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Prof. dr. C.R. (Celia) Berkers

Professor 
Veterinary Medicine
Department Biomolecular Health Sciences
Cell Biology, Metabolism & Cancer
Cell Biology, Metabolism & Cancer
Nieuw Gildestein
Yalelaan 2
Kamer 243
3584 CM Utrecht

Prof. dr. C.R. (Celia) Berkers

Professor
Cell Biology, Metabolism & Cancer
+31 30 253 5381
c.r.berkers@uu.nl
Profile CV Publications Research Teaching Ancillary activities Contact
Profile CV Publications Research Teaching Ancillary activities Contact
Areas of expertise
Research areas

Publications

2025

Scholarly publications

Kes, M. M. G., Morales-Rodriguez, F., Zaal, E. A., de Souza, T., Proost, N., van de Ven, M., van den Heuvel-Eibrink, M. M., Jansen, J. W. A., Berkers, C. R., & Drost, J. (2025). Metabolic profiling of patient-derived organoids reveals nucleotide synthesis as a metabolic vulnerability in malignant rhabdoid tumors. Cell Reports Medicine, Article 101878. Advance online publication. https://doi.org/10.1016/j.xcrm.2024.101878
Zaal, E. A., Jansen, J. W. A., & Berkers, C. R. (2025). Stable Isotope Tracing Experiments Using LC-MS. Methods in molecular biology (Clifton, N.J.), 2855, 103-116. https://doi.org/10.1007/978-1-0716-4116-3_6

