1
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Cardeira-da-Silva J, Wang Q, Sagvekar P, Mintcheva J, Latting S, Günther S, Ramadass R, Yekelchyk M, Preussner J, Looso M, Junker JP, Stainier DYR. Antigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish. Nat Commun 2024; 15:3637. [PMID: 38684665 PMCID: PMC11058276 DOI: 10.1038/s41467-024-47430-1] [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: 04/25/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
In contrast to adult mammals, adult zebrafish can fully regenerate injured cardiac tissue, and this regeneration process requires an adequate and tightly controlled immune response. However, which components of the immune response are required during regeneration is unclear. Here, we report positive roles for the antigen presentation-adaptive immunity axis during zebrafish cardiac regeneration. We find that following the initial innate immune response, activated endocardial cells (EdCs), as well as immune cells, start expressing antigen presentation genes. We also observe that T helper cells, a.k.a. Cd4+ T cells, lie in close physical proximity to these antigen-presenting EdCs. We targeted Major Histocompatibility Complex (MHC) class II antigen presentation by generating cd74a; cd74b mutants, which display a defective immune response. In these mutants, Cd4+ T cells and activated EdCs fail to efficiently populate the injured tissue and EdC proliferation is significantly decreased. cd74a; cd74b mutants exhibit additional defects in cardiac regeneration including reduced cardiomyocyte dedifferentiation and proliferation. Notably, Cd74 also becomes activated in neonatal mouse EdCs following cardiac injury. Altogether, these findings point to positive roles for antigen presentation during cardiac regeneration, potentially involving interactions between activated EdCs, classical antigen-presenting cells, and Cd4+ T cells.
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Affiliation(s)
- João Cardeira-da-Silva
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
| | - Qianchen Wang
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Pooja Sagvekar
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Janita Mintcheva
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt University of Berlin, Berlin, Germany
| | - Stephan Latting
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Radhan Ramadass
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michail Yekelchyk
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jens Preussner
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- DZHK German Centre for Cardiovascular Research, Partner Site Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- DZHK German Centre for Cardiovascular Research, Partner Site Rhine-Main, Bad Nauheim, Germany.
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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2
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Mitic N, Neuschulz A, Spanjaard B, Schneider J, Fresmann N, Novoselc KT, Strunk T, Münster L, Olivares-Chauvet P, Ninkovic J, Junker JP. Dissecting the spatiotemporal diversity of adult neural stem cells. Mol Syst Biol 2024; 20:321-337. [PMID: 38365956 PMCID: PMC10987636 DOI: 10.1038/s44320-024-00022-z] [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: 05/04/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
Adult stem cells are important for tissue turnover and regeneration. However, in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here, we dissected the diversity of neural stem cells in the adult zebrafish brain, an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single-cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze the regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells, with some subtypes being restricted to a single brain region, while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation, with different states being involved in proliferative and non-proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for the functional manipulation of neural stem cell subtypes.
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Affiliation(s)
- Nina Mitic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Anika Neuschulz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Humboldt Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Julia Schneider
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Nora Fresmann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Klara Tereza Novoselc
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
- Graduate School of Systemic Neurosciences, LMU, Munich, Germany
| | - Taraneh Strunk
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lisa Münster
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jovica Ninkovic
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Stem Cell Research, Munich, Germany
- Biomedical Center Munich (BMC), Department of Cell Biology and Anatomy, Medical Faculty, LMU, Munich, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Berlin, Germany.
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3
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Jumde G, Spanjaard B, Junker JP. Inference of differentiation trajectories by transfer learning across biological processes. Cell Syst 2024; 15:75-82.e5. [PMID: 38128536 DOI: 10.1016/j.cels.2023.12.002] [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: 03/13/2023] [Revised: 07/28/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Stem cells differentiate into distinct fates by transitioning through a series of transcriptional states. Current computational approaches allow reconstruction of differentiation trajectories from single-cell transcriptomics data, but it remains unknown to what degree differentiation can be predicted across biological processes. Here, we use transfer learning to infer differentiation processes and quantify predictability in early embryonic development and adult hematopoiesis. Overall, we find that non-linear methods outperform linear approaches, and we achieved the best predictions with a custom variational autoencoder that explicitly models changes in transcriptional variance. We observed a high accuracy of predictions in embryonic development, but we found somewhat lower agreement with the real data in adult hematopoiesis. We demonstrate that this discrepancy can be explained by a higher degree of concordant transcriptional processes along embryonic differentiation compared with adult homeostasis. In summary, we establish a framework for quantifying and exploiting predictability of cellular differentiation trajectories.
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Affiliation(s)
- Gaurav Jumde
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Humboldt Universität zu Berlin, Faculty of Life Sciences, Department of Biology, 10115 Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany; Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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4
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Neuschulz A, Bakina O, Badillo-Lisakowski V, Olivares-Chauvet P, Conrad T, Gotthardt M, Kettenmann H, Junker JP. A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation. Mol Syst Biol 2023; 19:e11147. [PMID: 36573354 PMCID: PMC9912023 DOI: 10.15252/msb.202211147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022] Open
Abstract
Tissue dissociation, a crucial step in single-cell sample preparation, can alter the transcriptional state of a sample through the intrinsic cellular stress response. Here we demonstrate a general approach for measuring transcriptional response during sample preparation. In our method, transcripts made during dissociation are labeled for later identification upon sequencing. We found general as well as cell-type-specific dissociation response programs in zebrafish larvae, and we observed sample-to-sample variation in the dissociation response of mouse cardiomyocytes despite well-controlled experimental conditions. Finally, we showed that dissociation of the mouse hippocampus can lead to the artificial activation of microglia. In summary, our approach facilitates experimental optimization of dissociation procedures as well as computational removal of transcriptional perturbation response.
