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2. Antibody-mediated delivery of viral epitopes to redirect EBV-specific CD8+ T-cell immunity towards cancer cells

Author

van der Wulp, Willemijn, primary, Remst, Dennis F. G., additional, Kester, Michel G. D., additional, Hagedoorn, Renate S., additional, Parren, Paul W. H. I., additional, van Kasteren, Sander I., additional, Schuurman, Janine, additional, Hoeben, Rob C., additional, Ressing, Maaike E., additional, Bleijlevens, Boris, additional, and Heemskerk, Mirjam H. M., additional

Published
2023
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3. Comparison of methods generating antibody-epitope conjugates for targeting cancer with virus-specific T cells

Author

van der Wulp, Willemijn, primary, Gram, Anna M., additional, Bleijlevens, Boris, additional, Hagedoorn, Renate S., additional, Araman, Can, additional, Kim, Robbert Q., additional, Drijfhout, Jan Wouter, additional, Parren, Paul W. H. I., additional, Hibbert, Richard G., additional, Hoeben, Rob C., additional, van Kasteren, Sander I., additional, Schuurman, Janine, additional, Ressing, Maaike E., additional, and Heemskerk, Mirjam H. M., additional

Published
2023
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4. Supplementary Data from Mesenchymal-Type Neuroblastoma Cells Escape ALK Inhibitors

Author

Westerhout, Ellen M., primary, Hamdi, Mohamed, primary, Stroeken, Peter, primary, Nowakowska, Natalia E., primary, Lakeman, Arjan, primary, van Arkel, Jennemiek, primary, Hasselt, Nancy E., primary, Bleijlevens, Boris, primary, Akogul, Nurdan, primary, Haneveld, Franciska, primary, Chan, Alvin, primary, van Sluis, Peter, primary, Zwijnenburg, Danny, primary, Volckmann, Richard, primary, van Noesel, Carel J.M., primary, Adameyko, Igor, primary, van Groningen, Tim, primary, Koster, Jan, primary, Valentijn, Linda J., primary, van Nes, Johan, primary, and Versteeg, Rogier, primary

Published
2023
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5. Data from Mesenchymal-Type Neuroblastoma Cells Escape ALK Inhibitors

Author

Westerhout, Ellen M., primary, Hamdi, Mohamed, primary, Stroeken, Peter, primary, Nowakowska, Natalia E., primary, Lakeman, Arjan, primary, van Arkel, Jennemiek, primary, Hasselt, Nancy E., primary, Bleijlevens, Boris, primary, Akogul, Nurdan, primary, Haneveld, Franciska, primary, Chan, Alvin, primary, van Sluis, Peter, primary, Zwijnenburg, Danny, primary, Volckmann, Richard, primary, van Noesel, Carel J.M., primary, Adameyko, Igor, primary, van Groningen, Tim, primary, Koster, Jan, primary, Valentijn, Linda J., primary, van Nes, Johan, primary, and Versteeg, Rogier, primary

Published
2023
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8. Antibody-mediated delivery of viral epitopes to redirect EBV-specific CD8+T-cell immunity towards cancer cells

Author

van der Wulp, Willemijn, Remst, Dennis F. G., Kester, Michel G. D., Hagedoorn, Renate S., Parren, Paul W. H. I., van Kasteren, Sander I., Schuurman, Janine, Hoeben, Rob C., Ressing, Maaike E., Bleijlevens, Boris, and Heemskerk, Mirjam H. M.