2024

Scholarly publications

Kes, M. M. G., Berkers, C. R., & Drost, J. (2024). Bridging the gap: advancing cancer cell culture to reveal key metabolic targets. Frontiers in Oncology, 14, Article 1480613. https://doi.org/10.3389/fonc.2024.1480613
https://research-portal.uu.nl/ws/files/242964347/fonc-1-1480613.pdf
de Kivit, S., Mensink, M., Kostidis, S., Derks, R. J. E., Zaal, E. A., Heijink, M., Verleng, L. J., de Vries, E., Schrama, E., Blomberg, N., Berkers, C. R., Giera, M., & Borst, J. (2024). Immune suppression by human thymus-derived effector Tregs relies on glucose/lactate-fueled fatty acid synthesis. Cell Reports, 43(9), Article 114681. https://doi.org/10.1016/j.celrep.2024.114681
https://research-portal.uu.nl/ws/files/241662475/PIIS2211124724010325.pdf
Jiang, X., Baig, A. H., Palazzo, G., Del Pizzo, R., Bortecen, T., Groessl, S., Zaal, E. A., Amaya Ramirez, C. C., Kowar, A., Aviles-Huerta, D., Berkers, C. R., Palm, W., Tschaharganeh, D., Krijgsveld, J., & Loayza-Puch, F. (2024). P53-dependent hypusination of eIF5A affects mitochondrial translation and senescence immune surveillance. Nature Communications, 15(1), Article 7458. https://doi.org/10.1038/s41467-024-51901-w
https://research-portal.uu.nl/ws/files/239226840/s41467-024-51901-w.pdf
Brombacher, E. C., Patente, T. A., van der Ham, A. J., Moll, T. J. A., Otto, F., Verheijen, F. W. M., Zaal, E. A., de Ru, A. H., Tjokrodirijo, R. T. N., Berkers, C. R., van Veelen, P. A., Guigas, B., & Everts, B. (2024). AMPK activation induces RALDH+ tolerogenic dendritic cells by rewiring glucose and lipid metabolism. The Journal of cell biology, 223(10), Article e202401024. https://doi.org/10.1083/jcb.202401024
https://research-portal.uu.nl/ws/files/238015864/jcb_202401024.pdf
Zhang, X., Greve, P. F., Minh, T. T. N., Wubbolts, R., Demir, A. Y., Zaal, E. A., Berkers, C. R., Boes, M., & Stoorvogel, W. (2024). Extracellular vesicles from seminal plasma interact with T cells in vitro and drive their differentiation into regulatory T-cells. Journal of Extracellular Vesicles, 13(7), 1-22. Article e12457. https://doi.org/10.1002/jev2.12457
https://research-portal.uu.nl/ws/files/233531407/J_of_Extracellular_Vesicle_-_2024_-_Zhang_-_Extracellular_vesicles_from_seminal_plasma_interact_with_T_cells_in_vitro_and_1_.pdf
von Hegedus, J. H., de Jong, A. J., Hoekstra, A. T., Spronsen, E., Zhu, W., Cabukusta, B., Kwekkeboom, J. C., Heijink, M., Bos, E., Berkers, C. R., Giera, M. A., Toes, R. E. M., & Ioan-Facsinay, A. (2024). Oleic acid enhances proliferation and calcium mobilization of CD3/CD28 activated CD4+ T cells through incorporation into membrane lipids. European Journal of Immunology, 54(9), Article 2350685. https://doi.org/10.1002/eji.202350685
https://research-portal.uu.nl/ws/files/239626521/Eur_J_Immunol_-_2024_-_Hegedus_-_Oleic_acid_enhances_proliferation_and_calcium_mobilization_of_CD3_CD28_activated_CD4_T.pdf
Díaz-Casado, M. E., González-García, P., López-Herrador, S., Hidalgo-Gutiérrez, A., Jiménez-Sánchez, L., Barriocanal-Casado, E., Bakkali, M., van de Lest, C. H. A., Corral-Sarasa, J., Zaal, E. A., Berkers, C. R., & López, L. C. (2024). Oral β-RA induces metabolic rewiring leading to the rescue of diet-induced obesity. Biochimica et Biophysica Acta. Molecular Basis of Disease, 1870(7), Article 167283. https://doi.org/10.1016/j.bbadis.2024.167283
https://research-portal.uu.nl/ws/files/227465666/1-s2.0-S0925443924002722-main.pdf
Yang, C., Pataskar, A., Feng, X., Montenegro Navarro, J., Paniagua, I., Jacobs, J. J. L., Zaal, E. A., Berkers, C. R., Bleijerveld, O. B., & Agami, R. (2024). Arginine deprivation enriches lung cancer proteomes with cysteine by inducing arginine-to-cysteine substitutants. Molecular Cell, 84(10), 1904-1916.e7. https://doi.org/10.1016/j.molcel.2024.04.012
https://dspace.library.uu.nl/bitstream/handle/1874/452572/1-s2.0-S1097276524003277-main.pdf?sequence=1
Markidi, A., Elford, J. D., Berkers, C., Kraneveld, A. D., & Perez-Pardo, P. (2024). Gut Microbes in Parkinson's Disease. In The Gut-Brain Axis: Dietary, Probiotic, and Prebiotic Interventions on the Microbiota (2 ed., pp. 217-240) https://doi.org/10.1016/b978-0-323-99971-7.00002-3
Wang, Y., Muylaert, C., Wyns, A., Vlummens, P., De Veirman, K., Vanderkerken, K., Zaal, E., Berkers, C., Moreaux, J., De Bruyne, E., & Menu, E. (2024). S-adenosylmethionine biosynthesis is a targetable metabolic vulnerability in multiple myeloma. Haematologica, 109(1), 256-271. https://doi.org/10.3324/haematol.2023.282866
https://dspace.library.uu.nl/bitstream/handle/1874/437456/11167-Article_Text-81546-2-10-20231227.pdf?sequence=1
Verheijen, F. W. M., Tran, T. N. M., Chang, J.-C., Broere, F., Zaal, E. A., & Berkers, C. R. (2024). Deciphering metabolic crosstalk in context: lessons from inflammatory diseases. Molecular Oncology, 18(7), 1759-1776. https://doi.org/10.1002/1878-0261.13588
https://research-portal.uu.nl/ws/files/230484345/Molecular_Oncology_-_2024_-_Verheijen_-_Deciphering_metabolic_crosstalk_in_context_lessons_from_inflammatory_diseases.pdf
Veth, T. S., Nouwen, L. V., Zwaagstra, M., Lyoo, H., Wierenga, K. A., Westendorp, B., Altelaar, M. A. F. M., Berkers, C., van Kuppeveld, F. J. M., & Heck, A. J. R. (2024). Assessment of Kinome-wide Activity Remodeling Upon Picornavirus Infection. Molecular and Cellular Proteomics, 23(5), Article 100757. https://doi.org/10.1016/j.mcpro.2024.100757
https://dspace.library.uu.nl/bitstream/handle/1874/451914/1-s2.0-S1535947624000471-main.pdf?sequence=1
Nouwen, L. V., Breeuwsma, M., Zaal, E. A., van de Lest, C. H. A., Buitendijk, I., Zwaagstra, M., Balić, P., Filippov, D. V., Berkers, C. R., & van Kuppeveld, F. J. M. (2024). Modulation of nucleotide metabolism by picornaviruses. PLoS Pathogens, 20(3 March), Article e1012036. https://doi.org/10.1371/journal.ppat.1012036
https://dspace.library.uu.nl/bitstream/handle/1874/436825/journal.ppat.1012036.pdf?sequence=1
Xu, Y., Wang, X., Zaal, E. A., Berkers, C. R., Lorent, J. H., Heise, T., Cox, R., Pieters, R. J., & Breukink, E. (2024). Specific labeling of newly synthesized lipopolysaccharide via metabolic incorporation of azido-galactose. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids, 1869(4), Article 159467. https://doi.org/10.1016/j.bbalip.2024.159467
https://dspace.library.uu.nl/bitstream/handle/1874/437146/1-s2.0-S1388198124000179-main.pdf?sequence=1

2023

Scholarly publications

Matamala Montoya, M., van Slobbe, G. J. J., Chang, J.-C., Zaal, E. A., & Berkers, C. R. (2023). Metabolic changes underlying drug resistance in the multiple myeloma tumor microenvironment. Frontiers in Oncology, 13, Article 1155621. https://doi.org/10.3389/fonc.2023.1155621
https://dspace.library.uu.nl/bitstream/handle/1874/437460/fonc-13-1155621.pdf?sequence=1
van Os, B. W., Vos, W. G., Bosmans, L. A., van Tiel, C. M., Lith, S. C., den Toom, M. S., Beckers, L., Levels, J. H. M., van Wouw, S. A. E., Zelcer, N., Zaal, E. A., Berkers, C. R., van der Lest, C. H. A., Helms, J. B., Weber, C., Atzler, D., de Winther, M. P. J., Baardman, J., & Lutgens, E. (2023). Hyperlipidaemia elicits an atypical, T helper 1-like CD4 + T-cell response: a key role for very low-density lipoprotein. European Heart Journal Open, 3(2), 1-14. Article oead013. https://doi.org/10.1093/ehjopen/oead013

2022

Scholarly publications

Mensink, M., Tran, T. N. M., Zaal, E. A., Schrama, E., Berkers, C. R., Borst, J., & de Kivit, S. (2022). TNFR2 Costimulation Differentially Impacts Regulatory and Conventional CD4+ T-Cell Metabolism. Frontiers in Immunology, 13, Article 881166. https://doi.org/10.3389/fimmu.2022.881166
https://dspace.library.uu.nl/bitstream/handle/1874/426206/fimmu_13_881166.pdf?sequence=1
González-García, P., Díaz-Casado, M. E., Hidalgo-Gutiérrez, A., Jiménez-Sánchez, L., Bakkali, M., Barriocanal-Casado, E., Escames, G., Chiozzi, R. Z., Völlmy, F., Zaal, E. A., Berkers, C. R., Heck, A. J. R., & López, L. C. (2022). The Q-junction and the inflammatory response are critical pathological and therapeutic factors in CoQ deficiency. Redox Biology, 55, Article 102403. https://doi.org/10.1016/j.redox.2022.102403
https://dspace.library.uu.nl/bitstream/handle/1874/426205/Q_junction.pdf?sequence=1
Peeters, R., Cuenca-Escalona, J., Zaal, E. A., Hoekstra, A. T., Balvert, A. C. G., Vidal-Manrique, M., Blomberg, N., van Deventer, S. J., Stienstra, R., Jellusova, J., Giera, M., Hannibal, L., Spiekerkoetter, U., ter Beest, M., Berkers, C. R., & van Spriel, A. B. (2022). Fatty acid metabolism in aggressive B-cell lymphoma is inhibited by tetraspanin CD37. Nature Communications, 13(1), 1-18. Article 5371. https://doi.org/10.1038/s41467-022-33138-7
https://dspace.library.uu.nl/bitstream/handle/1874/426118/s41467_022_33138_7.pdf?sequence=1
Van Nyen, T., Planque, M., van Wagensveld, L., Duarte, J. A. G., Zaal, E. A., Talebi, A., Rossi, M., Körner, P. R., Rizzotto, L., Moens, S., De Wispelaere, W., Baiden-Amissah, R. E. M., Sonke, G. S., Horlings, H. M., Eelen, G., Berardi, E., Swinnen, J. V., Berkers, C. R., Carmeliet, P., ... Amant, F. (2022). Serine metabolism remodeling after platinum-based chemotherapy identifies vulnerabilities in a subgroup of resistant ovarian cancers. Nature Communications, 13(1), 1-19. Article 4578. https://doi.org/10.1038/s41467-022-32272-6
https://dspace.library.uu.nl/bitstream/handle/1874/426114/s41467_022_32272_6.pdf?sequence=1
van Dijk, A., Anten, J., Bakker, A., Evers, N., Hoekstra, A. T., Chang, J.-C., Scheenstra, M. R., Veldhuizen, E. J. A., Netea, M. G., Berkers, C. R., & Haagsman, H. P. (2022). Innate Immune Training of Human Macrophages by Cathelicidin Analogs. Frontiers in Immunology, 13, 1-18. Article 777530. https://doi.org/10.3389/fimmu.2022.777530
https://dspace.library.uu.nl/bitstream/handle/1874/422314/fimmu_13_777530.pdf?sequence=1
Zaal, E. A., de Grooth, H.-J., Oudaert, I., Langerhorst, P., Levantovsky, S., van Slobbe, G. J. J., Jansen, J. W. A., Menu, E., Wu, W., & Berkers, C. R. (2022). Targeting coenzyme Q10 synthesis overcomes bortezomib resistance in multiple myeloma. Molecular Omics, 18(1), 19-30. https://doi.org/10.1039/d1mo00106j
https://dspace.library.uu.nl/bitstream/handle/1874/419215/d1mo00106j.pdf?sequence=1