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Affiliation(s)
- Anika Neuschulz
- Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Humboldt-Universität zu Berlin, Berlin, Germany
| | - Olga Bakina
- Cellular Neurosciences, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Victor Badillo-Lisakowski
- Humboldt-Universität zu Berlin, Berlin, Germany.,Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Thomas Conrad
- BIH/MDC Genomics Technology Platform, Berlin, Germany
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Helmut Kettenmann
- Cellular Neurosciences, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jan Philipp Junker
- Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
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5
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Preusser F, Neuschulz A, Junker JP, Rajewsky N, Preibisch S. Long-term imaging reveals behavioral plasticity during C. elegans dauer exit. BMC Biol 2022; 20:277. [PMID: 36514066 DOI: 10.1186/s12915-022-01471-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND During their lifetime, animals must adapt their behavior to survive in changing environments. This ability requires the nervous system to undergo adjustments at distinct temporal scales, from short-term dynamic changes in expression of neurotransmitters and receptors to longer-term growth, spatial and connectivity reorganization, while integrating external stimuli. The nematode Caenorhabditis elegans provides a model of nervous system plasticity, in particular its dauer exit decision. Under unfavorable conditions, larvae will enter the non-feeding and non-reproductive stress-resistant dauer stage and adapt their behavior to cope with the harsh new environment, with active reversal under improved conditions leading to resumption of reproductive development. However, how different environmental stimuli regulate the exit decision mechanism and thereby drive the larva's behavioral change is unknown. To fill this gap and provide insights on behavioral changes over extended periods of time, we developed a new open hardware method for long-term imaging (12h) of C. elegans larvae. RESULTS Our WormObserver platform comprises open hardware and software components for video acquisition, automated processing of large image data (> 80k images/experiment) and data analysis. We identified dauer-specific behavioral motifs and characterized the behavioral trajectory of dauer exit in different environments and genetic backgrounds to identify key decision points and stimuli promoting dauer exit. Combining long-term behavioral imaging with transcriptomics data, we find that bacterial ingestion triggers a change in neuropeptide gene expression to establish post-dauer behavior. CONCLUSIONS Taken together, we show how a developing nervous system can robustly integrate environmental changes activate a developmental switch and adapt the organism's behavior to a new environment. WormObserver is generally applicable to other research questions within and beyond the C. elegans field, having a modular and customizable character and allowing assessment of behavioral plasticity over longer periods.
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Affiliation(s)
- Friedrich Preusser
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany. .,Institute for Biology, Humboldt University of Berlin, 10099, Berlin, Germany.
| | - Anika Neuschulz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany.,Institute for Biology, Humboldt University of Berlin, 10099, Berlin, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Stephan Preibisch
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.
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6
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Hu B, Lelek S, Spanjaard B, El-Sammak H, Simões MG, Mintcheva J, Aliee H, Schäfer R, Meyer AM, Theis F, Stainier DYR, Panáková D, Junker JP. Origin and function of activated fibroblast states during zebrafish heart regeneration. Nat Genet 2022; 54:1227-1237. [PMID: 35864193 PMCID: PMC7613248 DOI: 10.1038/s41588-022-01129-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022]
Abstract
The adult zebrafish heart has a high capacity for regeneration following injury. However, the composition of the regenerative niche has remained largely elusive. Here, we dissected the diversity of activated cell states in the regenerating zebrafish heart based on single-cell transcriptomics and spatiotemporal analysis. We observed the emergence of several transient cell states with fibroblast characteristics following injury, and we outlined the proregenerative function of collagen-12-expressing fibroblasts. To understand the cascade of events leading to heart regeneration, we determined the origin of these cell states by high-throughput lineage tracing. We found that activated fibroblasts were derived from two separate sources: the epicardium and the endocardium. Mechanistically, we determined Wnt signalling as a regulator of the endocardial fibroblast response. In summary, our work identifies specialized activated fibroblast cell states that contribute to heart regeneration, thereby opening up possible approaches to modulating the regenerative capacity of the vertebrate heart. Single-cell RNA sequencing and spatiotemporal analysis of the regenerating zebrafish heart identify transient proregenerative fibroblast-like cells that are derived from the epicardium and the endocardium. Wnt signalling regulates the endocardial fibroblast response.
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Affiliation(s)
- Bo Hu
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Sara Lelek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research) partner site, Berlin, Germany
| | - Bastiaan Spanjaard
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Hadil El-Sammak
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,DZHK (German Centre for Cardiovascular Research) partner site Rhine/Main, Frankfurt, Germany
| | - Mariana Guedes Simões
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Janita Mintcheva
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Hananeh Aliee
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany
| | - Ronny Schäfer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Alexander M Meyer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Fabian Theis
- Helmholtz Center Munich - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Munich, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,DZHK (German Centre for Cardiovascular Research) partner site Rhine/Main, Frankfurt, Germany
| | - Daniela Panáková
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. .,DZHK (German Centre for Cardiovascular Research) partner site, Berlin, Germany.
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany. .,DZHK (German Centre for Cardiovascular Research) partner site, Berlin, Germany.
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7
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Singh SP, Chawla P, Hnatiuk A, Kamel M, Silva LD, Spanjaard B, Eski SE, Janjuha S, Olivares-Chauvet P, Kayisoglu O, Rost F, Bläsche J, Kränkel A, Petzold A, Kurth T, Reinhardt S, Junker JP, Ninov N. A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ-cells to diabetes recovery in zebrafish. Development 2022; 149:274140. [PMID: 35088828 DOI: 10.1242/dev.199853] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Regeneration-competent species possess the ability to reverse the progression of severe diseases by restoring the function of the damaged tissue. However, the cellular dynamics underlying this capability remain unexplored. Here, we have used single-cell transcriptomics to map de novo β-cell regeneration during induction and recovery from diabetes in zebrafish. We show that the zebrafish has evolved two distinct types of somatostatin-producing δ-cells, which we term δ1- and δ2-cells. Moreover, we characterize a small population of glucose-responsive islet cells, which share the hormones and fate-determinants of both β- and δ1-cells. The transcriptomic analysis of β-cell regeneration reveals that β/δ hybrid cells provide a prominent source of insulin expression during diabetes recovery. Using in vivo calcium imaging and cell tracking, we further show that the hybrid cells form de novo and acquire glucose-responsiveness in the course of regeneration. The overexpression of dkk3, a gene enriched in hybrid cells, increases their formation in the absence of β-cell injury. Finally, interspecies comparison shows that plastic δ1-cells are partially related to PP cells in the human pancreas. Our work provides an atlas of β-cell regeneration and indicates that the rapid formation of glucose-responsive hybrid cells contributes to the resolution of diabetes in zebrafish.
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Affiliation(s)
- Sumeet Pal Singh
- IRIBHM, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Prateek Chawla
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Alisa Hnatiuk
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Margrit Kamel
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Luis Delgadillo Silva
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Sema Elif Eski
- IRIBHM, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Sharan Janjuha
- Institute of Pharmacology and Toxicology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Pedro Olivares-Chauvet
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Oezge Kayisoglu
- The Julius Maximilian University of Wurzburg, 97070 Wurzburg, Germany
| | - Fabian Rost
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany.,DRESDEN-concept Genome Center, DFG NGS Competence Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, 01307 Dresden, Germany
| | - Juliane Bläsche
- DRESDEN-concept Genome Center, DFG NGS Competence Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, 01307 Dresden, Germany
| | - Annekathrin Kränkel
- DRESDEN-concept Genome Center, DFG NGS Competence Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Petzold
- DRESDEN-concept Genome Center, DFG NGS Competence Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, 01307 Dresden, Germany
| | - Thomas Kurth
- TUD, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, EM-Facility, Technische Universitaät Dresden, 01307 Dresden, Germany
| | - Susanne Reinhardt
- DRESDEN-concept Genome Center, DFG NGS Competence Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, 01307 Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 10115 Berlin, Germany
| | - Nikolay Ninov
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany.,Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of Technische Universität Dresden, 01307 Dresden, Germany
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8
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McGarvey AC, Kopp W, Vučićević D, Mattonet K, Kempfer R, Hirsekorn A, Bilić I, Gil M, Trinks A, Merks AM, Panáková D, Pombo A, Akalin A, Junker JP, Stainier DY, Garfield D, Ohler U, Lacadie SA. Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos. Cell Genom 2022; 2:100083. [PMID: 36777038 PMCID: PMC9903790 DOI: 10.1016/j.xgen.2021.100083] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/24/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022]
Abstract
DNA accessibility of cis-regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. While many genes regulating embryonic development have been identified, the underlying CRE dynamics controlling their expression remain largely uncharacterized. To address this, we produced a multimodal resource and genomic regulatory map for the zebrafish community, which integrates single-cell combinatorial indexing assay for transposase-accessible chromatin with high-throughput sequencing (sci-ATAC-seq) with bulk histone PTMs and Hi-C data to achieve a genome-wide classification of the regulatory architecture determining transcriptional activity in the 24-h post-fertilization (hpf) embryo. We characterized the genome-wide chromatin architecture at bulk and single-cell resolution, applying sci-ATAC-seq on whole 24-hpf stage zebrafish embryos, generating accessibility profiles for ∼23,000 single nuclei. We developed a genome segmentation method, ScregSeg (single-cell regulatory landscape segmentation), for defining regulatory programs, and candidate CREs, specific to one or more cell types. We integrated the ScregSeg output with bulk measurements for histone post-translational modifications and 3D genome organization and identified new regulatory principles between chromatin modalities prevalent during zebrafish development. Sci-ATAC-seq profiling of npas4l/cloche mutant embryos identified novel cellular roles for this hematovascular transcriptional master regulator and suggests an intricate mechanism regulating its expression. Our work defines regulatory architecture and principles in the zebrafish embryo and establishes a resource of cell-type-specific genome-wide regulatory annotations and candidate CREs, providing a valuable open resource for genomics, developmental, molecular, and computational biology.
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Affiliation(s)
- Alison C. McGarvey
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany,Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Wolfgang Kopp
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany,Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Berlin 10115, Germany
| | - Dubravka Vučićević
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Kenny Mattonet
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Rieke Kempfer
- Epigenetic Regulation and Chromatin Architecture, Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Berlin, Germany,Institute for Biology, Humboldt Universität Berlin, Berlin 10115, Germany
| | - Antje Hirsekorn
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Ilija Bilić
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Marine Gil
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Alexandra Trinks
- IRI Life Sciences, Humboldt Universität Berlin, Berlin 10115, Germany
| | - Anne Margarete Merks
- Electrochemical Signaling in Development and Disease, Max Delbrück Centre for Molecular Medicine, Berlin, Germany,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin 13125, Germany
| | - Daniela Panáková
- Electrochemical Signaling in Development and Disease, Max Delbrück Centre for Molecular Medicine, Berlin, Germany,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin 13125, Germany
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture, Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Berlin, Germany,Institute for Biology, Humboldt Universität Berlin, Berlin 10115, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Centre for Molecular Medicine, Berlin 10115, Germany
| | - Jan Philipp Junker
- Quantitative Developmental Biology, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Didier Y.R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - David Garfield
- IRI Life Sciences, Humboldt Universität Berlin, Berlin 10115, Germany
| | - Uwe Ohler
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany,Institute for Biology, Humboldt Universität Berlin, Berlin 10115, Germany,Corresponding author
| | - Scott Allen Lacadie
- Computational Regulatory Genomics, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany,Berlin Institute of Health, Berlin 10178, Germany,Corresponding author
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9
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Boogerd CJ, Lacraz GPA, Vértesy Á, van Kampen SJ, Perini I, de Ruiter H, Versteeg D, Brodehl A, van der Kraak P, Giacca M, de Jonge N, Junker JP, van Oudenaarden A, Vink A, van Rooij E. OUP accepted manuscript. Cardiovasc Res 2022; 119:477-491. [PMID: 35576477 PMCID: PMC10064846 DOI: 10.1093/cvr/cvac072] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
AIMS Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disorder that is characterized by progressive loss of myocardium that is replaced by fibro-fatty cells, arrhythmias, and sudden cardiac death. While myocardial degeneration and fibro-fatty replacement occur in specific locations, the underlying molecular changes remain poorly characterized. Here, we aim to delineate local changes in gene expression to identify new genes and pathways that are relevant for specific remodelling processes occurring during ACM. METHODS AND RESULTS Using Tomo-Seq, genome-wide transcriptional profiling with high spatial resolution, we created transmural epicardial-to-endocardial gene expression atlases of explanted ACM hearts to gain molecular insights into disease-driving processes. This enabled us to link gene expression profiles to the different regional remodelling responses and allowed us to identify genes that are potentially relevant for disease progression. In doing so, we identified distinct gene expression profiles marking regions of cardiomyocyte degeneration and fibro-fatty remodelling and revealed Zinc finger and BTB domain-containing protein 11 (ZBTB11) to be specifically enriched at sites of active fibro-fatty replacement of myocardium. Immunohistochemistry indicated ZBTB11 to be induced in cardiomyocytes flanking fibro-fatty areas, which could be confirmed in multiple cardiomyopathy patients. Forced overexpression of ZBTB11 induced autophagy and cell death-related gene programmes in human cardiomyocytes, leading to increased apoptosis. CONCLUSION Our study shows the power of Tomo-Seq to unveil new molecular mechanisms in human cardiomyopathy and uncovers ZBTB11 as a novel driver of cardiomyocyte loss.
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Affiliation(s)
| | | | | | - Sebastiaan J van Kampen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ilaria Perini
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hesther de Ruiter
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Danielle Versteeg
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andreas Brodehl
- Heart and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Bad Oeynhausen, Germany
| | - Petra van der Kraak
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mauro Giacca
- School of Cardiovascular Medicine and Sciences, King’s College London British Heart Foundation Centre, London, UK
| | - Nicolaas de Jonge
- Department of Cardiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands
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10
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Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M. Single cell biology-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:74-97. [PMID: 34605044 DOI: 10.1111/nyas.14692] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.
