J. Dengjel publications
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Selected publications
2025
Brunner, M., Hu, Z., Elkhaligy, H., Lampo, G., Roubaty, C., Vionnet, C., Sankar, D.S., McIlwain, S.J., Kaeser-Pebernard, S., Xing, Y., and Dengjel, J. (2025). Combination of in vivo and in vitro phosphoproteomics determines the PP2A target repertoire on proteome scale. Cell Rep Methods 5, 101084. pdf
Leytens, A., Benitez-Fernandez, R., Jimenez-Garcia, C., Roubaty, C., Stumpe, M., Boya, P., and Dengjel, J. (2025). Targeted proteomics addresses selectivity and complexity of protein degradation by autophagy. Autophagy 21, 460-475. pdf
Sander, S., Leytens, A., and Dengjel, J. (2025). Deep Proteome Profiling of Primary Skin Fibroblasts. Methods Mol Biol 2922, 197-207.
2024
Sankar, D.S., Kaeser-Pebernard, S., Vionnet, C., Favre, S., de Oliveira Marchioro, L., Pillet, B., Zhou, J., Stumpe, M., Kovacs, W.J., Kressler, D., Antonioli, M., Fimia, G. M., and Dengjel, J. (2024). The ULK1 effector BAG2 regulates autophagy initiation by modulating AMBRA1 localization. Cell Rep 43, 114689. pdf
2023
Kallergi, E., Siva Sankar, D., Matera, A., Kolaxi, A., Paolicelli, R.C., Dengjel, J., and Nikoletopoulou, V. (2023). Profiling of purified autophagic vesicle degradome in the maturing and aging brain. Neuron 111, 2329-2347 e2327. pdf
Zhou, J., Rasmussen, N.L., Olsvik, H.L., Akimov, V., Hu, Z., Evjen, G., Kaeser-Pebernard, S., Sankar, D.S., Roubaty, C., Verlhac, P., et al. (2023). TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1. J Cell Biol 222. pdf
2022
Kaeser-Pebernard, S., Vionnet, C., Mari, M., Sankar, D.S., Hu, Z., Roubaty, C., Martinez-Martinez, E., Zhao, H., Spuch-Calvar, M., Petri-Fink, A., Rainer, G., Steinberg, F., Reggiori, F., and Dengjel, J. (2022). mTORC1 controls Golgi architecture and vesicle secretion by phosphorylation of SCYL1. Nat Commun 13, 4685. pdf
Martinez-Martinez, E., Atzei, P., Vionnet, C., Roubaty, C., Kaeser-Pebernard, S., Naef, R., and Dengjel, J. (2022). A Dual-Acting Nitric Oxide Donor and Phosphodiesterase 5 Inhibitor Activates Autophagy in Primary Skin Fibroblasts. Int J Mol Sci 23.
Siva Sankar, D., Hu, Z., and Dengjel, J. (2022). The complex interplay between ULK1 and protein phosphatases in autophagy regulation. Autophagy 18, 455-456.
2021
Hu Z, Sankar DS, Vu B, Leytens A, Vionnet C, Wu W, Stumpe M, Martinez-Martinez E, Stork B, Dengjel J (2021) ULK1 phosphorylation of striatin activates protein phosphatase 2A and autophagy. Cell Rep 36: 109762. pdf
Martinez-Martinez E, Tolle R, Donauer J, Gretzmeier C, Bruckner-Tuderman L, Dengjel J (2021) Increased abundance of Cbl E3 ligases alters PDGFR signaling in recessive dystrophic epidermolysis bullosa. Matrix Biol 103-104: 58-73. pdf
Siva Sankar D, Dengjel J (2021) Protein complexes and neighborhoods driving autophagy. Autophagy 17: 2689-2705. pdf
Siva Sankar D, Hu Z, Dengjel J (2021) The complex interplay between ULK1 and protein phosphatases in autophagy regulation. Autophagy: 1-2. pdf
Vu B, Souza GR, Dengjel J (2021) Scaffold-free 3D cell culture of primary skin fibroblasts induces profound changes of the matrisome. Matrix Biol Plus 11: 100066. pdf
2020
Berberich, B, Thriene, K, Gretzmeier, C, Kuhl, T, Bayer, H, Athanasiou, I, Rafei-Shamsabadi, DA, Bruckner-Tuderman, L, Nystrom, A, Kiritsi, D, & Dengjel, J (2020). Proteomic Profiling of Fibroblasts Isolated from Chronic Wounds Identifies Disease-Relevant Signaling Pathways. J Invest Dermatol 140:2280-2290 e2284.