2021

Scholarly publications

Besse, L., Besse, A., Stolze, S. C., Sobh, A., Zaal, E. A., Ham, A. J. V. D., Ruiz, M., Phuyal, S., Buchler, L., Sathianathan, M., Florea, B. I., Boren, J., Hlman, M. S., Huber, J., Bolomsky, A., Ludwig, H., Hannich, J. T., Loguinov, A., Everts, B., ... Driessen, C. (2021). Treatment with HIV-protease inhibitor nelfinavir identifies membrane lipid composition and fluidity as a therapeutic target in advanced multiple myeloma. Cancer Research, 81(17), 4581-4593. https://doi.org/10.1158/0008-5472.CAN-20-3323
https://dspace.library.uu.nl/bitstream/handle/1874/416419/4581.full.pdf?sequence=1
Champagne, J., Pataskar, A., Blommaert, N., Nagel, R., Wernaart, D., Ramalho, S., Kenski, J., Bleijerveld, O. B., Zaal, E. A., Berkers, C. R., Altelaar, M., Peeper, D. S., Faller, W. J., & Agami, R. (2021). Oncogene-dependent sloppiness in mRNA translation. Molecular Cell, 81(22), 4709-4721. https://doi.org/10.1016/j.molcel.2021.09.002
https://dspace.library.uu.nl/bitstream/handle/1874/413475/PIIS109727652100736X.pdf?sequence=1
Chen, J., Zaal, E. A., Berkers, C. R., Ruijtenbeek, R., Garssen, J., & Redegeld, F. A. (2021). Omega-3 Fatty Acids DHA and EPA Reduce Bortezomib Resistance in Multiple Myeloma Cells by Promoting Glutathione Degradation. Cells, 10(9), Article 2287. https://doi.org/10.3390/cells10092287
https://dspace.library.uu.nl/bitstream/handle/1874/413132/cells_10_02287.pdf?sequence=1
Jamalpoor, A., van Gelder, C. A. G. H., Yousef Yengej, F. A., Zaal, E. A., Berlingerio, S. P., Veys, K. R., Pou Casellas, C., Voskuil, K., Essa, K., Ammerlaan, C. M. E., Rega, L. R., van der Welle, R. E. N., Lilien, M. R., Rookmaaker, M. B., Clevers, H., Klumperman, J., Levtchenko, E., Berkers, C. R., Verhaar, M. C., ... Janssen, M. J. (2021). Cysteamine–bicalutamide combination therapy corrects proximal tubule phenotype in cystinosis. EMBO Molecular Medicine, 13(7), 1-20. Article e13067. https://doi.org/10.15252/emmm.202013067
https://dspace.library.uu.nl/bitstream/handle/1874/412460/emmm.202013067.pdf?sequence=1
Ghanem, A., Melzer, A. M., Zaal, E., Neises, L., Baltissen, D., Matar, O., Glennemeier-Marke, H., Almouhanna, F., Theobald, J., Abu El Maaty, M. A., Berkers, C., & Wölfl, S. (2021). Ascorbate kills breast cancer cells by rewiring metabolism via redox imbalance and energy crisis. Free Radical Biology and Medicine, 163, 196-209. https://doi.org/10.1016/j.freeradbiomed.2020.12.012
https://dspace.library.uu.nl/bitstream/handle/1874/410951/1_s2.0_S0891584920316750_main.pdf?sequence=1
Bartok, O., Pataskar, A., Nagel, R., Laos, M., Goldfarb, E., Hayoun, D., Levy, R., Körner, P.-R., Kreuger, I. Z. M., Champagne, J., Zaal, E. A., Bleijerveld, O. B., Huang, X., Kenski, J., Wargo, J., Brandis, A., Levin, Y., Mizrahi, O., Alon, M., ... Agami, R. (2021). Anti-tumour immunity induces aberrant peptide presentation in melanoma. Nature, 590(7845), 332–337. https://doi.org/10.1038/s41586-020-03054-1
https://dspace.library.uu.nl/bitstream/handle/1874/410283/s41586_020_03054_1.pdf?sequence=1

2020

Scholarly publications

Jamalpoor, A., van Gelder, C. A. G. H., Yousef Yengej, F. A., Zaal, E. A., Berlingerio, S. P., Veys, K. R., Pou Casellas, C., Voskuil, K., Essa, K., Ammerlaan, C., Rega, L. R., van der Welle, R., Lilien, M. R., Rookmaaker, M. B., Clevers, H. C., Klumperman, J., Levtchenko, E., Berkers, C. R., Verhaar, M. C., ... Janssen, M. J. (2020). Cysteamine-bicalutamide combination treatment restores alpha-ketoglutarate and corrects proximal tubule phenotype in cystinosis. (pp. 1-53). bioRxiv. https://doi.org/10.1101/2020.02.10.941799
Ottria, A., Hoekstra, A. T., Zimmermann, M., van der Kroef, M., Vazirpanah, N., Cossu, M., Chouri, E., Rossato, M., Beretta, L., Tieland, R. G., Wichers, C. G. K., Stigter, E., Gulersonmez, C., Bonte-Mineur, F., Berkers, C. R., Radstake, T. R. D. J., & Marut, W. (2020). Fatty Acid and Carnitine Metabolism Are Dysregulated in Systemic Sclerosis Patients. Frontiers in Immunology, 11, Article 822. https://doi.org/10.3389/fimmu.2020.00822
https://dspace.library.uu.nl/bitstream/handle/1874/411080/fimmu_11_00822.pdf?sequence=1
de Kivit, S., Mensink, M., Hoekstra, A. T., Berlin, I., Derks, R. J. E., Both, D., Aslam, M. A., Amsen, D., Berkers, C. R., & Borst, J. (2020). Stable human regulatory T cells switch to glycolysis following TNF receptor 2 costimulation. Nature Metabolism, 2(10), 1046-1061. https://doi.org/10.1038/s42255-020-00271-w
https://dspace.library.uu.nl/bitstream/handle/1874/418729/s42255_020_00271_w.pdf?sequence=1
Jin, H., Wang, S., Zaal, E. A., Wang, C., Wu, H., Bosma, A., Jochems, F., Isima, N., Jin, G., Lieftink, C., Beijersbergen, R., Berkers, C. R., Qin, W., & Bernards, R. (2020). A powerful drug combination strategy targeting glutamine addiction for the treatment of human liver cancer. eLife, 9, Article e56749. https://doi.org/10.7554/eLife.56749
https://dspace.library.uu.nl/bitstream/handle/1874/410952/elife_56749_v1.pdf?sequence=1

2019

Scholarly publications

Milne, K., Sun, J., Zaal, E. A., Mowat, J., Celie, P. H. N., Fish, A., Berkers, C. R., Forlani, G., Loayza-Puch, F., Jamieson, C., & Agami, R. (2019). A fragment-like approach to PYCR1 inhibition. Bioorganic and Medicinal Chemistry Letters, 29(18), 2626-2631. https://doi.org/10.1016/j.bmcl.2019.07.047
https://dspace.library.uu.nl/bitstream/handle/1874/387540/fragment.pdf?sequence=1
Sun, J., Nagel, R., Zaal, E. A., Ugalde, A. P., Han, R., Proost, N., Song, J. Y., Pataskar, A., Burylo, A., Fu, H., Poelarends, G. J., van de Ven, M., van Tellingen, O., Berkers, C. R., & Agami, R. (2019). SLC1A3 contributes to L-asparaginase resistance in solid tumors. EMBO Journal, 38(21), Article e102147. https://doi.org/10.15252/embj.2019102147
https://dspace.library.uu.nl/bitstream/handle/1874/387793/Sun_et_al_2019_The_EMBO_Journal.pdf?sequence=1
Jansen, J., Jansen, K., Neven, E., Poesen, R., Othman, A., van Mil, A., Sluijter, J., Sastre Torano, J., Zaal, E. A., Berkers, C. R., Esser, D., Wichers, H. J., van Ede, K., van Duursen, M., Burtey, S., Verhaar, M. C., Meijers, B., & Masereeuw, R. (2019). Remote sensing and signaling in kidney proximal tubules stimulates gut microbiome-derived organic anion secretion. Proceedings of the National Academy of Sciences of the United States of America, 116(32), 16105-16110. https://doi.org/10.1073/pnas.1821809116
https://dspace.library.uu.nl/bitstream/handle/1874/384785/16105.full.pdf?sequence=1

2018

Scholarly publications

Zaal, E. A., & Berkers, C. R. (2018). The Influence of Metabolism on Drug Response in Cancer. Frontiers in Oncology, 8, Article 500. https://doi.org/10.3389/fonc.2018.00500
https://dspace.library.uu.nl/bitstream/handle/1874/374419/fonc_08_00500.pdf?sequence=1
Wu, W., Zaal, E. A., Berkers, C. R., Lemeer, S., & Heck, A. J. R. (2018). CTGF/VEGFA-activated fibroblasts promote tumor migration through micro-environmental modulation. Molecular and Cellular Proteomics, 17(8), 1502-1514. https://doi.org/10.1074/mcp.RA118.000708
https://dspace.library.uu.nl/bitstream/handle/1874/368260/1502.full.pdf?sequence=1
Oerlemans, R., Berkers, C. R., Assaraf, Y. G., Scheffer, G. L., Peters, G. J., Verbrugge, S. E., Cloos, J., Slootstra, J. W., Meloen, R. H., Shoemaker, R. H., Dijkmans, B. A. C., Scheper, R. J., Ovaa, H., & Jansen, G. (2018). Proteasome inhibition and mechanism of resistance to a synthetic, library-based hexapeptide. Investigational New Drugs, 36, 797–809. https://doi.org/10.1007/s10637-018-0569-x
https://research-portal.uu.nl/ws/files/247879313/s10637-018-0569-x.pdf

2017

Scholarly publications

Wisse, L. E., Penning, R., Zaal, E. A., van Berkel, C. G. M., ter Braak, T. J., Polder, E., Kenney, J. W., Proud, C. G., Berkers, C. R., Altelaar, M. A. F., Speijer, D., van der Knaap, M. S., & Abbink, T. E. M. (2017). Proteomic and metabolomic analyses of vanishing white matter mouse astrocytes reveal deregulation of ER functions. Frontiers in Cellular Neuroscience, 11, Article 411. https://doi.org/10.3389/fncel.2017.00411
https://dspace.library.uu.nl/bitstream/handle/1874/361198/wisse.pdf?sequence=1
Zaal, E. A., Wu, W., Jansen, G., Zweegman, S., Cloos, J., & Berkers, C. R. (2017). Bortezomib resistance in multiple myeloma is associated with increased serine synthesis. Cancer & metabolism, 5, Article 7. https://doi.org/10.1186/s40170-017-0169-9
https://dspace.library.uu.nl/bitstream/handle/1874/358231/Bortezomib.pdf?sequence=1
Loayza-Puch, F., Rooijers, K., Zijlstra, J. S., Moumbeini, B., Zaal, E. A., Oude Vrielink, J. F., Lopes, R. M., Ugalde, A. P., Berkers, C. R., & Agami, R. (2017). TGFβ1-induced leucine limitation uncovered by differential ribosome codon reading. EMBO Reports, 18(4), 549-557. https://doi.org/10.15252/embr.201744000
https://dspace.library.uu.nl/bitstream/handle/1874/358101/TGF.pdf?sequence=1
Welle, T., Hoekstra, A. T., Daemen, I. A. J. J. M., Berkers, C. R., & de Oliveira Costa, M. (2017). Metabolic response of porcine colon explants to in vitro infection by Brachyspira hyodysenteriae: a leap into disease pathophysiology. Metabolomics, 13(7), Article 83. https://doi.org/10.1007/s11306-017-1219-6
https://dspace.library.uu.nl/bitstream/handle/1874/358100/metabolic.pdf?sequence=1
Widjaja, C. E., Olvera, J. G., Metz, P. J., Phan, A. T., Savas, J. N., de Bruin, G., Leestemaker, Y., Berkers, C. R., De Jong, A., Florea, B. I., Fisch, K., Lopez, J., Kim, S. H., Garcia, D. A., Searles, S., Bui, J. D., Chang, A. N., Yates, J. R., Goldrath, A. W., ... Chang, J. T. (2017). Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. Journal of Clinical Investigation, 127(10), 3609-3623. https://doi.org/10.1172/JCI90895
https://dspace.library.uu.nl/bitstream/handle/1874/358099/proteasome.pdf?sequence=1
Ruprecht, B., Zaal, E. A., Zecha, J., Wu, W., Berkers, C. R., Kuster, B., & Lemeer, S. (2017). Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis. Cancer Research, 77(8), 1842-1853. https://doi.org/10.1158/0008-5472.CAN-16-2976
https://dspace.library.uu.nl/bitstream/handle/1874/357783/1842.full.pdf?sequence=1
Leestemaker, Y., de Jong, A., Witting, K. F., Penning, R., Schuurman, K., Rodenko, B., Zaal, E. A., van de Kooij, B., Laufer, S., Heck, A. J. R., Borst, J., Scheper, W., Berkers, C. R., & Ovaa, H. (2017). Proteasome Activation by Small Molecules. Cell Chemical Biology, 24(6), 725-736.e7. https://doi.org/10.1016/j.chembiol.2017.05.010
https://dspace.library.uu.nl/bitstream/handle/1874/352861/Protesame.pdf?sequence=1

2016

Scholarly publications

Becher, I., Werner, T., Doce, C., Zaal, E. A., Tögel, I., Khan, C. A., Rueger, A., Muelbaier, M., Salzer, E., Berkers, C. R., Fitzpatrick, P. F., Bantscheff, M., & Savitski, M. M. (2016). Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nature Chemical Biology, 12(11), 908-910. https://doi.org/10.1038/nchembio.2185
https://dspace.library.uu.nl/bitstream/handle/1874/345048/Thermal.pdf?sequence=1
Weijer, R., Clavier, S., Zaal, E. A., Pijls, M. M. E., van Kooten, R. T., Vermaas, K., Leen, R., Jongejan, A., Moerland, P. D., van Kampen, A. H. C., van Kuilenburg, A. B. P., Berkers, C. R., Lemeer, S., & Heger, M. (2016). Multi-OMIC profiling of survival and metabolic signaling networks in cells subjected to photodynamic therapy. Cellular and Molecular Life Sciences. https://doi.org/10.1007/s00018-016-2401-0
Liu, Y., Garcia Lopes Maia Rodrigues, J., Bonvin, A. M. J. J., Zaal, E. A., Berkers, C. R., Heger, M., Gawarecka, K., Swiezewska, E., Breukink, E., & Egmond, M. R. (2016). New insight into the catalytic mechanism of bacterial mray from enzyme kinetics and docking studies. Journal of Biological Chemistry, 291(29), 15057-15068. https://doi.org/10.1074/jbc.M116.717884
https://dspace.library.uu.nl/bitstream/handle/1874/337449/Insight.pdf?sequence=1

2015

Scholarly publications

Berkers, C. R., De Jong, A., Schuurman, K. G., Linnemann, C., Geenevasen, J. A. J., Schumacher, T. N. M., Rodenko, B., & Ovaa, H. (2015). Peptide splicing in the proteasome creates a novel type of antigen with an isopeptide linkage. Journal of Immunology, 195(9), 4075-4084. https://doi.org/10.4049/jimmunol.1402454
https://dspace.library.uu.nl/bitstream/handle/1874/330069/Peptide.pdf?sequence=1
Berkers, C. R., De Jong, A., Schuurman, K. G., Linnemann, C., Meiring, H. D., Janssen, L., Neefjes, J. J., Schumacher, T. N. M., Rodenko, B., & Ovaa, H. (2015). Definition of proteasomal peptide splicing rules for high-efficiency spliced peptide presentation by MHC class I molecules. Journal of Immunology, 195(9), 4085-4095. https://doi.org/10.4049/jimmunol.1402455
https://dspace.library.uu.nl/bitstream/handle/1874/327792/Proteasomal.pdf?sequence=1

2014

Scholarly publications

D'Alessandro, A., Amelio, I., Berkers, C. R., Antonov, A., Vousden, K. H., Melino, G., & Zolla, L. (2014). Metabolic effect of TAp63α: enhanced glycolysis and pentose phosphate pathway, resulting in increased antioxidant defense. Oncotarget, 5(17), 7722-7733. https://doi.org/10.18632/oncotarget.2300
https://dspace.library.uu.nl/bitstream/handle/1874/308017/oncotarget_05_7722.pdf?sequence=1

2013

Scholarly publications

Maddocks, O. D. K., Berkers, C. R., Mason, S. M., Zheng, L., Blyth, K., Gottlieb, E., & Vousden, K. H. (2013). Serine starvation induces stress and p53-dependent metabolic remodelling in cancer cells. Nature, 493(7433), 542-6. https://doi.org/10.1038/nature11743
Berkers, C. R., Maddocks, O. D. K., Cheung, E. C., Mor, I., & Vousden, K. H. (2013). Metabolic regulation by p53 family members. Cell Metabolism, 18(5), 617-633. https://doi.org/10.1016/j.cmet.2013.06.019
Gao, Y., Koppen, A., Rakhshandehroo, M., Tasdelen, I., van de Graaf, S. F. J., van Loosdregt, J., van Beekum, O., Hamers, N., van Leenen, D., Berkers, C. R., Berger, R., Holstege, F. C. P., Coffer, P. J., Brenkman, A. B., Ovaa, H., & Kalkhoven, E. (2013). Early adipogenesis is regulated through USP7-mediated deubiquitination of the histone acetyltransferase TIP60. Nature Communications [E], 4, 2656. https://doi.org/10.1038/ncomms3656
van Loosdregt, J., Fleskens, V., Fu, J., Brenkman, A. B., Bekker, C. P. J., Pals, C. E. G. M., Meerding, J. M., Berkers, C. R., Barbi, J., Grone, A., Sijts, E. J. A. M., Maurice, M. M., Kalkhoven, E., Prakken, A. B. J., Ovaa, H., Pan, F., Zaiss, D. M. W., & Coffer, P. J. (2013). Stabilization of the transcription factor Foxp3 by the deubiquitinase USP7 increases Treg-cell-suppressive capacity. Immunity, 39(2), 259-271. https://doi.org/10.1016/j.immuni.2013.05.018.

2012

Scholarly publications

De Jong, A., Schuurman, K. G., Rodenko, B., Ovaa, H., & Berkers, C. R. (2012). Fluorescence-based proteasome activity profiling. Humana Press. https://doi.org/10.1007/978-1-61779-364-6_13
Berkers, C. R., Leestemaker, Y., Schuurman, K. G., Ruggeri, B., Jones-Bolin, S., Williams, M., & Ovaa, H. (2012). Probing the specificity and activity profiles of the proteasome inhibitors bortezomib and delanzomib. Molecular Pharmaceutics, 9(5), 1126-1135. https://doi.org/10.1021/mp2004143

2011

Scholarly publications

Potts, B. C., Albitar, M. X., Anderson, K. C., Baritaki, S., Berkers, C., Bonavida, B., Chandra, J., Chauhan, D., Cusack, J. C., Fenical, W., Ghobrial, I. M., Groll, M., Jensen, P. R., Lam, K. S., Lloyd, G. K., McBride, W., McConkey, D. J., Miller, C. P., Neuteboom, S. T. C., ... Palladino, M. A. (2011). Marizomib, a proteasome inhibitor for all seasons: preclinical profile and a framework for clinical trials. Curr Cancer Drug Targets, 11(3), 254-84. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712795/
Nijholt, D. A. T., de Graaf, T. R., van Haastert, E. S., Oliveira, A. O., Berkers, C. R., Zwart, R., Ovaa, H., Baas, F., Hoozemans, J. J. M., & Scheper, W. (2011). Endoplasmic reticulum stress activates autophagy but not the proteasome in neuronal cells: implications for Alzheimer's disease. Cell Death and Differentiation, 18(6), 1071-81. https://doi.org/10.1038/cdd.2010.176

2010

Scholarly publications

Berkers, C. R., & Ovaa, H. (2010). Drug discovery and assay development in the ubiquitin-proteasome system. Biochemical Society Transactions, 38(Pt 1), 14-20. https://doi.org/10.1042/BST0380014
Pelletier, S., Schuurman, K. G., Berkers, C. R., Ovaa, H., Heck, A. J. R., & Raijmakers, R. (2010). Quantifying cross-tissue diversity in proteasome complexes by mass spectrometry. Molecular BioSystems, 6, 1450-1453.

2009

Scholarly publications

Berkers, C. R., de Jong, A., Ovaa, H., & Rodenko, B. (2009). Transpeptidation and reverse proteolysis and their consequences for immunity. International Journal of Biochemistry & Cell Biology, 41(1), 66-71. https://doi.org/10.1016/j.biocel.2008.08.036
Middeldorp, J., Kamphuis, W., Sluijs, J. A., Achoui, D., Leenaars, C., Feenstra, M. G. P., van Tijn, P., Fischer, D. F., Berkers, C., Ovaa, H., Quinlan, R. A., & Hol, E. M. (2009). Intermediate filament transcription in astrocytes is repressed by proteasome inhibition. FASEB Journal, 23(8), 2710-26. https://doi.org/10.1096/fj.08-127696

