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Article ; Online: Nucleocapsid protein accumulates in renal tubular epithelium of a post-COVID-19 patient.

Grootemaat, Anita E / Wiersma, Niek / van der Niet, Sanne / Schimmel, Irene M / Florquin, Sandrine / Reits, Eric A / Miller, Sara E / van der Wel, Nicole N

Microbiology spectrum

2023 Volume 11, Issue 6, Page(s) e0302923

Abstract: Importance: Even though the coronavirus disease 2019 (COVID-19) pandemic is slowly developing into a conventional infectious disease, the long-term effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infection are still not ... ...

Abstract	Importance: Even though the coronavirus disease 2019 (COVID-19) pandemic is slowly developing into a conventional infectious disease, the long-term effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infection are still not well understood. One of the problems is that many COVID-19 cases develop acute kidney injuries. Still, it is heavily debated whether SARS-CoV-2 virus enters and actively replicates in kidney tissue and if SARS-CoV-2 virus particles can be detected in kidney during or post-infection. Here, we demonstrated that nucleocapsid N protein was detected in kidney tubular epithelium of patients that already recovered form COVID-19. The presence of the abundantly produced N protein without signs of viral replication could have implications for the recurrence of kidney disease and have a continuing effect on the immune system.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Nucleocapsid Proteins ; Virus Replication ; Epithelium
Chemical Substances	Nucleocapsid Proteins
Language	English
Publishing date	2023-11-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03029-23
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Article ; Online: Lipid and Nucleocapsid N-Protein Accumulation in COVID-19 Patient Lung and Infected Cells.

Grootemaat, Anita E / van der Niet, Sanne / Scholl, Edwin R / Roos, Eva / Schurink, Bernadette / Bugiani, Marianna / Miller, Sara E / Larsen, Per / Pankras, Jeannette / Reits, Eric A / van der Wel, Nicole N

Microbiology spectrum

2022 Volume 10, Issue 1, Page(s) e0127121

Abstract: The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global outbreak and prompted an enormous research effort. Still, the subcellular localization of the coronavirus in lungs of COVID-19 patients is not well ... ...

Abstract	The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global outbreak and prompted an enormous research effort. Still, the subcellular localization of the coronavirus in lungs of COVID-19 patients is not well understood. Here, the localization of the SARS-CoV-2 proteins is studied in postmortem lung material of COVID-19 patients and in SARS-CoV-2-infected Vero cells, processed identically. Correlative light and electron microscopy on semithick cryo-sections demonstrated induction of electron-lucent, lipid-filled compartments after SARS-CoV-2 infection in both lung and cell cultures. In lung tissue, the nonstructural protein 4 and the stable nucleocapsid N-protein were detected on these novel lipid-filled compartments. The induction of such lipid-filled compartments and the localization of the viral proteins in lung of patients with fatal COVID-19 may explain the extensive inflammatory response and provide a new hallmark for SARS-CoV-2 infection at the final, fatal stage of infection.
MeSH term(s)	Adolescent ; Aged ; Animals ; COVID-19/metabolism ; COVID-19/pathology ; Child, Preschool ; Chlorocebus aethiops ; Disease Outbreaks ; Female ; Fluorescent Antibody Technique ; Humans ; Immunohistochemistry ; Lipid Metabolism/physiology ; Lipids/analysis ; Lung/cytology ; Lung/metabolism ; Lung/pathology ; Lung/ultrastructure ; Male ; Microscopy, Immunoelectron ; Middle Aged ; Nucleocapsid/analysis ; Nucleocapsid/metabolism ; Rabbits ; SARS-CoV-2/ultrastructure ; Vero Cells/virology
Chemical Substances	Lipids
Language	English
Publishing date	2022-02-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01271-21
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Article ; Online: Biomarkers, measured during therapy, for response of melanoma patients to immune checkpoint inhibitors: a systematic review.

Ouwerkerk, Wouter / van den Berg, Mirjam / van der Niet, Sanne / Limpens, Jacqueline / Luiten, Rosalie M

Melanoma research

2019 Volume 29, Issue 5, Page(s) 453–464

Abstract: Immune checkpoint inhibitors (ICIs), which target CTLA-4 or PD-(L)1 molecules, have shown impressive therapeutic results. Durable responses, however, are only observed in a segment of the patient population and must be offset against severe off-target ... ...

Abstract	Immune checkpoint inhibitors (ICIs), which target CTLA-4 or PD-(L)1 molecules, have shown impressive therapeutic results. Durable responses, however, are only observed in a segment of the patient population and must be offset against severe off-target immune toxicity and high costs. This calls for biomarkers that predict response during ICI treatment. Although many candidate biomarkers exist, as yet, there has been no systematic overview of biomarkers predictive during. Here, we provide a systematic review of the current literature of ICI treatment to establish an overview of candidate predictive biomarkers during ICI treatment in melanoma patients. We performed a systematic Medline search (2000-2018, 1 January) on biomarkers for survival or response to ICI treatment in melanoma patients. We retrieved 735 publications, of which 79 were finally included in this systematic review. Blood markers were largely studied for CTLA-4 ICI, whereas tumor tissue markers were analyzed for PD-(L)1 ICI. Blood cytology and soluble factors were more frequently correlated to overall survival (OS) than response, indicating their prognostic rather than predictive nature. An increase in tumor-infiltrating CD8 + T-cells and a decrease in regulatory T-cells were correlated to response, in addition to mutational load, neoantigen load, and immune-related gene expression. Immune-related adverse events were also associated frequently with a favorable response and OS. This review shows the great variety of potential biomarkers published to date, in an attempt to better understand response to ICI therapy; it also highlights the candidate markers for future research. The most promising biomarkers for response to ICI treatment are the occurrence of immune-related adverse events (especially vitiligo), lowering of lactate dehydrogenase, and increase in activated CD8 + and decrease in regulatory T-cells.
MeSH term(s)	Antibodies, Monoclonal/adverse effects ; Antineoplastic Agents, Immunological/therapeutic use ; B7-H1 Antigen/antagonists & inhibitors ; Biomarkers, Tumor/metabolism ; CD8-Positive T-Lymphocytes/cytology ; CTLA-4 Antigen/antagonists & inhibitors ; Cell Cycle ; Humans ; Immunotherapy/methods ; Melanoma/therapy ; Prognosis ; Skin Neoplasms/therapy ; T-Lymphocytes, Regulatory/cytology ; Treatment Outcome
Chemical Substances	Antibodies, Monoclonal ; Antineoplastic Agents, Immunological ; B7-H1 Antigen ; Biomarkers, Tumor ; CD274 protein, human ; CTLA-4 Antigen ; CTLA4 protein, human
Language	English
Publishing date	2019-03-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	1095779-0
ISSN	1473-5636 ; 0960-8931
ISSN (online)	1473-5636
ISSN	0960-8931
DOI	10.1097/CMR.0000000000000589
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Article ; Online: Identification of guanine nucleotide exchange factors that increase Cdc42 activity in primary human endothelial cells.

Reinhard, Nathalie R / Van Der Niet, Sanne / Chertkova, Anna / Postma, Marten / Hordijk, Peter L / Gadella, Theodorus W J / Goedhart, Joachim

Small GTPases

2019 Volume 12, Issue 3, Page(s) 226–240

Abstract: The Rho GTPase family is involved in actin dynamics and regulates the barrier function of the endothelium. One of the main barrier-promoting Rho GTPases is Cdc42, also known as cell division control protein 42 homolog. Currently, regulation of Cdc42- ... ...

Abstract	The Rho GTPase family is involved in actin dynamics and regulates the barrier function of the endothelium. One of the main barrier-promoting Rho GTPases is Cdc42, also known as cell division control protein 42 homolog. Currently, regulation of Cdc42-based signalling networks in endothelial cells (ECs) lack molecular details. To examine these, we focused on a subset of 15 Rho guanine nucleotide exchange factors (GEFs), which are expressed in the endothelium. By performing single cell FRET measurements with Rho GTPase biosensors in primary human ECs, we monitored GEF efficiency towards Cdc42 and Rac1. A new, single cell-based analysis was developed and used to enable the quantitative comparison of cellular activities of the overexpressed full-length GEFs. Our data reveal GEF dependent activation of Cdc42, with the most efficient Cdc42 activation induced by PLEKHG2, FGD1, PLEKHG1 and PREX1 and the highest selectivity for FGD1. Additionally, we generated truncated GEF constructs that comprise only the catalytic dbl homology (DH) domain or together with the adjacent pleckstrin homology domain (DHPH). The DH domain by itself did not activate Cdc42, whereas the DHPH domain of ITSN1, ITSN2 and PLEKHG1 showed activity towards Cdc42. Together, our study characterized endothelial GEFs that may directly or indirectly activate Cdc42, which will be of great value for the field of vascular biology.
MeSH term(s)	Amino Acid Sequence ; Animals ; Endothelium, Vascular/cytology ; Endothelium, Vascular/metabolism ; Fluorescence Resonance Energy Transfer/methods ; Guanine Nucleotide Exchange Factors/metabolism ; Human Umbilical Vein Endothelial Cells ; Humans ; Models, Molecular ; Protein Binding ; Sequence Homology, Amino Acid ; Single-Cell Analysis/methods ; cdc42 GTP-Binding Protein/metabolism ; rac1 GTP-Binding Protein/metabolism
Chemical Substances	Guanine Nucleotide Exchange Factors ; RAC1 protein, human ; CDC42 protein, human (EC 3.6.5.2) ; cdc42 GTP-Binding Protein (EC 3.6.5.2) ; rac1 GTP-Binding Protein (EC 3.6.5.2)
Language	English
Publishing date	2019-08-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2682247-7
ISSN	2154-1256 ; 2154-1248
ISSN (online)	2154-1256
ISSN	2154-1248
DOI	10.1080/21541248.2019.1658509
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Article ; Online: Endothelial Focal Adhesions Are Functional Obstacles for Leukocytes During Basolateral Crawling.

Arts, Janine J G / Mahlandt, Eike K / Schimmel, Lilian / Grönloh, Max L B / van der Niet, Sanne / Klein, Bart J A M / Fernandez-Borja, Mar / van Geemen, Daphne / Huveneers, Stephan / van Rijssel, Jos / Goedhart, Joachim / van Buul, Jaap D

Frontiers in immunology

2021 Volume 12, Page(s) 667213

Abstract: An inflammatory response requires leukocytes to migrate from the circulation across the vascular lining into the tissue to clear the invading pathogen. Whereas a lot of attention is focused on how leukocytes make their way through the endothelial ... ...

Abstract	An inflammatory response requires leukocytes to migrate from the circulation across the vascular lining into the tissue to clear the invading pathogen. Whereas a lot of attention is focused on how leukocytes make their way through the endothelial monolayer, it is less clear how leukocytes migrate underneath the endothelium before they enter the tissue. Upon finalization of the diapedesis step, leukocytes reside in the subendothelial space and encounter endothelial focal adhesions. Using TIRF microscopy, we show that neutrophils navigate around these focal adhesions. Neutrophils recognize focal adhesions as physical obstacles and deform to get around them. Increasing the number of focal adhesions by silencing the small GTPase RhoJ slows down basolateral crawling of neutrophils. However, apical crawling and diapedesis itself are not affected by RhoJ depletion. Increasing the number of focal adhesions drastically by expressing the Rac1 GEF Tiam1 make neutrophils to avoid migrating underneath these Tiam1-expressing endothelial cells. Together, our results show that focal adhesions mark the basolateral migration path of neutrophils.
MeSH term(s)	Cell Line ; Endothelial Cells/physiology ; Focal Adhesions/physiology ; Humans ; Leukocytes/physiology ; Neutrophils/physiology ; Transendothelial and Transepithelial Migration/physiology ; Umbilical Cord/pathology
Language	English
Publishing date	2021-05-18
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2021.667213
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Article ; Online: A terpene nucleoside from M. tuberculosis induces lysosomal lipid storage in foamy macrophages.

The Journal of clinical investigation

2023 Volume 133, Issue 6

Abstract: Induction of lipid-laden foamy macrophages is a cellular hallmark of tuberculosis (TB) disease, which involves the transformation of infected phagolysosomes from a site of killing into a nutrient-rich replicative niche. Here, we show that a terpenyl ... ...

Abstract	Induction of lipid-laden foamy macrophages is a cellular hallmark of tuberculosis (TB) disease, which involves the transformation of infected phagolysosomes from a site of killing into a nutrient-rich replicative niche. Here, we show that a terpenyl nucleoside shed from Mycobacterium tuberculosis, 1-tuberculosinyladenosine (1-TbAd), caused lysosomal maturation arrest and autophagy blockade, leading to lipid storage in M1 macrophages. Pure 1-TbAd, or infection with terpenyl nucleoside-producing M. tuberculosis, caused intralysosomal and peribacillary lipid storage patterns that matched both the molecules and subcellular locations known in foamy macrophages. Lipidomics showed that 1-TbAd induced storage of triacylglycerides and cholesterylesters and that 1-TbAd increased M. tuberculosis growth under conditions of restricted lipid access in macrophages. Furthermore, lipidomics identified 1-TbAd-induced lipid substrates that define Gaucher's disease, Wolman's disease, and other inborn lysosomal storage diseases. These data identify genetic and molecular causes of M. tuberculosis-induced lysosomal failure, leading to successful testing of an agonist of TRPML1 calcium channels that reverses lipid storage in cells. These data establish the host-directed cellular functions of an orphan effector molecule that promotes survival in macrophages, providing both an upstream cause and detailed picture of lysosome failure in foamy macrophages.
MeSH term(s)	Humans ; Mycobacterium tuberculosis ; Terpenes ; Nucleosides ; Tuberculosis ; Macrophages/microbiology ; Lipids ; Lysosomes
Chemical Substances	Terpenes ; Nucleosides ; Lipids
Language	English
Publishing date	2023-03-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI161944
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Article ; Online: Lipid and nucleocapsid N-protein accumulation in COVID-19 patient lung and infected cells

