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1,428 results on '"Afd Biomol.Mass Spect. and Proteomics"'

1. MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer

Author

Afd Biomol.Mass Spect. and Proteomics, Liao, HQ, Barra, C, Zhou, ZC, Peng, X, Woodhouse, I, Tailor, A, Parker, R, Carre, A, Borrow, P, Hogan, MJ, Paes, W, Eisenlohr, LC, Mallone, R, Nielsen, M, Ternette, N, Afd Biomol.Mass Spect. and Proteomics, Liao, HQ, Barra, C, Zhou, ZC, Peng, X, Woodhouse, I, Tailor, A, Parker, R, Carre, A, Borrow, P, Hogan, MJ, Paes, W, Eisenlohr, LC, Mallone, R, Nielsen, M, and Ternette, N

Published
2024

2. Genotype-dependent N-glycosylation and newly exposed O-glycosylation affect plasmin-induced cleavage of histidine-rich glycoprotein (HRG)

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Zou, Yang, Pronker, Matti F, Damen, J Mirjam A, Heck, Albert J R, Reiding, Karli R, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Zou, Yang, Pronker, Matti F, Damen, J Mirjam A, Heck, Albert J R, and Reiding, Karli R

Published
2024

4. Filamentous fungus-produced human monoclonal antibody provides protection against SARS-CoV-2 in hamster and non-human primate models

Author

Virologie, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Infectious Diseases and Immunology - Virology, Kaiser, Franziska K, Hernandez, Mariana Gonzalez, Krüger, Nadine, Englund, Ellinor, Du, Wenjuan, Mykytyn, Anna Z, Raadsen, Mathijs P, Lamers, Mart M, Rodrigues Ianiski, Francine, Shamorkina, Tatiana M, Snijder, Joost, Armando, Federico, Beythien, Georg, Ciurkiewicz, Malgorzata, Schreiner, Tom, Gruber-Dujardin, Eva, Bleyer, Martina, Batura, Olga, Erffmeier, Lena, Hinkel, Rabea, Rocha, Cheila, Mirolo, Monica, Drabek, Dubravka, Bosch, Berend-Jan, Emalfarb, Mark, Valbuena, Noelia, Tchelet, Ronen, Baumgärtner, Wolfgang, Saloheimo, Markku, Pöhlmann, Stefan, Grosveld, Frank, Haagmans, Bart L, Osterhaus, Albert D M E, Virologie, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Infectious Diseases and Immunology - Virology, Kaiser, Franziska K, Hernandez, Mariana Gonzalez, Krüger, Nadine, Englund, Ellinor, Du, Wenjuan, Mykytyn, Anna Z, Raadsen, Mathijs P, Lamers, Mart M, Rodrigues Ianiski, Francine, Shamorkina, Tatiana M, Snijder, Joost, Armando, Federico, Beythien, Georg, Ciurkiewicz, Malgorzata, Schreiner, Tom, Gruber-Dujardin, Eva, Bleyer, Martina, Batura, Olga, Erffmeier, Lena, Hinkel, Rabea, Rocha, Cheila, Mirolo, Monica, Drabek, Dubravka, Bosch, Berend-Jan, Emalfarb, Mark, Valbuena, Noelia, Tchelet, Ronen, Baumgärtner, Wolfgang, Saloheimo, Markku, Pöhlmann, Stefan, Grosveld, Frank, Haagmans, Bart L, and Osterhaus, Albert D M E

Published
2024

5. MUC13 negatively regulates tight junction proteins and intestinal epithelial barrier integrity via Protein Kinase C

Author

Infectiebiologie, Afd Biomol.Mass Spect. and Proteomics, Pathobiologie, Celbiologie, IOV CCB, Infectious Diseases and Immunology - Infection Biology, Cell Biology, Metabolism & Cancer - Cancer, Cell Biology, Metabolism & Cancer - Cellbiology, Segui-Perez, Celia, Stapels, Daphne A C, Ma, Ziliang, Su, Jinyi, Passchier, Elsemieke, Westendorp, Bart, Wubbolts, Richard W, Wu, Wei, van Putten, Jos P M, Strijbis, Karin, Infectiebiologie, Afd Biomol.Mass Spect. and Proteomics, Pathobiologie, Celbiologie, IOV CCB, Infectious Diseases and Immunology - Infection Biology, Cell Biology, Metabolism & Cancer - Cancer, Cell Biology, Metabolism & Cancer - Cellbiology, Segui-Perez, Celia, Stapels, Daphne A C, Ma, Ziliang, Su, Jinyi, Passchier, Elsemieke, Westendorp, Bart, Wubbolts, Richard W, Wu, Wei, van Putten, Jos P M, and Strijbis, Karin

Published
2024

6. Assessment of IgG-Fc glycosylation from individual RhD-specific B cell clones reveals regulation at clonal rather than clonotypic level

Author

Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, de Graaf, Erik L., Larsen, Mads Delbo, van der Bolt, Nieke, Visser, Remco, Verhagen, Onno J.H.M., Hipgrave Ederveen, Agnes L., Koeleman, Carolien A.M., van der Schoot, C. Ellen, Wuhrer, Manfred, Vidarsson, Gestur, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, de Graaf, Erik L., Larsen, Mads Delbo, van der Bolt, Nieke, Visser, Remco, Verhagen, Onno J.H.M., Hipgrave Ederveen, Agnes L., Koeleman, Carolien A.M., van der Schoot, C. Ellen, Wuhrer, Manfred, and Vidarsson, Gestur

Published
2024

7. Phosphoprotein dynamics of interacting T cells and tumor cells by HySic

Author

Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Ibáñez-Molero, Sofía, Pruijs, Joannes T.M., Atmopawiro, Alisha, Wang, Fujia, Terry, Alexandra M., Altelaar, Maarten, Peeper, Daniel S., Stecker, Kelly E., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Ibáñez-Molero, Sofía, Pruijs, Joannes T.M., Atmopawiro, Alisha, Wang, Fujia, Terry, Alexandra M., Altelaar, Maarten, Peeper, Daniel S., and Stecker, Kelly E.

Published
2024

8. Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Pharmaceutics, Biomolecular Mass Spectrometry and Proteomics, Pharmaceutics, Wienke, Judith, Visser, Lindy L, Kholosy, Waleed M, Keller, Kaylee M, Barisa, Marta, Poon, Evon, Munnings-Tomes, Sophie, Himsworth, Courtney, Calton, Elizabeth, Rodriguez, Ana, Bernardi, Ronald, van den Ham, Femke, van Hooff, Sander R, Matser, Yvette A H, Tas, Michelle L, Langenberg, Karin P S, Lijnzaad, Philip, Borst, Anne L, Zappa, Elisa, Bergsma, Francisca J, Strijker, Josephine G M, Verhoeven, Bronte M, Mei, Shenglin, Kramdi, Amira, Restuadi, Restuadi, Sanchez-Bernabeu, Alvaro, Cornel, Annelisa M, Holstege, Frank C P, Gray, Juliet C, Tytgat, Godelieve A M, Scheijde-Vermeulen, Marijn A, Wijnen, Marc H W A, Dierselhuis, Miranda P, Straathof, Karin, Behjati, Sam, Wu, Wei, Heck, Albert J R, Koster, Jan, Nierkens, Stefan, Janoueix-Lerosey, Isabelle, de Krijger, Ronald R, Baryawno, Ninib, Chesler, Louis, Anderson, John, Caron, Hubert N, Margaritis, Thanasis, van Noesel, Max M, Molenaar, Jan J, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Pharmaceutics, Biomolecular Mass Spectrometry and Proteomics, Pharmaceutics, Wienke, Judith, Visser, Lindy L, Kholosy, Waleed M, Keller, Kaylee M, Barisa, Marta, Poon, Evon, Munnings-Tomes, Sophie, Himsworth, Courtney, Calton, Elizabeth, Rodriguez, Ana, Bernardi, Ronald, van den Ham, Femke, van Hooff, Sander R, Matser, Yvette A H, Tas, Michelle L, Langenberg, Karin P S, Lijnzaad, Philip, Borst, Anne L, Zappa, Elisa, Bergsma, Francisca J, Strijker, Josephine G M, Verhoeven, Bronte M, Mei, Shenglin, Kramdi, Amira, Restuadi, Restuadi, Sanchez-Bernabeu, Alvaro, Cornel, Annelisa M, Holstege, Frank C P, Gray, Juliet C, Tytgat, Godelieve A M, Scheijde-Vermeulen, Marijn A, Wijnen, Marc H W A, Dierselhuis, Miranda P, Straathof, Karin, Behjati, Sam, Wu, Wei, Heck, Albert J R, Koster, Jan, Nierkens, Stefan, Janoueix-Lerosey, Isabelle, de Krijger, Ronald R, Baryawno, Ninib, Chesler, Louis, Anderson, John, Caron, Hubert N, Margaritis, Thanasis, van Noesel, Max M, and Molenaar, Jan J