2008

Scholarly publications

Bakker, A. H., Hoppes, R., Linnemann, C., Toebes, M., Rodenko, B., Berkers, C. R., Hadrup, S. R., Van Esch, W. J. E., Heemskerk, M. H. M., Ovaa, H., & Schumacher, T. N. M. (2008). Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7. Proceedings of the National Academy of Sciences of the United States of America, 105(10), 3825-3830. https://doi.org/10.1073/pnas.0709717105
Piva, R., Ruggeri, B., Williams, M., Costa, G., Tamagno, I., Ferrero, D., Giai, V., Coscia, M., Peola, S., Massaia, M., Pezzoni, G., Allievi, C., Pescalli, N., Cassin, M., di Giovine, S., Nicoli, P., de Feudis, P., Strepponi, I., Roato, I., ... Inghirami, G. (2008). CEP-18770: A novel, orally active proteasome inhibitor with a tumor-selective pharmacologic profile competitive with bortezomib. Blood, 111(5), 2765-75. https://doi.org/10.1182/blood-2007-07-100651
Oerlemans, R., Franke, N. E., Assaraf, Y. G., Cloos, J., van Zantwijk, I., Berkers, C. R., Scheffer, G. L., Debipersad, K., Vojtekova, K., Lemos, C., van der Heijden, J. W., Ylstra, B., Peters, G. J., Kaspers, G. L., Dijkmans, B. A. C., Scheper, R. J., & Jansen, G. (2008). Molecular basis of bortezomib resistance: proteasome subunit beta5 (PSMB5) gene mutation and overexpression of PSMB5 protein. Blood, 112(6), 2489-99. https://doi.org/10.1182/blood-2007-08-104950
Raijmakers, R., Berkers, C. R., de Jong, G. J., Ovaa, H., Heck, A. J. R., & Mohammed, S. (2008). Automated online sequential isotope labeling for protein quantitation applied to proteasome tissue specific diversity. Molecular & Cellular Proteomics, 7, 1755-1762.

2007

Scholarly publications

Kraus, M., Rückrich, T., Reich, M., Gogel, J., Beck, A., Kammer, W., Berkers, C. R., Burg, D., Overkleeft, H., Ovaa, H., & Driessen, C. (2007). Activity patterns of proteasome subunits reflect bortezomib sensitivity of hematologic malignancies and are variable in primary human leukemia cells. Leukemia, 21(1), 84-92. https://doi.org/10.1038/sj.leu.2404414
Berkers, C. R., van Leeuwen, F. W. B., Groothuis, T. A., Peperzak, V., van Tilburg, E. W., Borst, J., Neefjes, J. J., & Ovaa, H. (2007). Profiling proteasome activity in tissue with fluorescent probes. Molecular Pharmaceutics, 4(5), 739-48. https://doi.org/10.1021/mp0700256

2006

Scholarly publications

Verdoes, M., Berkers, C. R., Florea, B. I., van Swieten, P. F., Overkleeft, H. S., & Ovaa, H. (2006). Chemical proteomics profiling of proteasome activity. Methods in Molecular Biology, 328, 51-69. https://link.springer.com/protocol/10.1385%2F1-59745-026-X%3A51
Risseeuw, M. D. P., Berkers, C. R., Ploegh, H. L., & Ovaa, H. (2006). Synthesis of tritium labeled KRN7000. Tetrahedron Letters, 47(22), 3677-3679. https://doi.org/10.1016/j.tetlet.2006.03.131
Groll, M., Berkers, C. R., Ploegh, H. L., & Ovaa, H. (2006). Crystal structure of the boronic acid-based proteasome inhibitor bortezomib in complex with the yeast 20S proteasome. Structure, 14(3), 451-6. https://doi.org/10.1016/j.str.2005.11.019
Verdoes, M., Florea, B. I., Menendez-Benito, V., Maynard, C. J., Witte, M. D., van der Linden, W. A., van den Nieuwendijk, A. M. C. H., Hofmann, T., Berkers, C. R., van Leeuwen, F. W. B., Groothuis, T. A., Leeuwenburgh, M. A., Ovaa, H., Neefjes, J. J., Filippov, D. V., van der Marel, G. A., Dantuma, N. P., & Overkleeft, H. S. (2006). A fluorescent broad-spectrum proteasome inhibitor for labeling proteasomes in vitro and in vivo. Chemistry & Biology, 13(11), 1217-26. https://doi.org/10.1016/j.chembiol.2006.09.013

2005

Scholarly publications

Berkers, C. R., Verdoes, M., Lichtman, E., Fiebiger, E., Kessler, B. M., Anderson, K. C., Ploegh, H. L., Ovaa, H., & Galardy, P. J. (2005). Activity probe for in vivo profiling of the specificity of proteasome inhibitor bortezomib. Nature Methods, 2(5), 357-62. https://doi.org/10.1038/nmeth759
Berkers, C. R., & Ovaa, H. (2005). Immunotherapeutic potential for ceramide-based activators of iNKT cells. Trends in Pharmacological Sciences, 26(5), 252-7. https://doi.org/10.1016/j.tips.2005.03.005
Chauhan, D., Catley, L., Li, G., Podar, K., Hideshima, T., Velankar, M., Mitsiades, C., Mitsiades, N., Yasui, H., Letai, A., Ovaa, H., Berkers, C., Nicholson, B., Chao, T.-H., Neuteboom, S. T. C., Richardson, P., Palladino, M. A., & Anderson, K. C. (2005). A novel orally active proteasome inhibitor induces apoptosis in multiple myeloma cells with mechanisms distinct from Bortezomib. Cancer Cell, 8(5), 407-19. https://doi.org/10.1016/j.ccr.2005.10.013
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