35341793 PMCID: PMC9232975 DOI: 10.1016/j.kint.2022.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/14/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022]
Abstract
Oxidative metabolism in mitochondria regulates cellular differentiation and gene expression through intermediary metabolites and reactive oxygen species. Its role in kidney development and pathogenesis is not completely understood. Here we inactivated ubiquinone-binding protein QPC, a subunit of mitochondrial complex III, in two types of kidney progenitor cells to investigate the role of mitochondrial electron transport in kidney homeostasis. Inactivation of QPC in sine oculis-related homeobox 2 (SIX2)-expressing cap mesenchyme progenitors, which give rise to podocytes and all nephron segments except collecting ducts, resulted in perinatal death from severe kidney dysplasia. This was characterized by decreased proliferation of SIX2 progenitors and their failure to differentiate into kidney epithelium. QPC inactivation in cap mesenchyme progenitors induced activating transcription factor 4-mediated nutritional stress responses and was associated with a reduction in kidney tricarboxylic acid cycle metabolites and amino acid levels, which negatively impacted purine and pyrimidine synthesis. In contrast, QPC inactivation in ureteric tree epithelial cells, which give rise to the kidney collecting system, did not inhibit ureteric differentiation, and resulted in the development of functional kidneys that were smaller in size. Thus, our data demonstrate that mitochondrial oxidative metabolism is critical for the formation of cap mesenchyme-derived nephron segments but dispensable for formation of the kidney collecting system. Hence, our studies reveal compartment-specific needs for metabolic reprogramming during kidney development.
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Affiliation(s)
- Nan Guan
- Department of Medicine, Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Division of Nephrology, Huashan Hospital and Nephrology Research Institute, Fudan University, Shanghai, China; The Vanderbilt O'Brien Kidney Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Hanako Kobayashi
- Department of Medicine, Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee, USA; The Vanderbilt O'Brien Kidney Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Ken Ishii
- Department of Medicine, Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee, USA; The Vanderbilt O'Brien Kidney Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Olena Davidoff
- Department of Medicine, Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee, USA; The Vanderbilt O'Brien Kidney Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Feng Sha
- Department of Medicine, Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee, USA; The Vanderbilt O'Brien Kidney Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Talat A Ikizler
- Department of Medicine, Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee, USA; The Vanderbilt O'Brien Kidney Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Chuan-Ming Hao
- Division of Nephrology, Huashan Hospital and Nephrology Research Institute, Fudan University, Shanghai, China
| | - Navdeep S Chandel
- Department of Medicine, Feinberg School of Medicine, Northwestern University Chicago, Illinois, USA
| | - Volker H Haase
- Department of Medicine, Vanderbilt University Medical Center and Vanderbilt University School of Medicine, Nashville, Tennessee, USA; The Vanderbilt O'Brien Kidney Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Section of Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden.
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18
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Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 2022; 54:1037-1050. [PMID: 35789323 PMCID: PMC9279159 DOI: 10.1038/s41588-022-01089-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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Affiliation(s)
- Damir Baranasic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Piotr J Balwierz
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Zehnder
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Abdul Kadir Mukarram
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Chirag Nepal
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nan Li
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joseph Wragg
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabio M D'Orazio
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dorde Relic
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mikhail Pachkov
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Institute of Marine Sciences, Barcelona, Spain
| | | | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Marcus Stoiber
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michaël Dong
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Irene Stevens
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anne Eagle
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Ryan Martin
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Oluwapelumi Obasaju
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alison C McGarvey
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Wolfgang Kopp
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Emily Chambers
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Dennis Wang
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Hyejeong R Kim
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vanessa Chong
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Liège, Belgium
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Fondazione Human Technopole, Milano, Italy
| | - Uwe Ohler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Scott Allen Lacadie
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Shawn M Burgess
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Freek van Eeden
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Daria Onichtchouk
- Department of Developmental Biology, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ben James Brown
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Fiona C Wardle
- Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, London, UK
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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19
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Chen A, Liao S, Cheng M, Ma K, Wu L, Lai Y, Qiu X, Yang J, Xu J, Hao S, Wang X, Lu H, Chen X, Liu X, Huang X, Li Z, Hong Y, Jiang Y, Peng J, Liu S, Shen M, Liu C, Li Q, Yuan Y, Wei X, Zheng H, Feng W, Wang Z, Liu Y, Wang Z, Yang Y, Xiang H, Han L, Qin B, Guo P, Lai G, Muñoz-Cánoves P, Maxwell PH, Thiery JP, Wu QF, Zhao F, Chen B, Li M, Dai X, Wang S, Kuang H, Hui J, Wang L, Fei JF, Wang O, Wei X, Lu H, Wang B, Liu S, Gu Y, Ni M, Zhang W, Mu F, Yin Y, Yang H, Lisby M, Cornall RJ, Mulder J, Uhlén M, Esteban MA, Li Y, Liu L, Xu X, Wang J. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 2022; 185:1777-1792.e21. [PMID: 35512705 DOI: 10.1016/j.cell.2022.04.003] [Citation(s) in RCA: 294] [Impact Index Per Article: 147.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/24/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.
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Affiliation(s)
- Ao Chen
- BGI-Shenzhen, Shenzhen 518103, China; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Sha Liao
- BGI-Shenzhen, Shenzhen 518103, China
| | - Mengnan Cheng
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Liang Wu
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518120, China
| | - Yiwei Lai
- BGI-Shenzhen, Shenzhen 518103, China; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jin Yang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiangshan Xu
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Hao
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Wang
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Xi Chen
- BGI-Shenzhen, Shenzhen 518103, China
| | - Xing Liu
- BGI-Shenzhen, Shenzhen 518103, China
| | - Xin Huang
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhao Li
- BGI-Shenzhen, Shenzhen 518103, China
| | - Yan Hong
- BGI-Shenzhen, Shenzhen 518103, China
| | - Yujia Jiang
- BGI-Shenzhen, Shenzhen 518103, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Jian Peng
- BGI-Shenzhen, Shenzhen 518103, China
| | - Shuai Liu
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen 518103, China; Shenzhen Bay Laboratory, Shenzhen 518000, China
| | | | - Yue Yuan
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Huiwen Zheng
- BGI-Shenzhen, Shenzhen 518103, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Weimin Feng
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhifeng Wang
- BGI-Shenzhen, Shenzhen 518103, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518120, China
| | - Yang Liu
- BGI-Shenzhen, Shenzhen 518103, China
| | | | - Yunzhi Yang
- BGI-Shenzhen, Shenzhen 518103, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Han
- BGI-Shenzhen, Shenzhen 518103, China
| | - Baoming Qin
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Pengcheng Guo
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Guangyao Lai
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), ICREA and CIBERNED, Barcelona 08003, Spain; Spanish National Center on Cardiovascular Research (CNIC), Madrid 28029, Spain
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge CB2 0XY, UK
| | | | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | - Mei Li
- BGI-Shenzhen, Shenzhen 518103, China
| | - Xi Dai
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- BGI-Shenzhen, Shenzhen 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | | | - Liqun Wang
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Ji-Feng Fei
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Ou Wang
- BGI-Shenzhen, Shenzhen 518103, China
| | - Xiaofeng Wei
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Bo Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shiping Liu
- BGI-Shenzhen, Shenzhen 518103, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518120, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518103, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | - Ming Ni
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Wenwei Zhang
- BGI-Shenzhen, Shenzhen 518103, China; Shenzhen Key Laboratory of Neurogenomics, BGI-Shenzhen, Shenzhen 518103, China
| | - Feng Mu
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen 518103, China; BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518103, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Richard J Cornall
- Medical Research Council Human Immunology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Jan Mulder
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm 17121, Sweden; Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Mathias Uhlén
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm 17121, Sweden; Department of Neuroscience, Karolinska Institute, Stockholm 17177, Sweden
| | - Miguel A Esteban
- BGI-Shenzhen, Shenzhen 518103, China; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | | | - Longqi Liu
- BGI-Shenzhen, Shenzhen 518103, China; BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China; Shenzhen Bay Laboratory, Shenzhen 518000, China.
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518103, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China.