Dengjel, J, Bruckner-Tuderman, L, & Nystrom, A (2020). Skin proteomics - analysis of the extracellular matrix in health and disease. Expert Rev Proteomics 17:377-391. pdf
Siva Sankar, D & Dengjel, J (2020). Protein complexes and neighborhoods driving autophagy. Autophagy:1-17. pdf
2019
Hu, Z, Raucci, S, Jaquenoud, M, Hatakeyama, R, Stumpe, M, Rohr, R, Reggiori, F, De Virgilio, C, & Dengjel, J (2019). Multilayered Control of Protein Turnover by TORC1 and Atg1. Cell Rep 28:3486-3496 e3486. pdf
Tolle, RC & Dengjel, J (2019). Effects of the Extracellular Matrix on the Proteome of Primary Skin Fibroblasts. Methods Mol Biol 1993:193-204.
Kaeser-Pebernard, S, Diedrich, B, Dengjel, J (2019). Identification and Regulation of Multimeric Protein Complexes in Autophagy via SILAC-Based Mass Spectrometry Approaches. Methods Mol Biol 1880: 341-57, doi.org/10.1007/978-1-4939-8873-0_23. pdf
2018
Tölle, RC, Gaggioli C, Dengjel J. (2018). Three-Dimensional Cell Culture Conditions Affect the Proteome of Cancer-Associated Fibroblasts. J Proteome Res 17:2780-2789. pdf
Becker, AC, Gannage, M, Giese, S, Hu, Z, Abou-Eid, S, Roubaty, C, Paul, P, Buhler, LK, Gretzmeier, C, Dumit, VI, Kaeser-Pebernard, S, Schwemmle, M, Munz, C, & Dengjel, J (2018). Influenza A virus induces autophagosomal targeting of ribosomal proteins. Mol Cell Proteomics 17:1909-1921. pdf
Thriene, K, Gruning, BA, Bornert, O, Erxleben, A, Leppert, J, Athanasiou, I, Weber, E, Kiritsi, D, Nystrom, A, Reinheckel, T, Backofen, R, Has, C, Bruckner-Tuderman, L, & Dengjel, J (2018). Combinatorial Omics Analysis Reveals Perturbed Lysosomal Homeostasis in Collagen VII-deficient Keratinocytes. Mol Cell Proteomics 17:565-579. pdf
2017
Diedrich, B, Rigbolt, KT, Roring, M, Herr, R, Kaeser-Pebernard, S, Gretzmeier, C, Murphy, RF, Brummer, T, & Dengjel, J (2017). Discrete cytosolic macromolecular BRAF complexes exhibit distinct activities and composition. EMBO J 36:646-663. pdf
Diedrich, B & Dengjel, J (2017). Insights into autosomal dominant polycystic kidney disease by quantitative mass spectrometry-based proteomics. Cell Tissue Res 369:41-51. pdf
Dumit, VI, Zerbes, RM, Kaeser-Pebernard, S, Rackiewicz, M, Wall, MT, Gretzmeier, C, Kuttner, V, van der Laan, M, Braun, RJ, & Dengjel, J (2017). Respiratory status determines the effect of emodin on cell viability. Oncotarget 8:37478-37490.
Gretzmeier, C, Eiselein, S, Johnson, GR, Engelke, R, Nowag, H, Zarei, M, Kuttner, V, Becker, AC, Rigbolt, KTG, Hoyer-Hansen, M, Andersen, JS, Munz, C, Murphy, RF, & Dengjel, J (2017). Degradation of protein translation machinery by amino acid starvation-induced macroautophagy. Autophagy 13:1064-1075.
