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Article ; Online: Characterization of Commercially Available Human Primary Alveolar Epithelial Cells.

Herbst, Christopher J / Lopez-Rodriguez, Elena / Gluhovic, Vladimir / Schulz, Sabrina / Brandt, Raphael / Timm, Sara / Abledu, Jubilant / Falivene, Juliana / Pennitz, Peter / Kirsten, Holger / Nouailles, Geraldine / Witzenrath, Martin / Ochs, Matthias / Kuebler, Wolfgang M

American journal of respiratory cell and molecular biology

2024

Abstract: ... In ... ...

Abstract	In vitro
Language	English
Publishing date	2024-01-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1025960-0
ISSN	1535-4989 ; 1044-1549
ISSN (online)	1535-4989
ISSN	1044-1549
DOI	10.1165/rcmb.2023-0320MA
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Article ; Online: Protocol to dissociate healthy and infected murine- and hamster-derived lung tissue for single-cell transcriptome analysis.

Pennitz, Peter / Goekeri, Cengiz / Trimpert, Jakob / Wyler, Emanuel / Ebenig, Aileen / Weissfuss, Chantal / Mühlebach, Michael D / Witzenrath, Martin / Nouailles, Geraldine

STAR protocols

2022 Volume 4, Issue 1, Page(s) 101957

Abstract: In infectious disease research, single-cell RNA sequencing allows dissection of host-pathogen interactions. As a prerequisite, we provide a protocol to transform solid and complex organs such as lungs into representative diverse, viable single-cell ... ...

Abstract	In infectious disease research, single-cell RNA sequencing allows dissection of host-pathogen interactions. As a prerequisite, we provide a protocol to transform solid and complex organs such as lungs into representative diverse, viable single-cell suspensions. Our protocol describes performance of vascular perfusion, pneumonectomy, enzymatic digestion, and mechanical dissociation of lung tissue, as well as red blood cell lysis and counting of isolated cells. A challenge remains, however, to further increase the proportion of pulmonary endothelial cells without compromising on viability. For complete details on the use and execution of this protocol, please refer to Nouailles et al. (2021),
MeSH term(s)	Cricetinae ; Animals ; Mice ; Endothelial Cells ; Single-Cell Gene Expression Analysis ; Cell Death ; Dissection ; Lung
Language	English
Publishing date	2022-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101957
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: MicroRNA-223 Dampens Pulmonary Inflammation during Pneumococcal Pneumonia.

Goekeri, Cengiz / Pennitz, Peter / Groenewald, Wibke / Behrendt, Ulrike / Kirsten, Holger / Zobel, Christian M / Berger, Sarah / Heinz, Gitta A / Mashreghi, Mir-Farzin / Wienhold, Sandra-Maria / Dietert, Kristina / Dorhoi, Anca / Gruber, Achim D / Scholz, Markus / Rohde, Gernot / Suttorp, Norbert / Capnetz Study Group / Witzenrath, Martin / Nouailles, Geraldine

Cells

2023 Volume 12, Issue 6

Abstract: Community-acquired pneumonia remains a major contributor to global communicable disease-mediated mortality. Neutrophils play a leading role in trying to contain bacterial lung infection, but they also drive detrimental pulmonary inflammation, when ... ...

Abstract	Community-acquired pneumonia remains a major contributor to global communicable disease-mediated mortality. Neutrophils play a leading role in trying to contain bacterial lung infection, but they also drive detrimental pulmonary inflammation, when dysregulated. Here we aimed at understanding the role of microRNA-223 in orchestrating pulmonary inflammation during pneumococcal pneumonia. Serum microRNA-223 was measured in patients with pneumococcal pneumonia and in healthy subjects. Pulmonary inflammation in wild-type and microRNA-223-knockout mice was assessed in terms of disease course, histopathology, cellular recruitment and evaluation of inflammatory protein and gene signatures following pneumococcal infection. Low levels of serum microRNA-223 correlated with increased disease severity in pneumococcal pneumonia patients. Prolonged neutrophilic influx into the lungs and alveolar spaces was detected in pneumococci-infected microRNA-223-knockout mice, possibly accounting for aggravated histopathology and acute lung injury. Expression of microRNA-223 in wild-type mice was induced by pneumococcal infection in a time-dependent manner in whole lungs and lung neutrophils. Single-cell transcriptome analyses of murine lungs revealed a unique profile of antimicrobial and cellular maturation genes that are dysregulated in neutrophils lacking microRNA-223. Taken together, low levels of microRNA-223 in human pneumonia patient serum were associated with increased disease severity, whilst its absence provoked dysregulation of the neutrophil transcriptome in murine pneumococcal pneumonia.
MeSH term(s)	Animals ; Humans ; Mice ; Inflammation/genetics ; Inflammation/microbiology ; Inflammation/pathology ; Lung/pathology ; Mice, Knockout ; MicroRNAs/genetics ; Pneumonia, Pneumococcal/genetics ; Pneumonia, Pneumococcal/microbiology ; Pneumonia, Pneumococcal/pathology ; Streptococcus pneumoniae
Chemical Substances	MicroRNAs ; MIRN223 microRNA, human ; MIRN223 microRNA, mouse
Language	English
Publishing date	2023-03-21
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells12060959
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Article ; Online: Neural Network-Assisted Humanization of COVID-19 Hamster scRNAseq Data Reveals Matching Severity States in Human Disease