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518103, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
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20
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Lukowicz-Bedford RM, Farnsworth DR, Miller AC. Connexinplexity: the spatial and temporal expression of connexin genes during vertebrate organogenesis. G3 (Bethesda) 2022; 12:jkac062. [PMID: 35325106 PMCID: PMC9073686 DOI: 10.1093/g3journal/jkac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/24/2022] [Indexed: 11/28/2022]
Abstract
Animal development requires coordinated communication between cells. The Connexin family of proteins is a major contributor to intercellular communication in vertebrates by forming gap junction channels that facilitate the movement of ions, small molecules, and metabolites between cells. Additionally, individual hemichannels can provide a conduit to the extracellular space for paracrine and autocrine signaling. Connexin-mediated communication is widely used in epithelial, neural, and vascular development and homeostasis, and most tissues likely use this form of communication. In fact, Connexin disruptions are of major clinical significance contributing to disorders developing from all major germ layers. Despite the fact that Connexins serve as an essential mode of cellular communication, the temporal and cell-type-specific expression patterns of connexin genes remain unknown in vertebrates. A major challenge is the large and complex connexin gene family. To overcome this barrier, we determined the expression of all connexins in zebrafish using single-cell RNA-sequencing of entire animals across several stages of organogenesis. Our analysis of expression patterns has revealed that few connexins are broadly expressed, but rather, most are expressed in tissue- or cell-type-specific patterns. Additionally, most tissues possess a unique combinatorial signature of connexin expression with dynamic temporal changes across the organism, tissue, and cell. Our analysis has identified new patterns for well-known connexins and assigned spatial and temporal expression to genes with no-existing information. We provide a field guide relating zebrafish and human connexin genes as a critical step toward understanding how Connexins contribute to cellular communication and development throughout vertebrate organogenesis.
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Affiliation(s)
| | - Dylan R Farnsworth
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Adam C Miller
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
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21
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Wilson SB, Howden SE, Vanslambrouck JM, Dorison A, Alquicira-Hernandez J, Powell JE, Little MH. DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets. Genome Med 2022. [PMID: 35189942 DOI: 10.1101/2021.01.20.427346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND While single-cell transcriptional profiling has greatly increased our capacity to interrogate biology, accurate cell classification within and between datasets is a key challenge. This is particularly so in pluripotent stem cell-derived organoids which represent a model of a developmental system. Here, clustering algorithms and selected marker genes can fail to accurately classify cellular identity while variation in analyses makes it difficult to meaningfully compare datasets. Kidney organoids provide a valuable resource to understand kidney development and disease. However, direct comparison of relative cellular composition between protocols has proved challenging. Hence, an unbiased approach for classifying cell identity is required. METHODS The R package, scPred, was trained on multiple single cell RNA-seq datasets of human fetal kidney. A hierarchical model classified cellular subtypes into nephron, stroma and ureteric epithelial elements. This model, provided in the R package DevKidCC ( github.com/KidneyRegeneration/DevKidCC ), was then used to predict relative cell identity within published kidney organoid datasets generated using distinct cell lines and differentiation protocols, interrogating the impact of such variations. The package contains custom functions for the display of differential gene expression within cellular subtypes. RESULTS DevKidCC was used to directly compare between distinct kidney organoid protocols, identifying differences in relative proportions of cell types at all hierarchical levels of the model and highlighting variations in stromal and unassigned cell types, nephron progenitor prevalence and relative maturation of individual epithelial segments. Of note, DevKidCC was able to distinguish distal nephron from ureteric epithelium, cell types with overlapping profiles that have previously confounded analyses. When applied to a variation in protocol via the addition of retinoic acid, DevKidCC identified a consequential depletion of nephron progenitors. CONCLUSIONS The application of DevKidCC to kidney organoids reproducibly classifies component cellular identity within distinct single-cell datasets. The application of the tool is summarised in an interactive Shiny application, as are examples of the utility of in-built functions for data presentation. This tool will enable the consistent and rapid comparison of kidney organoid protocols, driving improvements in patterning to kidney endpoints and validating new approaches.
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Affiliation(s)
- Sean B Wilson
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia
| | - Sara E Howden
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia
| | | | - Aude Dorison
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia
| | - Jose Alquicira-Hernandez
- Garvan-Weizmann Centre for Cellular Genomics, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Flemington Rd, Parkville, Victoria, Australia.
- Department of Paediatrics, The University of Melbourne, Victoria, Parkville, Australia.
- Department of Anatomy and Neuroscience, The University of Melbourne, Victoria, Parkville, Australia.
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Copenhagen, Denmark.
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22
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Kirschner KM, Kelterborn S, Stehr H, Penzlin JLT, Jacobi CLJ, Endesfelder S, Sieg M, Kruppa J, Dame C, Sciesielski LK. Adaptation of the Oxygen Sensing System during Lung Development. Oxid Med Cell Longev 2022; 2022:9714669. [PMID: 35242281 PMCID: PMC8886745 DOI: 10.1155/2022/9714669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/18/2022] [Indexed: 12/22/2022]
Abstract
During gestation, the most drastic change in oxygen supply occurs with the onset of ventilation after birth. As the too early exposure of premature infants to high arterial oxygen pressure leads to characteristic diseases, we studied the adaptation of the oxygen sensing system and its targets, the hypoxia-inducible factor- (HIF-) regulated genes (HRGs) in the developing lung. We draw a detailed picture of the oxygen sensing system by integrating information from qPCR, immunoblotting, in situ hybridization, and single-cell RNA sequencing data in ex vivo and in vivo models. HIF1α protein was completely destabilized with the onset of pulmonary ventilation, but did not coincide with expression changes in bona fide HRGs. We observed a modified composition of the HIF-PHD system from intrauterine to neonatal phases: Phd3 was significantly decreased, while Hif2a showed a strong increase and the Hif3a isoform Ipas exclusively peaked at P0. Colocalization studies point to the Hif1a-Phd1 axis as the main regulator of the HIF-PHD system in mouse lung development, complemented by the Hif3a-Phd3 axis during gestation. Hif3a isoform expression showed a stepwise adaptation during the periods of saccular and alveolar differentiation. With a strong hypoxic stimulus, lung ex vivo organ cultures displayed a functioning HIF system at every developmental stage. Approaches with systemic hypoxia or roxadustat treatment revealed only a limited in vivo response of HRGs. Understanding the interplay of the oxygen sensing system components during the transition from saccular to alveolar phases of lung development might help to counteract prematurity-associated diseases like bronchopulmonary dysplasia.
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Affiliation(s)
- Karin M. Kirschner
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Simon Kelterborn
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Herrmann Stehr
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Johanna L. T. Penzlin
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Charlotte L. J. Jacobi
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Stefanie Endesfelder
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Miriam Sieg
- Institute of Biometry and Clinical Epidemiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Jochen Kruppa
- Institute of Medical Informatics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Christof Dame
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Lina K. Sciesielski
- Department of Neonatology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
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23
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Ahuja N, Cleaver O. The cell cortex as mediator of pancreatic epithelial development and endocrine differentiation. Curr Opin Genet Dev 2022; 72:118-127. [PMID: 34929610 PMCID: PMC8915777 DOI: 10.1016/j.gde.2021.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023]
Abstract
Organogenesis is the complex process of cells coordinating their own proliferation with changes to their shape, cell migration and cell-cell signaling, so that they transform into a three dimensional functional tissue, with its own custom range of differentiated cell types. Understanding when and where critical signals emanate from, and how those signals are transduced and interpreted, is the fundamental challenge of developmental biology. Here, we review recent findings regarding how progenitor cells interpret cues during pancreatic morphogenesis and how they coordinate cell fate determination. Recent evidence suggests that molecules located in the cell cortex play a crticial role in determining cellular behavior during pancreatic morphogenesis. Specifically, we find that control of cell adhesion, polarity, and constriction are all integral to both initiation of epithelial development and to later cell differentiation. Here, we review key molecules that coordinate these processes and suggest that the cell cortex acts as a signaling center that relays cues during pancreas development.
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Affiliation(s)
- Neha Ahuja
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Ondine Cleaver
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.
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24
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Triozzi PM, Irving TB, Schmidt HW, Keyser ZP, Chakraborty S, Balmant K, Pereira WJ, Dervinis C, Mysore KS, Wen J, Ané JM, Kirst M, Conde D. Spatiotemporal cytokinin response imaging and ISOPENTENYLTRANSFERASE 3 function in Medicago nodule development. Plant Physiol 2022; 188:560-575. [PMID: 34599592 PMCID: PMC8774767 DOI: 10.1093/plphys/kiab447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Most legumes can establish a symbiotic association with soil rhizobia that trigger the development of root nodules. These nodules host the rhizobia and allow them to fix nitrogen efficiently. The perception of bacterial lipo-chitooligosaccharides (LCOs) in the epidermis initiates a signaling cascade that allows rhizobial intracellular infection in the root and de-differentiation and activation of cell division that gives rise to the nodule. Thus, nodule organogenesis and rhizobial infection need to be coupled in space and time for successful nodulation. The plant hormone cytokinin (CK) contributes to the coordination of this process, acting as an essential positive regulator of nodule organogenesis. However, the temporal regulation of tissue-specific CK signaling and biosynthesis in response to LCOs or Sinorhizobium meliloti inoculation in Medicago truncatula remains poorly understood. In this study, using a fluorescence-based CK sensor (pTCSn::nls:tGFP), we performed a high-resolution tissue-specific temporal characterization of the sequential activation of CK response during root infection and nodule development in M. truncatula after inoculation with S. meliloti. Loss-of-function mutants of the CK-biosynthetic gene ISOPENTENYLTRANSFERASE 3 (IPT3) showed impairment of nodulation, suggesting that IPT3 is required for nodule development in M. truncatula. Simultaneous live imaging of pIPT3::nls:tdTOMATO and the CK sensor showed that IPT3 induction in the pericycle at the base of nodule primordium contributes to CK biosynthesis, which in turn promotes expression of positive regulators of nodule organogenesis in M. truncatula.
