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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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Wyler E, Mösbauer K, Franke V, Diag A, Gottula LT, Arsiè R, Klironomos F, Koppstein D, Hönzke K, Ayoub S, Buccitelli C, Hoffmann K, Richter A, Legnini I, Ivanov A, Mari T, Del Giudice S, Papies J, Praktiknjo S, Meyer TF, Müller MA, Niemeyer D, Hocke A, Selbach M, Akalin A, Rajewsky N, Drosten C, Landthaler M. Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy. iScience 2021; 24:102151. [PMID: 33585804 PMCID: PMC7866843 DOI: 10.1016/j.isci.2021.102151] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/20/2020] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Detailed knowledge of the molecular biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is crucial for understanding of viral replication, host responses, and disease progression. Here, we report gene expression profiles of three SARS-CoV- and SARS-CoV-2-infected human cell lines. SARS-CoV-2 elicited an approximately two-fold higher stimulation of the innate immune response compared to SARS-CoV in the human epithelial cell line Calu-3, including induction of miRNA-155. Single-cell RNA sequencing of infected cells showed that genes induced by virus infections were broadly upregulated, whereas interferon beta/lambda genes, a pro-inflammatory cytokines such as IL-6, were expressed only in small subsets of infected cells. Temporal analysis suggested that transcriptional activities of interferon regulatory factors precede those of nuclear factor κB. Lastly, we identified heat shock protein 90 (HSP90) as a protein relevant for the infection. Inhibition of the HSP90 activity resulted in a reduction of viral replication and pro-inflammatory cytokine expression in primary human airway epithelial cells.
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Affiliation(s)
- Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Kirstin Mösbauer
- Institute of Virology, Charité-Universitätsmedizin Berlin and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Vedran Franke
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Asija Diag
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Lina Theresa Gottula
- Institute of Virology, Charité-Universitätsmedizin Berlin and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Roberto Arsiè
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Filippos Klironomos
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
- Department of Pediatrics, Charité – University Hospital Berlin, 13353 Berlin, Germany
| | - David Koppstein
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Katja Hönzke
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine, Berlin, Germany
| | - Salah Ayoub
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Christopher Buccitelli
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Karen Hoffmann
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine, Berlin, Germany
| | - Anja Richter
- Institute of Virology, Charité-Universitätsmedizin Berlin and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Ivano Legnini
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Andranik Ivanov
- Core Unit Bioinformatics, Berlin Institute of Health, Charité – University Hospital Berlin, 10117 Berlin, Germany
| | - Tommaso Mari
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Simone Del Giudice
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Jan Papies
- Institute of Virology, Charité-Universitätsmedizin Berlin and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Samantha Praktiknjo
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Thomas F. Meyer
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, UKSH, Christian Albrechts University of Kiel, 24105 Kiel, Germany
| | - Marcel Alexander Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité-Universitätsmedizin Berlin and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Andreas Hocke
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité University Medicine, Berlin, Germany
| | - Matthias Selbach
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany
- IRI Life Sciences, Institut für Biologie, Humboldt Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
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