Abstract

Antibody-mediated delivery of immunogenic epitopes to redirect virus-specific CD8+T-cells towards cancer cells is an emerging and promising new therapeutic strategy. These so-called antibody-epitope conjugates (AECs) rely on the proteolytic release of the epitopes close to the tumor surface for presentation by HLA class I molecules to eventually redirect and activate virus-specific CD8+T-cells towards tumor cells. We fused the immunogenic EBV-BRLF1 epitope preceded by a protease cleavage site to the C-terminus of the heavy and/or light chains of cetuximab and trastuzumab. We evaluated these AECs and found that, even though all AECs were able to redirect the EBV-specific T-cells, AECs with an epitope fused to the C-terminus of the heavy chain resulted in higher levels of T-cell activation compared to AECs with the same epitope fused to the light chain of an antibody. We observed that all AECs were depending on the presence of the antibody target, that the level of T-cell activation correlated with expression levels of the antibody target, and that our AECs could efficiently deliver the BRLF1 epitope to cancer cell lines from different origins (breast, ovarian, lung, and cervical cancer and a multiple myeloma). Moreover, in vivo, the AECs efficiently reduced tumor burden and increased the overall survival, which was prolonged even further in combination with immune checkpoint blockade. We demonstrate the potential of these genetically fused AECs to redirect the potent EBV-specific T-cells towards cancer in vitro and in vivo.

Published
2024
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10. Comparative Analysis of Antibodies and Heavily Glycosylated Macromolecular Immune Complexes by Size-Exclusion Chromatography Multi-Angle Light Scattering, Native Charge Detection Mass Spectrometry, and Mass Photometry

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Boer, Maurits A. den, Lai, Szu-Hsueh, Xue, Xiaoguang, Kampen, Muriel D. van, Bleijlevens, Boris, Heck, Albert J. R., Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Boer, Maurits A. den, Lai, Szu-Hsueh, Xue, Xiaoguang, Kampen, Muriel D. van, Bleijlevens, Boris, and Heck, Albert J. R.

Published
2022

12. Comparative Analysis of Antibodies and Heavily Glycosylated Macromolecular Immune Complexes by Size-Exclusion Chromatography Multi-Angle Light Scattering, Native Charge Detection Mass Spectrometry, and Mass Photometry

Author

Boer, Maurits A. den, Lai, Szu-Hsueh, Xue, Xiaoguang, Kampen, Muriel D. van, Bleijlevens, Boris, Heck, Albert J. R., Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, and Biomolecular Mass Spectrometry and Proteomics

Subjects
Photometry, Glycosylation, Chromatography, Gel, Antigen-Antibody Complex, Article, Mass Spectrometry, Analytical Chemistry
Abstract

Qualitative and quantitative mass analysis of antibodies and related macromolecular immune complexes is a prerequisite for determining their identity, binding partners, stoichiometries, and affinities. A plethora of bioanalytical technologies exist to determine such characteristics, typically based on size, interaction with functionalized surfaces, light scattering, or direct mass measurements. While these methods are highly complementary, they also exhibit unique strengths and weaknesses. Here, we benchmark mass photometry (MP), a recently introduced technology for mass measurement, against native mass spectrometry (MS) and size exclusion chromatography multi-angle light scattering (SEC-MALS). We examine samples of variable complexity, namely, IgG4Δhinge dimerizing half-bodies, IgG-RGY hexamers, heterogeneously glycosylated IgG:sEGFR antibody–antigen complexes, and finally megadalton assemblies involved in complement activation. We thereby assess the ability to determine (1) binding affinities and stoichiometries, (2) accurate masses, for extensively glycosylated species, and (3) assembly pathways of large heterogeneous immune complexes. We find that MP provides a sensitive approach for characterizing antibodies and stable assemblies, with dissociation correction enabling us to expand the measurable affinity range. In terms of mass resolution and accuracy, native MS performs the best but is occasionally hampered by artifacts induced by electrospray ionization, and its resolving power diminishes when analyzing extensively glycosylated proteins. In the latter cases, MP performs well, but single-particle charge detection MS can also be useful in this respect, measuring masses of heterogeneous assemblies even more accurately. Both methods perform well compared to SEC-MALS, still being the most established method in biopharma. Together, our data highlight the complementarity of these approaches, each having its unique strengths and weaknesses.

Published
2022

14. Mesenchymal-Type Neuroblastoma Cells Escape ALK Inhibitors

Author

Westerhout, Ellen M., primary, Hamdi, Mohamed, additional, Stroeken, Peter, additional, Nowakowska, Natalia E., additional, Lakeman, Arjan, additional, van Arkel, Jennemiek, additional, Hasselt, Nancy E., additional, Bleijlevens, Boris, additional, Akogul, Nurdan, additional, Haneveld, Franciska, additional, Chan, Alvin, additional, van Sluis, Peter, additional, Zwijnenburg, Danny, additional, Volckmann, Richard, additional, van Noesel, Carel J.M., additional, Adameyko, Igor, additional, van Groningen, Tim, additional, Koster, Jan, additional, Valentijn, Linda J., additional, van Nes, Johan, additional, and Versteeg, Rogier, additional

Published
2021
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24. Involvement of hyp gene products in maturation of the H(sub)2-sensing [NiFe] hydrogenase of Ralstonia eutropha

Author

Buhrke, Thorsten, Bleijlevens, Boris, Albracht, Simon P.J., and Friedrich, Barbel

Subjects
Enzymes -- Regulation, Gene expression -- Analysis, Structure-activity relationships (Biochemistry) -- Analysis, Cellular signal transduction -- Physiological aspects, Biological sciences
Abstract

Results demonstrate that the complete set of Hyp proteins, with the exception of the HypX, mediates the incorporation of the hydrogen-activating [NiFe] site into the regulatory hydrogenase in Ralstonia eutropha. Data indicate that HypF elimination causes a 90% reduction in the regulatory hydrogenase activity.

Published
2001

29. Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

Author

Hoefsloot Huub CJ, de Koster Chris G, Bleijlevens Boris, van Themaat Emiel, Buist Marrije R, Moerland Perry D, Wegdam Wouter, and Aerts Johannes MFG

Subjects
Cytology, QH573-671
Abstract

Abstract Background Mass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Results Two in-house generated clinical SELDI-TOF MS datasets are used in this study as an example of high throughput mass-spectrometry data. We perform a systematic comparison of two commonly used pre-processing methods as implemented in Ciphergen ProteinChip Software and in the Cromwell package. With respect to reproducibility, Ciphergen and Cromwell pre-processing are largely comparable. We find that the overlap between peaks detected by either Ciphergen ProteinChip Software or Cromwell is large. This is especially the case for the more stringent peak detection settings. Moreover, similarity of the estimated intensities between matched peaks is high. We evaluate the pre-processing methods using five different classification methods. Classification is done in a double cross-validation protocol using repeated random sampling to obtain an unbiased estimate of classification accuracy. No pre-processing method significantly outperforms the other for all peak detection settings evaluated. Conclusion We use classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods. Both pre-processing methods lead to similar classification results on an ovarian cancer and a Gaucher disease dataset. However, the settings for pre-processing parameters lead to large differences in classification accuracy and are therefore of crucial importance. We advocate the evaluation over a range of parameter settings when comparing pre-processing methods. Our analysis also demonstrates that reliable classification results can be obtained with a combination of strict sample handling and a well-defined classification protocol on clinical samples.

Published
2009
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30. SELDI-TOF mass spectrometry of High-Density Lipoprotein

Author

Rezaee Farhad, Bleijlevens Boris, Levels Johannes HM, Aerts Johannes MFG, and Meijers Joost CM

Subjects
Cytology, QH573-671
Abstract

Abstract Background High-Density Lipoprotein (HDL), one of the main plasma lipoproteins, serves as a docking station for proteins involved in inflammation, coagulation, and lipid metabolism. Methods To elucidate the protein composition of HDL, we employed SELDI-TOF mass spectrometry as a potential high-throughput proteomic candidate for protein profiling of HDL. HDL derived from normolipemic individuals was captured on PS20 protein-chips using covalently bound antibodies against apo A-I or A-II. Results After optimisation, on-chip capture of HDL particles directly from plasma or from pre-purified HDL resulted in comparable fingerprints confirming specific capture of HDL. Depending on the capture antibody some differences in the fingerprint were observed. The most detailed fingerprint was observed up to 50 kDa; approximately 95 peaks were detected in the 3–50 kDa molecular mass range. Between 50 and 160 kDa, 27 more peaks were detected. Conclusion Based on these results, SELDI-TOF MS may be a suitable high-throughput candidate for HDL protein profiling and marker search. This approach may be used to i) investigate the underlying mechanisms that lead to increased atherothrombotic risk and ii) to investigate the atherothrombotic state of an individual.