Rackiewicz, M, Grosse-Hovest, L, Alpert, AJ, Zarei, M, & Dengjel, J (2017). Hydrophobic Interaction Chromatography for Bottom-Up Proteomics Analysis of Single Proteins and Protein Complexes. J Proteome Res 16:2318-2323. pdf
Stork, B & Dengjel, J (2017). Study of ULK1 Catalytic Activity and Its Regulation. Methods Enzymol 587:391-404.
2016
Zarei, M, Sprenger, A, Rackiewicz, M, & Dengjel, J (2016). Fast and easy phosphopeptide fractionation by combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis. Nat Protoc 11:37-45.
2014
Becker, AC & Dengjel, J (2014). Autophagosomal proteome analysis by protein correlation profiling-SILAC. Methods Mol Biol 1188:271-279.
Dumit, VI & Dengjel, J (2014). The cup of youth. Cell Cycle 13:2021.
Dumit, VI, Kuttner, V, Kappler, J, Piera-Velazquez, S, Jimenez, SA, Bruckner-Tuderman, L, Uitto, J, & Dengjel, J (2014). Altered MCM protein levels and autophagic flux in aged and systemic sclerosis dermal fibroblasts. J Invest Dermatol 134:2321-2330.
Kuttner, V, Mack, C, Gretzmeier, C, Bruckner-Tuderman, L, & Dengjel, J (2014). Loss of collagen VII is associated with reduced transglutaminase 2 abundance and activity. J Invest Dermatol 134:2381-2389.
Rigbolt, KT, Zarei, M, Sprenger, A, Becker, AC, Diedrich, B, Huang, X, Eiselein, S, Kristensen, AR, Gretzmeier, C, Andersen, JS, Zi, Z, & Dengjel, J (2014). Characterization of early autophagy signaling by quantitative phosphoproteomics. Autophagy 10:356-371.
2013
Halbach, S, Rigbolt, KT, Wohrle, FU, Diedrich, B, Gretzmeier, C, Brummer, T, & Dengjel, J (2013). Alterations of Gab2 signalling complexes in imatinib and dasatinib treated chronic myeloid leukaemia cells. Cell Commun Signal 11:30.
Kuttner, V, Mack, C, Rigbolt, KT, Kern, JS, Schilling, O, Busch, H, Bruckner-Tuderman, L, & Dengjel, J (2013). Global remodelling of cellular microenvironment due to loss of collagen VII. Mol Syst Biol 9:657.
Sprenger, A, Weber, S, Zarai, M, Engelke, R, Nascimento, JM, Gretzmeier, C, Hilpert, M, Boerries, M, Has, C, Busch, H, Bruckner-Tuderman, L, & Dengjel, J (2013). Consistency of the proteome in primary human keratinocytes with respect to gender, age, and skin localization. Mol Cell Proteomics 12:2509-2521.
Sprenger, A, Kuttner, V, Bruckner-Tuderman, L, & Dengjel, J (2013). Global proteome analyses of SILAC-labeled skin cells. Methods Mol Biol 961:179-191.
Zarei, M, Sprenger, A, Gretzmeier, C, & Dengjel, J (2013). Rapid combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis. J Proteome Res 12:5989-5995.
2012
Becker, AC, Bunkenborg, J, Eisenberg, T, Harder, LM, Schroeder, S, Madeo, F, Andersen, JS, & Dengjel, J (2012). Friend or food: different cues to the autophagosomal proteome. Autophagy 8:995-996.
Dengjel, J, Hoyer-Hansen, M, Nielsen, MO, Eisenberg, T, Harder, LM, Schandorff, S, Farkas, T, Kirkegaard, T, Becker, AC, Schroeder, S, Vanselow, K, Lundberg, E, Nielsen, MM, Kristensen, AR, Akimov, V, Bunkenborg, J, Madeo, F, Jaattela, M, & Andersen, JS (2012). Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens. Mol Cell Proteomics 11:M111 014035.
Dumit, VI & Dengjel, J (2012). Autophagosomal protein dynamics and influenza virus infection. Front Immunol 3:43.
Engelke, R, Becker, AC, & Dengjel, J (2012). The degradative inventory of the cell: proteomic insights. Antioxid Redox Signal 17:803-812.
Zarei, M, Sprenger, A, Gretzmeier, C, & Dengjel, J (2012). Combinatorial use of electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) and strong cation exchange (SCX) chromatography for in-depth phosphoproteome analysis. J Proteome Res 11:4269-4276.
2011
Zarei, M, Sprenger, A, Metzger, F, Gretzmeier, C, & Dengjel, J (2011). Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches. J Proteome Res 10:3474-3483.
2010
Dengjel, J, Kratchmarova, I, & Blagoev, B (2010). Mapping protein-protein interactions by quantitative proteomics. Methods Mol Biol 658:267-278.
Dengjel, J, Jakobsen, L, & Andersen, JS (2010). Organelle proteomics by label-free and SILAC-based protein correlation profiling. Methods Mol Biol 658:255-265.
Sprenger, A, Kuttner, V, Biniossek, ML, Gretzmeier, C, Boerries, M, Mack, C, Has, C, Bruckner-Tuderman, L, & Dengjel, J (2010). Comparative quantitation of proteome alterations induced by aging or immortalization in primary human fibroblasts and keratinocytes for clinical applications. Mol Biosyst 6:1579-1582.
Zimmermann, AC, Zarei, M, Eiselein, S, & Dengjel, J (2010). Quantitative proteomics for the analysis of spatio-temporal protein dynamics during autophagy. Autophagy 6:1009-1016.
2009
Dengjel, J, Kratchmarova, I, & Blagoev, B (2009). Receptor tyrosine kinase signaling: a view from quantitative proteomics. Mol Biosyst 5:1112-1121.
2008
Dengjel, J, Kristensen, AR, & Andersen, JS (2008). Ordered bulk degradation via autophagy. Autophagy 4:1057-1059.
Kristensen, AR, Schandorff, S, Hoyer-Hansen, M, Nielsen, MO, Jaattela, M, Dengjel, J, & Andersen, JS (2008). Ordered organelle degradation during starvation-induced autophagy. Mol Cell Proteomics 7:2419-2428.
2007
Dengjel, J, Akimov, V, Olsen, JV, Bunkenborg, J, Mann, M, Blagoev, B, & Andersen, JS (2007). Quantitative proteomic assessment of very early cellular signaling events. Nat Biotechnol 25:566-568.
Dengjel, J, Akimov, V, Blagoev, B, & Andersen, JS (2007). Signal transduction by growth factor receptors: signaling in an instant. Cell Cycle 6:2913-2916.
2006
Dengjel, J, Nastke, MD, Gouttefangeas, C, Gitsioudis, G, Schoor, O, Altenberend, F, Muller, M, Kramer, B, Missiou, A, Sauter, M, Hennenlotter, J, Wernet, D, Stenzl, A, Rammensee, HG, Klingel, K, & Stevanovic, S (2006). Unexpected abundance of HLA class II presented peptides in primary renal cell carcinomas. Clin Cancer Res 12:4163-4170.
Dengjel, J, Stevanovic S (2006). Naturally presented MHC ligands carrying glycans. Transfus Med Hemother. 33: 38-44.
2005
Dengjel, J, Schoor, O, Fischer, R, Reich, M, Kraus, M, Muller, M, Kreymborg, K, Altenberend, F, Brandenburg, J, Kalbacher, H, Brock, R, Driessen, C, Rammensee, HG, & Stevanovic, S (2005). Autophagy promotes MHC class II presentation of peptides from intracellular source proteins. Proc Natl Acad Sci U S A 102:7922-7927.
Dengjel, J, Rammensee, HG, & Stevanovic, S (2005). Glycan side chains on naturally presented MHC class II ligands. J Mass Spectrom 40:100-104.
2004
Dengjel, J, Decker, P, Schoor, O, Altenberend, F, Weinschenk, T, Rammensee, HG, & Stevanovic, S (2004). Identification of a naturally processed cyclin D1 T-helper epitope by a novel combination of HLA class II targeting and differential mass spectrometry. Eur J Immunol 34:3644-3651.