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Affiliation(s)
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California
| | - Ana I Domingos
- Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, United Kingdom.,The Howard Hughes Medical Institute, New York, New York
| | - Naomi Habib
- Cell Circuits Program, Broad Institute, Cambridge, Massachusetts.,Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Homaira Hamidzada
- Toronto General Hospital Research Institute, University Health Network; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, New York
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Jessica Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Aaron Streets
- Department of Bioengineering and Center for Computational Biology, University of California, Berkeley, Berkeley, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington; and Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Clarice Kit Yee Hong
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, and Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Uri Alon
- Faculty of Sciences, Department of Human Biology, University of Haifa, Haifa, Israel
| | - Alex K Shalek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Regan Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Pfau
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts
| | - Arjun Raj
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, California.,Department of Bioengineering, Stanford University, Stanford, California.,Department of Applied Physics, Stanford University, Stanford, California
| | - Nancy R Zhang
- Graduate Group in Genomics and Computational Biology and Department of Statistics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine; and Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | | | | | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Hernan G Garcia
- Department of Physics; Biophysics Graduate Group; Department of Molecular and Cell Biology; and Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California
| | | | - Federico Gaiti
- New York Genome Center and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, and Center for Systems Biology Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Allon M Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Samantha A Morris
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri.,Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - John I Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Merrit Romeike
- Max Perutz Laboratories Vienna, University of Vienna, Vienna, Austria
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11
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Holler K, Neuschulz A, Drewe-Boß P, Mintcheva J, Spanjaard B, Arsiè R, Ohler U, Landthaler M, Junker JP. Spatio-temporal mRNA tracking in the early zebrafish embryo. Nat Commun 2021; 12:3358. [PMID: 34099733 PMCID: PMC8184788 DOI: 10.1038/s41467-021-23834-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 11/05/2020] [Accepted: 05/18/2021] [Indexed: 01/17/2023] Open
Abstract
Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.
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Affiliation(s)
- Karoline Holler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Anika Neuschulz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Philipp Drewe-Boß
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Janita Mintcheva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Roberto Arsiè
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Humboldt University, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- IRI Life Science, Institute of Biology, Humboldt University, Berlin, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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12
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Buchumenski I, Holler K, Appelbaum L, Eisenberg E, Junker JP, Levanon EY. Systematic identification of A-to-I RNA editing in zebrafish development and adult organs. Nucleic Acids Res 2021; 49:4325-4337. [PMID: 33872356 PMCID: PMC8096273 DOI: 10.1093/nar/gkab247] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/05/2021] [Accepted: 04/15/2021] [Indexed: 11/18/2022] Open
Abstract
A-to-I RNA editing is a common post transcriptional mechanism, mediated by the Adenosine deaminase that acts on RNA (ADAR) enzymes, that increases transcript and protein diversity. The study of RNA editing is limited by the absence of editing maps for most model organisms, hindering the understanding of its impact on various physiological conditions. Here, we mapped the vertebrate developmental landscape of A-to-I RNA editing, and generated the first comprehensive atlas of editing sites in zebrafish. Tens of thousands unique editing events and 149 coding sites were identified with high-accuracy. Some of these edited sites are conserved between zebrafish and humans. Sequence analysis of RNA over seven developmental stages revealed high levels of editing activity in early stages of embryogenesis, when embryos rely on maternal mRNAs and proteins. In contrast to the other organisms studied so far, the highest levels of editing were detected in the zebrafish ovary and testes. This resource can serve as the basis for understanding of the role of editing during zebrafish development and maturity.
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Affiliation(s)
- Ilana Buchumenski
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Karoline Holler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Lior Appelbaum
- The Faculty of Life Sciences and the Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
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13
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Moreno-Ayala R, Junker JP. Single-cell genomics to study developmental cell fate decisions in zebrafish. Brief Funct Genomics 2021:elab018. [PMID: 33782691 DOI: 10.1093/bfgp/elab018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022] Open
Abstract
New developments in single-cell genomics have transformed developmental biology in recent years by enabling systematic analysis of embryonic cell types and differentiation trajectories. Ongoing efforts in experimental and computational method development aim to reveal gene-regulatory mechanisms and to provide additional spatio-temporal information about developmental cell fate decisions. Here, we discuss recent technological developments as well as biological applications of single-cell genomics, with a particular focus on analysis of developmental cell fate decisions. Although the approaches described here are generally applicable to a broad range of model systems, we focus our discussion on applications in zebrafish, which has proven to be a particularly powerful model organism for establishing novel methods in single-cell genomics.
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14
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Schwabe D, Formichetti S, Philipp Junker J, Falcke M, Rajewsky N. The Transcriptome Dynamics of Single Cells During the Cell Cycle. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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Moreno-Ayala R, Olivares-Chauvet P, Schäfer R, Junker JP. Variability of an Early Developmental Cell Population Underlies Stochastic Laterality Defects. Cell Rep 2021; 34:108606. [PMID: 33440143 PMCID: PMC7809618 DOI: 10.1016/j.celrep.2020.108606] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/28/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Embryonic development seemingly proceeds with almost perfect precision. However, it is largely unknown how much underlying microscopic variability is compatible with normal development. Here, we quantify embryo-to-embryo variability in vertebrate development by studying cell number variation in the zebrafish endoderm. We notice that the size of a sub-population of the endoderm, the dorsal forerunner cells (DFCs, which later form the left-right organizer), exhibits significantly more embryo-to-embryo variation than the rest of the endoderm. We find that, with incubation of the embryos at elevated temperature, the frequency of left-right laterality defects is increased drastically in embryos with a low number of DFCs. Furthermore, we observe that these fluctuations have a large stochastic component among fish of the same genetic background. Hence, a stochastic variation in early development leads to a remarkably strong macroscopic phenotype. These fluctuations appear to be associated with maternal effects in the specification of the DFCs. High embryo-to-embryo variability of dorsal forerunner cell numbers Fluctuations of dorsal forerunner cells have a large stochastic component Embryos with fewer dorsal forerunner cells frequently develop laterality defects Variability of dorsal forerunner cell numbers is associated to maternal effects
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Affiliation(s)
- Roberto Moreno-Ayala
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany
| | - Pedro Olivares-Chauvet
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany
| | - Ronny Schäfer
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany
| | - Jan Philipp Junker
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Hannoversche Strasse 28, 10115 Berlin, Germany.
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16
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Schwabe D, Formichetti S, Junker JP, Falcke M, Rajewsky N. The transcriptome dynamics of single cells during the cell cycle. Mol Syst Biol 2020; 16:e9946. [PMID: 33205894 PMCID: PMC7672610 DOI: 10.15252/msb.20209946] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 08/24/2020] [Revised: 09/12/2020] [Accepted: 09/22/2020] [Indexed: 11/28/2022] Open
Abstract
The cell cycle is among the most basic phenomena in biology. Despite advances in single-cell analysis, dynamics and topology of the cell cycle in high-dimensional gene expression space remain largely unknown. We developed a linear analysis of transcriptome data which reveals that cells move along a planar circular trajectory in transcriptome space during the cycle. Non-cycling gene expression adds a third dimension causing helical motion on a cylinder. We find in immortalized cell lines that cell cycle transcriptome dynamics occur largely independently from other cellular processes. We offer a simple method ("Revelio") to order unsynchronized cells in time. Precise removal of cell cycle effects from the data becomes a straightforward operation. The shape of the trajectory implies that each gene is upregulated only once during the cycle, and only two dynamic components represented by groups of genes drive transcriptome dynamics. It indicates that the cell cycle has evolved to minimize changes of transcriptional activity and the related regulatory effort. This design principle of the cell cycle may be of relevance to many other cellular differentiation processes.
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Affiliation(s)
- Daniel Schwabe
- Mathematical Cell PhysiologyMax Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Sara Formichetti
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Epigenetics and Neurobiology Unit, European Molecular Biology LaboratoryMonterotondoItaly
- Collaboration for Joint PhD Degree between European Molecular Biology Laboratory and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Jan Philipp Junker
- Quantitative Developmental Biology, Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
| | - Martin Falcke
- Mathematical Cell PhysiologyMax Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Department of PhysicsHumboldt University BerlinBerlinGermany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
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17
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Olivares-Chauvet P, Junker JP. Inclusion of temporal information in single cell transcriptomics. Int J Biochem Cell Biol 2020; 122:105745. [PMID: 32283227 DOI: 10.1016/j.biocel.2020.105745] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/25/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
Abstract
Single cell transcriptomics has emerged as a powerful method for dissecting cell type diversity and for understanding mechanisms of cell fate decisions. However, inclusion of temporal information remains challenging, since each cell can be measured only once by sequencing analysis. Here, we discuss recent progress and current efforts towards inclusion of temporal information in single cell transcriptomics. Even from snapshot data, temporal dynamics can be computationally inferred via pseudo-temporal ordering of single cell transcriptomes. Temporal information can also come from analysis of intronic reads or from RNA metabolic labeling, which can provide additional evidence for pseudo-time trajectories and enable more fine-grained analysis of gene regulatory interactions. These approaches measure dynamics on short timescales of hours. Emerging methods for high-throughput lineage tracing now enable information storage over long timescales by using CRISPR/Cas9 to record information in the genome, which can later be read out by sequencing.
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Affiliation(s)
- Pedro Olivares-Chauvet
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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18
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Abstract
Embryonic development is heavily dependent on temporally and spatially restricted gene expression. Spatially resolved measurements of gene expression are therefore crucial for identifying novel regulators and the understanding of their function. However, in situ methods do not resolve global gene expression, and sequencing-based methods usually do not provide spatial information. Here, we describe tomo-seq, a method that combines classical histological sectioning of embryos or tissues with a highly sensitive RNA-sequencing technique. Application of tomo-seq to zebrafish embryos allows reconstructing the spatial gene expression of thousands of genes.
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Affiliation(s)
- Karoline Holler
- Berlin Institute for Medical Systems Biology, MDC Berlin, Berlin, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, MDC Berlin, Berlin, Germany.
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19
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Ebbing A, Vértesy Á, Betist MC, Spanjaard B, Junker JP, Berezikov E, van Oudenaarden A, Korswagen HC. Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns. Dev Cell 2018; 47:801-813.e6. [DOI: 10.1016/j.devcel.2018.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/31/2018] [Accepted: 10/12/2018] [Indexed: 12/15/2022]
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20
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Spanjaard B, Hu B, Mitic N, Olivares-Chauvet P, Janjuha S, Ninov N, Junker JP. Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol 2018; 36:469-473. [PMID: 29644996 PMCID: PMC5942543 DOI: 10.1038/nbt.4124] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/15/2018] [Indexed: 12/12/2022]
Abstract
A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ1. However, organizing the resulting taxonomy of cell types into lineage trees to understand developmental origin of cells remains challenging. Here we present LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)—a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
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Affiliation(s)
- Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bo Hu
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nina Mitic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sharan Janjuha
- DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Nikolay Ninov
- DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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21
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Spanjaard B, Junker JP. Methods for lineage tracing on the organism-wide level. Curr Opin Cell Biol 2017; 49:16-21. [PMID: 29175321 DOI: 10.1016/j.ceb.2017.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 01/22/2023]
Abstract
Determining the lineage origin of cell types is a major goal in developmental biology. Furthermore, lineage tracing is a powerful approach for understanding the origin of developmental defects as well as the origin of diseases such as cancer. There is now a variety of complementary approaches for identifying lineage relationships, ranging from direct observation of cell divisions by light microscopy to genetic labeling of cells using inducible recombinases and fluorescent reporters. A recent development, and the main topic of this review article, is the use of high-throughput sequencing data for lineage analysis. This emerging approach holds the promise of increased multiplexing capacity, allowing lineage analysis of large cell numbers up to the organism-wide level combined with simultaneous transcription profiling by single cell RNA sequencing.
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Affiliation(s)
- Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin-Buch, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin-Buch, Germany.
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22
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Lacraz GP, Junker JP, Gladka MM, Molenaar B, Scholman KT, Vigil-Garcia M, Versteeg D, de Ruiter H, Vermunt MW, Creyghton MP, Huibers MM, de Jonge N, van Oudenaarden A, van Rooij E. Tomo-Seq Identifies SOX9 as a Key Regulator of Cardiac Fibrosis During Ischemic Injury. Circulation 2017; 136:1396-1409. [DOI: 10.1161/circulationaha.117.027832] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022]
Abstract
Background:
Cardiac ischemic injury induces a pathological remodeling response, which can ultimately lead to heart failure. Detailed mechanistic insights into molecular signaling pathways relevant for different aspects of cardiac remodeling will support the identification of novel therapeutic targets.
Methods:
Although genome-wide transcriptome analysis on diseased tissues has greatly advanced our understanding of the regulatory networks that drive pathological changes in the heart, this approach has been disadvantaged by the fact that the signals are derived from tissue homogenates. Here we used tomo-seq to obtain a genome-wide gene expression signature with high spatial resolution spanning from the infarcted area to the remote to identify new regulators of cardiac remodeling. Cardiac tissue samples from patients suffering from ischemic heart disease were used to validate our findings.
Results:
Tracing transcriptional differences with a high spatial resolution across the infarcted heart enabled us to identify gene clusters that share a comparable expression profile. The spatial distribution patterns indicated a separation of expressional changes for genes involved in specific aspects of cardiac remodeling, such as fibrosis, cardiomyocyte hypertrophy, and calcium handling (
Col1a2
,
Nppa
, and
Serca2
). Subsequent correlation analysis allowed for the identification of novel factors that share a comparable transcriptional regulation pattern across the infarcted tissue. The strong correlation between the expression levels of these known marker genes and the expression of the coregulated genes could be confirmed in human ischemic cardiac tissue samples. Follow-up analysis identified SOX9 as common transcriptional regulator of a large portion of the fibrosis-related genes that become activated under conditions of ischemic injury. Lineage-tracing experiments indicated that the majority of COL1-positive fibroblasts stem from a pool of SOX9-expressing cells, and in vivo loss of
Sox9
blunted the cardiac fibrotic response on ischemic injury. The colocalization between SOX9 and COL1 could also be confirmed in patients suffering from ischemic heart disease.
Conclusions:
Based on the exact local expression cues, tomo-seq can serve to reveal novel genes and key transcription factors involved in specific aspects of cardiac remodeling. Using tomo-seq, we were able to unveil the unknown relevance of SOX9 as a key regulator of cardiac fibrosis, pointing to SOX9 as a potential therapeutic target for cardiac fibrosis.