Published
2007
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32. Targeting CD40-Induced TRAF6 Signaling in Macrophages Reduces Atherosclerosis

Author

Seijkens, Tom T.P., primary, van Tiel, Claudia M., additional, Kusters, Pascal J.H., additional, Atzler, Dorothee, additional, Soehnlein, Oliver, additional, Zarzycka, Barbara, additional, Aarts, Suzanne A.B.M., additional, Lameijer, Marnix, additional, Gijbels, Marion J., additional, Beckers, Linda, additional, den Toom, Myrthe, additional, Slütter, Bram, additional, Kuiper, Johan, additional, Duchene, Johan, additional, Aslani, Maria, additional, Megens, Remco T.A., additional, van ‘t Veer, Cornelis, additional, Kooij, Gijs, additional, Schrijver, Roy, additional, Hoeksema, Marten A., additional, Boon, Louis, additional, Fay, Francois, additional, Tang, Jun, additional, Baxter, Samantha, additional, Jongejan, Aldo, additional, Moerland, Perry D., additional, Vriend, Gert, additional, Bleijlevens, Boris, additional, Fisher, Edward A., additional, Duivenvoorden, Raphael, additional, Gerdes, Norbert, additional, de Winther, Menno P.J., additional, Nicolaes, Gerry A., additional, Mulder, Willem J.M., additional, Weber, Christian, additional, and Lutgens, Esther, additional

Published
2018
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33. Stabilization of Glucocerebrosidase by Active Site Occupancy

Author

Ben Bdira, Fredj, primary, Kallemeijn, Wouter W., additional, Oussoren, Saskia V., additional, Scheij, Saskia, additional, Bleijlevens, Boris, additional, Florea, Bogdan I., additional, van Roomen, Cindy P. A. A., additional, Ottenhoff, Roelof, additional, van Kooten, Marielle J. F. M., additional, Walvoort, Marthe T. C., additional, Witte, Martin D., additional, Boot, Rolf G., additional, Ubbink, Marcellus, additional, Overkleeft, Herman S., additional, and Aerts, Johannes M. F. G., additional

Published
2017
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34. Abstract 224: TRAF-STOP-RHDL-Nanoparticles Reduce Atherosclerosis

Author

van Tiel, Claudia M, primary, Seijkens, Tom T, additional, Kusters, Pascal J, additional, Zarzycka, Barbara, additional, Soehnlein, Oliver, additional, Gijbels, Marion J, additional, Fay, Francois, additional, Bleijlevens, Boris, additional, Gerdes, Norbert, additional, de Winther, Menno P, additional, Nicholaes, Gerry A, additional, Mulder, Willem J, additional, Weber, Christian, additional, and Lutgens, Esther, additional

Published
2017
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37. A multi-infrastructure gateway for virtual drug screening

Author

Jaghoori, Mohammad Mahdi, van Altena, Allard J., Bleijlevens, Boris, Ramezani, Sara, Font, Juan Luis, Olabarriaga, Silvia D., Other Research, Epidemiology and Data Science, Other departments, Amsterdam Gastroenterology Endocrinology Metabolism, Medical Biochemistry, and Amsterdam Public Health

