J. Dengjel publications

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Publication list

2024

Da Silva Andre, G., Paganella, L.G., Badolato, A., Sander, S., Giampietro, C., Tibbitt, M.W., Dengjel, J., and Labouesse, C. (2024). Protein Isolation from 3D Hydrogel Scaffolds. Curr Protoc 4, e966.

Maas-Bauer, K., Stell, A.V., Yan, K.L., de Vega, E., Vinnakota, J.M., Unger, S., Nunez, N., Norona, J., Talvard-Balland, N., Kossmann, S., et al. (2024). ROCK1/2 signaling contributes to corticosteroid-refractory acute graft-versus-host disease. Nat Commun 15, 446.

Mandhair, H.K., Radpour, R., Westerhuis, M., Banz, Y., Humbert, M., Arambasic, M., Dengjel, J., Davies, A., Tschan, M.P., and Novak, U. (2024). Analysis of autophagy in DLBCL reveals subtype-specific differences and the preferential targeting of ULK1 inhibition in GCB-DLBCL provides a rationale as a new therapeutic approach. Leukemia in press.

2023

Akkoc, Y., Dalci, K., Karakas, H.E., Erbil-Bilir, S., Yalav, O., Sakman, G., Celik, F., Arikan, S., Zeybek, U., Ergin, M., et al. (2023). Tumor-derived CTF1 (cardiotrophin 1) is a critical mediator of stroma-assisted and autophagy-dependent breast cancer cell migration, invasion and metastasis. Autophagy 19, 306-323.

Arlt, H., Raman, B., Filali-Mouncef, Y., Hu, Y., Leytens, A., Hardenberg, R., Guimaraes, R., Kriegenburg, F., Mari, M., Smaczynska-de, R., II, et al. (2023). The dynamin Vps1 mediates Atg9 transport to the sites of autophagosome formation. J Biol Chem 299, 104712.

Bahl, A., Ibrahim, C., Plate, K., Haase, A., Dengjel, J., Nymark, P., and Dumit, V.I. (2023). PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping. J Cheminform 15, 34.

Caligaris, M., Nicastro, R., Hu, Z., Tripodi, F., Hummel, J.E., Pillet, B., Deprez, M.A., Winderickx, J., Rospert, S., Coccetti, P., et al. (2023). Snf1/AMPK fine-tunes TORC1 signaling in response to glucose starvation. Elife 12.

Faienza, F., Polverino, F., Rajendraprasad, G., Milletti, G., Hu, Z., Colella, B., Gargano, D., Strappazzon, F., Rizza, S., Vistesen, M.V., et al. (2023). AMBRA1 phosphorylation by CDK1 and PLK1 regulates mitotic spindle orientation. Cell Mol Life Sci 80, 251.

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.

Kolitsida, P., Nolic, V., Zhou, J., Stumpe, M., Niemi, N.M., Dengjel, J., and Abeliovich, H. (2023). The pyruvate dehydrogenase complex regulates mitophagic trafficking and protein phosphorylation. Life Sci Alliance 6.

Krivitsky, V., Krivitsky, A., Mantella, V., Ben-Yehuda Greenwald, M., Sankar, D.S., Betschmann, J., Bader, J., Zoratto, N., Schreier, K., Feiss, S., et al. (2023). Ultrafast and Controlled Capturing, Loading, and Release of Extracellular Vesicles by a Portable Microstructured Electrochemical Fluidic Device. Adv Mater 35, e2212000.

Lauinger, M., Christen, D., Klar, R.F.U., Roubaty, C., Heilig, C.E., Stumpe, M., Knox, J.J., Radulovich, N., Tamblyn, L., Xie, I.Y., et al. (2023). BRAF(Deltabeta3-alphaC) in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability. Sci Adv 9, eade7486.

Nivoit, P., Mathivet, T., Wu, J., Salemkour, Y., Sankar, D.S., Baudrie, V., Bourreau, J., Guihot, A.L., Vessieres, E., Lemitre, M., et al. (2023). Autophagy protein 5 controls flow-dependent endothelial functions. Cell Mol Life Sci 80, 210.

Pena-Francesch, M., Vanoaica, L.D., Zhu, G.F., Stumpe, M., Sankar, D.S., Nowag, H., Valencia-Camargo, A.D., Hammerschmidt, W., Dengjel, J., Ligeon, L.A., et al. (2023). The autophagy machinery interacts with EBV capsids during viral envelope release. Proc Natl Acad Sci U S A 120, e2211281120.

Rasmussen, N.L., Zhou, J., Olsvik, H., Kaeser-Pebernard, S., Lamark, T., Dengjel, J., and Johansen, T. (2023). The inflammation repressor TNIP1/ABIN-1 is degraded by autophagy following TBK1 phosphorylation of its LIR. Autophagy 19, 2819-2820.

Sanger, C.S., Cernakova, M., Wietecha, M.S., Garau Paganella, L., Labouesse, C., Dudaryeva, O.Y., Roubaty, C., Stumpe, M., Mazza, E., Tibbitt, M.W., et al. (2023). Serine protease 35 regulates the fibroblast matrisome in response to hyperosmotic stress. Sci Adv 9, eadh9219.

Tarnutzer, K., Siva Sankar, D., Dengjel, J., and Ewald, C.Y. (2023). Collagen constitutes about 12% in females and 17% in males of the total protein in mice. Sci Rep 13, 4490.

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.

2022

Akkoc, Y., Dalci, K., Karakas, H.E., Erbil-Bilir, S., Yalav, O., Sakman, G., Celik, F., Arikan, S., Zeybek, U., Ergin, M., Akkiz, H., Dilege, E., Dengjel, J., Dogan-Ekici, A.I., and Gozuacik, D. (2022). Tumor-derived CTF1 (cardiotrophin 1) is a critical mediator of stroma-assisted and autophagy-dependent breast cancer cell migration, invasion and metastasis. Autophagy, 1-18.

Borrego, I., Frobert, A., Ajalbert, G., Valentin, J., Kaltenrieder, C., Fellay, B., Stumpe, M., Cook, S., Dengjel, J., and Giraud, M.N. (2022). Fibrin, Bone Marrow Cells and Macrophages Interactively Modulate Cardiomyoblast Fate. Biomedicines 10.

Demirbag-Sarikaya, S., Akkoc, Y., Turgut, S., Erbil-Bilir, S., Kocaturk, N.M., Dengjel, J., and Gozuacik, D. (2022). A novel ATG5 interaction with Ku70 potentiates DNA repair upon genotoxic stress. Sci Rep 12, 8134.

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.

Karamash, M., Stumpe, M., Dengjel, J., Salgueiro, C.A., Giese, B., and Fromm, K.M. (2022). Reduction Kinetic of Water Soluble Metal Salts by Geobacter sulfurreducens: Fe(2+)/Hemes Stabilize and Regulate Electron Flux Rates. Front Microbiol 13, 909109.

Lahiri, V., Metur, S.P., Hu, Z., Song, X., Mari, M., Hawkins, W.D., Bhattarai, J., Delorme-Axford, E., Reggiori, F., Tang, D., Dengjel, J., and Klionsky, D.J. (2022). Post-transcriptional regulation of ATG1 is a critical node that modulates autophagy during distinct nutrient stresses. Autophagy 18, 1694-1714.

Leytens, A., and Dengjel, J. (2022). DRAMing for autophagy. FEBS J 289, 3731-3734.

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.

Pantasis, S., Friemel, J., Brutsch, S.M., Hu, Z., Krautbauer, S., Liebisch, G., Dengjel, J., Weber, A., Werner, S., and Bordoli, M.R. (2022). Vertebrate lonesome kinase modulates the hepatocyte secretome to prevent perivascular liver fibrosis and inflammation. J Cell Sci 135.

Ring, J., Tadic, J., Ristic, S., Poglitsch, M., Bergmann, M., Radic, N., Mossmann, D., Liang, Y., Maglione, M., Jerkovic, A., Hajiraissi, R., Hanke, M., Kuttner, V., Wolinski, H., Zimmermann, A., Domuz Trifunovic, L., Mikolasch, L., Moretti, D.N., Broeskamp, F., Westermayer, J., Abraham, C., Schauer, S., Dammbrueck, C., Hofer, S.J., Abdellatif, M., Grundmeier, G., Kroemer, G., Braun, R.J., Hansen, N., Sommer, C., Ninkovic, M., Seba, S., Rockenfeller, P., Vogtle, F.N., Dengjel, J., Meisinger, C., Keller, A., Sigrist, S.J., Eisenberg, T., and Madeo, F. (2022). The HSP40 chaperone Ydj1 drives amyloid beta 42 toxicity. EMBO Mol Med 14, e13952.

Seiler, K., Humbert, M., Minder, P., Mashimo, I., Schlafli, A.M., Krauer, D., Federzoni, E.A., Vu, B., Moresco, J.J., Yates, J.R., 3rd, Sadowski, M.C., Radpour, R., Kaufmann, T., Sarry, J.E., Dengjel, J., Tschan, M.P., and Torbett, B.E. (2022). Hexokinase 3 enhances myeloid cell survival via non-glycolytic functions. Cell Death Dis 13, 448.

Siva Sankar, D., Hu, Z., and Dengjel, J. (2022). The complex interplay between ULK1 and protein phosphatases in autophagy regulation. Autophagy 18, 455-456.

Strohm, L., Hu, Z., Suk, Y., Ruhmkorf, A., Sternburg, E., Gattringer, V., Riemenschneider, H., Berutti, R., Graf, E., Weishaupt, J.H., Brill, M.S., Harbauer, A.B., Dormann, D., Dengjel, J., Edbauer, D., and Behrends, C. (2022). Multi-omics profiling identifies a deregulated FUS-MAP1B axis in ALS/FTD-associated UBQLN2 mutants. Life Sci Alliance 5.

Thuenauer, R., Kuhn, K., Guo, Y., Kotsis, F., Xu, M., Trefzer, A., Altmann, S., Wehrum, S., Heshmatpour, N., Faust, B., Landi, A., Diedrich, B., Dengjel, J., Kuehn, E.W., Imberty, A., and Romer, W. (2022). The Lectin LecB Induces Patches with Basolateral Characteristics at the Apical Membrane to Promote Pseudomonas aeruginosa Host Cell Invasion. mBio 13, e0081922.

2021

Chen, Z., Malia, P.C., Hatakeyama, R., Nicastro, R., Hu, Z., Peli-Gulli, M.P., Gao, J., Nishimura, T., Eskes, E., Stefan, C.J., Winderickx, J., Dengjel, J., De Virgilio, C., and Ungermann, C. (2021). TORC1 Determines Fab1 Lipid Kinase Function at Signaling Endosomes and Vacuoles. Curr Biol 31, 297-309 e298.

Akimov V, Fehling-Kaschek M, Barrio-Hernandez I, Puglia M, Bunkenborg J, Nielsen MM, Timmer J, Dengjel J, Blagoev B (2021) Magnitude of Ubiquitination Determines the Fate of Epidermal Growth Factor Receptor Upon Ligand Stimulation. J Mol Biol 433: 167240

Bernasconi R, Thriene K, Romero-Fernandez E, Gretzmeier C, Kuhl T, Maler M, Nauroy P, Kleiser S, Ruhl-Muth AC, Stumpe M, Kiritsi D, Martin SF, Hinz B, Bruckner-Tuderman L, Dengjel J, Nystrom A (2021) Pro-inflammatory immunity supports fibrosis advancement in epidermolysis bullosa: intervention with Ang-(1-7). EMBO Mol Med 13: e14392

Dokladal L, Stumpe M, Hu Z, Jaquenoud M, Dengjel J, De Virgilio C (2021) Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast. Cell Rep 37: 110149.  pdf 

Frensch M, Jager C, Muller PF, Tadic A, Wilhelm I, Wehrum S, Diedrich B, Fischer B, Melendez AV, Dengjel J, Eibel H, Romer W (2021) Bacterial lectin BambL acts as a B cell superantigen. Cell Mol Life Sci 78: 8165-8186

Hofer SJ, Liang Y, Zimmermann A, Schroeder S, Dengjel J, Kroemer G, Eisenberg T, Sigrist SJ, Madeo F (2021) Spermidine-induced hypusination preserves mitochondrial and cognitive function during aging. Autophagy 17: 2037-2039

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 

Lahiri V, Metur SP, Hu Z, Song X, Mari M, Hawkins WD, Bhattarai J, Delorme-Axford E, Reggiori F, Tang D, Dengjel J, Klionsky DJ (2021) Post-transcriptional regulation of ATG1 is a critical node that modulates autophagy during distinct nutrient stresses. Autophagy: 1-21

Manganelli V, Matarrese P, Antonioli M, Gambardella L, Vescovo T, Gretzmeier C, Longo A, Capozzi A, Recalchi S, Riitano G, Misasi R, Dengjel J, Malorni W, Fimia GM, Sorice M, Garofalo T (2021) Raft-like lipid microdomains drive autophagy initiation via AMBRA1-ERLIN1 molecular association within MAMs. Autophagy 17: 2528-2548

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 

Walter C, Marada A, Suhm T, Ernsberger R, Muders V, Kucukkose C, Sanchez-Martin P, Hu Z, Aich A, Loroch S, Solari FA, Poveda-Huertes D, Schwierzok A, Pommerening H, Matic S, Brix J, Sickmann A, Kraft C, Dengjel J, Dennerlein S et al (2021) Global kinome profiling reveals DYRK1A as critical activator of the human mitochondrial import machinery. Nat Commun 12: 428

Dokladal, L., Stumpe, M., Pillet, B., Hu, Z., Garcia Osuna, G.M., Kressler, D., Dengjel, J., and De Virgilio, C. (2021). Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control. Mol Cell 81, 1879-1889 e1876.  pdf 

Feng, Y., Ariosa, A.R., Yang, Y., Hu, Z., Dengjel, J., and Klionsky, D.J. (2021). Downregulation of autophagy by Met30-mediated Atg9 ubiquitination. Proc Natl Acad Sci U S A 118.  pdf 

Klionsky, D.J., Abdel-Aziz, A.K., Abdelfatah, S., Abdellatif, M., Abdoli, A., Abel, S., Abeliovich, H., Abildgaard, M.H., Abudu, Y.P., Acevedo-Arozena, A., Adamopoulos, I.E., Adeli, K., Adolph, T.E., Adornetto, A., Aflaki, E., Agam, G., Agarwal, A., Aggarwal, B.B., Agnello, M., Agostinis, P., Agrewala, J.N., Agrotis, A., Aguilar, P.V., Ahmad, S.T., Ahmed, Z.M., Ahumada-Castro, U., Aits, S., Aizawa, S., Akkoc, Y., Akoumianaki, T., Akpinar, H.A., Al-Abd, A.M., Al-Akra, L., Al-Gharaibeh, A., Alaoui-Jamali, M.A., Alberti, S., Alcocer-Gomez, E., Alessandri, C., Ali, M., Alim Al-Bari, M.A., Aliwaini, S., Alizadeh, J., Almacellas, E., Almasan, A., Alonso, A., Alonso, G.D., Altan-Bonnet, N., Altieri, D.C., Alvarez, E.M.C., Alves, S., et al. (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)(1). Autophagy 17, 1-382.

Maier, J.I., Rogg, M., Helmstadter, M., Sammarco, A., Schilling, O., Sabass, B., Miner, J.H., Dengjel, J., Walz, G., Werner, M., Huber, T.B., and Schell, C. (2021). EPB41L5 controls podocyte extracellular matrix assembly by adhesome-dependent force transmission. Cell Rep 34, 108883.

Schroeder, S., Hofer, S.J., Zimmermann, A., Pechlaner, R., Dammbrueck, C., Pendl, T., Marcello, G.M., Pogatschnigg, V., Bergmann, M., Muller, M., Gschiel, V., Ristic, S., Tadic, J., Iwata, K., Richter, G., Farzi, A., Ucal, M., Schafer, U., Poglitsch, M., Royer, P., Mekis, R., Agreiter, M., Tolle, R.C., Sotonyi, P., Willeit, J., Mairhofer, B., Niederkofler, H., Pallhuber, I., Rungger, G., Tilg, H., Defrancesco, M., Marksteiner, J., Sinner, F., Magnes, C., Pieber, T.R., Holzer, P., Kroemer, G., Carmona-Gutierrez, D., Scorrano, L., Dengjel, J., Madl, T., Sedej, S., Sigrist, S.J., Racz, B., Kiechl, S., Eisenberg, T., and Madeo, F. (2021). Dietary spermidine improves cognitive function. Cell Rep 35, 108985.

2020

Barrio-Hernandez, I, Jafari, A, Rigbolt, KTG, Hallenborg, P, Sanchez-Quiles, V, Skovrind, I, Akimov, V, Kratchmarova, I, Dengjel, J, Kassem, M, & Blagoev, B (2020). Phosphoproteomic profiling reveals a defined genetic program for osteoblastic lineage commitment of human bone marrow-derived stromal stem cells. Genome Res 30:127-137.

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.

Chen, Z, Malia, PC, Hatakeyama, R, Nicastro, R, Hu, Z, Peli-Gulli, MP, Gao, J, Nishimura, T, Eskes, E, Stefan, CJ, Winderickx, J, Dengjel, J, De Virgilio, C, & Ungermann, C (2020). TORC1 Determines Fab1 Lipid Kinase Function at Signaling Endosomes and Vacuoles. Curr Biol.

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 

Duman, M, Vaquie, A, Nocera, G, Heller, M, Stumpe, M, Siva Sankar, D, Dengjel, J, Meijer, D, Yamaguchi, T, Matthias, P, Zeis, T, Schaeren-Wiemers, N, Hayoz, A, Ruff, S, & Jacob, C (2020). EEF1A1 deacetylation enables transcriptional activation of remyelination. Nat Commun 11:3420.

Estrada Mallarino, L, Engel, C, Ilik, IA, Maticzka, D, Heyl, F, Muller, B, Yakulov, TA, Dengjel, J, Backofen, R, Akhtar, A, & Walz, G (2020). Nephronophthisis gene products display RNA-binding properties and are recruited to stress granules. Sci Rep 10:15954.

Finger, Y, Habich, M, Gerlich, S, Urbanczyk, S, van de Logt, E, Koch, J, Schu, L, Lapacz, KJ, Ali, M, Petrungaro, C, Salscheider, SL, Pichlo, C, Baumann, U, Mielenz, D, Dengjel, J, Brachvogel, B, Hofmann, K, & Riemer, J (2020). Proteasomal degradation induced by DPP9-mediated processing competes with mitochondrial protein import. EMBO J 39:e103889.

Manganelli, V, Matarrese, P, Antonioli, M, Gambardella, L, Vescovo, T, Gretzmeier, C, Longo, A, Capozzi, A, Recalchi, S, Riitano, G, Misasi, R, Dengjel, J, Malorni, W, Fimia, GM, Sorice, M, & Garofalo, T (2020). Raft-like lipid microdomains drive autophagy initiation via AMBRA1-ERLIN1 molecular association within MAMs. Autophagy:1-21.

Siva Sankar, D & Dengjel, J (2020). Protein complexes and neighborhoods driving autophagy. Autophagy:1-17.          pdf 

Stekovic, S, Hofer, SJ, Tripolt, N, Aon, MA, Royer, P, Pein, L, Stadler, JT, Pendl, T, Prietl, B, Url, J, Schroeder, S, Tadic, J, Eisenberg, T, Magnes, C, Stumpe, M, Zuegner, E, Bordag, N, Riedl, R, Schmidt, A, Kolesnik, E, Verheyen, N, Springer, A, Madl, T, Sinner, F, de Cabo, R, Kroemer, G, Obermayer-Pietsch, B, Dengjel, J, Sourij, H, Pieber, TR, & Madeo, F (2020). Alternate Day Fasting Improves Physiological and Molecular Markers of Aging in Healthy, Non-obese Humans. Cell Metab 31:878-881.

Thuenauer, R, Landi, A, Trefzer, A, Altmann, S, Wehrum, S, Eierhoff, T, Diedrich, B, Dengjel, J, Nystrom, A, Imberty, A, & Romer, W (2020). The Pseudomonas aeruginosa Lectin LecB Causes Integrin Internalization and Inhibits Epithelial Wound Healing. mBio 11.

Wen, X, Gatica, D, Yin, Z, Hu, Z, Dengjel, J, & Klionsky, DJ (2020). The transcription factor Spt4-Spt5 complex regulates the expression of ATG8 and ATG41. Autophagy 16:1172-1185.

2019

Brenna, A, Olejniczak, I, Chavan, R, Ripperger, JA, Langmesser, S, Cameroni, E, Hu, Z, De Virgilio, C, Dengjel, J, & Albrecht, U (2019). Cyclin dependent kinase 5 (CDK5) regulates the circadian clock. Elife 8.

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 

Kolitsida, P, Zhou, J, Rackiewicz, M, Nolic, V, Dengjel, J, & Abeliovich, H (2019). Phosphorylation of mitochondrial matrix proteins regulates their selective mitophagic degradation. Proc Natl Acad Sci USA.

Kvainickas, A, Nagele, H, Qi, W, Dokladal, L, Jimenez-Orgaz, A, Stehl, L, Gangurde, D, Zhao, Q, Hu, Z, Dengjel, J, De Virgilio, C, Baumeister, R, & Steinberg, F (2019). Retromer and TBC1D5 maintain late endosomal RAB7 domains to enable amino acid-induced mTORC1 signaling. J Cell Biol 218:3019-3038.

Stekovic, S, Hofer, SJ, Tripolt, N, Aon, MA, Royer, P, Pein, L, Stadler, JT, Pendl, T, Prietl, B, Url, J, Schroeder, S, Tadic, J, Eisenberg, T, Magnes, C, Stumpe, M, Zuegner, E, Bordag, N, Riedl, R, Schmidt, A, Kolesnik, E, Verheyen, N, Springer, A, Madl, T, Sinner, F, de Cabo, R, Kroemer, G, Obermayer-Pietsch, B, Dengjel, J, Sourij, H, Pieber, TR, & Madeo, F (2019). Alternate Day Fasting Improves Physiological and Molecular Markers of Aging in Healthy, Non-obese Humans. Cell Metab 30:462-476 e465.   pdf 

Wen, X, Gatica, D, Yin, Z, Hu, