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1. The accumulation of erythrocytes quantified and visualized by Glycophorin C in carotid atherosclerotic plaque reflects intraplaque hemorrhage and pre-procedural neurological symptoms

Author

Mekke, Joost M., Sakkers, Tim R., Verwer, Maarten C., van den Dungen, Noortje A. M., Song, Yipei, Miller, Clint L., Finn, Aloke V., Pasterkamp, Gerard, Mokry, Michal, den Ruijter, Hester M., Vink, Aryan, de Kleijn, Dominique P. V., de Borst, Gert J., Haitjema, Saskia, and van der Laan, Sander W.

Published
2023
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3. Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation

Author

Mokry, Michal, Boltjes, Arjan, Slenders, Lotte, Bel-Bordes, Gemma, Cui, Kai, Brouwer, Eli, Mekke, Joost M., Depuydt, Marie A. C., Timmerman, Nathalie, Waissi, Farahnaz, Verwer, Maarten C., Turner, Adam W., Khan, Mohammad Daud, Hodonsky, Chani J., Diez Benavente, Ernest, Hartman, Robin J. G., van den Dungen, Noortje A. M., Lansu, Nico, Nagyova, Emilia, Prange, Koen H. M., Kovacic, Jason C., Björkegren, Johan L. M., Pavlos, Eleftherios, Andreakos, Evangelos, Schunkert, Heribert, Owens, Gary K., Monaco, Claudia, Finn, Aloke V., Virmani, Renu, Leeper, Nicholas J., de Winther, Menno P. J., Kuiper, Johan, de Borst, Gert J., Stroes, Erik S. G., Civelek, Mete, de Kleijn, Dominique P. V., den Ruijter, Hester M., Asselbergs, Folkert W., van der Laan, Sander W., Miller, Clint L., and Pasterkamp, Gerard

Published
2022
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5. N6-Methyladenosine Promotes TNF mRNA Degradation In CD4+ T Lymphocytes

Author

CTI Van Loosdregt, Immuno/reuma onderzoek 3 (Loosdregt), Infection & Immunity, CDL Research analisten, Cancer, CDL Onderzoek Pasterkamp, Experimentele Afd. Cardiologie 1, Child Health, Circulatory Health, MMB Research line 3a, CMM Groep Coffer, Regenerative Medicine and Stem Cells, CMM Sectie Stem Cells, Onderzoek, Immuno/reuma onderzoek 1 (Vastert), Immunologie/Reumatologie, CTI Research, van Vroonhoven, Ellen C N, Picavet, Lucas W, Scholman, Rianne C, Sijbers, Lyanne J P M, Kievit, Corlinda R E, van den Dungen, Noortje A M, Mokry, Michal, Evers, Anouk, Lebbink, Robert J, Mocholi, Enric, Coffer, Paul J, Calis, Jorg J A, Vastert, Sebastiaan J, van Loosdregt, Jorg, CTI Van Loosdregt, Immuno/reuma onderzoek 3 (Loosdregt), Infection & Immunity, CDL Research analisten, Cancer, CDL Onderzoek Pasterkamp, Experimentele Afd. Cardiologie 1, Child Health, Circulatory Health, MMB Research line 3a, CMM Groep Coffer, Regenerative Medicine and Stem Cells, CMM Sectie Stem Cells, Onderzoek, Immuno/reuma onderzoek 1 (Vastert), Immunologie/Reumatologie, CTI Research, van Vroonhoven, Ellen C N, Picavet, Lucas W, Scholman, Rianne C, Sijbers, Lyanne J P M, Kievit, Corlinda R E, van den Dungen, Noortje A M, Mokry, Michal, Evers, Anouk, Lebbink, Robert J, Mocholi, Enric, Coffer, Paul J, Calis, Jorg J A, Vastert, Sebastiaan J, and van Loosdregt, Jorg

Published
2024

6. N6-methyladenosine promotes TNF mRNA degradation in CD4+T lymphocytes

Author

van Vroonhoven, Ellen C N, Picavet, Lucas W, Scholman, Rianne C, Sijbers, Lyanne J P M, Kievit, Corlinda R E, van den Dungen, Noortje A M, Mokry, Michal, Evers, Anouk, Lebbink, Robert J, Mocholi, Enric, Coffer, Paul J, Calis, Jorg J A, Vastert, Sebastiaan J, and van Loosdregt, Jorg

Abstract

N6-methyladenosine (m6A) is a RNA modification that can regulate post-transcriptional processes including RNA stability, translation, splicing, and nuclear export. In CD4+lymphocytes, m6A modifications have been demonstrated to play a role in early differentiation processes. The role of m6A in CD4+T cell activation and effector function remains incompletely understood. To assess the role of m6A in CD4+T lymphocyte activation and function, we assessed the transcriptome-wide m6A landscape of human primary CD4+T cells by methylated RNA immunoprecipitation sequencing. Stimulation of the T cells impacted the m6A pattern of hundreds of transcripts including tumor necrosis factor (TNF). m6A methylation was increased on TNFmessenger RNA (mRNA) after activation, predominantly in the 3′ untranslated region of the transcript. Manipulation of m6A levels in primary human T cells, the directly affected the expression of TNF. Furthermore, we identified that the m6A reader protein YTHDF2 binds m6A-methylated TNFmRNA, and promotes its degradation. Taken together, this study demonstrates that TNF expression in CD4+T lymphocytes is regulated via m6A and YTHDF2, thereby providing novel insight into the regulation of T cell effector functions.This study demonstrates that tumor necrosis factor expression in CD4+ T lymphocytes is regulated via N6-methyladenosine and YTHDF2, thereby providing novel insight into the regulation of T cell effector functions.T helper cells are immune cells of the adaptive immune system. These cells are activated by antigen presenting cells that have engulfed invading pathogens. When the T helper cell is activated, it will produce and excrete signaling molecules (cytokines) that activate other immune cells in order to eradicate these pathogens. Cytokines are formed after translation of RNA molecules that encode for these cytokines. In this study it was found that a modification (N6-methyladenosine) on RNA molecules is involved in the regulation of the life cycle of these RNA molecules. It was found that the degradation of RNA encoding for cytokine tumor necrosis factor (TNF) was mediated through N6-methyladenosine and its “reader” protein YTHDF2 in activated T helper cells. As TNF promotes inflammation, reduction of TNF production through this mechanism dampens the immune response and therefore prevents chronic inflammation.

Published
2024
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7. Human Plaque Myofibroblasts to Study Mechanisms of Atherosclerosis

Author

Buono, Michele F., primary, Benavente, Ernest Diez, additional, Slenders, Lotte, additional, Methorst, Daisey, additional, Tessels, Daniëlle, additional, Mili, Eloi, additional, Finger, Roxy, additional, Kapteijn, Daniek, additional, Daniels, Mark, additional, van den Dungen, Noortje A. M., additional, Calis, Jorg J. A., additional, Mol, Barend M., additional, de Borst, Gert J., additional, de Kleijn, Dominique P. V., additional, Pasterkamp, Gerard, additional, den Ruijter, Hester M., additional, and Mokry, Michal, additional

Published
2023
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Author

Zorgeenheid Vaatchirurgie Medisch, Experimentele Afd. Cardiologie 1, Circulatory Health, CDL Research analisten, Cancer, CDL Onderzoek Pasterkamp, Centraal Diagnostisch Laboratorium, Child Health, Onderzoek Vrouw Hart & Vaatziekten, Pathologie Pathologen staf, Infection & Immunity, Regenerative Medicine and Stem Cells, CDL Cluster Speciële Diagnostiek, Mekke, Joost M, Sakkers, Tim R, Verwer, Maarten C, van den Dungen, Noortje A M, Song, Yipei, Miller, Clint L, Finn, Aloke V, Pasterkamp, Gerard, Mokry, Michal, den Ruijter, Hester M, Vink, Aryan, de Kleijn, Dominique P V, de Borst, Gert J, Haitjema, Saskia, van der Laan, Sander W, Zorgeenheid Vaatchirurgie Medisch, Experimentele Afd. Cardiologie 1, Circulatory Health, CDL Research analisten, Cancer, CDL Onderzoek Pasterkamp, Centraal Diagnostisch Laboratorium, Child Health, Onderzoek Vrouw Hart & Vaatziekten, Pathologie Pathologen staf, Infection & Immunity, Regenerative Medicine and Stem Cells, CDL Cluster Speciële Diagnostiek, Mekke, Joost M, Sakkers, Tim R, Verwer, Maarten C, van den Dungen, Noortje A M, Song, Yipei, Miller, Clint L, Finn, Aloke V, Pasterkamp, Gerard, Mokry, Michal, den Ruijter, Hester M, Vink, Aryan, de Kleijn, Dominique P V, de Borst, Gert J, Haitjema, Saskia, and van der Laan, Sander W

Published
2023

10. Locational memory of macrovessel vascular cells is transcriptionally imprinted

Author

Spanjersberg, Talitha C F, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van den Dungen, Noortje A M, Vernooij, Johannes C M, Asselbergs, Folkert W, Mokry, Michal, Spee, Bart, Harakalova, Magdalena, van Steenbeek, Frank G, Spanjersberg, Talitha C F, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van den Dungen, Noortje A M, Vernooij, Johannes C M, Asselbergs, Folkert W, Mokry, Michal, Spee, Bart, Harakalova, Magdalena, and van Steenbeek, Frank G

Abstract

Vascular pathologies show locational predisposition throughout the body; further insights into the transcriptomics basis of this vascular heterogeneity are needed. We analyzed transcriptomes from cultured endothelial cells and vascular smooth muscle cells from nine adult canine macrovessels: the aorta, coronary artery, vena cava, portal vein, femoral artery, femoral vein, saphenous vein, pulmonary vein, and pulmonary artery. We observed that organ-specific expression patterns persist in vitro, indicating that these genes are not regulated by blood flow or surrounding cell types but are likely fixed in the epigenetic memory. We further demonstrated the preserved location-specific expression of GATA4 protein in cultured cells and in the primary adult vessel. On a functional level, arterial and venous endothelial cells differed in vascular network morphology as the arterial networks maintained a higher complexity. Our findings prompt the rethinking of the extrapolation of results from single-origin endothelial cell systems.

Published
2023

11. Transcriptome sequencing reveals two subtypes of cortisol-secreting adrenocortical tumours in dogs and identifies CYP26B1 as a potential new therapeutic target

Author

Sanders, Karin, Kooistra, Hans S, van den Heuvel, Marieke, Mokry, Michal, Grinwis, Guy C M, van den Dungen, Noortje A M, van Steenbeek, Frank G, Galac, Sara, Sanders, Karin, Kooistra, Hans S, van den Heuvel, Marieke, Mokry, Michal, Grinwis, Guy C M, van den Dungen, Noortje A M, van Steenbeek, Frank G, and Galac, Sara

Abstract

Cushing's syndrome (CS) is a serious endocrine disorder that is relatively common in dogs, but rare in humans. In ~15%–20% of cases, CS is caused by a cortisol-secreting adrenocortical tumour (csACT). To identify differentially expressed genes that can improve prognostic predictions after surgery and represent novel treatment targets, we performed RNA sequencing on csACTs (n = 48) and normal adrenal cortices (NACs; n = 10) of dogs. A gene was declared differentially expressed when the adjusted p-value was <.05 and the log2 fold change was >2 or < −2. Between NACs and csACTs, 98 genes were differentially expressed. Based on the principal component analysis (PCA) the csACTs were separated in two groups, of which Group 1 had significantly better survival after adrenalectomy (p =.002) than Group 2. Between csACT Group G1 and Group 2, 77 genes were differentially expressed. One of these, cytochrome P450 26B1 (CYP26B1), was significantly associated with survival in both our canine csACTs and in a publicly available data set of 33 human cortisol-secreting adrenocortical carcinomas. In the validation cohort, CYP26B1 was also expressed significantly higher (p =.012) in canine csACTs compared with NACs. In future studies it would be interesting to determine whether CYP26B1 inhibitors could inhibit csACT growth in both dogs and humans.

Published
2023

12. Locational memory of macrovessel vascular cells is transcriptionally imprinted

Author

Internal Medicine of Companion Animals, Interne geneeskunde GD, FAH Evidence based Veterinary Medicine, CS_STEAM, CS_Genetics, Genetics, STEAM, Welfare & Emerging Diseases, Spanjersberg, Talitha C F, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van den Dungen, Noortje A M, Vernooij, Johannes C M, Asselbergs, Folkert W, Mokry, Michal, Spee, Bart, Harakalova, Magdalena, van Steenbeek, Frank G, Internal Medicine of Companion Animals, Interne geneeskunde GD, FAH Evidence based Veterinary Medicine, CS_STEAM, CS_Genetics, Genetics, STEAM, Welfare & Emerging Diseases, Spanjersberg, Talitha C F, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van den Dungen, Noortje A M, Vernooij, Johannes C M, Asselbergs, Folkert W, Mokry, Michal, Spee, Bart, Harakalova, Magdalena, and van Steenbeek, Frank G

Published
2023

13. Transcriptome sequencing reveals two subtypes of cortisol-secreting adrenocortical tumours in dogs and identifies CYP26B1 as a potential new therapeutic target

Author

CS_Cancer, Interne geneeskunde GD, CS_Welfare & emerging diseases, VPDC pathologie, dPB CR, VP pathologie, CS_Genetics, Pathology, Genetics, OnGo, Welfare & Emerging Diseases, Sanders, Karin, Kooistra, Hans S, van den Heuvel, Marieke, Mokry, Michal, Grinwis, Guy C M, van den Dungen, Noortje A M, van Steenbeek, Frank G, Galac, Sara, CS_Cancer, Interne geneeskunde GD, CS_Welfare & emerging diseases, VPDC pathologie, dPB CR, VP pathologie, CS_Genetics, Pathology, Genetics, OnGo, Welfare & Emerging Diseases, Sanders, Karin, Kooistra, Hans S, van den Heuvel, Marieke, Mokry, Michal, Grinwis, Guy C M, van den Dungen, Noortje A M, van Steenbeek, Frank G, and Galac, Sara

Published
2023

14. Locational memory of macrovessel vascular cells is transcriptionally imprinted

Author

Onderzoek Precision medicine, CDL Research analisten, Cancer, CDL Onderzoek Pasterkamp, Experimentele Afd. Cardiologie 1, Child Health, Circulatory Health, Spanjersberg, Talitha C F, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van den Dungen, Noortje A M, Vernooij, Johannes C M, Asselbergs, Folkert W, Mokry, Michal, Spee, Bart, Harakalova, Magdalena, van Steenbeek, Frank G, Onderzoek Precision medicine, CDL Research analisten, Cancer, CDL Onderzoek Pasterkamp, Experimentele Afd. Cardiologie 1, Child Health, Circulatory Health, Spanjersberg, Talitha C F, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van den Dungen, Noortje A M, Vernooij, Johannes C M, Asselbergs, Folkert W, Mokry, Michal, Spee, Bart, Harakalova, Magdalena, and van Steenbeek, Frank G

Published
2023

15. Human Plaque Myofibroblasts to Study Mechanisms of Atherosclerosis

Author

Experimentele Afd. Cardiologie 1, CDL Onderzoek Pasterkamp, CDL Research analisten, Cancer, Immuno/reuma onderzoek 1 (Vastert), Zorgeenheid Vaatchirurgie Medisch, Circulatory Health, Regenerative Medicine and Stem Cells, Infection & Immunity, Centraal Diagnostisch Laboratorium, Onderzoek Vrouw Hart & Vaatziekten, Child Health, Buono, Michele F, Benavente, Ernest Diez, Slenders, Lotte, Methorst, Daisey, Tessels, Daniëlle, Mili, Eloi, Finger, Roxy, Kapteijn, Daniek, Daniels, Mark, van den Dungen, Noortje A M, Calis, Jorg J A, Mol, Barend M, de Borst, Gert J, de Kleijn, Dominique P V, Pasterkamp, Gerard, den Ruijter, Hester M, Mokry, Michal, Experimentele Afd. Cardiologie 1, CDL Onderzoek Pasterkamp, CDL Research analisten, Cancer, Immuno/reuma onderzoek 1 (Vastert), Zorgeenheid Vaatchirurgie Medisch, Circulatory Health, Regenerative Medicine and Stem Cells, Infection & Immunity, Centraal Diagnostisch Laboratorium, Onderzoek Vrouw Hart & Vaatziekten, Child Health, Buono, Michele F, Benavente, Ernest Diez, Slenders, Lotte, Methorst, Daisey, Tessels, Daniëlle, Mili, Eloi, Finger, Roxy, Kapteijn, Daniek, Daniels, Mark, van den Dungen, Noortje A M, Calis, Jorg J A, Mol, Barend M, de Borst, Gert J, de Kleijn, Dominique P V, Pasterkamp, Gerard, den Ruijter, Hester M, and Mokry, Michal

Published
2023

16. Human primary plaque cell cultures to study mechanisms of atherosclerosis

Author

Buono, Michele F., primary, Benavente, Ernest Diez, additional, Slenders, Lotte, additional, Methorst, Daisey, additional, Tessels, Daniёlle, additional, Mili, Eloi, additional, Finger, Roxy, additional, Kapteijn, Daniek, additional, Daniels, Mark, additional, van den Dungen, Noortje A. M., additional, Calis, Jorg J. A., additional, Mol, Barend M., additional, de Borst, Gert J., additional, de Kleijn, Dominique P. V., additional, Pasterkamp, Gerard, additional, den Ruijter, Hester M., additional, and Mokry, Michal, additional

Published
2023
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18. N 6 -Methyladenosine Directly Regulates CD40L Expression in CD4 + T Lymphocytes.

Author

van Vroonhoven, Ellen C. N., Picavet, Lucas W., Scholman, Rianne C., van den Dungen, Noortje A. M., Mokry, Michal, Evers, Anouk, Lebbink, Robert J., Calis, Jorg J. A., Vastert, Sebastiaan J., and van Loosdregt, Jorg

Subjects
GENE expression, T cells, RNA-binding proteins, GENETIC regulation, T cell differentiation, CYTOKINE receptors, T cell receptors
Abstract

Simple Summary: The tight regulation of the expression of cytokines, surface receptors and co-stimulatory and co-inhibitory molecules is necessary for a well-functioning immune system. There are various cellular processes that regulate the expression of these immune regulatory proteins, for instance at the RNA transcript level. Epitranscriptomic regulation, involving RNA binding proteins and modifications, can determine the turnover and translation of mRNA transcripts. N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotic cells and it was demonstrated that m6A is involved in the early differentiation of CD4+ T lymphocytes. However, the function of m6A in CD4+ T cell activation and function is still incompletely understood. Here, we demonstrate that m6A regulates the activation of CD4+ T lymphocytes via the regulation of CD40 ligand expression, a key co-stimulatory molecule expressed on the cell surface of CD4+ T cells. The discovery of this novel function of m6A and its regulatory proteins contributes to our general understanding of CD4+ T cell activation, gene expression regulation and autoimmune disease pathogenesis. T cell activation is a highly regulated process, modulated via the expression of various immune regulatory proteins including cytokines, surface receptors and co-stimulatory proteins. N6-methyladenosine (m6A) is an RNA modification that can directly regulate RNA expression levels and it is associated with various biological processes. However, the function of m6A in T cell activation remains incompletely understood. We identify m6A as a novel regulator of the expression of the CD40 ligand (CD40L) in human CD4+ lymphocytes. Manipulation of the m6A 'eraser' fat mass and obesity-associated protein (FTO) and m6A 'writer' protein methyltransferase-like 3 (METTL3) directly affects the expression of CD40L. The m6A 'reader' protein YT521-B homology domain family-2 (YTHDF2) is hypothesized to be able to recognize and bind m6A specific sequences on the CD40L mRNA and promotes its degradation. This study demonstrates that CD40L expression in human primary CD4+ T lymphocytes is regulated via m6A modifications, elucidating a new regulatory mechanism in CD4+ T cell activation that could possibly be leveraged in the future to modulate T cell responses in patients with immune-related diseases. [ABSTRACT FROM AUTHOR]

Published
2023
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19. Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation

Author

CDL Onderzoek Pasterkamp, Experimentele Afd. Cardiologie 1, Child Health, Circulatory Health, CDL Cluster Onderzoek en Onderwijs, Onderzoek Precision medicine, Zorgeenheid Vaatchirurgie Medisch, Cancer, Regenerative Medicine and Stem Cells, Infection & Immunity, Onderzoek Vrouw Hart & Vaatziekten, Team Medisch, Centraal Diagnostisch Laboratorium, Mokry, Michal, Boltjes, Arjan, Slenders, Lotte, Bel-Bordes, Gemma, Cui, Kai, Brouwer, Eli, Mekke, Joost M., Depuydt, Marie A. C., Timmerman, Nathalie, Waissi, Farahnaz, Verwer, Maarten C., Turner, Adam W., Khan, Mohammad Daud, Hodonsky, Chani J., Diez Benavente, Ernest, Hartman, Robin J. G., van den Dungen, Noortje A. M., Lansu, Nico, Nagyova, Emilia, Prange, Koen H. M., Kovacic, Jason C., Björkegren, Johan L. M., Pavlos, Eleftherios, Andreakos, Evangelos, Schunkert, Heribert, Owens, Gary K., Monaco, Claudia, Finn, Aloke V., Virmani, Renu, Leeper, Nicholas J., de Winther, Menno P. J., Kuiper, Johan, de Borst, Gert J., Stroes, Erik S. G., Civelek, Mete, de Kleijn, Dominique P. V., den Ruijter, Hester M., Asselbergs, Folkert W., van der Laan, Sander W., Miller, Clint L., Pasterkamp, Gerard, CDL Onderzoek Pasterkamp, Experimentele Afd. Cardiologie 1, Child Health, Circulatory Health, CDL Cluster Onderzoek en Onderwijs, Onderzoek Precision medicine, Zorgeenheid Vaatchirurgie Medisch, Cancer, Regenerative Medicine and Stem Cells, Infection & Immunity, Onderzoek Vrouw Hart & Vaatziekten, Team Medisch, Centraal Diagnostisch Laboratorium, Mokry, Michal, Boltjes, Arjan, Slenders, Lotte, Bel-Bordes, Gemma, Cui, Kai, Brouwer, Eli, Mekke, Joost M., Depuydt, Marie A. C., Timmerman, Nathalie, Waissi, Farahnaz, Verwer, Maarten C., Turner, Adam W., Khan, Mohammad Daud, Hodonsky, Chani J., Diez Benavente, Ernest, Hartman, Robin J. G., van den Dungen, Noortje A. M., Lansu, Nico, Nagyova, Emilia, Prange, Koen H. M., Kovacic, Jason C., Björkegren, Johan L. M., Pavlos, Eleftherios, Andreakos, Evangelos, Schunkert, Heribert, Owens, Gary K., Monaco, Claudia, Finn, Aloke V., Virmani, Renu, Leeper, Nicholas J., de Winther, Menno P. J., Kuiper, Johan, de Borst, Gert J., Stroes, Erik S. G., Civelek, Mete, de Kleijn, Dominique P. V., den Ruijter, Hester M., Asselbergs, Folkert W., van der Laan, Sander W., Miller, Clint L., and Pasterkamp, Gerard

Published
2022

20. Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis

Author

Onderzoek Precision medicine, CDL Onderzoek Pasterkamp, Zorgeenheid Vaatchirurgie Medisch, Cancer, Brain, Circulatory Health, Regenerative Medicine and Stem Cells, Infection & Immunity, Team Medisch, Onderzoek Vrouw Hart & Vaatziekten, Child Health, Centraal Diagnostisch Laboratorium, Experimentele Afd. Cardiologie 1, Slenders, Lotte, Landsmeer, Lennart P L, Cui, Kai, Depuydt, Marie A C, Verwer, Maarten, Mekke, Joost, Timmerman, Nathalie, van den Dungen, Noortje A M, Kuiper, Johan, de Winther, Menno P J, Prange, Koen H M, Ma, Wei Feng, Miller, Clint L, Aherrahrou, Redouane, Civelek, Mete, de Borst, Gert J, de Kleijn, Dominique P V, Asselbergs, Folkert W, den Ruijter, Hester M, Boltjes, Arjan, Pasterkamp, Gerard, van der Laan, Sander W, Mokry, Michal, Onderzoek Precision medicine, CDL Onderzoek Pasterkamp, Zorgeenheid Vaatchirurgie Medisch, Cancer, Brain, Circulatory Health, Regenerative Medicine and Stem Cells, Infection & Immunity, Team Medisch, Onderzoek Vrouw Hart & Vaatziekten, Child Health, Centraal Diagnostisch Laboratorium, Experimentele Afd. Cardiologie 1, Slenders, Lotte, Landsmeer, Lennart P L, Cui, Kai, Depuydt, Marie A C, Verwer, Maarten, Mekke, Joost, Timmerman, Nathalie, van den Dungen, Noortje A M, Kuiper, Johan, de Winther, Menno P J, Prange, Koen H M, Ma, Wei Feng, Miller, Clint L, Aherrahrou, Redouane, Civelek, Mete, de Borst, Gert J, de Kleijn, Dominique P V, Asselbergs, Folkert W, den Ruijter, Hester M, Boltjes, Arjan, Pasterkamp, Gerard, van der Laan, Sander W, and Mokry, Michal

Published
2022

21. Chromatin Immunoprecipitation Sequencing (ChIP-seq) Protocol for Small Amounts of Frozen Biobanked Cardiac Tissue

Author

Onderzoek Precision medicine, CDL Onderzoek Pasterkamp, Cancer, Team Medisch, Circulatory Health, Experimentele Afd. Cardiologie 1, Child Health, Horsfield, Julia, Marsman, Judith, Pei, Jiayi, van den Dungen, Noortje A M, Asselbergs, Folkert W, Mokry, Michal, Harakalova, Magdalena, Onderzoek Precision medicine, CDL Onderzoek Pasterkamp, Cancer, Team Medisch, Circulatory Health, Experimentele Afd. Cardiologie 1, Child Health, Horsfield, Julia, Marsman, Judith, Pei, Jiayi, van den Dungen, Noortje A M, Asselbergs, Folkert W, Mokry, Michal, and Harakalova, Magdalena

Published
2022

22. Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis

Author

Slenders, Lotte, primary, Landsmeer, Lennart P L, additional, Cui, Kai, additional, Depuydt, Marie A C, additional, Verwer, Maarten, additional, Mekke, Joost, additional, Timmerman, Nathalie, additional, van den Dungen, Noortje A M, additional, Kuiper, Johan, additional, de Winther, Menno P J, additional, Prange, Koen H M, additional, Ma, Wei Feng, additional, Miller, Clint L, additional, Aherrahrou, Redouane, additional, Civelek, Mete, additional, de Borst, Gert J, additional, de Kleijn, Dominique P V, additional, Asselbergs, Folkert W, additional, den Ruijter, Hester M, additional, Boltjes, Arjan, additional, Pasterkamp, Gerard, additional, van der Laan, Sander W, additional, and Mokry, Michal, additional

Published
2021
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23. Transcriptomic-based clustering of advanced atherosclerotic plaques identifies subgroups of plaques with differential underlying biology that associate with clinical presentation

Author

Mokry, Michal, primary, Boltjes, Arjan, additional, Cui, Kai, additional, Slenders, Lotte, additional, Mekke, Joost M., additional, depuydt, Marie A.C., additional, Timmerman, Nathalie M., additional, Waissi, Farahnaz, additional, Verwer, Maarten C., additional, Turner, Adam W., additional, Khan, Mohammad D., additional, Hodonsky, Chani J., additional, Diez Benavente, Ernest, additional, Hartman, Robin J. G., additional, van den Dungen, Noortje A. M., additional, Lansu, Nico, additional, Nagyova, Emilia, additional, Prange, Koen H. M., additional, Pavlos, Eleftherios, additional, Andreakos, Evangelos, additional, Schunkert, Heribert, additional, Owens, Gary K., additional, Monaco, Claudia, additional, Finn, Aloke V., additional, Virmani, Renu, additional, Leeper, Nicholas J., additional, de Winther, Menno P. J., additional, Kuiper, Johan, additional, de Borst, Gert J., additional, Stroes, Erik S. G., additional, Civelek, Mete, additional, de Kleijn, Dominique P. V., additional, den Ruijter, Hester M., additional, Asselbergs, Folkert W., additional, van der Laan, Sander W., additional, Miller, Clint L., additional, and Pasterkamp, Gerard, additional

Published
2021
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24. Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels

Author

Oosterhoff, Loes A, Kruitwagen, Hedwig S, van Wolferen, Monique E, van Balkom, Bas W M, Mokry, Michal, Lansu, Nico, van den Dungen, Noortje A M, Penning, Louis C, Spanjersberg, Talitha C F, de Graaf, Johannes W, Veenendaal, Tomas, Zomerdijk, Flin, Fledderus, Joost O, Spee, Bart, van Steenbeek, Frank G, Biochemisch laboratorium, dCSCA RMSC-1, LS Interne geneeskunde, Sub Biomol.Mass Spect. and Proteomics, dCSCA AVR, Onderzoek, Undergraduate School, Biochemisch laboratorium, dCSCA RMSC-1, LS Interne geneeskunde, Sub Biomol.Mass Spect. and Proteomics, dCSCA AVR, Onderzoek, and Undergraduate School

Subjects
0301 basic medicine, Cell type, Vascular smooth muscle, Endothelium, Physiology, Angiogenesis, Biology, lcsh:Physiology, Transcriptome, 03 medical and health sciences, angiogenesis, 0302 clinical medicine, Tissue engineering, cell model system, vascular cell interaction, Physiology (medical), medicine, vascular smooth muscle cells, vascular smooth, Tissue homeostasis, Original Research, lcsh:QP1-981, Vascular disease, medicine.disease, endothelial cells, Cell biology, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, cardiovascular system
Abstract

Vasculature performs a critical function in tissue homeostasis, supply of oxygen and nutrients, and the removal of metabolic waste products. Vascular problems are implicated in a large variety of pathologies and accurate in vitro models resembling native vasculature are of great importance. Unfortunately, existing in vitro models do not sufficiently reflect their in vivo counterpart. The complexity of vasculature requires the examination of multiple cell types including endothelial cells (ECs) and vascular smooth muscle cells (VSMCs), as well as vessel location in the body from which they originate. The use of canine blood vessels provides a way to study vasculature with similar vessel size and physiology compared to human vasculature. We report an isolation procedure that provides the possibility to isolate both the endothelial and smooth muscle cells from the same vessels simultaneously, enabling new opportunities in investigating vasculature behavior. Canine primary ECs and VSMCs were isolated from the vena cava, vena porta and aorta. All tissue sources were derived from three donors for accurate comparison and to reduce inter-animal variation. The isolation and purification of the two distinct cell types was confirmed by morphology, gene- and protein-expression and function. As both cell types can be derived from the same vessel, this approach allows accurate modeling of vascular diseases and can also be used more widely, for example, in vascular bioreactors and tissue engineering designs. Additionally, we identified several new genes that were highly expressed in canine ECs, which may become candidate genes for novel EC markers. In addition, we observed transcriptional and functional differences between arterial- and venous-derived endothelium. Further exploration of the transcriptome and physiology of arteriovenous differentiation of primary cells may have important implications for a better understanding of the fundamental behavior of the vasculature and pathogenesis of vascular disease.

Published
2019
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25. Characterization of Endothelial and Smooth Muscle Cells From Different Canine Vessels

Author

Biochemisch laboratorium, dCSCA RMSC-1, LS Interne geneeskunde, Sub Biomol.Mass Spect. and Proteomics, dCSCA AVR, Onderzoek, Undergraduate School, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van Wolferen, Monique E, van Balkom, Bas W M, Mokry, Michal, Lansu, Nico, van den Dungen, Noortje A M, Penning, Louis C, Spanjersberg, Talitha C F, de Graaf, Johannes W, Veenendaal, Tomas, Zomerdijk, Flin, Fledderus, Joost O, Spee, Bart, van Steenbeek, Frank G, Biochemisch laboratorium, dCSCA RMSC-1, LS Interne geneeskunde, Sub Biomol.Mass Spect. and Proteomics, dCSCA AVR, Onderzoek, Undergraduate School, Oosterhoff, Loes A, Kruitwagen, Hedwig S, van Wolferen, Monique E, van Balkom, Bas W M, Mokry, Michal, Lansu, Nico, van den Dungen, Noortje A M, Penning, Louis C, Spanjersberg, Talitha C F, de Graaf, Johannes W, Veenendaal, Tomas, Zomerdijk, Flin, Fledderus, Joost O, Spee, Bart, and van Steenbeek, Frank G

Published
2019

26. Stem Cells are the Principal Intestinal Epithelial Responders to Bacterial Antigens

Author

Meddens, Claartje A., primary, de Vries, Maaike H., additional, Hijma, Hemme J., additional, Berrens, Anne Claire, additional, Westendorp, Bart, additional, van der Spek, Jet, additional, Kooiman, Berend A. P., additional, Schreurs, Renée R. C. E., additional, Lijster, Erik, additional, Prelic, Sinisa, additional, Nieuwenhuis, Ninke M., additional, Mijnders, Marjolein, additional, Vega, Miguel, additional, Jansen, Suze A., additional, Hanemaaijer, Evelyn S., additional, Lansu, Nico, additional, van den Dungen, Noortje A. M., additional, Bunders, Madeleine J., additional, Middendorp, Sabine, additional, Clevers, Hans, additional, Mokry, Michal, additional, and Nieuwenhuis, Edward E. S., additional

Published
2019
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27. Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease

Author

Meddens, Claartje A, Harakalova, Magdalena, van den Dungen, Noortje A M, Foroughi Asl, Hassan, Hijma, Hemme J, Cuppen, Edwin P J G, Björkegren, Johan L M, Asselbergs, Folkert W, Nieuwenhuis, Edward E S, Mokry, Michal, Meddens, Claartje A, Harakalova, Magdalena, van den Dungen, Noortje A M, Foroughi Asl, Hassan, Hijma, Hemme J, Cuppen, Edwin P J G, Björkegren, Johan L M, Asselbergs, Folkert W, Nieuwenhuis, Edward E S, and Mokry, Michal

Published
2016

28. Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease

Author

MDL onderzoek 3, Child Health, Cardiologie Arts-onderzoekers, CMM, Circulatory Health, Cancer, Brain, Cardiologie, Zorg en O&O, Regenerative Medicine and Stem Cells, Infection & Immunity, Meddens, Claartje A, Harakalova, Magdalena, van den Dungen, Noortje A M, Foroughi Asl, Hassan, Hijma, Hemme J, Cuppen, Edwin P J G, Björkegren, Johan L M, Asselbergs, Folkert W, Nieuwenhuis, Edward E S, Mokry, Michal, MDL onderzoek 3, Child Health, Cardiologie Arts-onderzoekers, CMM, Circulatory Health, Cancer, Brain, Cardiologie, Zorg en O&O, Regenerative Medicine and Stem Cells, Infection & Immunity, Meddens, Claartje A, Harakalova, Magdalena, van den Dungen, Noortje A M, Foroughi Asl, Hassan, Hijma, Hemme J, Cuppen, Edwin P J G, Björkegren, Johan L M, Asselbergs, Folkert W, Nieuwenhuis, Edward E S, and Mokry, Michal

Published
2016

29. Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease

Author

Meddens, Claartje A., primary, Harakalova, Magdalena, additional, van den Dungen, Noortje A. M., additional, Foroughi Asl, Hassan, additional, Hijma, Hemme J., additional, Cuppen, Edwin P. J. G., additional, Björkegren, Johan L. M., additional, Asselbergs, Folkert W., additional, Nieuwenhuis, Edward E. S., additional, and Mokry, Michal, additional

Published
2016
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30. N6-methyladenosine promotes TNF mRNA degradation in CD4+ T lymphocytes.

Author

van Vroonhoven ECN, Picavet LW, Scholman RC, Sijbers LJPM, Kievit CRE, van den Dungen NAM, Mokry M, Evers A, Lebbink RJ, Mocholi E, Coffer PJ, Calis JJA, Vastert SJ, and van Loosdregt J

Subjects
Humans, Methylation, Lymphocyte Activation, Gene Expression Regulation, Adenosine analogs & derivatives, Adenosine metabolism, CD4-Positive T-Lymphocytes metabolism, CD4-Positive T-Lymphocytes immunology, RNA Stability, RNA, Messenger genetics, RNA, Messenger metabolism, Tumor Necrosis Factor-alpha metabolism, RNA-Binding Proteins metabolism, RNA-Binding Proteins genetics
Abstract

N6-methyladenosine (m6A) is a RNA modification that can regulate post-transcriptional processes including RNA stability, translation, splicing, and nuclear export. In CD4+ lymphocytes, m6A modifications have been demonstrated to play a role in early differentiation processes. The role of m6A in CD4+ T cell activation and effector function remains incompletely understood. To assess the role of m6A in CD4+ T lymphocyte activation and function, we assessed the transcriptome-wide m6A landscape of human primary CD4+ T cells by methylated RNA immunoprecipitation sequencing. Stimulation of the T cells impacted the m6A pattern of hundreds of transcripts including tumor necrosis factor (TNF). m6A methylation was increased on TNF messenger RNA (mRNA) after activation, predominantly in the 3' untranslated region of the transcript. Manipulation of m6A levels in primary human T cells, the directly affected the expression of TNF. Furthermore, we identified that the m6A reader protein YTHDF2 binds m6A-methylated TNF mRNA, and promotes its degradation. Taken together, this study demonstrates that TNF expression in CD4+ T lymphocytes is regulated via m6A and YTHDF2, thereby providing novel insight into the regulation of T cell effector functions., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Leukocyte Biology.)

Published
2024
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31. Chromatin Immunoprecipitation Sequencing (ChIP-seq) Protocol for Small Amounts of Frozen Biobanked Cardiac Tissue.

Author

Pei J, van den Dungen NAM, Asselbergs FW, Mokry M, and Harakalova M

Subjects
Chromatin genetics, Chromatin Immunoprecipitation methods, Genome, High-Throughput Nucleotide Sequencing methods, Humans, Protein Processing, Post-Translational, Chromatin Immunoprecipitation Sequencing, Histone Code
Abstract

Chromatin immunoprecipitation and sequencing (ChIP-seq) is a well-established method to study the epigenetic profile at the genome-wide scale, including histone modifications and DNA-protein interactions. It provides valuable insights to better understand disease mechanisms. Here we present an optimized ChIP-seq protocol suitable for human cardiac tissues, especially the frozen biobanked small biopsy samples., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2022
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32. Chromatin Conformation Links Distal Target Genes to CKD Loci.

Author

Brandt MM, Meddens CA, Louzao-Martinez L, van den Dungen NAM, Lansu NR, Nieuwenhuis EES, Duncker DJ, Verhaar MC, Joles JA, Mokry M, and Cheng C

Subjects
Animals, Biosynthetic Pathways genetics, Cells, Cultured, Databases, Genetic, Endothelial Cells, Genetic Predisposition to Disease genetics, Genotype, Homeostasis genetics, Humans, Kidney Tubules, Mice, Polymorphism, Single Nucleotide, Quantitative Trait Loci, RNA, Messenger metabolism, Sequence Analysis, DNA methods, Chromatin chemistry, DNA chemistry, Nucleic Acid Conformation, Renal Insufficiency, Chronic genetics
Abstract

Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes. To identify target genes of these DREs, we used circular chromosome conformation capture (4C) sequencing on glomerular endothelial cells and renal tubular epithelial cells. Our 4C analyses revealed interactions of CKD-associated susceptibility regions with the transcriptional start sites of 304 target genes. Overlap with multiple databases confirmed that many of these target genes are involved in kidney homeostasis. Expression quantitative trait loci analysis revealed that mRNA levels of many target genes are genotype dependent. Pathway analyses showed that target genes were enriched in processes crucial for renal function, identifying dysregulated geranylgeranyl diphosphate biosynthesis as a potential disease mechanism. Overall, our data annotated multiple genes to previously reported CKD-associated single-nucleotide polymorphisms and provided evidence for interaction between these loci and target genes. This pipeline provides a novel technique for hypothesis generation and complements classic GWAS interpretation. Future studies are required to specify the implications of our dataset and further reveal the complex roles that common variants have in complex diseases, such as CKD., (Copyright © 2018 by the American Society of Nephrology.)

Published
2018
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