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Affiliation(s)
- Paolo M Triozzi
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Henry W Schmidt
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Zachary P Keyser
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sanhita Chakraborty
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kelly Balmant
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Wendell J Pereira
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | - Christopher Dervinis
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
| | | | - Jiangqi Wen
- Noble Research Institute, Ardmore, Oklahoma 73401, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Matias Kirst
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Daniel Conde
- School of Forest, Fisheries and Geomatics Sciences, University of Florida, Gainesville, Florida 32611, USA
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25
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Li J, Glover JD, Zhang H, Peng M, Tan J, Mallick CB, Hou D, Yang Y, Wu S, Liu Y, Peng Q, Zheng SC, Crosse EI, Medvinsky A, Anderson RA, Brown H, Yuan Z, Zhou S, Xu Y, Kemp JP, Ho YYW, Loesch DZ, Wang L, Li Y, Tang S, Wu X, Walters RG, Lin K, Meng R, Lv J, Chernus JM, Neiswanger K, Feingold E, Evans DM, Medland SE, Martin NG, Weinberg SM, Marazita ML, Chen G, Chen Z, Zhou Y, Cheeseman M, Wang L, Jin L, Headon DJ, Wang S. Limb development genes underlie variation in human fingerprint patterns. Cell 2022; 185:95-112.e18. [PMID: 34995520 PMCID: PMC8740935 DOI: 10.1016/j.cell.2021.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022]
Abstract
Fingerprints are of long-standing practical and cultural interest, but little is known about the mechanisms that underlie their variation. Using genome-wide scans in Han Chinese cohorts, we identified 18 loci associated with fingerprint type across the digits, including a genetic basis for the long-recognized “pattern-block” correlations among the middle three digits. In particular, we identified a variant near EVI1 that alters regulatory activity and established a role for EVI1 in dermatoglyph patterning in mice. Dynamic EVI1 expression during human development supports its role in shaping the limbs and digits, rather than influencing skin patterning directly. Trans-ethnic meta-analysis identified 43 fingerprint-associated loci, with nearby genes being strongly enriched for general limb development pathways. We also found that fingerprint patterns were genetically correlated with hand proportions. Taken together, these findings support the key role of limb development genes in influencing the outcome of fingerprint patterning. GWAS identifies variants associated with fingerprint type across all digits Fingerprint-associated genes are strongly enriched for limb development functions Evi1 alters dermatoglyphs in mice by modulating limb rather than skin development Fingerprint patterns are genetically correlated with hand and finger proportions
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Affiliation(s)
- Jinxi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - James D Glover
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Haiguo Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Meifang Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Chandana Basu Mallick
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK; Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Dan Hou
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Sijie Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Edie I Crosse
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, PRC
| | - Shen Zhou
- Shanghai Foreign Language School, Shanghai 200083, PRC
| | - Yanqing Xu
- Forest Ridge School of the Sacred Heart, Bellevue, WA 98006, USA
| | - John P Kemp
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia
| | - Yvonne Y W Ho
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | - Danuta Z Loesch
- Psychology Department, La Trobe University, Melbourne, VIC, Australia
| | | | | | | | - Xiaoli Wu
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ruogu Meng
- Center for Data Science in Health and Medicine, Peking University, Beijing 100191, PRC
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, PRC
| | - Jonathan M Chernus
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Katherine Neiswanger
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | | | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mary L Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Clinical and Translational Science, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Gang Chen
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yong Zhou
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PRC
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Lan Wang
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai 200438, PRC.
| | - Denis J Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, PRC.
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26
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Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CHL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nat Biotechnol 2022; 40:74-85. [PMID: 34489600 PMCID: PMC8763645 DOI: 10.1038/s41587-021-01006-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.
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Affiliation(s)
- T Lohoff
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - S Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - A Missarova
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - N Koulena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - N Pierson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - J A Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Genomics Plc, Cambridge, UK
| | - E S Bardot
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C-H L Eng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - R C V Tyser
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - R Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - C Guibentif
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - S Srinivas
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - J Briscoe
- The Francis Crick Institute, London, UK
| | - B D Simons
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - A-K Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Göttgens
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - W Reik
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - J Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - L Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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27
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Negretti NM, Plosa EJ, Benjamin JT, Schuler BA, Habermann AC, Jetter CS, Gulleman P, Bunn C, Hackett AN, Ransom M, Taylor CJ, Nichols D, Matlock BK, Guttentag SH, Blackwell TS, Banovich NE, Kropski JA, Sucre JMS. A single-cell atlas of mouse lung development. Development 2021; 148:dev199512. [PMID: 34927678 PMCID: PMC8722390 DOI: 10.1242/dev.199512] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022]
Abstract
Lung organogenesis requires precise timing and coordination to effect spatial organization and function of the parenchymal cells. To provide a systematic broad-based view of the mechanisms governing the dynamic alterations in parenchymal cells over crucial periods of development, we performed a single-cell RNA-sequencing time-series yielding 102,571 epithelial, endothelial and mesenchymal cells across nine time points from embryonic day 12 to postnatal day 14 in mice. Combining computational fate-likelihood prediction with RNA in situ hybridization and immunofluorescence, we explore lineage relationships during the saccular to alveolar stage transition. The utility of this publicly searchable atlas resource (www.sucrelab.org/lungcells) is exemplified by discoveries of the complexity of type 1 pneumocyte function and characterization of mesenchymal Wnt expression patterns during the saccular and alveolar stages - wherein major expansion of the gas-exchange surface occurs. We provide an integrated view of cellular dynamics in epithelial, endothelial and mesenchymal cell populations during lung organogenesis.
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Affiliation(s)
- Nicholas M. Negretti
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Erin J. Plosa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John T. Benjamin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bryce A. Schuler
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Christopher S. Jetter
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Peter Gulleman
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Claire Bunn
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alice N. Hackett
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Meaghan Ransom
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Chase J. Taylor
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David Nichols
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Brittany K. Matlock
- Vanderbilt Ingram Cancer Center and Vanderbilt Digestive Disease Research Center, Flow Cytometry Shared Resource, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Susan H. Guttentag
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Timothy S. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Nicholas E. Banovich
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Jonathan A. Kropski
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Jennifer M. S. Sucre
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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28
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Nasri A, Foisset F, Ahmed E, Lahmar Z, Vachier I, Jorgensen C, Assou S, Bourdin A, De Vos J. Roles of Mesenchymal Cells in the Lung: From Lung Development to Chronic Obstructive Pulmonary Disease. Cells 2021; 10:3467. [PMID: 34943975 PMCID: PMC8700565 DOI: 10.3390/cells10123467] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Mesenchymal cells are an essential cell type because of their role in tissue support, their multilineage differentiation capacities and their potential clinical applications. They play a crucial role during lung development by interacting with airway epithelium, and also during lung regeneration and remodeling after injury. However, much less is known about their function in lung disease. In this review, we discuss the origins of mesenchymal cells during lung development, their crosstalk with the epithelium, and their role in lung diseases, particularly in chronic obstructive pulmonary disease.