Friedrich, Vincent D / Pennitz, Peter / Wyler, Emanuel / Adler, Julia M / Postmus, Dylan / Alves, Luiz Gustavo Teixeira / Prigann, Julia / Pott, Fabian / Vladimirova, Daria / Hoefler, Thomas / Goekeri, Cengiz / Landthaler, Markus / Goffinet, Christine / Saliba, Antoine-Emmanuel / Scholz, Markus / Witzenrath, Martin / Trimpert, Jakob / Kirsten, Holger / Nouailles, Geraldine

bioRxiv

Abstract: Translating findings from animal models to human disease is essential for dissecting disease mechanisms, developing and testing precise therapeutic strategies. The coronavirus disease 2019 (COVID-19) pandemic has highlighted this need, particularly for ... ...

Abstract	Translating findings from animal models to human disease is essential for dissecting disease mechanisms, developing and testing precise therapeutic strategies. The coronavirus disease 2019 (COVID-19) pandemic has highlighted this need, particularly for models showing disease severity-dependent immune responses. Single-cell transcriptomics (scRNAseq) is well poised to reveal similarities and differences between species at the molecular and cellular level with unprecedented resolution. However, computational methods enabling detailed matching are still scarce. Here, we provide a structured scRNAseq-based approach that we applied to scRNAseq from blood leukocytes originating from humans and hamsters affected with moderate or severe COVID-19. Integration of COVID-19 patient data with two hamster models that develop moderate (Syrian hamster, Mesocricetus auratus) or severe (Roborovski hamster, Phodopus roborovskii) disease revealed that most cellular states are shared across species. A neural network-based analysis using variational autoencoders quantified the overall transcriptomic similarity across species and severity levels, showing highest similarity between neutrophils of Roborovski hamsters and severe COVID-19 patients, while Syrian hamsters better matched patients with moderate disease, particularly in classical monocytes. We further used transcriptome-wide differential expression analysis to identify which disease stages and cell types display strongest transcriptional changes. Consistently, hamster9s response to COVID-19 was most similar to humans in monocytes and neutrophils. Disease-linked pathways found in all species specifically related to interferon response or inhibition of viral replication. Analysis of candidate genes and signatures supported the results. Our structured neural network-supported workflow could be applied to other diseases, allowing better identification of suitable animal models with similar pathomechanisms across species.
Keywords	covid19
Language	English
Publishing date	2024-01-12
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.01.11.574849
Database	COVID19

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Book ; Online: Supplementary scRNA data for manuscript "MicroRNA-223 dampens neutrophil-mediated lung inflammation during pneumococcal pneumonia" ; Regulation of acute lung inflammation by microRNA-223

Gökeri, Cengiz / Pennitz, Peter / Groenewald, Wibke / Behrendt, Ulrike / Kirsten, Holger / Zobel, Christian M. / Berger, Sarah / Heinz, Gitta A. / Mashreghi, Mir-Farzin / Wienhold, Sandra-Maria / Dietert, Kristina / Gruber, Achim D. / Scholz, Markus / Rohde, Gernot / Suttorp, Norbert / CAPNETZ Study Group / Witzenrath, Martin / Nouailles, Geraldine

2023

Keywords	PhysicalObject ; ddc:570 ; microRNA-223 -- pneumonia -- Streptococcus pneumoniae -- inflammation
Language	English
Publishing date	2023-01-31
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: MicroRNA-223 Dampens Pulmonary Inflammation during Pneumococcal Pneumonia

Goekeri, Cengiz / Pennitz, Peter / Groenewald, Wibke / Behrendt, Ulrike / Kirsten, Holger / Zobel, Christian M. / Berger, Sarah / Heinz, Gitta A. / Mashreghi, Mir-Farzin / Wienhold, Sandra-Maria / Dietert, Kristina / Dorhoi, Anca / Gruber, Achim D. / Scholz, Markus / Rohde, Gernot / Suttorp, Norbert / CAPNETZ Study Group: / Witzenrath, Martin / Nouailles, Geraldine