Published
2024

9. Into the dark serum proteome: personalized features of IgG1 and IgA1 repertoires in severe COVID-19 patients

Author

Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Bondt, Albert, Hoek, Max, Dingess, Kelly, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, den Boer, Maurits A, Damen, Mirjam, Zwart, Ceri, Barendregt, Arjan, van Rijswijck, Danique M H, Schulte, Douwe, Grobben, Marloes, Tejjani, Khadija, van Rijswijk, Jacqueline, Völlmy, Franziska, Snijder, Joost, Fortini, Francesca, Papi, Alberto, Volta, Carlo Alberto, Campo, Gianluca, Contoli, Marco, van Gils, Marit J, Spadaro, Savino, Rizzo, Paola, Heck, Albert J R, Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Bondt, Albert, Hoek, Max, Dingess, Kelly, Tamara, Sem, de Graaf, Bastiaan, Peng, Weiwei, den Boer, Maurits A, Damen, Mirjam, Zwart, Ceri, Barendregt, Arjan, van Rijswijck, Danique M H, Schulte, Douwe, Grobben, Marloes, Tejjani, Khadija, van Rijswijk, Jacqueline, Völlmy, Franziska, Snijder, Joost, Fortini, Francesca, Papi, Alberto, Volta, Carlo Alberto, Campo, Gianluca, Contoli, Marco, van Gils, Marit J, Spadaro, Savino, Rizzo, Paola, and Heck, Albert J R

Published
2024

10. Direct Comparison of the Hinge-Cleaving Proteases IgdE and BdpK for LC-MS-Based IgG1 Clonal Profiling

Author

Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, van Rijswijck, Danique M H, Bondt, Albert, de Kat, Naomi, Lood, Rolf, Heck, Albert J R, Biomolecular Mass Spectrometry and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, van Rijswijck, Danique M H, Bondt, Albert, de Kat, Naomi, Lood, Rolf, and Heck, Albert J R

Published
2024

11. Region-specific and age-related differences in astrocytes in the human brain

Author

Afd Biomol.Mass Spect. and Proteomics, Man, Jodie H.K., Breur, Marjolein, van Gelder, Charlotte A.G.H., Marcon, Gabriella, Maderna, Emanuela, Giaccone, Giorgio, Altelaar, Maarten, van der Knaap, Marjo S., Bugiani, Marianna, Afd Biomol.Mass Spect. and Proteomics, Man, Jodie H.K., Breur, Marjolein, van Gelder, Charlotte A.G.H., Marcon, Gabriella, Maderna, Emanuela, Giaccone, Giorgio, Altelaar, Maarten, van der Knaap, Marjo S., and Bugiani, Marianna

Published
2024

12. Mesenchymal stromal/stem cells promote intestinal epithelium regeneration after chemotherapy-induced damage

Author

Pathobiologie, Cell Biology, Metabolism and Cancer, Afd Biomol.Mass Spect. and Proteomics, Cell Biology, Metabolism & Cancer - Cancer, Yetkin-Arik, B, Jansen, S A, Varderidou-Minasian, S, Westendorp, B, Skarp, K-P, Altelaar, M, Lindemans, C A, Lorenowicz, M J, Pathobiologie, Cell Biology, Metabolism and Cancer, Afd Biomol.Mass Spect. and Proteomics, Cell Biology, Metabolism & Cancer - Cancer, Yetkin-Arik, B, Jansen, S A, Varderidou-Minasian, S, Westendorp, B, Skarp, K-P, Altelaar, M, Lindemans, C A, and Lorenowicz, M J

Published
2024

13. Generation of human antibodies targeting human platelet antigen (HPA)-1a

Author

Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Oosterhoff, Janita J., Linty, Federica, Visser, Remco, de Vos, Thijs, Hofstede-van Egmond, Suzanne, van de Weerd, Miranda, Porcelijn, Leendert, de Haas, Masja, van der Schoot, Ellen, Vidarsson, Gestur, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Oosterhoff, Janita J., Linty, Federica, Visser, Remco, de Vos, Thijs, Hofstede-van Egmond, Suzanne, van de Weerd, Miranda, Porcelijn, Leendert, de Haas, Masja, van der Schoot, Ellen, and Vidarsson, Gestur

Published
2024

14. Assessment of Kinome-wide Activity Remodeling Upon Picornavirus Infection

Author

Afd Biomol.Mass Spect. and Proteomics, Virologie, Pathobiologie, Faculteit Diergeneeskunde, Veterinaire biochemie, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Infectious Diseases and Immunology - Virology, Cell Biology, Metabolism & Cancer - Cancer, Cell Biology, Metabolism & Cancer - Metabolomics, Veth, Tim S, Nouwen, Lonneke V, Zwaagstra, Marleen, Lyoo, Heyrhyoung, Wierenga, Kathryn A, Westendorp, Bart, Altelaar, Maarten A F M, Berkers, Celia, van Kuppeveld, Frank J M, Heck, Albert J R, Afd Biomol.Mass Spect. and Proteomics, Virologie, Pathobiologie, Faculteit Diergeneeskunde, Veterinaire biochemie, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Infectious Diseases and Immunology - Virology, Cell Biology, Metabolism & Cancer - Cancer, Cell Biology, Metabolism & Cancer - Metabolomics, Veth, Tim S, Nouwen, Lonneke V, Zwaagstra, Marleen, Lyoo, Heyrhyoung, Wierenga, Kathryn A, Westendorp, Bart, Altelaar, Maarten A F M, Berkers, Celia, van Kuppeveld, Frank J M, and Heck, Albert J R

Published
2024

15. The physiological interactome of TCR-like antibody therapeutics in human tissues

Author

Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Marrer-Berger, Estelle, Nicastri, Annalisa, Augustin, Angelique, Kramar, Vesna, Liao, Hanqing, Hanisch, Lydia Jasmin, Carpy, Alejandro, Weinzierl, Tina, Durr, Evelyne, Schaub, Nathalie, Nudischer, Ramona, Ortiz-Franyuti, Daniela, Breous-Nystrom, Ekaterina, Stucki, Janick, Hobi, Nina, Raggi, Giulia, Cabon, Lauriane, Lezan, Emmanuelle, Umaña, Pablo, Woodhouse, Isaac, Bujotzek, Alexander, Klein, Christian, Ternette, Nicola, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Marrer-Berger, Estelle, Nicastri, Annalisa, Augustin, Angelique, Kramar, Vesna, Liao, Hanqing, Hanisch, Lydia Jasmin, Carpy, Alejandro, Weinzierl, Tina, Durr, Evelyne, Schaub, Nathalie, Nudischer, Ramona, Ortiz-Franyuti, Daniela, Breous-Nystrom, Ekaterina, Stucki, Janick, Hobi, Nina, Raggi, Giulia, Cabon, Lauriane, Lezan, Emmanuelle, Umaña, Pablo, Woodhouse, Isaac, Bujotzek, Alexander, Klein, Christian, and Ternette, Nicola

Published
2024

16. Complex N-glycans are important for interspecies transmission of H7 influenza A viruses

Author

Chemical Biology and Drug Discovery, Biomolecular Mass Spectrometry and Proteomics, Afd Chemical Biology and Drug Discovery, Afd Biomol.Mass Spect. and Proteomics, Sub Chemical Biology and Drug Discovery, Spruit, Cindy M, Palme, Diana I, Li, Tiehai, Ríos Carrasco, María, Gabarroca García, Alba, Sweet, Igor R, Kuryshko, Maryna, Maliepaard, Joshua C L, Reiding, Karli R, Scheibner, David, Boons, Geert-Jan, Abdelwhab, Elsayed M, de Vries, Robert P, Chemical Biology and Drug Discovery, Biomolecular Mass Spectrometry and Proteomics, Afd Chemical Biology and Drug Discovery, Afd Biomol.Mass Spect. and Proteomics, Sub Chemical Biology and Drug Discovery, Spruit, Cindy M, Palme, Diana I, Li, Tiehai, Ríos Carrasco, María, Gabarroca García, Alba, Sweet, Igor R, Kuryshko, Maryna, Maliepaard, Joshua C L, Reiding, Karli R, Scheibner, David, Boons, Geert-Jan, Abdelwhab, Elsayed M, and de Vries, Robert P

Published
2024

17. Thrombin activation of the factor XI dimer is a multistaged process for each subunit

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Bar Barroeta, Awital, Albanese, Pascal, Kadavá, Tereza, Jankevics, Andris, Marquart, J. Arnoud, Meijers, Joost C.M., Scheltema, Richard A., Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Bar Barroeta, Awital, Albanese, Pascal, Kadavá, Tereza, Jankevics, Andris, Marquart, J. Arnoud, Meijers, Joost C.M., and Scheltema, Richard A.

Published
2024

19. The pleiotropic phenotype of FlbA of Aspergillus niger is explained in part by the activity of seven of its downstream-regulated transcription factors

Author

Sub Molecular Microbiology, Afd Biomol.Mass Spect. and Proteomics, Molecular Microbiology, Chen, Xiaoyi, Moran Torres, Juan P., Jan Vonk, Peter, Damen, J. Mirjam A., Reiding, Karli R., Dijksterhuis, Jan, Lugones, Luis G., Wösten, Han A.B., Sub Molecular Microbiology, Afd Biomol.Mass Spect. and Proteomics, Molecular Microbiology, Chen, Xiaoyi, Moran Torres, Juan P., Jan Vonk, Peter, Damen, J. Mirjam A., Reiding, Karli R., Dijksterhuis, Jan, Lugones, Luis G., and Wösten, Han A.B.

Published
2024

20. Impact of structural modifications of IgG antibodies on effector functions

Author

Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Damelang, T, Brinkhaus, M, van Osch, TLJ, Schuurman, J, Labrijn, AF, Rispens, T, Vidarsson, G, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Damelang, T, Brinkhaus, M, van Osch, TLJ, Schuurman, J, Labrijn, AF, Rispens, T, and Vidarsson, G

Published
2024

21. Ultralong transients enhance sensitivity and resolution in Orbitrap-based single-ion mass spectrometry

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Deslignière, Evolène, Yin, Victor C, Ebberink, Eduard H T M, Rolland, Amber D, Barendregt, Arjan, Wörner, Tobias P, Nagornov, Konstantin O, Kozhinov, Anton N, Fort, Kyle L, Tsybin, Yury O, Makarov, Alexander A, Heck, Albert J R, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Deslignière, Evolène, Yin, Victor C, Ebberink, Eduard H T M, Rolland, Amber D, Barendregt, Arjan, Wörner, Tobias P, Nagornov, Konstantin O, Kozhinov, Anton N, Fort, Kyle L, Tsybin, Yury O, Makarov, Alexander A, and Heck, Albert J R

Published
2024

22. Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness

Author

Sub Biomol.Mass Spect. and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Lin, Chun Pu, Levy, Pierre L., Alflen, Astrid, Apriamashvili, Georgi, Ligtenberg, Maarten A., Vredevoogd, David W., Bleijerveld, Onno B., Alkan, Ferhat, Malka, Yuval, Hoekman, Liesbeth, Markovits, Ettai, George, Austin, Traets, Joleen J.H., Krijgsman, Oscar, van Vliet, Alex, Poźniak, Joanna, Pulido-Vicuña, Carlos Ariel, de Bruijn, Beaunelle, van Hal-van Veen, Susan E., Boshuizen, Julia, van der Helm, Pim W., Díaz-Gómez, Judit, Warda, Hamdy, Behrens, Leonie M., Mardesic, Paula, Dehni, Bilal, Visser, Nils L., Marine, Jean Christophe, Markel, Gal, Faller, William J., Altelaar, Maarten, Agami, Reuven, Besser, Michal J., Peeper, Daniel S., Sub Biomol.Mass Spect. and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Lin, Chun Pu, Levy, Pierre L., Alflen, Astrid, Apriamashvili, Georgi, Ligtenberg, Maarten A., Vredevoogd, David W., Bleijerveld, Onno B., Alkan, Ferhat, Malka, Yuval, Hoekman, Liesbeth, Markovits, Ettai, George, Austin, Traets, Joleen J.H., Krijgsman, Oscar, van Vliet, Alex, Poźniak, Joanna, Pulido-Vicuña, Carlos Ariel, de Bruijn, Beaunelle, van Hal-van Veen, Susan E., Boshuizen, Julia, van der Helm, Pim W., Díaz-Gómez, Judit, Warda, Hamdy, Behrens, Leonie M., Mardesic, Paula, Dehni, Bilal, Visser, Nils L., Marine, Jean Christophe, Markel, Gal, Faller, William J., Altelaar, Maarten, Agami, Reuven, Besser, Michal J., and Peeper, Daniel S.

Published
2024

23. Antigen-specific Fab profiling achieves molecular-resolution analysis of human autoantibody repertoires in rheumatoid arthritis

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Stork, Eva Maria, van Rijswijck, Danique M H, van Schie, Karin A, Hoek, Max, Kissel, Theresa, Scherer, Hans Ulrich, Huizinga, Tom W J, Heck, Albert J R, Toes, Rene E M, Bondt, Albert, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Stork, Eva Maria, van Rijswijck, Danique M H, van Schie, Karin A, Hoek, Max, Kissel, Theresa, Scherer, Hans Ulrich, Huizinga, Tom W J, Heck, Albert J R, Toes, Rene E M, and Bondt, Albert

Published
2024

24. Size matters: Functional differences of small extracellular vesicle subpopulations in cardiac repair responses

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Pharmaceutics, Sub General Pharmaceutics, van de Wakker, Simonides Immanuel, Bauzá-Martinez, Julia, Ríos Arceo, Carla, Manjikian, Herak, Snijders Blok, Christian Jamie Bernard, Roefs, Marieke Theodora, Willms, Eduard, Maas, Renee Goverdina Catharina, Pronker, Matti Feije, de Jong, Olivier Gerrit, Wu, Wei, Görgens, André, El Andaloussi, Samir, Sluijter, Joost Petrus Gerardus, Vader, Pieter, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Afd Pharmaceutics, Sub General Pharmaceutics, van de Wakker, Simonides Immanuel, Bauzá-Martinez, Julia, Ríos Arceo, Carla, Manjikian, Herak, Snijders Blok, Christian Jamie Bernard, Roefs, Marieke Theodora, Willms, Eduard, Maas, Renee Goverdina Catharina, Pronker, Matti Feije, de Jong, Olivier Gerrit, Wu, Wei, Görgens, André, El Andaloussi, Samir, Sluijter, Joost Petrus Gerardus, and Vader, Pieter

Published
2024

25. Lipidome characterisation and sex-specific differences in type 1 and type 2 diabetes mellitus

Author

Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Barranco-Altirriba, Maria, Alonso, Núria, Weber, Ralf J.M., Lloyd, Gavin R., Hernandez, Marta, Yanes, Oscar, Capellades, Jordi, Jankevics, Andris, Winder, Catherine, Falguera, Mireia, Franch-Nadal, Josep, Dunn, Warwick B., Perera-Lluna, Alexandre, Castelblanco, Esmeralda, Mauricio, Didac, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Barranco-Altirriba, Maria, Alonso, Núria, Weber, Ralf J.M., Lloyd, Gavin R., Hernandez, Marta, Yanes, Oscar, Capellades, Jordi, Jankevics, Andris, Winder, Catherine, Falguera, Mireia, Franch-Nadal, Josep, Dunn, Warwick B., Perera-Lluna, Alexandre, Castelblanco, Esmeralda, and Mauricio, Didac

Published
2024

26. Structural basis for recognition of the FLAG-tag by anti-FLAG M2

Author

Sub Structural Biochemistry, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Structural Biochemistry, Biomolecular Mass Spectrometry and Proteomics, Beugelink, J. Wouter, Sweep, Els, Janssen, Bert J.C., Snijder, Joost, Pronker, Matti F., Sub Structural Biochemistry, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Structural Biochemistry, Biomolecular Mass Spectrometry and Proteomics, Beugelink, J. Wouter, Sweep, Els, Janssen, Bert J.C., Snijder, Joost, and Pronker, Matti F.

Published
2024

27. Proteoform-resolved profiling of plasminogen activation reveals novel abundant phosphorylation site and primary N-terminal cleavage site

Author

Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Cramer, Dario A T, Yin, Victor, Caval, Tomislav, Franc, Vojtech, Yu, Dingyi, Wu, Guojie, Lloyd, Gordon, Langendorf, Christopher, Whisstock, James C, Law, Ruby H P, Heck, Albert J R, Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Cramer, Dario A T, Yin, Victor, Caval, Tomislav, Franc, Vojtech, Yu, Dingyi, Wu, Guojie, Lloyd, Gordon, Langendorf, Christopher, Whisstock, James C, Law, Ruby H P, and Heck, Albert J R

Published
2024

28. Relative impact of three growth conditions on the Escherichia coli protein acetylome.

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Lozano-Terol, Gema, Chiozzi, Riccardo Zenezini, Gallego-Jara, Julia, Sola-Martínez, Rosa Alba, Vivancos, Adrián Martínez, Ortega, Álvaro, Heck, Albert J R, Díaz, Manuel Cánovas, de Diego Puente, Teresa, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Lozano-Terol, Gema, Chiozzi, Riccardo Zenezini, Gallego-Jara, Julia, Sola-Martínez, Rosa Alba, Vivancos, Adrián Martínez, Ortega, Álvaro, Heck, Albert J R, Díaz, Manuel Cánovas, and de Diego Puente, Teresa

Published
2024

29. Innovative strategies for measuring kinase activity to accelerate the next wave of novel kinase inhibitors

Author

Afd Biomol.Mass Spect. and Proteomics, Afd Chemical Biology and Drug Discovery, Biomolecular Mass Spectrometry and Proteomics, Chemical Biology and Drug Discovery, Veth, Tim S., Kannegieter, Nynke M., de Graaf, Erik L., Ruijtenbeek, Rob, Joore, Jos, Ressa, Anna, Altelaar, Maarten, Afd Biomol.Mass Spect. and Proteomics, Afd Chemical Biology and Drug Discovery, Biomolecular Mass Spectrometry and Proteomics, Chemical Biology and Drug Discovery, Veth, Tim S., Kannegieter, Nynke M., de Graaf, Erik L., Ruijtenbeek, Rob, Joore, Jos, Ressa, Anna, and Altelaar, Maarten

Published
2024

30. Human fetal brain self-organizes into long-term expanding organoids

Author

Afd Biomol.Mass Spect. and Proteomics, Faculteit Diergeneeskunde, Biomolecular Mass Spectrometry and Proteomics, Hendriks, Delilah, Pagliaro, Anna, Andreatta, Francesco, Ma, Ziliang, van Giessen, Joey, Massalini, Simone, López-Iglesias, Carmen, van Son, Gijs J.F., DeMartino, Jeff, Damen, J. Mirjam A., Zoutendijk, Iris, Staliarova, Nadzeya, Bredenoord, Annelien L., Holstege, Frank C.P., Peters, Peter J., Margaritis, Thanasis, Chuva de Sousa Lopes, Susana, Wu, Wei, Clevers, Hans, Artegiani, Benedetta, Afd Biomol.Mass Spect. and Proteomics, Faculteit Diergeneeskunde, Biomolecular Mass Spectrometry and Proteomics, Hendriks, Delilah, Pagliaro, Anna, Andreatta, Francesco, Ma, Ziliang, van Giessen, Joey, Massalini, Simone, López-Iglesias, Carmen, van Son, Gijs J.F., DeMartino, Jeff, Damen, J. Mirjam A., Zoutendijk, Iris, Staliarova, Nadzeya, Bredenoord, Annelien L., Holstege, Frank C.P., Peters, Peter J., Margaritis, Thanasis, Chuva de Sousa Lopes, Susana, Wu, Wei, Clevers, Hans, and Artegiani, Benedetta

Published
2024

31. Epidermal growth factor receptor (EGFR) is a target of the tumor-suppressor E3 ligase FBXW7

Author

Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Boretto, Matteo, Geurts, Maarten H., Gandhi, Shashank, Ma, Ziliang, Staliarova, Nadzeya, Celotti, Martina, Lim, Sangho, He, Gui Wei, Millen, Rosemary, Driehuis, Else, Begthel, Harry, Smabers, Lidwien, Roodhart, Jeanine, van Es, Johan, Wu, Wei, Clevers, Hans, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Boretto, Matteo, Geurts, Maarten H., Gandhi, Shashank, Ma, Ziliang, Staliarova, Nadzeya, Celotti, Martina, Lim, Sangho, He, Gui Wei, Millen, Rosemary, Driehuis, Else, Begthel, Harry, Smabers, Lidwien, Roodhart, Jeanine, van Es, Johan, Wu, Wei, and Clevers, Hans

Published
2024

32. Adipocyte p53 coordinates the response to intermittent fasting by regulating adipose tissue immune cell landscape

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Reinisch, Isabel, Michenthaler, Helene, Sulaj, Alba, Moyschewitz, Elisabeth, Krstic, Jelena, Galhuber, Markus, Xu, Ruonan, Riahi, Zina, Wang, Tongtong, Vujic, Nemanja, Amor, Melina, Zenezini Chiozzi, Riccardo, Wabitsch, Martin, Kolb, Dagmar, Georgiadi, Anastasia, Glawitsch, Lisa, Heitzer, Ellen, Schulz, Tim J., Schupp, Michael, Sun, Wenfei, Dong, Hua, Ghosh, Adhideb, Hoffmann, Anne, Kratky, Dagmar, Hinte, Laura C., von Meyenn, Ferdinand, Heck, Albert J.R., Blüher, Matthias, Herzig, Stephan, Wolfrum, Christian, Prokesch, Andreas, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Reinisch, Isabel, Michenthaler, Helene, Sulaj, Alba, Moyschewitz, Elisabeth, Krstic, Jelena, Galhuber, Markus, Xu, Ruonan, Riahi, Zina, Wang, Tongtong, Vujic, Nemanja, Amor, Melina, Zenezini Chiozzi, Riccardo, Wabitsch, Martin, Kolb, Dagmar, Georgiadi, Anastasia, Glawitsch, Lisa, Heitzer, Ellen, Schulz, Tim J., Schupp, Michael, Sun, Wenfei, Dong, Hua, Ghosh, Adhideb, Hoffmann, Anne, Kratky, Dagmar, Hinte, Laura C., von Meyenn, Ferdinand, Heck, Albert J.R., Blüher, Matthias, Herzig, Stephan, Wolfrum, Christian, and Prokesch, Andreas

Published
2024

33. Antibody glycosylation in COVID-19

Author

Pongracz, Tamas, Vidarsson, Gestur, Wuhrer, Manfred, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, and Biomolecular Mass Spectrometry and Proteomics

Subjects
Glycomics, biomarker, Glycosylation, animal structures, SARS-CoV-2, Mini Review, IgG glycosylation, COVID-19, Cell Biology, macromolecular substances, Antibodies, Viral, Biochemistry, carbohydrates (lipids), Immunoglobulin G, Antibody glycosylation, Humans, biomarker, lipids (amino acids, peptides, and proteins), Molecular Biology, Glycomics
Abstract

Antibody glycosylation has received considerable attention in coronavirus disease 2019 (COVID-19) infections and recently also in vaccination. Antibody glycosylation and in particular immunoglobulin G1 fucosylation levels influence effector functions and are therefore key parameters for assessing the efficacy and safety of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directed immune responses. This review article summarizes and interprets recent research into antibody glycosylation in COVID-19. Experimental approaches for analyzing the glycosylation of SARS-CoV-2-directed antibody responses are evaluated. The pronounced dynamics, effector functions, clinical utility, and regulation of antibody glycosylation in COVID-19 are assessed. Future research on the role of antibody glycosylation in COVID may cover the glycosylation of other antibody classes beyond immunoglobulin G, the regulation of antibody glycosylation, and the role of non-canonical antibody receptors in determining effector functions. Graphical abstract

Published
2022

34. Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy

Author

Subramaniam, Gunasekaran, Schleicher, Katharina, Kovanich, Duangnapa, Zerio, Anna, Folkmanaite, Milda, Chao, Ying-Chi, Surdo, Nicoletta C, Koschinski, Andreas, Hu, Jianshu, Scholten, Arjen, Heck, Albert J R, Ercu, Maria, Sholokh, Anastasiia, Chan Park, Kyung, Klussmann, Enno, Meraviglia, Viviana, Bellin, Milena, Zanivan, Sara, Hester, Svenja, Mohammed, Shabaz, Zaccolo, Manuela, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Subjects
adrenergic agents, hypertrophy, phosphoric diester hydrolases, protein isoforms, rodentia, Cardiovascular and Metabolic Diseases, Physiology, Cardiology and Cardiovascular Medicine
Abstract

Background: Signaling by cAMP is organized in multiple distinct subcellular nanodomains regulated by cAMP-hydrolyzing PDEs (phosphodiesterases). Cardiac β-adrenergic signaling has served as the prototypical system to elucidate cAMP compartmentalization. Although studies in cardiac myocytes have provided an understanding of the location and properties of a handful of cAMP subcellular compartments, an overall view of the cellular landscape of cAMP nanodomains is missing. Methods: Here, we combined an integrated phosphoproteomics approach that takes advantage of the unique role that individual PDEs play in the control of local cAMP, with network analysis to identify previously unrecognized cAMP nanodomains associated with β-adrenergic stimulation. We then validated the composition and function of one of these nanodomains using biochemical, pharmacological, and genetic approaches and cardiac myocytes from both rodents and humans. Results: We demonstrate the validity of the integrated phosphoproteomic strategy to pinpoint the location and provide critical cues to determine the function of previously unknown cAMP nanodomains. We characterize in detail one such compartment and demonstrate that the PDE3A2 isoform operates in a nuclear nanodomain that involves SMAD4 (SMAD family member 4) and HDAC-1 (histone deacetylase 1). Inhibition of PDE3 results in increased HDAC-1 phosphorylation, leading to inhibition of its deacetylase activity, derepression of gene transcription, and cardiac myocyte hypertrophic growth. Conclusions: We developed a strategy for detailed mapping of subcellular PDE-specific cAMP nanodomains. Our findings reveal a mechanism that explains the negative long-term clinical outcome observed in patients with heart failure treated with PDE3 inhibitors.

Published
2023

35. Promoting Fc-Fc interactions between anti-capsular antibodies provides strong immune protection against Streptococcus pneumoniae

Author

Aguinagalde Salazar, Leire, den Boer, Maurits A, Castenmiller, Suzanne M, Zwarthoff, Seline A, de Haas, Carla, Aerts, Piet C, Beurskens, Frank J, Schuurman, Janine, Heck, Albert J R, van Kessel, Kok, Rooijakkers, Suzan H M, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Subjects
Hexamer-enhancing mutations, Complement system, General Immunology and Microbiology, Biochemistry, Genetics and Molecular Biology(all), Neutrophils, General Neuroscience, Neuroscience(all), General Medicine, Serogroup, General Biochemistry, Genetics and Molecular Biology, Pneumoniae, Mice, Streptococcus pneumoniae, Immunology and Microbiology(all), Immunoglobulin G, Humans, Animals, Monoclonal antibodies, Other, Pneumococcal Infections/prevention & control
Abstract

Streptococcus pneumoniae is the leading cause of community-acquired pneumonia and an important cause of childhood mortality. Despite the introduction of successful vaccines, the global spread of both non-vaccine serotypes and antibiotic-resistant strains reinforce the development of alternative therapies against this pathogen. One possible route is the development of monoclonal antibodies (mAbs) that induce killing of bacteria via the immune system. Here we investigate whether mAbs can be used to induce killing of pneumococcal serotypes for which the current vaccines show unsuccessful protection. Our study demonstrates that when human mAbs against pneumococcal capsule polysaccharides (CPS) have a poor capacity to induce complement activation, a critical process for immune protection against pneumococci, their activity can be strongly improved by hexamerization-enhancing mutations. Our data indicate that anti-capsular antibodies may have a low capacity to form higher-order oligomers (IgG hexamers) that are needed to recruit complement component C1. Indeed, specific point mutations in the IgG-Fc domain that strengthen hexamerization strongly enhance C1 recruitment and downstream complement activation on encapsulated pneumococci. Specifically, hexamerization-enhancing mutations E430G or E345K in CPS6-IgG strongly potentiate complement activation on S. pneumoniae strains that express capsular serotype 6 (CPS6), and the highly invasive serotype 19A strain. Furthermore, these mutations improve complement activation via mAbs recognizing CPS3 and CPS8 strains. Importantly, hexamer-enhancing mutations enable mAbs to induce strong phagocytosis and intracellular killing by human neutrophils. Finally, passive immunization with CPS6-IgG1-E345K protected mice from developing severe pneumonia. Altogether, this work provides an important proof-of-concept for future optimization of antibody therapies against encapsulated bacteria.

Published
2023

36. MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex

Author

Hevler, Johannes F, Albanese, Pascal, Cabrera-Orefice, Alfredo, Potter, Alisa, Jankevics, Andris, Misic, Jelena, Scheltema, Richard A, Brandt, Ulrich, Arnold, Susanne, Heck, Albert J R, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Subjects
Biochemistry, Genetics and Molecular Biology(all), General Neuroscience, Neuroscience(all), complexome profiling, cross-linking mass spectrometry, Immunology, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Biochemistry, General Biochemistry, Genetics and Molecular Biology, tricarboxylic acid (TCA) cycle, MRPS36, All institutes and research themes of the Radboud University Medical Center, structural biology, 2-oxoglutarate dehydrogenase (OGDHC), Genetics and Molecular Biology(all)
Abstract

Contains fulltext : 290938.pdf (Publisher’s version ) (Open Access) The tricarboxylic acid cycle is the central pathway of energy production in eukaryotic cells and plays a key part in aerobic respiration throughout all kingdoms of life. One of the pivotal enzymes in this cycle is 2-oxoglutarate dehydrogenase complex (OGDHC), which generates NADH by oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. OGDHC is a megadalton protein complex originally thought to be assembled from three catalytically active subunits (E1o, E2o, E3). In fungi and animals, however, the protein MRPS36 has more recently been proposed as a putative additional component. Based on extensive cross-linking mass spectrometry data supported by phylogenetic analyses, we provide evidence that MRPS36 is an important member of the eukaryotic OGDHC, with no prokaryotic orthologues. Comparative sequence analysis and computational structure predictions reveal that, in contrast with bacteria and archaea, eukaryotic E2o does not contain the peripheral subunit-binding domain (PSBD), for which we propose that MRPS36 evolved as an E3 adaptor protein, functionally replacing the PSBD. We further provide a refined structural model of the complete eukaryotic OGDHC of approximately 3.45 MDa with novel mechanistic insights.

Published
2023

37. Sodium stibogluconate and CD47-SIRPα blockade overcome resistance of anti-CD20–opsonized B cells to neutrophil killing

Author

Rees, Dieke J. van, Brinkhaus, Maximilian, Klein, Bart, Verkuijlen, Paul, Tool, Anton T.J., Schornagel, Karin, Treffers, Louise W., Houdt, Michel van, Kater, Arnon P., Vidarsson, Gestur, Gennery, Andrew R., Kuijpers, Taco W., Bruggen, Robin van, Matlung, Hanke L., Berg, Timo K. van den, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Graduate School, AII - Inflammatory diseases, AII - Cancer immunology, AII - Infectious diseases, CCA - Cancer biology and immunology, Experimental Immunology, Clinical Haematology, Landsteiner Laboratory, Paediatric Infectious Diseases / Rheumatology / Immunology, ARD - Amsterdam Reproduction and Development, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, and Molecular cell biology and Immunology

Subjects
Neutrophils, Complement, Phosphatase inhibitor, Antibody-Dependent Cell Cytotoxicity, Expression, CD47 Antigen, Hematology, Fc-gamma-r, Antimony Sodium Gluconate, immune system diseases, hemic and lymphatic diseases, Cd20, Dependent cellular cytotoxicity, Rituximab, Antibody, Sirp-alpha, Therapeutic activity
Abstract

Anti-CD20 antibodies such as rituximab are broadly used to treat B-cell malignancies. These antibodies can induce various effector functions, including immune cell-mediated antibody-dependent cellular cytotoxicity (ADCC). Neutrophils can induce ADCC toward solid cancer cells by trogoptosis, a cytotoxic mechanism known to be dependent on trogocytosis. However, neutrophils seem to be incapable of killing rituximab-opsonized B-cell lymphoma cells. Nevertheless, neutrophils do trogocytose rituximab-opsonized B-cell lymphoma cells, but this only reduces CD20 surface expression and is thought to render tumor cells therapeutically resistant to further rituximab-dependent destruction. Here, we demonstrate that resistance of B-cell lymphoma cells toward neutrophil killing can be overcome by a combination of CD47-SIRPα checkpoint blockade and sodium stibogluconate (SSG), an anti-leishmaniasis drug and documented inhibitor of the tyrosine phosphatase SHP-1. SSG enhanced neutrophil-mediated ADCC of solid tumor cells but enabled trogoptotic killing of B-cell lymphoma cells by turning trogocytosis from a mechanism that contributes to resistance into a cytotoxic anti-cancer mechanism. Tumor cell killing in the presence of SSG required both antibody opsonization of the target cells and disruption of CD47-SIRPα interactions. These results provide a more detailed understanding of the role of neutrophil trogocytosis in antibody-mediated destruction of B cells and clues on how to further optimize antibody therapy of B-cell malignancies.

Published
2022

38. Decreased antibody response after severe acute respiratory syndrome coronavirus 2 vaccination in patients with Down syndrom

Author

Streng, Bianca M M, Bont, Marin, Delemarre, Eveline M, Binnendijk, Rob S, Smit, Gaby, den Hartog, Gerco, Coppus, Antonia M W, de Vries, Esther, Weijerman, Michel E, Lamberts, Regina, de Graaf, Gert, van der Klis, Fiona R, Vidarsson, Gestur, Rave, Neele, Bont, Louis J, Wildenbeest, Joanne G, LS IRAS Tox Algemeen, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, AII - Inflammatory diseases, Landsteiner Laboratory, LS IRAS Tox Algemeen, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Huisarts & Ziekenhuis, and Tranzo, Scientific center for care and wellbeing

Subjects
Adult, COVID-19 Vaccines, COVID-19 vaccination, SARS-CoV-2, COVID-19/prevention & control, Messenger, Vaccination, COVID-19, antibody response, Antibodies, Viral, Antibodies, Healthcare improvement science Radboud Institute for Health Sciences [Radboudumc 18], Infectious Diseases, Antibody Formation, Immunology and Allergy, Humans, RNA, RNA, Messenger, Viral, Prospective Studies, Down Syndrome, BNT162 Vaccine
Abstract

The risk of a severe course of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in adults with Down syndrome is increased, resulting in an up to 10-fold increase in mortality, in particular in those >40 years of age. After primary SARS-CoV-2 vaccination, the higher risks remain. In this prospective observational cohort study, SARS-CoV-2 spike S1–specific antibody responses after routine SARS-CoV-2 vaccination (BNT162b2, messenger RNA [mRNA]–1273, or ChAdOx1) in adults with Down syndrome and healthy controls were compared. Adults with Down syndrome showed lower antibody concentrations after 2 mRNA vaccinations or after 2 ChAdOx1 vaccinations. After 2 mRNA vaccinations, lower antibody concentrations were seen with increasing age. Clinical Trials Registration NCT05145348.

Published
2022

39. Heterogeneity in Spore Aggregation and Germination Results in Different Sized, Cooperative Microcolonies in an Aspergillus niger Culture

Author

Lyu, Jun, Tegelaar, Martin, Post, Harm, Moran Torres, Juan, Torchia, Costanza, Altelaar, A F Maarten, Bleichrodt, Robert-Jan, de Cock, Hans, Lugones, Luis G, Wösten, Han A B, Molecular Microbiology, Biomolecular Mass Spectrometry and Proteomics, Sub Molecular Microbiology, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spect. and Proteomics, Molecular Microbiology, Biomolecular Mass Spectrometry and Proteomics, Sub Molecular Microbiology, Afd Biomol.Mass Spect. and Proteomics, and Sub Biomol.Mass Spect. and Proteomics

Subjects
spores, fungus, conidia, Microbiology, secretome, stress survival, colony morphology, Virology, protein secretion, Aspergillus niger, heterogeneity, cell factory, stress resistance
Abstract

The fungus Aspergillus niger is among the most abundant fungi in the world and is widely used as a cell factory for protein and metabolite production. This fungus forms asexual spores called conidia that are used for dispersal. Notably, part of the spores and germlings aggregate in an aqueous environment. The aggregated conidia/ germlings give rise to large microcolonies, while the nonaggregated spores/germlings result in small microcolonies. Here, it is shown that small microcolonies release a larger variety and quantity of secreted proteins compared to large microcolonies. Yet, the secretome of large microcolonies has complementary cellulase activity with that of the small microcolonies. Also, large microcolonies are more resistant to heat and oxidative stress compared to small microcolonies, which is partly explained by the presence of nongerminated spores in the core of the large microcolonies. Together, it is proposed that heterogeneity in germination and aggregation has evolved to form a population of different sized A. niger microcolonies, thereby increasing stress survival and producing a meta-secretome more optimally suited to degrade complex substrates.

Published
2023

40. Characterization of high-molecular weight by-products in the production of a trivalent bispecific 2+1 heterodimeric antibody

Author

Cramer, Dario A T, Franc, Vojtech, Heidenreich, Anna-Katharina, Hook, Michaela, Adibzadeh, Mahdi, Reusch, Dietmar, Heck, Albert J R, Haberger, Markus, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Subjects
mass photometry, Immunology, Immunology and Allergy, Native MS, bispecific antibodies, HMW by-products
Abstract

The development of increasingly complex antibody formats, such as bispecifics, can lead to the formation of increasingly complex high- and low-molecular-weight by-products. Here, we focus on the characterization of high molecular weight species (HMWs) representing the highest complexity of size variants. Standard methods used for product release, such as size exclusion chromatography (SEC), can separate HMW by-products from the main product, but cannot distinguish smaller changes in mass. Here, for the identification of the diverse and complex HMW variants of a trivalent bispecific CrossMAb antibody, offline fractionation, as well as production of HMW by-products combined with comprehensive analytical testing, was applied. Furthermore, HMW variants were analyzed regarding their chemical binding nature and tested in functional assays regarding changes in potency of the variants. Changes in potency were explained by detailed characterization using mass photometry, SDS-PAGE analysis, native mass spectrometry (MS) coupled to SEC and bottom-up proteomics. We identified a major portion of the HMW by-products to be non-covalently linked, leading to dissociation and changes in activity. We also identified and localized high heterogeneity of a by-product of concern and applied a CD3 affinity column coupled to native MS to annotate unexpected by-products. We present here a multi-method approach for the characterization of complex HMW by-products. A better understanding of these by-products is beneficial to guide analytical method development and proper specification setting for therapeutic bispecific antibodies to ensure constant efficacy and patient safety of the product through the assessment of by-products.

Published
2023

41. A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution

Author

Chen, Yen-Hsi, Tian, Weihua, Yasuda, Makiko, Ye, Zilu, Song, Ming, Mandel, Ulla, Kristensen, Claus, Povolo, Lorenzo, Marques, André R A, Čaval, Tomislav, Heck, Albert J R, Sampaio, Julio Lopes, Johannes, Ludger, Tsukimura, Takahiro, Desnick, Robert, Vakhrushev, Sergey Y, Yang, Zhang, Clausen, Henrik, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Subjects
glycoprotein therapeutics, Histology, lysosomal storage disease, Enzyme replacement therapy, Glycoengineering, Biomedical Engineering, Glycoprotein therapeutics, Bioengineering, glycoengineering, Lysosymal storage disease, enzyme replacement therapy, Biotechnology
Abstract

Currently available enzyme replacement therapies for lysosomal storage diseases are limited in their effectiveness due in part to short circulation times and suboptimal biodistribution of the therapeutic enzymes. We previously engineered Chinese hamster ovary (CHO) cells to produce α-galactosidase A (GLA) with various N-glycan structures and demonstrated that elimination of mannose-6-phosphate (M6P) and conversion to homogeneous sialylated N-glycans prolonged circulation time and improved biodistribution of the enzyme following a single-dose infusion into Fabry mice. Here, we confirmed these findings using repeated infusions of the glycoengineered GLA into Fabry mice and further tested whether this glycoengineering approach, Long-Acting-GlycoDesign (LAGD), could be implemented on other lysosomal enzymes. LAGD-engineered CHO cells stably expressing a panel of lysosomal enzymes [aspartylglucosamine (AGA), beta-glucuronidase (GUSB), cathepsin D (CTSD), tripeptidyl peptidase (TPP1), alpha-glucosidase (GAA) or iduronate 2-sulfatase (IDS)] successfully converted all M6P-containing N-glycans to complex sialylated N-glycans. The resulting homogenous glycodesigns enabled glycoprotein profiling by native mass spectrometry. Notably, LAGD extended the plasma half-life of all three enzymes tested (GLA, GUSB, AGA) in wildtype mice. LAGD may be widely applicable to lysosomal replacement enzymes to improve their circulatory stability and therapeutic efficacy.

Published
2023

42. Co-display of diverse spike proteins on nanoparticles broadens sarbecovirus neutralizing antibody responses

Author

Brinkkemper, Mitch, Veth, Tim S, Brouwer, Philip J M, Turner, Hannah, Poniman, Meliawati, Burger, Judith A, Bouhuijs, Joey H, Olijhoek, Wouter, Bontjer, Ilja, Snitselaar, Jonne L, Caniels, Tom G, van der Linden, Cynthia A, Ravichandran, Rashmi, Villaudy, Julien, van der Velden, Yme U, Sliepen, Kwinten, van Gils, Marit J, Ward, Andrew B, King, Neil P, Heck, Albert J R, Sanders, Rogier W, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Graduate School, Medical Microbiology and Infection Prevention, AII - Infectious diseases, AII - Inflammatory diseases, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Subjects
Multidisciplinary, Virology, Immunology, Immune response, General, Microbiology
Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses continuous challenges in combating the virus. Here, we describe vaccination strategies to broaden SARS-CoV-2 and sarbecovirus immunity by combining spike proteins based on different viruses or viral strains displayed on two-component protein nanoparticles. First, we combined spike proteins based on ancestral and Beta SARS-CoV-2 strains to broaden SARS-CoV-2 immune responses. Inclusion of Beta spike improved neutralizing antibody responses against SARS-CoV-2 Beta, Gamma, and Omicron BA.1 and BA.4/5. A third vaccination with ancestral SARS-CoV-2 spike also improved cross-neutralizing antibody responses against SARS-CoV-2 variants, in particular against the Omicron sublineages. Second, we combined SARS-CoV and SARS-CoV-2 spike proteins to broaden sarbecovirus immune responses. Adding SARS-CoV spike to a SARS-CoV-2 spike vaccine improved neutralizing responses against SARS-CoV and SARS-like bat sarbecoviruses SHC014 and WIV1. These results should inform the development of broadly active SARS-CoV-2 and pan-sarbecovirus vaccines and highlight the versatility of two-component nanoparticles for displaying diverse antigens.