Grootemaat, Anita / van der Niet, Sanne / Scholl, Edwin R. / Roos, Eva / Schurink, Bernadette / Bugiani, Marianna / Miller, Sara E. / Larsen, Per W / Pankras, Jeannette / Reits, Eric E / van der Wel, Nicole N

bioRxiv

Abstract: The trafficking of coronaviruses in lung of COVID-19 patients is not well understood and virus particles are difficult to find. Here we have visualized virus particles in SARS-CoV-2 infected cells by focusing on viral protein detection, in combination ... ...

Abstract	The trafficking of coronaviruses in lung of COVID-19 patients is not well understood and virus particles are difficult to find. Here we have visualized virus particles in SARS-CoV-2 infected cells by focusing on viral protein detection, in combination with ultrastructure. We studied how the virus is altering the cell morphology and determined that in Vero cells, lipid filled compartments contained various viral proteins. In these cells, also membrane enclosed multi-virus bodies were visible that contain a different set of viral proteins. We demonstrated that lipid filled compartments are novel viral induced compartments, as no known cellular marker such as lipid droplet or lysosomal marker was present. Using this knowledge, we then studied lung tissue from patients with a fatal SARS-Cov-2 infection, processed in a similar manner. Again we detected lipid filled compartments with viral proteins nsp4 and the stable nucleocapsid N-protein. The presence of these lipid filled compartments with viral proteins induced by SARS-CoV-2 infections, could be why the immune response of the COVID-19 patients is so strong, resulting in a fatal infection, and should be considered for new therapeutic strategies.
Keywords	covid19
Language	English
Publishing date	2021-06-24
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2021.06.24.449252
Database	COVID19

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Article ; Online: IL-1R1-Dependent Signals Improve Control of Cytosolic Virulent Mycobacteria

van der Niet, Sanne / van Zon, Maaike / de Punder, Karin / Grootemaat, Anita / Rutten, Sofie / Moorlag, Simone J C F M / Houben, Diane / van der Sar, Astrid M / Bitter, Wilbert / Brosch, Roland / Hernandez Pando, Rogelio / Pena, Maria T / Peters, Peter J / Reits, Eric A / Mayer-Barber, Katrin D / van der Wel, Nicole N

mSphere

2021 Volume 6, Issue 3

Abstract: Mycobacterium ... ...

Abstract	Mycobacterium tuberculosis
MeSH term(s)	Animals ; Armadillos/microbiology ; Bacterial Translocation ; Cytosol/immunology ; Cytosol/microbiology ; Female ; Humans ; Leprosy/microbiology ; Male ; Mice ; Mice, Inbred BALB C ; Mice, SCID ; Mycobacterium/classification ; Mycobacterium/immunology ; Mycobacterium/pathogenicity ; Phagosomes/immunology ; Phagosomes/microbiology ; Receptors, Interleukin-1/genetics ; Receptors, Interleukin-1/immunology ; Signal Transduction/immunology ; Skin/microbiology ; Skin/pathology ; THP-1 Cells ; Zebrafish
Chemical Substances	Receptors, Interleukin-1
Language	English
Publishing date	2021-05-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ISSN	2379-5042
ISSN (online)	2379-5042
DOI	10.1128/mSphere.00153-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Nucleocapsid protein accumulates in renal tubular epithelium of a post-COVID-19 patient.

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Article ; Online: Lipid and Nucleocapsid N-Protein Accumulation in COVID-19 Patient Lung and Infected Cells.

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Article ; Online: Biomarkers, measured during therapy, for response of melanoma patients to immune checkpoint inhibitors: a systematic review.

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Article ; Online: Identification of guanine nucleotide exchange factors that increase Cdc42 activity in primary human endothelial cells.

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Article ; Online: Endothelial Focal Adhesions Are Functional Obstacles for Leukocytes During Basolateral Crawling.

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Article ; Online: A terpene nucleoside from M. tuberculosis induces lysosomal lipid storage in foamy macrophages.

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Article ; Online: Lipid and nucleocapsid N-protein accumulation in COVID-19 patient lung and infected cells

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Article ; Online: IL-1R1-Dependent Signals Improve Control of Cytosolic Virulent Mycobacteria

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