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Affiliation(s)
- Grégory P.A. Lacraz
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Jan Philipp Junker
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Monika M. Gladka
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Bas Molenaar
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Koen T. Scholman
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Marta Vigil-Garcia
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Danielle Versteeg
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Hesther de Ruiter
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Marit W. Vermunt
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Menno P. Creyghton
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Manon M.H. Huibers
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Nicolaas de Jonge
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Alexander van Oudenaarden
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
| | - Eva van Rooij
- From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.)
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23
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Adolphe C, Junker JP, Lyubimova A, van Oudenaarden A, Wainwright B. Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient. J Invest Dermatol 2016; 137:179-186. [PMID: 27498049 DOI: 10.1016/j.jid.2016.06.632] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 06/01/2016] [Accepted: 06/14/2016] [Indexed: 01/24/2023]
Abstract
By using the sensitivity of single-molecule fluorescent in situ hybridization, we have precisely quantified the levels and defined the temporal and spatial distribution of Hedgehog signaling activity during embryonic skin development and discovered that there is a Hedgehog signaling gradient along the proximal-distal axis of developing hair follicles. To explore the contribution of Hedgehog receptors Ptch1 and Ptch2 in establishing the epidermal signaling gradient, we quantitated the level of pathway activity generated in Ptch1- and Ptch1;Ptch2-deficient skin and defined the contribution of each receptor to regulation of the levels of Hedgehog signaling identified in wild-type skin. Moreover, we show that both the cellular phenotype and level of pathway activity featured in Ptch1;Ptch2-deficient cells faithfully recapitulates the Peak level of endogenous Hedgehog signaling detected at the base of developing follicles, where the concentration of endogenous Shh is predicted to be highest. Taken together, these data show that both Ptch1 and Ptch2 play a crucial role in sensing the concentration of Hedgehog ligand and regulating the appropriate dose-dependent response.
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Affiliation(s)
- Christelle Adolphe
- Division of Molecular Genetics and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jan Philipp Junker
- Hubrecht Institute, KNAW and University Medical Centre Utrecht, Utrecht, The Netherlands; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Anna Lyubimova
- Hubrecht Institute, KNAW and University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Brandon Wainwright
- Division of Molecular Genetics and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
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24
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Abstract
To improve our understanding of pattern formation during development and disease we heavily rely on the identification of novel regulators and pathways. While RNA sequencing yields genome-wide expression data that suit this purpose, it lacks spatial resolution. Such spatial resolution can be obtained by microscopy-based methods like in situ hybridization, but these fail to provide information on more than a few genes at a time. Here, we describe tomo-seq, a technique that combines the advantages of the above-mentioned approaches and provides genome-wide expression data with spatial information. The tomo-seq technique is based on cryosectioning of an embryo or tissue of interest and performing RNA-seq on individual sections. Using this method, we have generated genome-wide transcriptomics with high spatial resolution of the whole zebrafish embryo at various stages of development (Junker et al., 2014) and of adult zebrafish hearts after injury (Wu et al., 2016).
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Affiliation(s)
- F Kruse
- Hubrecht Institute and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J P Junker
- Hubrecht Institute and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A van Oudenaarden
- Hubrecht Institute and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J Bakkers
- Hubrecht Institute and University Medical Centre Utrecht, Utrecht, The Netherlands
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25
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Wu CC, Kruse F, Vasudevarao MD, Junker JP, Zebrowski DC, Fischer K, Noël ES, Grün D, Berezikov E, Engel FB, van Oudenaarden A, Weidinger G, Bakkers J. Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration. Dev Cell 2015; 36:36-49. [PMID: 26748692 DOI: 10.1016/j.devcel.2015.12.010] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 10/14/2015] [Accepted: 11/20/2015] [Indexed: 12/21/2022]
Abstract
In contrast to mammals, zebrafish regenerate heart injuries via proliferation of cardiomyocytes located near the wound border. To identify regulators of cardiomyocyte proliferation, we used spatially resolved RNA sequencing (tomo-seq) and generated a high-resolution genome-wide atlas of gene expression in the regenerating zebrafish heart. Interestingly, we identified two wound border zones with distinct expression profiles, including the re-expression of embryonic cardiac genes and targets of bone morphogenetic protein (BMP) signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast, we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation, ultimately compromising myocardial regeneration, while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non-regenerative hearts.
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Affiliation(s)
- Chi-Chung Wu
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Fabian Kruse
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | | | - Jan Philipp Junker
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - David C Zebrowski
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Krankenhausstr 8-10, 91054 Erlangen, Germany
| | - Kristin Fischer
- Institute of Clinical Genetics, Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany
| | - Emily S Noël
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - Dominic Grün
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands; Skolkovo Institute of Science and Technology (Skoltech), Novaya Street 100, Skolkovo, Moscow Region 143025, Russia
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Krankenhausstr 8-10, 91054 Erlangen, Germany
| | - Alexander van Oudenaarden
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands
| | - Gilbert Weidinger
- Institute for Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Jeroen Bakkers
- Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands; Medical Physiology, University Medical Centre Utrecht, Yalelaan 50, 3584 CM Utrecht, the Netherlands.
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26
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Yvernogeau L, Junker JP, van Oudenaarden A, Robin C. Genome-wide RNA tomography analysis of the microenvironment promoting hematopoietic stem cell emergence in the embryo aorta. Exp Hematol 2015. [DOI: 10.1016/j.exphem.2015.06.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Abstract
Two publications in the current issue of Cell introduce novel methods for high-throughput single-cell transcriptomics by using droplet microfluidics and sophisticated barcoding schemes for transcriptional profiling of thousands of individual cells.
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Affiliation(s)
- Jan Philipp Junker
- Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13092 Berlin-Buch, Germany.
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28
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Lacraz G, Junker JP, Scholman K, Versteeg D, van Oudenaarden A, van Rooij E. Abstract 373: Spatial Expression Analysis of the Ischemic Heart Identifies Novel Factors Involved in Cardiac Remodeling and Disease. Circ Res 2015. [DOI: 10.1161/res.117.suppl_1.373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cardiac ischemic injury is associated with expressional changes in a broad range of coding and non-coding genes. While genome-wide expression techniques like RNA sequencing, give valuable information about the transcriptional activity of genes, spatial clues are lost.
