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Article ; Online: Advancing lung organoids for COVID-19 research

Jelte van der Vaart / Mart M. Lamers / Bart L. Haagmans / Hans Clevers

Disease Models & Mechanisms, Vol 14, Iss

2021 Volume 6

Abstract: The COVID-19 pandemic has emphasised the need to develop effective treatments to combat emerging viruses. Model systems that poorly represent a virus' cellular environment, however, may impede research and waste resources. Collaborations between cell ... ...

Abstract	The COVID-19 pandemic has emphasised the need to develop effective treatments to combat emerging viruses. Model systems that poorly represent a virus' cellular environment, however, may impede research and waste resources. Collaborations between cell biologists and virologists have led to the rapid development of representative organoid model systems to study severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We believe that lung organoids, in particular, have advanced our understanding of SARS-CoV-2 pathogenesis, and have laid a foundation to study future pandemic viruses and develop effective treatments.
Keywords	Medicine ; R ; Pathology ; RB1-214
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	The Company of Biologists
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Glycosylated extracellular mucin domains protect against SARS-CoV-2 infection at the respiratory surface.

Maitrayee Chatterjee / Liane Z X Huang / Anna Z Mykytyn / Chunyan Wang / Mart M Lamers / Bart Westendorp / Richard W Wubbolts / Jos P M van Putten / Berend-Jan Bosch / Bart L Haagmans / Karin Strijbis

PLoS Pathogens, Vol 19, Iss 8, p e

2023 Volume 1011571

Abstract: Mucins play an essential role in protecting the respiratory tract against microbial infections while also acting as binding sites for bacterial and viral adhesins. The heavily O-glycosylated gel-forming mucins MUC5AC and MUC5B eliminate pathogens by ... ...

Abstract	Mucins play an essential role in protecting the respiratory tract against microbial infections while also acting as binding sites for bacterial and viral adhesins. The heavily O-glycosylated gel-forming mucins MUC5AC and MUC5B eliminate pathogens by mucociliary clearance. Transmembrane mucins MUC1, MUC4, and MUC16 can restrict microbial invasion at the apical surface of the epithelium. In this study, we determined the impact of host mucins and mucin glycans on epithelial entry of SARS-CoV-2. Human lung epithelial Calu-3 cells express the SARS-CoV-2 entry receptor ACE2 and high levels of glycosylated MUC1, but not MUC4 and MUC16, on their cell surface. The O-glycan-specific mucinase StcE specifically removed the glycosylated part of the MUC1 extracellular domain while leaving the underlying SEA domain and cytoplasmic tail intact. StcE treatment of Calu-3 cells significantly enhanced infection with SARS-CoV-2 pseudovirus and authentic virus, while removal of terminal mucin glycans sialic acid and fucose from the epithelial surface did not impact viral entry. In Calu-3 cells, the transmembrane mucin MUC1 and ACE2 are located to the apical surface in close proximity and StcE treatment results in enhanced binding of purified spike protein. Both MUC1 and MUC16 are expressed on the surface of human organoid-derived air-liquid interface (ALI) differentiated airway cultures and StcE treatment led to mucin removal and increased levels of SARS-CoV-2 replication. In these cultures, MUC1 was highly expressed in non-ciliated cells while MUC16 was enriched in goblet cells. In conclusion, the glycosylated extracellular domains of different transmembrane mucins might have similar protective functions in different respiratory cell types by restricting SARS-CoV-2 binding and entry.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens.

Karel Bezstarosti / Mart M Lamers / Wouter A S Doff / Peter C Wever / Khoa T D Thai / Jeroen J A van Kampen / Bart L Haagmans / Jeroen A A Demmers

PLoS ONE, Vol 16, Iss 11, p e

2021 Volume 0259165

Abstract: The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS- ... ...

Abstract	The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site

Anna Z Mykytyn / Tim I Breugem / Samra Riesebosch / Debby Schipper / Petra B van den Doel / Robbert J Rottier / Mart M Lamers / Bart L Haagmans

eLife, Vol

2021 Volume 10

Abstract: Coronavirus entry is mediated by the spike protein that binds the receptor and mediates fusion after cleavage by host proteases. The proteases that mediate entry differ between cell lines, and it is currently unclear which proteases are relevant in vivo. ...