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Affiliation(s)
- Amel Nasri
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Florent Foisset
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Engi Ahmed
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
- PhyMedExp, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
| | - Zakaria Lahmar
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
- PhyMedExp, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
| | - Isabelle Vachier
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
| | - Christian Jorgensen
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Said Assou
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Arnaud Bourdin
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
- PhyMedExp, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
| | - John De Vos
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
- Department of Cell and Tissue Engineering, Université de Montpellier, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France
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29
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Li D, Xu J, Yang MQ. Gene Regulation Analysis Reveals Perturbations of Autism Spectrum Disorder during Neural System Development. Genes (Basel) 2021; 12:genes12121901. [PMID: 34946850 PMCID: PMC8700980 DOI: 10.3390/genes12121901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 01/21/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that impedes patients' cognition, social, speech and communication skills. ASD is highly heterogeneous with a variety of etiologies and clinical manifestations. The prevalence rate of ASD increased steadily in recent years. Presently, molecular mechanisms underlying ASD occurrence and development remain to be elucidated. Here, we integrated multi-layer genomics data to investigate the transcriptome and pathway dysregulations in ASD development. The RNA sequencing (RNA-seq) expression profiles of induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs) and neuron cells from ASD and normal samples were compared in our study. We found that substantially more genes were differentially expressed in the NPCs than the iPSCs. Consistently, gene set variation analysis revealed that the activity of the known ASD pathways in NPCs and neural cells were significantly different from the iPSCs, suggesting that ASD occurred at the early stage of neural system development. We further constructed comprehensive brain- and neural-specific regulatory networks by incorporating transcription factor (TF) and gene interactions with long 5 non-coding RNA(lncRNA) and protein interactions. We then overlaid the transcriptomes of different cell types on the regulatory networks to infer the regulatory cascades. The variations of the regulatory cascades between ASD and normal samples uncovered a set of novel disease-associated genes and gene interactions, particularly highlighting the functional roles of ELF3 and the interaction between STAT1 and lncRNA ELF3-AS 1 in the disease development. These new findings extend our understanding of ASD and offer putative new therapeutic targets for further studies.
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Affiliation(s)
- Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA;
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA;
- Correspondence: (J.X.); (M.Q.Y.)
| | - Mary Qu Yang
- MidSouth Bioinformatics Center, Joint Bioinformatics Graduate Program of University of Arkansas at Little Rock, University of Arkansas for Medical Sciences, Little Rock, AR 72204, USA
- Correspondence: (J.X.); (M.Q.Y.)
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30
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Murugapoopathy V, Cammisotto PG, Mossa AH, Campeau L, Gupta IR. Osr1 Is Required for Mesenchymal Derivatives That Produce Collagen in the Bladder. Int J Mol Sci 2021; 22:ijms222212387. [PMID: 34830270 PMCID: PMC8619163 DOI: 10.3390/ijms222212387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/24/2022] Open
Abstract
The extracellular matrix of the bladder consists mostly of type I and III collagen, which are required during loading. During bladder injury, there is an accumulation of collagen that impairs bladder function. Little is known about the genes that regulate production of collagens in the bladder. We demonstrate that the transcription factor Odd-skipped related 1 (Osr1) is expressed in the bladder mesenchyme and epithelium at the onset of development. As development proceeds, Osr1 is mainly expressed in mesenchymal progenitors and their derivatives. We hypothesized that Osr1 regulates mesenchymal cell differentiation and production of collagens in the bladder. To test this hypothesis, we examined newborn and adult mice heterozygous for Osr1, Osr1+/−. The bladders of newborn Osr1+/− mice had a decrease in collagen I by western blot analysis and a global decrease in collagens using Sirius red staining. There was also a decrease in the cellularity of the lamina propria, where most collagen is synthesized. This was not due to decreased proliferation or increased apoptosis in this cell population. Surprisingly, the bladders of adult Osr1+/− mice had an increase in collagen that was associated with abnormal bladder function; they also had a decrease in bladder capacity and voided more frequently. The results suggest that Osr1 is important for the differentiation of mesenchymal cells that give rise to collagen-producing cells.
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Affiliation(s)
| | - Philippe G. Cammisotto
- Lady Davis Research Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (P.G.C.); (A.H.M.); (L.C.)
| | - Abubakr H. Mossa
- Lady Davis Research Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (P.G.C.); (A.H.M.); (L.C.)
| | - Lysanne Campeau
- Lady Davis Research Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (P.G.C.); (A.H.M.); (L.C.)
- Division of Urology, Department of Surgery, Jewish General Hospital, McGill University, Montreal, QCH3T 1E2, Canada
| | - Indra R. Gupta
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada;
- Research Institute of the McGill University Health Center, Montreal, QC H3H 2R9, Canada
- Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada
- Correspondence:
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31
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Rippa AL, Alpeeva EV, Vasiliev AV, Vorotelyak EA. Alveologenesis: What Governs Secondary Septa Formation. Int J Mol Sci 2021; 22:ijms222212107. [PMID: 34829987 PMCID: PMC8618598 DOI: 10.3390/ijms222212107] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/30/2022] Open
Abstract
The simplification of alveoli leads to various lung pathologies such as bronchopulmonary dysplasia and emphysema. Deep insight into the process of emergence of the secondary septa during development and regeneration after pneumonectomy, and into the contribution of the drivers of alveologenesis and neo-alveolarization is required in an efficient search for therapeutic approaches. In this review, we describe the formation of the gas exchange units of the lung as a multifactorial process, which includes changes in the actomyosin cytoskeleton of alveocytes and myofibroblasts, elastogenesis, retinoic acid signaling, and the contribution of alveolar mesenchymal cells in secondary septation. Knowledge of the mechanistic context of alveologenesis remains incomplete. The characterization of the mechanisms that govern the emergence and depletion of αSMA will allow for an understanding of how the niche of fibroblasts is changing. Taking into account the intense studies that have been performed on the pool of lung mesenchymal cells, we present data on the typing of interstitial fibroblasts and their role in the formation and maintenance of alveoli. On the whole, when identifying cell subpopulations in lung mesenchyme, one has to consider the developmental context, the changing cellular functions, and the lability of gene signatures.
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Littleford HE, Kiontke K, Fitch DHA, Greenwald I. hlh-12, a gene that is necessary and sufficient to promote migration of gonadal regulatory cells in Caenorhabditis elegans, evolved within the Caenorhabditis clade. Genetics 2021; 219:iyab127. [PMID: 34740245 PMCID: PMC8570790 DOI: 10.1093/genetics/iyab127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/30/2021] [Indexed: 11/12/2022] Open
Abstract
Specialized cells of the somatic gonad primordium of nematodes play important roles in the final form and function of the mature gonad. Caenorhabditis elegans hermaphrodites are somatic females that have a two-armed, U-shaped gonad that connects to the vulva at the midbody. The outgrowth of each gonad arm from the somatic gonad primordium is led by two female distal tip cells (fDTCs), while the anchor cell (AC) remains stationary and central to coordinate uterine and vulval development. The bHLH protein HLH-2 and its dimerization partners LIN-32 and HLH-12 had previously been shown to be required for fDTC specification. Here, we show that ectopic expression of both HLH-12 and LIN-32 in cells with AC potential transiently transforms them into fDTC-like cells. Furthermore, hlh-12 was known to be required for the fDTCs to sustain gonad arm outgrowth. Here, we show that ectopic expression of HLH-12 in the normally stationary AC causes displacement from its normal position and that displacement likely results from activation of the leader program of fDTCs because it requires genes necessary for gonad arm outgrowth. Thus, HLH-12 is both necessary and sufficient to promote gonadal regulatory cell migration. As differences in female gonadal morphology of different nematode species reflect differences in the fate or migratory properties of the fDTCs or of the AC, we hypothesized that evolutionary changes in the expression of hlh-12 may underlie the evolution of such morphological diversity. However, we were unable to identify an hlh-12 ortholog outside of Caenorhabditis. Instead, by performing a comprehensive phylogenetic analysis of all Class II bHLH proteins in multiple nematode species, we found that hlh-12 evolved within the Caenorhabditis clade, possibly by duplicative transposition of hlh-10. Our analysis suggests that control of gene regulatory hierarchies for gonadogenesis can be remarkably plastic during evolution without adverse phenotypic consequence.
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Affiliation(s)
- Hana E Littleford
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Karin Kiontke
- Department of Biology, Center for Developmental Genetics, New York University, New York, NY 10003, USA
| | - David H A Fitch
- Department of Biology, Center for Developmental Genetics, New York University, New York, NY 10003, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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Schweiggert J, Habeck G, Hess S, Mikus F, Beloshistov R, Meese K, Hata S, Knobeloch K, Melchior F. SCF Fbxw5 targets kinesin-13 proteins to facilitate ciliogenesis. EMBO J 2021; 40:e107735. [PMID: 34368969 PMCID: PMC8441365 DOI: 10.15252/embj.2021107735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022] Open
Abstract
Microtubule depolymerases of the kinesin-13 family play important roles in various cellular processes and are frequently overexpressed in different cancer types. Despite the importance of their correct abundance, remarkably little is known about how their levels are regulated in cells. Using comprehensive screening on protein microarrays, we identified 161 candidate substrates of the multi-subunit ubiquitin E3 ligase SCFFbxw5 , including the kinesin-13 member Kif2c/MCAK. In vitro reconstitution assays demonstrate that MCAK and its closely related orthologs Kif2a and Kif2b become efficiently polyubiquitylated by neddylated SCFFbxw5 and Cdc34, without requiring preceding modifications. In cells, SCFFbxw5 targets MCAK for proteasomal degradation predominantly during G2 . While this seems largely dispensable for mitotic progression, loss of Fbxw5 leads to increased MCAK levels at basal bodies and impairs ciliogenesis in the following G1 /G0 , which can be rescued by concomitant knockdown of MCAK, Kif2a or Kif2b. We thus propose a novel regulatory event of ciliogenesis that begins already within the G2 phase of the preceding cell cycle.