Here, we use a novel method (TomoSEQ) based on traditional histological techniques with low-input RNA sequencing to generate a spatial gene expression atlas for the infarcted heart. Transcriptome profiling of 50 consecutive sections from hearts exposed to ischemia reperfusion or sham surgery, allowed us to trace differential gene regulation throughout the infarct, borderzone and remote area. Fourteen days post-injury, we clearly observed differential expression curves specific for genes known to be relevant for cardiac function and disease, like
Nppa
(remodeling/hypertrophy),
Col3a1
(fibrosis) and
Atp2a2
(calcium handling), with the first two being more abundantly expressed in the infarct, and the latter more dominant towards the remote. Interestingly, the exact spatial information on these 3 reference genes enabled us to identify a set of genes that show an identical regulation, potentially linking these transcripts to the aforementioned biological function of the reference genes. The validity of using this method to identify genes that are expressionally linked was underscored by the observation that the correlation between the expression level of the
Nppa
,
Col3a1
,
Atp2a2
and the newly identified genes could be confirmed in human cardiac tissue samples from patients suffering from ischemic heart disease. We next used an
in silico
approach to identify common transcription factors among the co-regulated genes. TomoSEQ analysis revealed a strong spatial correlation between these identified transcription factors and their target genes. This provides further support for our methodology, but also provides an opportunity to identify novel transcription factors relevant for cardiac function and disease.
Our study shows the power of spatial transcriptome profiling throughout the infarcted heart by giving local clues on changes in gene expression and allowing for the identification of novel genes and key transcription factors that could be relevant for cardiac repair upon injury.
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29
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Welling M, Chen HH, Muñoz J, Musheev MU, Kester L, Junker JP, Mischerikow N, Arbab M, Kuijk E, Silberstein L, Kharchenko PV, Geens M, Niehrs C, van de Velde H, van Oudenaarden A, Heck AJR, Geijsen N. DAZL regulates Tet1 translation in murine embryonic stem cells. EMBO Rep 2015; 16:791-802. [PMID: 26077710 DOI: 10.15252/embr.201540538] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 05/08/2015] [Indexed: 11/09/2022] Open
Abstract
Embryonic stem cell (ESC) cultures display a heterogeneous gene expression profile, ranging from a pristine naïve pluripotent state to a primed epiblast state. Addition of inhibitors of GSK3β and MEK (so-called 2i conditions) pushes ESC cultures toward a more homogeneous naïve pluripotent state, but the molecular underpinnings of this naïve transition are not completely understood. Here, we demonstrate that DAZL, an RNA-binding protein known to play a key role in germ-cell development, marks a subpopulation of ESCs that is actively transitioning toward naïve pluripotency. Moreover, DAZL plays an essential role in the active reprogramming of cytosine methylation. We demonstrate that DAZL associates with mRNA of Tet1, a catalyst of 5-hydroxylation of methyl-cytosine, and enhances Tet1 mRNA translation. Overexpression of DAZL in heterogeneous ESC cultures results in elevated TET1 protein levels as well as increased global hydroxymethylation. Conversely, null mutation of Dazl severely stunts 2i-mediated TET1 induction and hydroxymethylation. Our results provide insight into the regulation of the acquisition of naïve pluripotency and demonstrate that DAZL enhances TET1-mediated cytosine hydroxymethylation in ESCs that are actively reprogramming to a pluripotent ground state.
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Affiliation(s)
- Maaike Welling
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hsu-Hsin Chen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Javier Muñoz
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Centre, Utrecht, The Netherlands
| | | | - Lennart Kester
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan Philipp Junker
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nikolai Mischerikow
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Mandana Arbab
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ewart Kuijk
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lev Silberstein
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Mieke Geens
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Christof Niehrs
- Institute of Molecular Biology, Mainz, Germany Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hilde van de Velde
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Niels Geijsen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands Department of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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30
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Hu YC, Nicholls PK, Soh YQS, Daniele JR, Junker JP, van Oudenaarden A, Page DC. Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling. PLoS Genet 2015; 11:e1005019. [PMID: 25739037 PMCID: PMC4349450 DOI: 10.1371/journal.pgen.1005019] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/22/2015] [Indexed: 01/07/2023] Open
Abstract
In mouse embryos at mid-gestation, primordial germ cells (PGCs) undergo licensing to become gametogenesis-competent cells (GCCs), gaining the capacity for meiotic initiation and sexual differentiation. GCCs then initiate either oogenesis or spermatogenesis in response to gonadal cues. Germ cell licensing has been considered to be a cell-autonomous and gonad-independent event, based on observations that some PGCs, having migrated not to the gonad but to the adrenal gland, nonetheless enter meiosis in a time frame parallel to ovarian germ cells -- and do so regardless of the sex of the embryo. Here we test the hypothesis that germ cell licensing is cell-autonomous by examining the fate of PGCs in Gata4 conditional mutant (Gata4 cKO) mouse embryos. Gata4, which is expressed only in somatic cells, is known to be required for genital ridge initiation. PGCs in Gata4 cKO mutants migrated to the area where the genital ridge, the precursor of the gonad, would ordinarily be formed. However, these germ cells did not undergo licensing and instead retained characteristics of PGCs. Our results indicate that licensing is not purely cell-autonomous but is induced by the somatic genital ridge. During embryonic development, stem cell-like primordial germ cells travel across the developing embryo to the genital ridge, which gives rise to the gonad. Around the time of their arrival, the primordial germ cells gain the capacity to undertake sexual specialization and meiosis—a process called germ cell licensing. Based on the observation that meiosis and sexual differentiation can occur when primordial germ cells stray into the area of the adrenal gland, the primordial germ cell has been thought to be responsible for its own licensing. We tested this notion by examining the licensing process in mutant mouse embryos that did not form a genital ridge. We discovered that in the absence of the genital ridge, primordial germ cells migrate across the developing embryo properly, but instead of undergoing licensing, these cells retain their primordial germ cell characteristics. We conclude that licensing of embryonic primordial germ cells for gametogenesis is dependent on signaling from the genital ridge.
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Affiliation(s)
- Yueh-Chiang Hu
- Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Peter K. Nicholls
- Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Y. Q. Shirleen Soh
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Joseph R. Daniele
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jan Philipp Junker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Hubrecht Institute—KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, Netherlands
| | - Alexander van Oudenaarden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Hubrecht Institute—KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, Netherlands
| | - David C. Page
- Whitehead Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
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Schuijers J, Junker JP, Mokry M, Hatzis P, Koo BK, Sasselli V, van der Flier LG, Cuppen E, van Oudenaarden A, Clevers H. Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts. Cell Stem Cell 2015; 16:158-70. [PMID: 25620640 DOI: 10.1016/j.stem.2014.12.006] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/18/2014] [Accepted: 12/17/2014] [Indexed: 01/14/2023]
Abstract
The Wnt signaling pathway controls stem cell identity in the intestinal epithelium and in many other adult organs. The transcription factor Ascl2 (a Wnt target gene) is a master regulator of intestinal stem cell identity. It is unclear how the continuous Wnt gradient along the crypt axis is translated into discrete expression of Ascl2 and discrete specification of stem cells at crypt bottoms. We show that (1) Ascl2 is regulated in a direct autoactivatory loop, leading to a distinct on/off expression pattern, and (2) Wnt/R-spondin can activate this regulatory loop. This mechanism interprets the Wnt levels in the intestinal crypt and translates the continuous Wnt signal into a discrete Ascl2 "on" or "off" decision. In turn, Ascl2, together with β-catenin/Tcf, activates the genes fundamental to the stem cell state. In this manner, Ascl2 forms a transcriptional switch that is both Wnt responsive and Wnt dependent to define stem cell identity.