2023

Abstract	Community-acquired pneumonia remains a major contributor to global communicable disease-mediated mortality. Neutrophils play a leading role in trying to contain bacterial lung infection, but they also drive detrimental pulmonary inflammation, when dysregulated. Here we aimed at understanding the role of microRNA-223 in orchestrating pulmonary inflammation during pneumococcal pneumonia. Serum microRNA-223 was measured in patients with pneumococcal pneumonia and in healthy subjects. Pulmonary inflammation in wild-type and microRNA-223-knockout mice was assessed in terms of disease course, histopathology, cellular recruitment and evaluation of inflammatory protein and gene signatures following pneumococcal infection. Low levels of serum microRNA-223 correlated with increased disease severity in pneumococcal pneumonia patients. Prolonged neutrophilic influx into the lungs and alveolar spaces was detected in pneumococci-infected microRNA-223-knockout mice, possibly accounting for aggravated histopathology and acute lung injury. Expression of microRNA-223 in wild-type mice was induced by pneumococcal infection in a time-dependent manner in whole lungs and lung neutrophils. Single-cell transcriptome analyses of murine lungs revealed a unique profile of antimicrobial and cellular maturation genes that are dysregulated in neutrophils lacking microRNA-223. Taken together, low levels of microRNA-223 in human pneumonia patient serum were associated with increased disease severity, whilst its absence provoked dysregulation of the neutrophil transcriptome in murine pneumococcal pneumonia.
Keywords	Text ; ddc:570 ; microRNA-223 -- pneumonia -- Streptococcus pneumoniae -- neutrophils -- inflammation
Subject code	610
Language	English
Publishing date	2023-03-21
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Single-cell-resolved interspecies comparison identifies a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19

Peidli, Stefan / Nouailles, Geraldine / Wyler, Emanuel / Adler, Julia M. / Kunder, Sandra / Voss, Anne / Kazmierski, Julia / Pott, Fabian / Pennitz, Peter / Postmus, Dylan / Teixeira Alves, Luiz Gustavo / Goffinet, Christine / Gruber, Achim D. / Bluethgen, Nils / Witzenrath, Martin / Trimpert, Jakob / Landthaler, Markus / Praktiknjo, Samantha D.

bioRxiv

Abstract: Key issues for research of COVID-19 pathogenesis are the lack of biopsies from patients and of samples at the onset of infection. To overcome these hurdles, hamsters were shown to be useful models for studying this disease. Here, we further leveraged the ...

Abstract	Key issues for research of COVID-19 pathogenesis are the lack of biopsies from patients and of samples at the onset of infection. To overcome these hurdles, hamsters were shown to be useful models for studying this disease. Here, we further leveraged the model to molecularly survey the disease progression from time-resolved single-cell RNA-sequencing data collected from healthy and SARS-CoV-2-infected Syrian and Roborovski hamster lungs. We compared our data to human COVID-19 studies, including BALF, nasal swab, and post-mortem lung tissue, and identified a shared axis of inflammation dominated by macrophages, neutrophils, and endothelial cells, which we show to be transient in Syrian and terminal in Roborovski hamsters. Our data suggest that, following SARS-CoV-2 infection, commitment to a type 1 or type 3-biased immunity determines moderate versus severe COVID-19 outcomes, respectively.
Keywords	covid19
Language	English
Publishing date	2023-08-27
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.08.25.551434
Database	COVID19

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Article ; Online: A pulmonologist's guide to perform and analyse cross-species single lung cell transcriptomics.

European respiratory review : an official journal of the European Respiratory Society

2022 Volume 31, Issue 165

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 ... ...

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 (
MeSH term(s)	Animals ; Base Sequence ; Chlorocebus aethiops ; Cricetinae ; Humans ; Lung ; Mice ; Pulmonologists ; Rats ; Species Specificity ; Swine ; Transcriptome
Language	English
Publishing date	2022-07-27
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1077620-5
ISSN	1600-0617 ; 0905-9180
ISSN (online)	1600-0617
ISSN	0905-9180
DOI	10.1183/16000617.0056-2022
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Zs.A 3265: Show issues

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Article ; Online: Key benefits of dexamethasone and antibody treatment in COVID-19 hamster models revealed by single-cell transcriptomics.

Wyler, Emanuel / Adler, Julia M / Eschke, Kathrin / Teixeira Alves, G / Peidli, Stefan / Pott, Fabian / Kazmierski, Julia / Michalick, Laura / Kershaw, Olivia / Bushe, Judith / Andreotti, Sandro / Pennitz, Peter / Abdelgawad, Azza / Postmus, Dylan / Goffinet, Christine / Kreye, Jakob / Reincke, S Momsen / Prüss, Harald / Blüthgen, Nils /

Gruber, Achim D / Kuebler, Wolfgang M / Witzenrath, Martin / Landthaler, Markus / Nouailles, Geraldine / Trimpert, Jakob

Molecular therapy : the journal of the American Society of Gene Therapy

2022 Volume 30, Issue 5, Page(s) 1952–1965

Abstract: For coronavirus disease 2019 (COVID-19), effective and well-understood treatment options are still scarce. Since vaccine efficacy is challenged by novel variants, short-lasting immunity, and vaccine hesitancy, understanding and optimizing therapeutic ... ...

Abstract	For coronavirus disease 2019 (COVID-19), effective and well-understood treatment options are still scarce. Since vaccine efficacy is challenged by novel variants, short-lasting immunity, and vaccine hesitancy, understanding and optimizing therapeutic options remains essential. We aimed at better understanding the effects of two standard-of-care drugs, dexamethasone and anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies, on infection and host responses. By using two COVID-19 hamster models, pulmonary immune responses were analyzed to characterize effects of single or combinatorial treatments. Pulmonary viral burden was reduced by anti-SARS-CoV-2 antibody treatment and unaltered or increased by dexamethasone alone. Dexamethasone exhibited strong anti-inflammatory effects and prevented fulminant disease in a severe disease model. Combination therapy showed additive benefits with both anti-viral and anti-inflammatory potency. Bulk and single-cell transcriptomic analyses confirmed dampened inflammatory cell recruitment into lungs upon dexamethasone treatment and identified a specifically responsive subpopulation of neutrophils, thereby indicating a potential mechanism of action. Our analyses confirm the anti-inflammatory properties of dexamethasone and suggest possible mechanisms, validate anti-viral effects of anti-SARS-CoV-2 antibody treatment, and reveal synergistic effects of a combination therapy, thus informing more effective COVID-19 therapies.
MeSH term(s)	Animals ; Anti-Inflammatory Agents/pharmacology ; Anti-Inflammatory Agents/therapeutic use ; Antibodies, Viral ; Antiviral Agents ; Cricetinae ; Dexamethasone/pharmacology ; SARS-CoV-2 ; Transcriptome ; COVID-19 Drug Treatment
Chemical Substances	Anti-Inflammatory Agents ; Antibodies, Viral ; Antiviral Agents ; Dexamethasone (7S5I7G3JQL)
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2022.03.014
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Zs.A 5640: Show issues

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Article ; Online: Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters.

Nouailles, Geraldine / Adler, Julia M / Pennitz, Peter / Peidli, Stefan / Teixeira Alves, Luiz Gustavo / Baumgardt, Morris / Bushe, Judith / Voss, Anne / Langenhagen, Alina / Langner, Christine / Martin Vidal, Ricardo / Pott, Fabian / Kazmierski, Julia / Ebenig, Aileen / Lange, Mona V / Mühlebach, Michael D / Goekeri, Cengiz / Simmons, Szandor / Xing, Na /

Abdelgawad, Azza / Herwig, Susanne / Cichon, Günter / Niemeyer, Daniela / Drosten, Christian / Goffinet, Christine / Landthaler, Markus / Blüthgen, Nils / Wu, Haibo / Witzenrath, Martin / Gruber, Achim D / Praktiknjo, Samantha D / Osterrieder, Nikolaus / Wyler, Emanuel / Kunec, Dusan / Trimpert, Jakob

Nature microbiology

2023 Volume 8, Issue 5, Page(s) 860–874

Abstract: Vaccines play a critical role in combating the COVID-19 pandemic. Future control of the pandemic requires improved vaccines with high efficacy against newly emerging SARS-CoV-2 variants and the ability to reduce virus transmission. Here we compare immune ...

Abstract	Vaccines play a critical role in combating the COVID-19 pandemic. Future control of the pandemic requires improved vaccines with high efficacy against newly emerging SARS-CoV-2 variants and the ability to reduce virus transmission. Here we compare immune responses and preclinical efficacy of the mRNA vaccine BNT162b2, the adenovirus-vectored spike vaccine Ad2-spike and the live-attenuated virus vaccine candidate sCPD9 in Syrian hamsters, using both homogeneous and heterologous vaccination regimens. Comparative vaccine efficacy was assessed by employing readouts from virus titrations to single-cell RNA sequencing. Our results show that sCPD9 vaccination elicited the most robust immunity, including rapid viral clearance, reduced tissue damage, fast differentiation of pre-plasmablasts, strong systemic and mucosal humoral responses, and rapid recall of memory T cells from lung tissue after challenge with heterologous SARS-CoV-2. Overall, our results demonstrate that live-attenuated vaccines offer advantages over currently available COVID-19 vaccines.
MeSH term(s)	Animals ; Cricetinae ; Humans ; Vaccines, Attenuated ; SARS-CoV-2 ; COVID-19/prevention & control ; COVID-19 Vaccines ; BNT162 Vaccine ; Pandemics ; Mesocricetus
Chemical Substances	sCPD9 COVID-19 vaccine ; Vaccines, Attenuated ; COVID-19 Vaccines ; BNT162 Vaccine
Language	English
Publishing date	2023-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-023-01352-8
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