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Affiliation(s)
- Jörg Schweiggert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Gregor Habeck
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Sandra Hess
- Institute of NeuropathologyFaculty of MedicineUniversity of FreiburgFreiburgGermany
- Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Felix Mikus
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Roman Beloshistov
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Klaus Meese
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | - Shoji Hata
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
| | | | - Frauke Melchior
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH)University of HeidelbergDKFZ ‐ ZMBH AllianceHeidelbergGermany
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El-Khairi R, Olszanowski E, Muraro D, Madrigal P, Tilgner K, Chhatriwala M, Vyas S, Chia CY, Vallier L, Rodríguez-Seguí SA. Modeling HNF1B-associated monogenic diabetes using human iPSCs reveals an early stage impairment of the pancreatic developmental program. Stem Cell Reports 2021; 16:2289-2304. [PMID: 34450036 PMCID: PMC8452540 DOI: 10.1016/j.stemcr.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 01/20/2023] Open
Abstract
Heterozygous mutations in HNF1B in humans result in a multisystem disorder, including pancreatic hypoplasia and diabetes mellitus. Here we used a well-controlled human induced pluripotent stem cell pancreatic differentiation model to elucidate the molecular mechanisms underlying HNF1B-associated diabetes. Our results show that lack of HNF1B blocks specification of pancreatic fate from the foregut progenitor (FP) stage, but HNF1B haploinsufficiency allows differentiation of multipotent pancreatic progenitor cells (MPCs) and insulin-secreting β-like cells. We show that HNF1B haploinsufficiency impairs cell proliferation in FPs and MPCs. This could be attributed to impaired induction of key pancreatic developmental genes, including SOX11, ROBO2, and additional TEAD1 target genes whose function is associated with MPC self-renewal. In this work we uncover an exhaustive list of potential HNF1B gene targets during human pancreas organogenesis whose downregulation might underlie HNF1B-associated diabetes onset in humans, thus providing an important resource to understand the pathogenesis of this disease.
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Affiliation(s)
- Ranna El-Khairi
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Evelyn Olszanowski
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniele Muraro
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Pedro Madrigal
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - Mariya Chhatriwala
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Sapna Vyas
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Crystal Y Chia
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ludovic Vallier
- Wellcome Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK.
| | - Santiago A Rodríguez-Seguí
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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Kretzschmar K, Boonekamp KE, Bleijs M, Asra P, Koomen M, Chuva de Sousa Lopes SM, Giovannone B, Clevers H. Troy/Tnfrsf19 marks epidermal cells that govern interfollicular epidermal renewal and cornification. Stem Cell Reports 2021; 16:2379-2394. [PMID: 34358453 PMCID: PMC8452520 DOI: 10.1016/j.stemcr.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/01/2023] Open
Abstract
The skin epidermis is a highly compartmentalized tissue consisting of a cornifying epithelium called the interfollicular epidermis (IFE) and associated hair follicles (HFs). Several stem cell populations have been described that mark specific compartments in the skin but none of them is specific to the IFE. Here, we identify Troy as a marker of IFE and HF infundibulum basal layer cells in developing and adult human and mouse epidermis. Genetic lineage-tracing experiments demonstrate that Troy-expressing basal cells contribute to long-term renewal of all layers of the cornifying epithelium. Single-cell transcriptomics and organoid assays of Troy-expressing cells, as well as their progeny, confirmed stem cell identity as well as the ability to generate differentiating daughter cells. In conclusion, we define Troy as a marker of epidermal basal cells that govern interfollicular epidermal renewal and cornification.
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Affiliation(s)
- Kai Kretzschmar
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands; Mildred Scheel Early Career Centre (MSNZ) for Cancer Research Würzburg, University Hospital Würzburg, 97080 Würzburg, Germany.
| | - Kim E Boonekamp
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands; German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
| | - Margit Bleijs
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Priyanca Asra
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands
| | - Mandy Koomen
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands
| | | | | | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre (UMC) Utrecht, 3584 CT Utrecht, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands.
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He H, Chen J, Zhao J, Zhang P, Qiao Y, Wan H, Wang J, Mei M, Bao S, Li Q. PRMT7 targets of Foxm1 controls alveolar myofibroblast proliferation and differentiation during alveologenesis. Cell Death Dis 2021; 12:841. [PMID: 34497269 PMCID: PMC8426482 DOI: 10.1038/s41419-021-04129-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/23/2021] [Indexed: 02/05/2023]
Abstract
Although aberrant alveolar myofibroblasts (AMYFs) proliferation and differentiation are often associated with abnormal lung development and diseases, such as bronchopulmonary dysplasia (BPD), chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF), epigenetic mechanisms regulating proliferation and differentiation of AMYFs remain poorly understood. Protein arginine methyltransferase 7 (PRMT7) is the only reported type III enzyme responsible for monomethylation of arginine residue on both histone and nonhistone substrates. Here we provide evidence for PRMT7's function in regulating AMYFs proliferation and differentiation during lung alveologenesis. In PRMT7-deficient mice, we found reduced AMYFs proliferation and differentiation, abnormal elastin deposition, and failure of alveolar septum formation. We further shown that oncogene forkhead box M1 (Foxm1) is a direct target of PRMT7 and that PRMT7-catalyzed monomethylation at histone H4 arginine 3 (H4R3me1) directly associate with chromatin of Foxm1 to activate its transcription, and thereby regulate of cell cycle-related genes to inhibit AMYFs proliferation and differentiation. Overexpression of Foxm1 in isolated myofibroblasts (MYFs) significantly rescued PRMT7-deficiency-induced cell proliferation and differentiation defects. Thus, our results reveal a novel epigenetic mechanism through which PRMT7-mediated histone arginine monomethylation activates Foxm1 transcriptional expression to regulate AMYFs proliferation and differentiation during lung alveologenesis and may represent a potential target for intervention in pulmonary diseases.
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Affiliation(s)
- Huacheng He
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, P.R. China
| | - Jilin Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, P.R. China
| | - Jian Zhao
- Department of Health Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Peizhun Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, P.R. China
| | - Yulong Qiao
- Department of Health Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China
| | - Huajing Wan
- Laboratory of Pulmonary Immunology and Inflammation, Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Jincheng Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, P.R. China
| | - Mei Mei
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, P.R. China
| | - Shilai Bao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, P.R. China.
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100101, P.R. China.
| | - Qiuling Li
- Department of Health Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601, P.R. China.
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Abstract
BACKGROUND Standard preprocessing of single-cell RNA-seq UMI data includes normalization by sequencing depth to remove this technical variability, and nonlinear transformation to stabilize the variance across genes with different expression levels. Instead, two recent papers propose to use statistical count models for these tasks: Hafemeister and Satija (Genome Biol 20:296, 2019) recommend using Pearson residuals from negative binomial regression, while Townes et al. (Genome Biol 20:295, 2019) recommend fitting a generalized PCA model. Here, we investigate the connection between these approaches theoretically and empirically, and compare their effects on downstream processing. RESULTS We show that the model of Hafemeister and Satija produces noisy parameter estimates because it is overspecified, which is why the original paper employs post hoc smoothing. When specified more parsimoniously, it has a simple analytic solution equivalent to the rank-one Poisson GLM-PCA of Townes et al. Further, our analysis indicates that per-gene overdispersion estimates in Hafemeister and Satija are biased, and that the data are in fact consistent with the overdispersion parameter being independent of gene expression. We then use negative control data without biological variability to estimate the technical overdispersion of UMI counts, and find that across several different experimental protocols, the data are close to Poisson and suggest very moderate overdispersion. Finally, we perform a benchmark to compare the performance of Pearson residuals, variance-stabilizing transformations, and GLM-PCA on scRNA-seq datasets with known ground truth. CONCLUSIONS We demonstrate that analytic Pearson residuals strongly outperform other methods for identifying biologically variable genes, and capture more of the biologically meaningful variation when used for dimensionality reduction.
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Affiliation(s)
- Jan Lause
- University of Tübingen, Institute for Ophthalmic Research, Tübingen, Germany
| | - Philipp Berens
- University of Tübingen, Institute for Ophthalmic Research, Tübingen, Germany
- University of Tübingen, Institute for Bioinformatics and Medical Informatics, Tübingen, Germany
- University of Tübingen, Bernstein Center for Computational Neuroscience, Tübingen, Germany
- University of Tübingen, Center for Integrative Neuroscience, Tübingen, Germany
| | - Dmitry Kobak
- University of Tübingen, Institute for Ophthalmic Research, Tübingen, Germany
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Abstract
The kidney is among the best characterized developing tissues, with the genes and signaling pathways that regulate embryonic and adult kidney patterning and development having been extensively identified. It is now widely understood that DNA methylation and histone modification patterns are imprinted during embryonic development and must be maintained in adult cells for appropriate gene transcription and phenotypic stability. A compelling question then is how these epigenetic mechanisms play a role in kidney development. In this review, we describe the major genes and pathways that have been linked to epigenetic mechanisms in kidney development. We also discuss recent applications of single-cell RNA sequencing (scRNA-seq) techniques in the study of kidney development. Additionally, we summarize the techniques of single-cell epigenomics, which can potentially be used to characterize epigenomes at single-cell resolution in embryonic and adult kidneys. The combination of scRNA-seq and single-cell epigenomics will help facilitate the further understanding of early cell lineage specification at the level of epigenetic modifications in embryonic and adult kidney development, which may also be used to investigate epigenetic mechanisms in kidney diseases.
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Affiliation(s)
- Katrina Chan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA;
| | - Xiaogang Li
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA;
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: ; Tel.: +1-507-266-0110
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Abstract
During liver organogenesis, cellular transcriptional profiles are constantly reshaped by the action of hepatic transcriptional regulators, including FoxA1-3, GATA4/6, HNF1α/β, HNF4α, HNF6, OC-2, C/EBPα/β, Hex, and Prox1. These factors are crucial for the activation of hepatic genes that, in the context of compact chromatin, cannot access their targets. The initial opening of highly condensed chromatin is executed by a special class of transcription factors known as pioneer factors. They bind and destabilize highly condensed chromatin and facilitate access to other "non-pioneer" factors. The association of target genes with pioneer and non-pioneer transcription factors takes place long before gene activation. In this way, the underlying gene regulatory regions are marked for future activation. The process is called "bookmarking", which confers transcriptional competence on target genes. Developmental bookmarking is accompanied by a dynamic maturation process, which prepares the genomic loci for stable and efficient transcription. Stable hepatic expression profiles are maintained during development and adulthood by the constant availability of the main regulators. This is achieved by a self-sustaining regulatory network that is established by complex cross-regulatory interactions between the major regulators. This network gradually grows during liver development and provides an epigenetic memory mechanism for safeguarding the optimal expression of the regulators.
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Affiliation(s)
- Evangelia C. Tachmatzidi
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Ourania Galanopoulou
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Iannis Talianidis
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Correspondence:
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Casey MA, Lusk S, Kwan KM. Build me up optic cup: Intrinsic and extrinsic mechanisms of vertebrate eye morphogenesis. Dev Biol 2021; 476:128-136. [PMID: 33811855 PMCID: PMC8848517 DOI: 10.1016/j.ydbio.2021.03.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/16/2022]
Abstract
The basic structure of the eye, which is crucial for visual function, is established during the embryonic process of optic cup morphogenesis. Molecular pathways of specification and patterning are integrated with spatially distinct cell and tissue shape changes to generate the eye, with discrete domains and structural features: retina and retinal pigment epithelium enwrap the lens, and the optic fissure occupies the ventral surface of the eye and optic stalk. Interest in the underlying cell biology of eye morphogenesis has led to a growing body of work, combining molecular genetics and imaging to quantify cellular processes such as adhesion and actomyosin activity. These studies reveal that intrinsic machinery and spatiotemporally specific extrinsic inputs collaborate to control dynamics of cell movements and morphologies. Here we consider recent advances in our understanding of eye morphogenesis, with a focus on the mechanics of eye formation throughout vertebrate systems, including insights and potential opportunities using organoids, which may provide a tractable system to test hypotheses from embryonic models.
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Affiliation(s)
- Macaulie A Casey
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Sarah Lusk
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Kristen M Kwan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.
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Seese SE, Deml B, Muheisen S, Sorokina E, Semina EV. Genetic disruption of zebrafish mab21l1 reveals a conserved role in eye development and affected pathways. Dev Dyn 2021; 250:1056-1073. [PMID: 33570754 PMCID: PMC8349561 DOI: 10.1002/dvdy.312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The male-abnormal 21 like (MAB21L) genes are important in human ocular development. Homozygous loss of MAB21L1 leads to corneal dystrophy in all affected individuals along with cataracts and buphthalmos in some. The molecular function and downstream pathways of MAB21L factors are largely undefined. RESULTS We generated the first mab21l1 zebrafish mutant carrying a putative loss-of-function allele, c.107delA p.(Lys36Argfs*7). At the final stages of embryonic development, homozygous mab21l1c.107delA fish displayed enlarged anterior chambers and corneal thinning which progressed with age. Additional studies revealed increased cell death in the mutant corneas, transformation of the cornea into a skin-like epithelium, and progressive lens degeneration with development of fibrous masses in the anterior chamber. RNA-seq of wild-type and mutant ocular transcriptomes revealed significant changes in expression of several genes, including irf1a and b, stat1, elf3, krt17, tlr9, and loxa associated with immunity and/or corneal function. Abnormal expression of lysyl oxidases have been previously linked with corneal thinning, fibrosis, and lens defects in mammals, suggesting a role for loxa misexpression in the progressive mab21l1c.107delA eye phenotype. CONCLUSIONS Zebrafish mab21l1 is essential for normal corneal development, similar to human MAB21L1. The identified molecular changes in mab21l1c.107delA mutants provide the first clues about possible affected pathways.
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Affiliation(s)
- Sarah E. Seese
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Brett Deml
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- PreventionGenetics, Marshfield, Wisconsin
| | - Sanaa Muheisen
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena Sorokina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elena V. Semina
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Cell Biology, Neurobiology and Anatomy, The Medical College of Wisconsin, Milwaukee, Wisconsin
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
- Children's Research Institute, Medical College of Wisconsin, Children's of Wisconsin, Milwaukee, Wisconsin
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Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C, Göttgens B. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome Biol 2021; 22:197. [PMID: 34225769 PMCID: PMC8258993 DOI: 10.1186/s13059-021-02414-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept to an extended timecourse dataset covering mouse gastrulation and early organogenesis. RESULTS Intriguingly, RNA velocity correctly identifies epiblast cells as the starting point, but several trajectory predictions at later stages are inconsistent with both real-time ordering and existing knowledge. The most striking discrepancy concerns red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes reveals a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulator Gata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be upregulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, the Gata1-chimera dataset reveals induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression. CONCLUSIONS By identifying a limitation of the current velocity framework coupled with in vivo analysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.
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Affiliation(s)
- Melania Barile
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
| | - Isabella Inzani
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Cambridge, CB2 0QQ UK
| | - Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - Jennifer Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, CB10 1SD UK
| | - Carolina Guibentif
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
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Nakano H, Fajardo VM, Nakano A. The role of glucose in physiological and pathological heart formation. Dev Biol 2021; 475:222-233. [PMID: 33577830 PMCID: PMC8107118 DOI: 10.1016/j.ydbio.2021.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/30/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023]
Abstract
Cells display distinct metabolic characteristics depending on its differentiation stage. The fuel type of the cells serves not only as a source of energy but also as a driver of differentiation. Glucose, the primary nutrient to the cells, is a critical regulator of rapidly growing embryos. This metabolic change is a consequence as well as a cause of changes in genetic program. Disturbance of fetal glucose metabolism such as in diabetic pregnancy is associated with congenital heart disease. In utero hyperglycemia impacts the left-right axis establishment, migration of cardiac neural crest cells, conotruncal formation and mesenchymal formation of the cardiac cushion during early embryogenesis and causes cardiac hypertrophy in late fetal stages. In this review, we focus on the role of glucose in cardiogenesis and the molecular mechanisms underlying heart diseases associated with hyperglycemia.
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Affiliation(s)
- Haruko Nakano
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Viviana M Fajardo
- Department of Pediatrics, Division of Neonatology and Developmental Biology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Atsushi Nakano
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, Division of Cardiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA.
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Li E, Ustiyan V, Wen B, Kalin GT, Whitsett JA, Kalin TV, Kalinichenko VV. Blastocyst complementation reveals that NKX2-1 establishes the proximal-peripheral boundary of the airway epithelium. Dev Dyn 2021; 250:1001-1020. [PMID: 33428297 DOI: 10.1002/dvdy.298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Distinct boundaries between the proximal conducting airways and more peripheral-bronchial regions of the lung are established early in foregut embryogenesis, demarcated in part by the distribution of SOX family and NKX2-1 transcription factors along the cephalo-caudal axis of the lung. We used blastocyst complementation to identify the role of NKX2-1 in the formation of the proximal-peripheral boundary of the airways in mouse chimeric embryos. RESULTS While Nkx2-1-/- mouse embryos form primordial tracheal cysts, peripheral pulmonary structures are entirely lacking in Nkx2-1-/- mice. Complementation of Nkx2-1-/- embryos with NKX2-1-sufficient embryonic stem cells (ESCs) enabled the formation of all tissue components of the peripheral lung but did not enhance ESC colonization of the most proximal regions of the airways. In chimeric mice, a precise boundary was formed between NKX2-1-deficient basal cells co-expressing SOX2 and SOX9 in large airways and ESC-derived NKX2-1+ SOX9+ epithelial cells of smaller airways. NKX2-1-sufficient ESCs were able to selectively complement peripheral, rather than most proximal regions of the airways. ESC complementation did not prevent ectopic expression of SOX9 but restored β-catenin signaling in Nkx2-1-/- basal cells of large airways. CONCLUSIONS NKX2-1 and β-catenin function in an epithelial cell-autonomous manner to establish the proximal-peripheral boundary along developing airways.
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Affiliation(s)
- Enhong Li
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
| | - Vladimir Ustiyan
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
| | - Bingqiang Wen
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
| | - Gregory T Kalin
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
| | - Jeffrey A Whitsett
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Tanya V Kalin
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Vladimir V Kalinichenko
- Center for Lung Regenerative Medicine, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
- Division of Pulmonary Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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45
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Arnold F, Mahaddalkar PU, Kraus JM, Zhong X, Bergmann W, Srinivasan D, Gout J, Roger E, Beutel AK, Zizer E, Tharehalli U, Daiss N, Russell R, Perkhofer L, Oellinger R, Lin Q, Azoitei N, Weiss F, Lerch MM, Liebau S, Katz S, Lechel A, Rad R, Seufferlein T, Kestler HA, Ott M, Sharma AD, Hermann PC, Kleger A. Functional Genomic Screening During Somatic Cell Reprogramming Identifies DKK3 as a Roadblock of Organ Regeneration. Adv Sci (Weinh) 2021; 8:2100626. [PMID: 34306986 PMCID: PMC8292873 DOI: 10.1002/advs.202100626] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 05/06/2023]
Abstract
Somatic cell reprogramming and tissue repair share relevant factors and molecular programs. Here, Dickkopf-3 (DKK3) is identified as novel factor for organ regeneration using combined transcription-factor-induced reprogramming and RNA-interference techniques. Loss of Dkk3 enhances the generation of induced pluripotent stem cells but does not affect de novo derivation of embryonic stem cells, three-germ-layer differentiation or colony formation capacity of liver and pancreatic organoids. However, DKK3 expression levels in wildtype animals and serum levels in human patients are elevated upon injury. Accordingly, Dkk3-null mice display less liver damage upon acute and chronic failure mediated by increased proliferation in hepatocytes and LGR5+ liver progenitor cell population, respectively. Similarly, recovery from experimental pancreatitis is accelerated. Regeneration onset occurs in the acinar compartment accompanied by virtually abolished canonical-Wnt-signaling in Dkk3-null animals. This results in reduced expression of the Hedgehog repressor Gli3 and increased Hedgehog-signaling activity upon Dkk3 loss. Collectively, these data reveal Dkk3 as a key regulator of organ regeneration via a direct, previously unacknowledged link between DKK3, canonical-Wnt-, and Hedgehog-signaling.
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Affiliation(s)
- Frank Arnold
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Pallavi U Mahaddalkar
- Institute for Diabetes and RegenerationHelmholtz Zentrum MünchenIngolstädter Landstraße 185764 NeuherbergGermany
| | - Johann M. Kraus
- Institute of Medical Systems BiologyUlm UniversityAlbert‐Einstein Allee 1189081 UlmGermany
| | - Xiaowei Zhong
- Department of GastroenterologyHepatology and EndocrinologyHannover Medical SchoolFeodor‐Lynen‐Str. 730625 HannoverGermany
| | - Wendy Bergmann
- Core Facility for Cell Sorting and Cell AnalysisUniversity Medical Center RostockSchillingallee 7018057 RostockGermany
| | - Dharini Srinivasan
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Johann Gout
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Elodie Roger
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Alica K. Beutel
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Eugen Zizer
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Umesh Tharehalli
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Nora Daiss
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Ronan Russell
- Diabetes CenterUniversity of CaliforniaSan FranciscoCA94143USA
| | - Lukas Perkhofer
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Rupert Oellinger
- Institute of Molecular Oncology and Functional GenomicsTranslaTUM Cancer CenterTechnical University of MunichIsmaninger Str. 2281675 MunichGermany
| | - Qiong Lin
- Bayer AG Research & DevelopmentPharmaceuticalsMüllerstraße 17813353 BerlinGermany
| | - Ninel Azoitei
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Frank‐Ulrich Weiss
- Department of Medicine AUniversity Medicine GreifswaldFerdinand‐Sauerbruch‐Straße17475 GreifswaldGermany
| | - Markus M. Lerch
- Department of Medicine AUniversity Medicine GreifswaldFerdinand‐Sauerbruch‐Straße17475 GreifswaldGermany
- Klinikum der Ludwig‐Maximilians‐Universität München‐GroßhadernMarchioninistraße 1581377 MünchenGermany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology INDBEberhard Karls University TübingenÖsterbergstr. 372074 TübingenGermany
| | - Sarah‐Fee Katz
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - André Lechel
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Roland Rad
- Institute of Molecular Oncology and Functional GenomicsTranslaTUM Cancer CenterTechnical University of MunichIsmaninger Str. 2281675 MunichGermany
| | - Thomas Seufferlein
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Hans A. Kestler
- Institute of Medical Systems BiologyUlm UniversityAlbert‐Einstein Allee 1189081 UlmGermany
| | - Michael Ott
- Department of GastroenterologyHepatology and EndocrinologyHannover Medical SchoolFeodor‐Lynen‐Str. 730625 HannoverGermany
| | - Amar Deep Sharma
- Department of GastroenterologyHepatology and EndocrinologyHannover Medical SchoolFeodor‐Lynen‐Str. 730625 HannoverGermany
| | - Patrick C. Hermann
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Alexander Kleger
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
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46
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Beckert V, Rassmann S, Kayvanjoo AH, Klausen C, Bonaguro L, Botermann DS, Krause M, Moreth K, Spielmann N, da Silva-Buttkus P, Fuchs H, Gailus-Durner V, de Angelis MH, Händler K, Ulas T, Aschenbrenner AC, Mass E, Wachten D. Creld1 regulates myocardial development and function. J Mol Cell Cardiol 2021; 156:45-56. [PMID: 33773996 DOI: 10.1016/j.yjmcc.2021.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/25/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022]
Abstract
CRELD1 (Cysteine-Rich with EGF-Like Domains 1) is a risk gene for non-syndromic atrioventricular septal defects in human patients. In a mouse model, Creld1 has been shown to be essential for heart development, particularly in septum and valve formation. However, due to the embryonic lethality of global Creld1 knockout (KO) mice, its cell type-specific function during peri- and postnatal stages remains unknown. Here, we generated conditional Creld1 KO mice lacking Creld1 either in the endocardium (KOTie2) or the myocardium (KOMyHC). Using a combination of cardiac phenotyping, histology, immunohistochemistry, RNA-sequencing, and flow cytometry, we demonstrate that Creld1 function in the endocardium is dispensable for heart development. Lack of myocardial Creld1 causes extracellular matrix remodeling and trabeculation defects by modulation of the Notch1 signaling pathway. Hence, KOMyHC mice die early postnatally due to myocardial hypoplasia. Our results reveal that Creld1 not only controls the formation of septa and valves at an early stage during heart development, but also cardiac maturation and function at a later stage. These findings underline the central role of Creld1 in mammalian heart development and function.
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Affiliation(s)
- Vera Beckert
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Sebastian Rassmann
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Amir Hossein Kayvanjoo
- Life & Medical Institute (LIMES), Developmental Biology of the Immune System, University of Bonn, 53115 Bonn, Germany
| | - Christina Klausen
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Lorenzo Bonaguro
- Life & Medical Institute (LIMES), Genomics and Immunoregulation, University of Bonn, 53115 Bonn, Germany
| | - Dominik Simon Botermann
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Melanie Krause
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Kristin Moreth
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Patricia da Silva-Buttkus
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Experimental Genetics, School of Life Science Weihenstephan, Technical University Munich, 85354 Freising, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Single Cell Genomics and Epigenomics at the DZNE and the University of Bonn, 53127 Bonn, Germany
| | - Thomas Ulas
- Life & Medical Institute (LIMES), Genomics and Immunoregulation, University of Bonn, 53115 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Single Cell Genomics and Epigenomics at the DZNE and the University of Bonn, 53127 Bonn, Germany
| | - Anna C Aschenbrenner
- Life & Medical Institute (LIMES), Genomics and Immunoregulation, University of Bonn, 53115 Bonn, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6500HB Nijmegen, the Netherlands
| | - Elvira Mass
- Life & Medical Institute (LIMES), Developmental Biology of the Immune System, University of Bonn, 53115 Bonn, Germany.
| | - Dagmar Wachten
- Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
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Ghilardi A, Diana A, Bacchetta R, Santo N, Ascagni M, Prosperi L, Del Giacco L. Inner Ear and Muscle Developmental Defects in Smpx-Deficient Zebrafish Embryos. Int J Mol Sci 2021; 22:ijms22126497. [PMID: 34204426 PMCID: PMC8235540 DOI: 10.3390/ijms22126497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 12/20/2022] Open
Abstract
The last decade has witnessed the identification of several families affected by hereditary non-syndromic hearing loss (NSHL) caused by mutations in the SMPX gene and the loss of function has been suggested as the underlying mechanism. In the attempt to confirm this hypothesis we generated an Smpx-deficient zebrafish model, pointing out its crucial role in proper inner ear development. Indeed, a marked decrease in the number of kinocilia together with structural alterations of the stereocilia and the kinocilium itself in the hair cells of the inner ear were observed. We also report the impairment of the mechanotransduction by the hair cells, making SMPX a potential key player in the construction of the machinery necessary for sound detection. This wealth of evidence provides the first possible explanation for hearing loss in SMPX-mutated patients. Additionally, we observed a clear muscular phenotype consisting of the defective organization and functioning of muscle fibers, strongly suggesting a potential role for the protein in the development of muscle fibers. This piece of evidence highlights the need for more in-depth analyses in search for possible correlations between SMPX mutations and muscular disorders in humans, thus potentially turning this non-syndromic hearing loss-associated gene into the genetic cause of dysfunctions characterized by more than one symptom, making SMPX a novel syndromic gene.
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Affiliation(s)
- Anna Ghilardi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; (A.G.); (A.D.); (L.P.)
| | - Alberto Diana
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; (A.G.); (A.D.); (L.P.)
| | - Renato Bacchetta
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milan, Italy;
| | - Nadia Santo
- Unitech NOLIMITS, Università degli Studi di Milano, 20133 Milan, Italy; (N.S.); (M.A.)
| | - Miriam Ascagni
- Unitech NOLIMITS, Università degli Studi di Milano, 20133 Milan, Italy; (N.S.); (M.A.)
| | - Laura Prosperi
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; (A.G.); (A.D.); (L.P.)
| | - Luca Del Giacco
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; (A.G.); (A.D.); (L.P.)
- Correspondence:
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48
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Kaufman ML, Goodson NB, Park KU, Schwanke M, Office E, Schneider SR, Abraham J, Hensley A, Jones KL, Brzezinski JA. Initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity. Development 2021; 148:dev199399. [PMID: 34143204 PMCID: PMC8254865 DOI: 10.1242/dev.199399] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/10/2021] [Indexed: 11/20/2022]
Abstract
During retinal development, a large subset of progenitors upregulates the transcription factor Otx2, which is required for photoreceptor and bipolar cell formation. How these retinal progenitor cells initially activate Otx2 expression is unclear. To address this, we investigated the cis-regulatory network that controls Otx2 expression in mice. We identified a minimal enhancer element, DHS-4D, that drove expression in newly formed OTX2+ cells. CRISPR/Cas9-mediated deletion of DHS-4D reduced OTX2 expression, but this effect was diminished in postnatal development. Systematic mutagenesis of the enhancer revealed that three basic helix-loop-helix (bHLH) transcription factor-binding sites were required for its activity. Single cell RNA-sequencing of nascent Otx2+ cells identified the bHLH factors Ascl1 and Neurog2 as candidate regulators. CRISPR/Cas9 targeting of these factors showed that only the simultaneous loss of Ascl1 and Neurog2 prevented OTX2 expression. Our findings suggest that Ascl1 and Neurog2 act either redundantly or in a compensatory fashion to activate the DHS-4D enhancer and Otx2 expression. We observed redundancy or compensation at both the transcriptional and enhancer utilization levels, suggesting that the mechanisms governing Otx2 regulation in the retina are flexible and robust.
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Affiliation(s)
- Michael L. Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Noah B. Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emma Office
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sophia R. Schneider
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joy Abraham
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Austin Hensley
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth L. Jones
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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49
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DeLaForest A, Kohlnhofer BM, Franklin OD, Stavniichuk R, Thompson CA, Pulakanti K, Rao S, Battle MA. GATA4 Controls Epithelial Morphogenesis in the Developing Stomach to Promote Establishment of Glandular Columnar Epithelium. Cell Mol Gastroenterol Hepatol 2021; 12:1391-1413. [PMID: 34111600 PMCID: PMC8479485 DOI: 10.1016/j.jcmgh.2021.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND & AIMS The transcription factor GATA4 is broadly expressed in nascent foregut endoderm. As development progresses, GATA4 is lost in the domain giving rise to the stratified squamous epithelium of the esophagus and forestomach (FS), while it is maintained in the domain giving rise to the simple columnar epithelium of the hindstomach (HS). Differential GATA4 expression within these domains coincides with the onset of distinct tissue morphogenetic events, suggesting a role for GATA4 in diversifying foregut endoderm into discrete esophageal/FS and HS epithelial tissues. The goal of this study was to determine how GATA4 regulates differential morphogenesis of the mouse gastric epithelium. METHODS We used a Gata4 conditional knockout mouse line to eliminate GATA4 in the developing HS and a Gata4 conditional knock-in mouse line to express GATA4 in the developing FS. RESULTS We found that GATA4-deficient HS epithelium adopted a FS-like fate, and conversely, that GATA4-expressing FS epithelium adopted a HS-like fate. Underlying structural changes in these epithelia were broad changes in gene expression networks attributable to GATA4 directly activating or repressing expression of HS or FS defining transcripts. Our study implicates GATA4 as having a primary role in suppressing an esophageal/FS transcription factor network during HS development to promote columnar epithelium. Moreover, GATA4-dependent phenotypes in developmental mutants reflected changes in gene expression associated with Barrett's esophagus. CONCLUSIONS This study demonstrates that GATA4 is necessary and sufficient to activate the development of simple columnar epithelium, rather than stratified squamous epithelium, in the embryonic stomach. Moreover, similarities between mutants and Barrett's esophagus suggest that developmental biology can provide insight into human disease mechanisms.
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Affiliation(s)
- Ann DeLaForest
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Bridget M Kohlnhofer
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Olivia D Franklin
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Roman Stavniichuk
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Cayla A Thompson
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kirthi Pulakanti
- Blood Research Institute, Versiti Wisconsin, Milwaukee, Wisconsin
| | - Sridhar Rao
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin; Blood Research Institute, Versiti Wisconsin, Milwaukee, Wisconsin; Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, Medical College of Wisconsin and Children's Wisconsin, Milwaukee, Wisconsin
| | - Michele A Battle
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin.
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Abstract
Alternative splicing (AS) is pervasive in mammalian genomes, yet cross-species comparisons have been largely restricted to adult tissues and the functionality of most AS events remains unclear. We assessed AS patterns across pre- and postnatal development of seven organs in six mammals and a bird. Our analyses revealed that developmentally dynamic AS events, which are especially prevalent in the brain, are substantially more conserved than nondynamic ones. Cassette exons with increasing inclusion frequencies during development show the strongest signals of conserved and regulated AS. Newly emerged cassette exons are typically incorporated late in testis development, but those retained during evolution are predominantly brain specific. Our work suggests that an intricate interplay of programs controlling gene expression levels and AS is fundamental to organ development, especially for the brain and heart. In these regulatory networks, AS affords substantial functional diversification of genes through the generation of tissue- and time-specific isoforms from broadly expressed genes.
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Affiliation(s)
- Pavel V Mazin
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Philipp Khaitovich
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Margarida Cardoso-Moreira
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
- Evolutionary Developmental Biology Laboratory, The Francis Crick Institute, London, UK.
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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