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Pennitz P, Kirsten H, Friedrich VD, Wyler E, Goekeri C, Obermayer B, Heinz GA, Mashreghi MF, Büttner M, Trimpert J, Landthaler M, Suttorp N, Hocke AC, Hippenstiel S, Tönnies M, Scholz M, Kuebler WM, Witzenrath M, Hoenzke K, Nouailles G. A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics. Eur Respir Rev 2022; 31:31/165/220056. [PMID: 35896273 DOI: 10.1183/16000617.0056-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 11/05/2022] Open
Abstract
Single-cell ribonucleic acid sequencing is becoming widely employed to study biological processes at a novel resolution depth. The ability to analyse transcriptomes of multiple heterogeneous cell types in parallel is especially valuable for cell-focused lung research where a variety of resident and recruited cells are essential for maintaining organ functionality. We compared the single-cell transcriptomes from publicly available and unpublished datasets of the lungs in six different species: human (Homo sapiens), African green monkey (Chlorocebus sabaeus), pig (Sus domesticus), hamster (Mesocricetus auratus), rat (Rattus norvegicus) and mouse (Mus musculus) by employing RNA velocity and intercellular communication based on ligand-receptor co-expression, among other techniques. Specifically, we demonstrated a workflow for interspecies data integration, applied a single unified gene nomenclature, performed cell-specific clustering and identified marker genes for each species. Overall, integrative approaches combining newly sequenced as well as publicly available datasets could help identify species-specific transcriptomic signatures in both healthy and diseased lung tissue and select appropriate models for future respiratory research.
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Affiliation(s)
- Peter Pennitz
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,Both authors contributed equally to this work
| | - Holger Kirsten
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.,Both authors contributed equally to this work
| | - Vincent D Friedrich
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany.,Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig, Germany
| | - Emanuel Wyler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Cengiz Goekeri
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,Cyprus International University, Faculty of Medicine, Nicosia, Cyprus
| | - Benedikt Obermayer
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Bioinformatics, Berlin, Germany
| | - Gitta A Heinz
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), A Leibniz Institute, Therapeutic Gene Regulation, Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Maren Büttner
- University of Bonn, Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, Bonn, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Systems Medicine, Bonn, Germany
| | - Jakob Trimpert
- Freie Universität Berlin, Institute of Virology, Berlin, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Humboldt-Universität zu Berlin, Institute for Biology, IRI Life Sciences, Berlin, Germany
| | - Norbert Suttorp
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Andreas C Hocke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Stefan Hippenstiel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Mario Tönnies
- HELIOS Clinic Emil von Behring, Department of Pneumology and Department of Thoracic Surgery, Chest Hospital Heckeshorn, Berlin, Germany
| | - Markus Scholz
- University of Leipzig, Institute for Medical Informatics, Statistics, and Epidemiology, Leipzig, Germany
| | - Wolfgang M Kuebler
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Physiology, Berlin, Germany.,German Center for Lung Research (DZL), Berlin, Germany
| | - Martin Witzenrath
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany.,German Center for Lung Research (DZL), Berlin, Germany
| | - Katja Hoenzke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Geraldine Nouailles
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
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