Abstract

In computer-aided drug design, software tools are used to narrow down possible drug candidates, thereby reducing the amount of expensive in vitro research, by a process called virtual screening. This process includes large computations that require advanced computing infrastructure; however, using rapidly evolving high-performance computing platforms can be difficult for biochemists. In this paper, we present a science gateway for virtual screening that has been tailored to the specific needs of our local users. The gateway provides user-friendly access to distributed computing infrastructures for high-throughput experiments with a few clicks. Its design is based on the generic layer developed for another gateway for neuroimaging data analysis, including data and computation management, as well as support for its operation. To facilitate scalability, the system architecture allows for adding new computing platforms to the back-end without affecting the front-end, from which the user can dynamically choose the preferred infrastructure. This paper describes the user-centered design process, the system architecture and a performance assessment using gLite grid, Hadoop, and a local cluster. The empirical results show considerable speed-ups and ease of use, as well as user satisfaction. Copyright (c) 2015John Wiley & Sons, Ltd

Published
2015

39. Variable Major Proteins as Targets for Specific Antibodies against Borrelia miyamotoi

Author

Wagemakers, Alex, primary, Koetsveld, Joris, additional, Narasimhan, Sukanya, additional, Wickel, Melvin, additional, Deponte, Kathleen, additional, Bleijlevens, Boris, additional, Jahfari, Seta, additional, Sprong, Hein, additional, Karan, Lyudmila S., additional, Sarksyan, Denis S., additional, van der Poll, Tom, additional, Bockenstedt, Linda K., additional, Bins, Adriaan D., additional, Platonov, Alexander E., additional, Fikrig, Erol, additional, and Hovius, Joppe W., additional

Published
2016
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40. Class effects of SGLT2 inhibitors in mouse cardiomyocytes and hearts: inhibition of Na+/H+ exchanger, lowering of cytosolic Na+ and vasodilation.

Author

Uthman, Laween, Baartscheer, Antonius, Bleijlevens, Boris, Schumacher, Cees A., Fiolet, Jan W. T., Koeman, Anneke, Jancev, Milena, Hollmann, Markus W., Weber, Nina C., Coronel, Ruben, and Zuurbier, Coert J.

Abstract

Aims/hypothesis: Sodium–glucose cotransporter 2 (SGLT2) inhibitors (SGLT2i) constitute a novel class of glucose-lowering (type 2) kidney-targeted agents. We recently reported that the SGLT2i empagliflozin (EMPA) reduced cardiac cytosolic Na+ ([Na+]c) and cytosolic Ca2+ ([Ca2+]c) concentrations through inhibition of Na+/H+ exchanger (NHE). Here, we examine (1) whether the SGLT2i dapagliflozin (DAPA) and canagliflozin (CANA) also inhibit NHE and reduce [Na+]c; (2) a structural model for the interaction of SGLT2i to NHE; (3) to what extent SGLT2i affect the haemodynamic and metabolic performance of isolated hearts of healthy mice.Methods: Cardiac NHE activity and [Na+]c in mouse cardiomyocytes were measured in the presence of clinically relevant concentrations of EMPA (1 μmol/l), DAPA (1 μmol/l), CANA (3 μmol/l) or vehicle. NHE docking simulation studies were applied to explore potential binding sites for SGTL2i. Constant-flow Langendorff-perfused mouse hearts were subjected to SGLT2i for 30 min, and cardiovascular function, O2 consumption and energetics (phosphocreatine (PCr)/ATP) were determined.Results: EMPA, DAPA and CANA inhibited NHE activity (measured through low pH recovery after NH4+ pulse: EMPA 6.69 ± 0.09, DAPA 6.77 ± 0.12 and CANA 6.80 ± 0.18 vs vehicle 7.09 ± 0.09; p < 0.001 for all three comparisons) and reduced [Na+]c (in mmol/l: EMPA 10.0 ± 0.5, DAPA 10.7 ± 0.7 and CANA 11.0 ± 0.9 vs vehicle 12.7 ± 0.7; p < 0.001). Docking studies provided high binding affinity of all three SGLT2i with the extracellular Na+-binding site of NHE. EMPA and CANA, but not DAPA, induced coronary vasodilation of the intact heart. PCr/ATP remained unaffected.Conclusions/interpretation: EMPA, DAPA and CANA directly inhibit cardiac NHE flux and reduce [Na+]c, possibly by binding with the Na+-binding site of NHE-1. Furthermore, EMPA and CANA affect the healthy heart by inducing vasodilation. The [Na+]c-lowering class effect of SGLT2i is a potential approach to combat elevated [Na+]c that is known to occur in heart failure and diabetes. [ABSTRACT FROM AUTHOR]