Published
2022

43. The encephalomyocarditis virus Leader promotes the release of virions inside extracellular vesicles via the induction of secretory autophagy

Author

van der Grein, Susanne G, Defourny, Kyra A Y, Rabouw, Huib H, Goerdayal, Soenita S, van Herwijnen, Martijn J C, Wubbolts, Richard W, Altelaar, Maarten, van Kuppeveld, Frank J M, Nolte-'t Hoen, Esther N M, Virologie, Celbiologie, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, IOV CCB, Virologie, Celbiologie, Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, and IOV CCB

Subjects
Lysis, Picornavirus, viruses, Viral Proteins/metabolism, Mutant, General Physics and Astronomy, Antiviral Agents, General Biochemistry, Genetics and Molecular Biology, Virus, Flow cytometry, Virion/metabolism, Extracellular Vesicles, Viral Proteins, medicine, Autophagy, Encephalomyocarditis virus, Multidisciplinary, medicine.diagnostic_test, biology, Chemistry, Antiviral Agents/metabolism, Virion, Wild type, Extracellular Vesicles/metabolism, General Chemistry, Encephalomyocarditis virus/metabolism, biology.organism_classification, Virus Release, Cell biology
Abstract

Naked viruses can escape host cells before the induction of lysis via release in extracellular vesicles (EVs). These nanosized EVs cloak the secreted virus particles in a host-derived membrane, which alters virus-host interactions that affect infection efficiency and antiviral immunity. Currently, little is known about the viral and host factors regulating this form of virus release. Here, we assessed the role of the encephalomyocarditis virus (EMCV) Leader protein, a ‘viral security protein’ that subverts the host antiviral response. EV release upon infection with wildtype virus or a Leader-deficient mutant was characterized at the single particle level using high-resolution flow cytometry. Inactivation of the Leader abolished EV induction during infection and strongly reduced EV-enclosed virus release. We demonstrate that the Leader promotes the release of virions within EVs by stimulating a secretory arm of autophagy. This newly discovered role of the EMCV Leader adds to the variety of mechanisms via which this protein affects virus-host interactions. Moreover, these data provide first evidence for a crucial role of a non-structural viral protein in the non-lytic release of picornaviruses via packaging in EVs.

Published
2022

44. Heterogeneity in Spore Aggregation and Germination Results in Different Sized, Cooperative Microcolonies in an Aspergillus niger Culture

Author

Molecular Microbiology, Biomolecular Mass Spectrometry and Proteomics, Sub Molecular Microbiology, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spect. and Proteomics, Lyu, Jun, Tegelaar, Martin, Post, Harm, Moran Torres, Juan, Torchia, Costanza, Altelaar, A F Maarten, Bleichrodt, Robert-Jan, de Cock, Hans, Lugones, Luis G, Wösten, Han A B, Molecular Microbiology, Biomolecular Mass Spectrometry and Proteomics, Sub Molecular Microbiology, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spect. and Proteomics, Lyu, Jun, Tegelaar, Martin, Post, Harm, Moran Torres, Juan, Torchia, Costanza, Altelaar, A F Maarten, Bleichrodt, Robert-Jan, de Cock, Hans, Lugones, Luis G, and Wösten, Han A B

Published
2023

45. Promoting Fc-Fc interactions between anti-capsular antibodies provides strong immune protection against Streptococcus pneumoniae.

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Aguinagalde Salazar, Leire, den Boer, Maurits A, Castenmiller, Suzanne M, Zwarthoff, Seline A, de Haas, Carla, Aerts, Piet C, Beurskens, Frank J, Schuurman, Janine, Heck, Albert J R, van Kessel, Kok, Rooijakkers, Suzan H M, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Aguinagalde Salazar, Leire, den Boer, Maurits A, Castenmiller, Suzanne M, Zwarthoff, Seline A, de Haas, Carla, Aerts, Piet C, Beurskens, Frank J, Schuurman, Janine, Heck, Albert J R, van Kessel, Kok, and Rooijakkers, Suzan H M

Published
2023

46. A universal GlycoDesign for lysosomal replacement enzymes to improve circulation time and biodistribution

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Chen, Yen-Hsi, Tian, Weihua, Yasuda, Makiko, Ye, Zilu, Song, Ming, Mandel, Ulla, Kristensen, Claus, Povolo, Lorenzo, Marques, André R A, Čaval, Tomislav, Heck, Albert J R, Sampaio, Julio Lopes, Johannes, Ludger, Tsukimura, Takahiro, Desnick, Robert, Vakhrushev, Sergey Y, Yang, Zhang, Clausen, Henrik, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Chen, Yen-Hsi, Tian, Weihua, Yasuda, Makiko, Ye, Zilu, Song, Ming, Mandel, Ulla, Kristensen, Claus, Povolo, Lorenzo, Marques, André R A, Čaval, Tomislav, Heck, Albert J R, Sampaio, Julio Lopes, Johannes, Ludger, Tsukimura, Takahiro, Desnick, Robert, Vakhrushev, Sergey Y, Yang, Zhang, and Clausen, Henrik

Published
2023

47. IgG Fab Glycans Hinder FcRn-Mediated Placental Transport

Author

Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Volkov, Mikhail, Brinkhaus, Maximilian, van Schie, Karin A, Bondt, Albert, Kissel, Theresa, van der Kooi, Elvera J, Bentlage, Arthur E H, Koeleman, Carolien A M, de Taeye, Steven W, Derksen, Ninotska I, Dolhain, Radboud J E M, Braig-Scherer, Ute, Huizinga, Tom W J, Wuhrer, Manfred, Toes, René E M, Vidarsson, Gestur, van der Woude, Diane, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, Biomolecular Mass Spectrometry and Proteomics, Volkov, Mikhail, Brinkhaus, Maximilian, van Schie, Karin A, Bondt, Albert, Kissel, Theresa, van der Kooi, Elvera J, Bentlage, Arthur E H, Koeleman, Carolien A M, de Taeye, Steven W, Derksen, Ninotska I, Dolhain, Radboud J E M, Braig-Scherer, Ute, Huizinga, Tom W J, Wuhrer, Manfred, Toes, René E M, Vidarsson, Gestur, and van der Woude, Diane

Published
2023

48. Characterization of high-molecular weight by-products in the production of a trivalent bispecific 2+1 heterodimeric antibody

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Cramer, Dario A T, Franc, Vojtech, Heidenreich, Anna-Katharina, Hook, Michaela, Adibzadeh, Mahdi, Reusch, Dietmar, Heck, Albert J R, Haberger, Markus, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Cramer, Dario A T, Franc, Vojtech, Heidenreich, Anna-Katharina, Hook, Michaela, Adibzadeh, Mahdi, Reusch, Dietmar, Heck, Albert J R, and Haberger, Markus

Published
2023

49. MRPS36 provides a structural link in the eukaryotic 2-oxoglutarate dehydrogenase complex

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Hevler, Johannes F, Albanese, Pascal, Cabrera-Orefice, Alfredo, Potter, Alisa, Jankevics, Andris, Misic, Jelena, Scheltema, Richard A, Brandt, Ulrich, Arnold, Susanne, Heck, Albert J R, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Hevler, Johannes F, Albanese, Pascal, Cabrera-Orefice, Alfredo, Potter, Alisa, Jankevics, Andris, Misic, Jelena, Scheltema, Richard A, Brandt, Ulrich, Arnold, Susanne, and Heck, Albert J R

Published
2023

50. Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy

Author

Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Subramaniam, Gunasekaran, Schleicher, Katharina, Kovanich, Duangnapa, Zerio, Anna, Folkmanaite, Milda, Chao, Ying-Chi, Surdo, Nicoletta C, Koschinski, Andreas, Hu, Jianshu, Scholten, Arjen, Heck, Albert J R, Ercu, Maria, Sholokh, Anastasiia, Chan Park, Kyung, Klussmann, Enno, Meraviglia, Viviana, Bellin, Milena, Zanivan, Sara, Hester, Svenja, Mohammed, Shabaz, Zaccolo, Manuela, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Subramaniam, Gunasekaran, Schleicher, Katharina, Kovanich, Duangnapa, Zerio, Anna, Folkmanaite, Milda, Chao, Ying-Chi, Surdo, Nicoletta C, Koschinski, Andreas, Hu, Jianshu, Scholten, Arjen, Heck, Albert J R, Ercu, Maria, Sholokh, Anastasiia, Chan Park, Kyung, Klussmann, Enno, Meraviglia, Viviana, Bellin, Milena, Zanivan, Sara, Hester, Svenja, Mohammed, Shabaz, and Zaccolo, Manuela

Published
2023

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