Abstract	Coronavirus entry is mediated by the spike protein that binds the receptor and mediates fusion after cleavage by host proteases. The proteases that mediate entry differ between cell lines, and it is currently unclear which proteases are relevant in vivo. A remarkable feature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the presence of a multibasic cleavage site (MBCS), which is absent in the SARS-CoV spike. Here, we report that the SARS-CoV-2 spike MBCS increases infectivity on human airway organoids (hAOs). Compared with SARS-CoV, SARS-CoV-2 entered faster into Calu-3 cells and, more frequently, formed syncytia in hAOs. Moreover, the MBCS increased entry speed and plasma membrane serine protease usage relative to cathepsin-mediated endosomal entry. Blocking serine proteases, but not cathepsins, effectively inhibited SARS-CoV-2 entry and replication in hAOs. Our findings demonstrate that SARS-CoV-2 enters relevant airway cells using serine proteases, and suggest that the MBCS is an adaptation to this viral entry strategy.
Keywords	COVID-19 ; SARS-CoV-2 ; SARS-CoV ; multibasic cleavage site ; serine proteases ; airway organoids ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation

Mart M Lamers / Anna Z Mykytyn / Tim I Breugem / Yiquan Wang / Douglas C Wu / Samra Riesebosch / Petra B van den Doel / Debby Schipper / Theo Bestebroer / Nicholas C Wu / Bart L Haagmans

eLife, Vol

2021 Volume 10

Abstract: Virus propagation methods generally use transformed cell lines to grow viruses from clinical specimens, which may force viruses to rapidly adapt to cell culture conditions, a process facilitated by high viral mutation rates. Upon propagation in VeroE6 ... ...

Abstract	Virus propagation methods generally use transformed cell lines to grow viruses from clinical specimens, which may force viruses to rapidly adapt to cell culture conditions, a process facilitated by high viral mutation rates. Upon propagation in VeroE6 cells, SARS-CoV-2 may mutate or delete the multibasic cleavage site (MBCS) in the spike protein. Previously, we showed that the MBCS facilitates serine protease-mediated entry into human airway cells (Mykytyn et al., 2021). Here, we report that propagating SARS-CoV-2 on the human airway cell line Calu-3 – that expresses serine proteases – prevents cell culture adaptations in the MBCS and directly adjacent to the MBCS (S686G). Similar results were obtained using a human airway organoid-based culture system for SARS-CoV-2 propagation. Thus, in-depth knowledge on the biology of a virus can be used to establish methods to prevent cell culture adaptation.
Keywords	COVID-19 ; SARS-CoV-2 ; cell culture adaptation ; furin cleavage site ; serine proteases ; airway organoids ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

Karel Bezstarosti / Mart M. Lamers / Wouter A. S. Doff / Peter C. Wever / Khoa T. D. Thai / Jeroen J. A. van Kampen / Bart L. Haagmans / Jeroen A. A. Demmers

PLoS ONE, Vol 16, Iss

2021 Volume 11

Abstract	The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry (MS) based proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was estimated to be in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 Omicron variant causes mild pathology in the upper and lower respiratory tract of hamsters

Federico Armando / Georg Beythien / Franziska K. Kaiser / Lisa Allnoch / Laura Heydemann / Malgorzata Rosiak / Svenja Becker / Mariana Gonzalez-Hernandez / Mart M. Lamers / Bart L. Haagmans / Kate Guilfoyle / Geert van Amerongen / Malgorzata Ciurkiewicz / Albert D.M.E. Osterhaus / Wolfgang Baumgärtner

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 15

Abstract: Since the emergence of SARS-CoV-2 several variants of concerns have been identified, with altered disease progression and transmission dynamics. Here, Armando et al. compare virus spread and pathology in the upper and lower respiratory tracts of Syrian ... ...

Abstract	Since the emergence of SARS-CoV-2 several variants of concerns have been identified, with altered disease progression and transmission dynamics. Here, Armando et al. compare virus spread and pathology in the upper and lower respiratory tracts of Syrian golden hamster after 4 days post infection for VOCs Gamma, Delta and Omicron and find milder pathology for Omicron.
Keywords	Science ; Q
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Independent Effects of a Herbivore’s Bacterial Symbionts on Its Performance and Induced Plant Defences

Heike Staudacher / Bernardus C. J. Schimmel / Mart M. Lamers / Nicky Wybouw / Astrid T. Groot / Merijn R. Kant

International Journal of Molecular Sciences, Vol 18, Iss 1, p

2017 Volume 182

Abstract: It is well known that microbial pathogens and herbivores elicit defence responses in plants. Moreover, microorganisms associated with herbivores, such as bacteria or viruses, can modulate the plant’s response to herbivores. Herbivorous spider mites can ... ...