Published
2018
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43. Ultrasensitive in situ visualization of active glucocerebrosidase molecules

Author

Witte, Martin D., Kallemeijn, Wouter W., Aten, Jan, Li, Kah-Yee, Strijland, Anneke, Donker-Koopman, Wilma E., Nieuwendijk, Adrianus M.C.H. van den, Bleijlevens, Boris, Kramer, Gertjan, Florea, Bogdan I., Hooibrink, Berend, Hollak, Carla E.M., Ottenhoff, Roelof, Boot, Rolf G., Marel, Gijsbert A. van der, Overkleeft, Herman S., Aerts, Johannes M.F.G., Witte, Martin D., Kallemeijn, Wouter W., Aten, Jan, Li, Kah-Yee, Strijland, Anneke, Donker-Koopman, Wilma E., Nieuwendijk, Adrianus M.C.H. van den, Bleijlevens, Boris, Kramer, Gertjan, Florea, Bogdan I., Hooibrink, Berend, Hollak, Carla E.M., Ottenhoff, Roelof, Boot, Rolf G., Marel, Gijsbert A. van der, Overkleeft, Herman S., and Aerts, Johannes M.F.G.

Abstract

Deficiency of glucocerebrosidase (GBA) underlies Gaucher disease, a common lysosomal storage disorder. Carriership for Gaucher disease has recently been identified as major risk for parkinsonism. Presently, no method exists to visualize active GBA molecules in situ. We here report the design, synthesis and application of two fluorescent activity-based probes allowing highly specific labeling of active GBA molecules in vitro and in cultured cells and mice in vivo. Detection of in vitro labeled recombinant GBA on slab gels after electrophoresis is in the low attomolar range. Using cell or tissue lysates, we obtained exclusive labeling of GBA molecules. We present evidence from fluorescence-activated cell sorting analysis, fluorescence microscopy and pulse-chase experiments of highly efficient labeling of GBA molecules in intact cells as well as tissues of mice. In addition, we illustrate the use of the fluorescent probes to study inhibitors and tentative chaperones in living cells.

Published
2010

45. Ultrasensitive in situ visualization of active glucocerebrosidase molecules

Author

Witte, Martin D, primary, Kallemeijn, Wouter W, additional, Aten, Jan, additional, Li, Kah-Yee, additional, Strijland, Anneke, additional, Donker-Koopman, Wilma E, additional, van den Nieuwendijk, Adrianus M C H, additional, Bleijlevens, Boris, additional, Kramer, Gertjan, additional, Florea, Bogdan I, additional, Hooibrink, Berend, additional, Hollak, Carla E M, additional, Ottenhoff, Roelof, additional, Boot, Rolf G, additional, van der Marel, Gijsbert A, additional, Overkleeft, Herman S, additional, and Aerts, Johannes M F G, additional

Published
2010
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48. Characterization of a cyanobacterial-like uptake [NiFe] hydrogenase: EPR and FTIR spectroscopic studies of the enzyme from Acidithiobacillus ferrooxidans

Author

Schröder, Olga, primary, Bleijlevens, Boris, additional, de Jongh, Thyra E., additional, Chen, Zhujun, additional, Li, Tianshu, additional, Fischer, Jörg, additional, Förster, Jochen, additional, Friedrich, Cornelius G., additional, Bagley, Kimberly A., additional, Albracht, Simon P. J., additional, and Lubitz, Wolfgang, additional

Published
2006
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