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Affiliation(s)
- Jurian Schuijers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jan Philipp Junker
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, 3508 AB Utrecht, the Netherlands
| | - Pantelis Hatzis
- Biomedical Sciences Research Center "Alexander Fleming," 16672 Vari, Greece
| | - Bon-Kyoung Koo
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Valentina Sasselli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Laurens G van der Flier
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; SomantiX B.V., Utrecht, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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Junker JP, Peterson KA, Nishi Y, Mao J, McMahon AP, van Oudenaarden A. A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning. Dev Cell 2014; 31:448-60. [PMID: 25458012 DOI: 10.1016/j.devcel.2014.10.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/05/2014] [Accepted: 10/24/2014] [Indexed: 11/26/2022]
Abstract
Hedgehog signaling controls pattern formation in many vertebrate tissues. The downstream effectors of the pathway are the bifunctional Gli transcription factors, which, depending on hedgehog concentration, act as either transcriptional activators or repressors. Quantitatively understanding the interplay between Gli activator and repressor forms for patterning complex tissues is an open challenge. Here, we describe a reductionist mathematical model for how Gli activators and repressors are integrated in space and time to regulate transcriptional outputs of hedgehog signaling, using the pathway readouts Gli1 and Ptch1 as a model system. Spatially resolved measurements of absolute transcript numbers for these genes allow us to infer spatiotemporal variations of Gli activator and repressor levels. We validate our model by successfully predicting expression changes of Gli1 and Ptch1 in mutants at different developmental stages and in different tissues. Our results provide a starting point for understanding gene regulation by bifunctional transcription factors during mammalian development.
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Affiliation(s)
- Jan Philipp Junker
- Departments of Physics and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Hubrecht Institute, KNAW, and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Kevin A Peterson
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Yuichi Nishi
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Junhao Mao
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Alexander van Oudenaarden
- Departments of Physics and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Hubrecht Institute, KNAW, and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
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Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, McMahon AP. Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev 2013; 26:2802-16. [PMID: 23249739 DOI: 10.1101/gad.207142.112] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In the vertebrate neural tube, regional Sonic hedgehog (Shh) signaling invokes a time- and concentration-dependent induction of six different cell populations mediated through Gli transcriptional regulators. Elsewhere in the embryo, Shh/Gli responses invoke different tissue-appropriate regulatory programs. A genome-scale analysis of DNA binding by Gli1 and Sox2, a pan-neural determinant, identified a set of shared regulatory regions associated with key factors central to cell fate determination and neural tube patterning. Functional analysis in transgenic mice validates core enhancers for each of these factors and demonstrates the dual requirement for Gli1 and Sox2 inputs for neural enhancer activity. Furthermore, through an unbiased determination of Gli-binding site preferences and analysis of binding site variants in the developing mammalian CNS, we demonstrate that differential Gli-binding affinity underlies threshold-level activator responses to Shh input. In summary, our results highlight Sox2 input as a context-specific determinant of the neural-specific Shh response and differential Gli-binding site affinity as an important cis-regulatory property critical for interpreting Shh morphogen action in the mammalian neural tube.
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Affiliation(s)
- Kevin A Peterson
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Abstract
In this issue of Molecular Cell, Stewart-Ornstein et al. (2012) use systematic pair-wise correlation analysis of expression noise in a large number of yeast genes to identify clusters of functionally related genes and signaling pathways responsible for elevated noise.
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Affiliation(s)
- Jan Philipp Junker
- Departments of Physics and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Abstract
Single-molecule force spectroscopy allows superb mechanical control of protein conformation. We used a custom-built low-drift atomic force microscope to observe mechanically induced conformational equilibrium fluctuations of single molecules of the eukaryotic calcium-dependent signal transducer calmodulin (CaM). From this data, the ligand dependence of the full energy landscape can be reconstructed. We find that calcium ions affect the folding kinetics of the individual CaM domains, whereas target peptides stabilize the already folded structure. Single-molecule data of full length CaM reveal that a wasp venom peptide binds noncooperatively to CaM with 2:1 stoichiometry, whereas a target enzyme peptide binds cooperatively with 1:1 stoichiometry. If mechanical load is applied directly to the target peptide, real-time binding/unbinding transitions can be observed.
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Affiliation(s)
- Jan Philipp Junker
- Physik Department E22, Technische Universität München, James-Franck-Strasse, 85748 München, Germany
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36
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Dietz H, Bertz M, Schlierf M, Berkemeier F, Bornschlögl T, Junker JP, Rief M. Cysteine engineering of polyproteins for single-molecule force spectroscopy. Nat Protoc 2006; 1:80-4. [PMID: 17406215 DOI: 10.1038/nprot.2006.12] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Single-molecule methods such as force spectroscopy give experimental access to the mechanical properties of protein molecules. So far, owing to the limitations of recombinant construction of polyproteins, experimental access has been limited to mostly the N-to-C terminal direction of force application. This protocol gives a fast and simple alternative to current recombinant strategies for preparing polyproteins. We describe in detail the method to construct polyproteins with precisely controlled linkage topologies, based on the pairwise introduction of cysteines into protein structure and subsequent polymerization in solution. Stretching such constructed polyproteins in an atomic force microscope allows mechanical force application to a single protein structure via two precisely controlled amino acid positions in the functional three-dimensional protein structure. The capability for site-directed force application can provide valuable information about both protein structure and directional protein mechanics. This protocol should be applicable to almost any protein that can be point mutated. Given correct setup of all necessary reagents, this protocol can be accomplished in fewer than 10 d.
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Affiliation(s)
- Hendrik Dietz
- Physik Department, Technische Universität München, James-Franck-Strasse, D-85748 Garching bei München, Germany.
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37
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Abstract
We investigated the effect of substrate binding on the mechanical stability of mouse dihydrofolate reductase using single-molecule force spectroscopy by atomic force microscopy. We find that under mechanical forces dihydrofolate reductase unfolds via a metastable intermediate with lifetimes on the millisecond timescale. Based on the measured length increase of approximately 22 nm we suggest a structure for this intermediate with intact substrate binding sites. In the presence of the substrate analog methotrexate and the cofactor NADPH lifetimes of this intermediate are increased by up to a factor of two. Comparing mechanical and thermodynamic stabilization effects of substrate binding suggests mechanical stability is dominated by local interactions within the protein structure. These experiments demonstrate that protein mechanics can be used to probe the substrate binding status of an enzyme.
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Affiliation(s)
- J P Junker
- Physik-Department E22, Technische Universität München, D-85748 Garching, Germany
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