Abstract	It is well known that microbial pathogens and herbivores elicit defence responses in plants. Moreover, microorganisms associated with herbivores, such as bacteria or viruses, can modulate the plant’s response to herbivores. Herbivorous spider mites can harbour different species of bacterial symbionts and exert a broad range of effects on host-plant defences. Hence, we tested the extent to which such symbionts affect the plant’s defences induced by their mite host and assessed if this translates into changes in plant resistance. We assessed the bacterial communities of two strains of the common mite pest Tetranychus urticae. We found that these strains harboured distinct symbiotic bacteria and removed these using antibiotics. Subsequently, we tested to which extent mites with and without symbiotic bacteria induce plant defences in terms of phytohormone accumulation and defence gene expression, and assessed mite oviposition and survival as a measure for plant resistance. We observed that the absence/presence of these bacteria altered distinct plant defence parameters and affected mite performance but we did not find indications for a causal link between the two. We argue that although bacteria-related effects on host-induced plant defences may occur, these do not necessarily affect plant resistance concomitantly.
Keywords	Tetranychus urticae ; Wolbachia ; Cardinium ; Spiroplasma ; symbiosis ; plant–herbivore interaction ; plant defence ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Development of immunohistochemistry and in situ hybridisation for the detection of SARS-CoV and SARS-CoV-2 in formalin-fixed paraffin-embedded specimens

Fabian Z. X. Lean / Mart M. Lamers / Samuel P. Smith / Rebecca Shipley / Debby Schipper / Nigel Temperton / Bart L. Haagmans / Ashley C. Banyard / Kevin R. Bewley / Miles W. Carroll / Sharon M. Brookes / Ian Brown / Alejandro Nuñez

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 9

Abstract: Abstract The rapid emergence of SARS-CoV-2, the causative agent of COVID-19, and its dissemination globally has caused an unprecedented strain on public health. Animal models are urgently being developed for SARS-CoV-2 to aid rational design of vaccines ... ...

Abstract	Abstract The rapid emergence of SARS-CoV-2, the causative agent of COVID-19, and its dissemination globally has caused an unprecedented strain on public health. Animal models are urgently being developed for SARS-CoV-2 to aid rational design of vaccines and therapeutics. Immunohistochemistry and in situ hybridisation techniques that facilitate reliable and reproducible detection of SARS-CoV and SARS-CoV-2 viral products in formalin-fixed paraffin-embedded (FFPE) specimens would be of great utility. A selection of commercial antibodies generated against SARS-CoV spike protein and nucleoprotein, double stranded RNA, and RNA probe for spike genes were evaluated for the ability to detect FFPE infected cells. We also tested both heat- and enzymatic-mediated virus antigen retrieval methods to determine the optimal virus antigen recovery as well as identifying alternative retrieval methods to enable flexibility of IHC methods. In addition to using native virus infected cells as positive control material, the evaluation of non-infected cells expressing coronavirus (SARS, MERS) spike as a biosecure alternative to assays involving live virus was undertaken. Optimized protocols were successfully applied to experimental animal-derived tissues. The diverse techniques for virus detection and control material generation demonstrated in this study can be applied to investigations of coronavirus pathogenesis and therapeutic research in animal models.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: SARS-CoV-2 is transmitted via contact and via the air between ferrets

Mathilde Richard / Adinda Kok / Dennis de Meulder / Theo M. Bestebroer / Mart M. Lamers / Nisreen M. A. Okba / Martje Fentener van Vlissingen / Barry Rockx / Bart L. Haagmans / Marion P. G. Koopmans / Ron A. M. Fouchier / Sander Herfst

Nature Communications, Vol 11, Iss 1, Pp 1-

2020 Volume 6

Abstract: SARS-CoV-2 has rapidly spread globally and animal models to study transmission are needed. Here, Richard et al. show efficient transmission of SARS-CoV-2 between ferrets via direct contact and via the air, through respiratory droplets and/or aerosols. ...

Abstract	SARS-CoV-2 has rapidly spread globally and animal models to study transmission are needed. Here, Richard et al. show efficient transmission of SARS-CoV-2 between ferrets via direct contact and via the air, through respiratory droplets and/or aerosols.
Keywords	Science ; Q ; covid19
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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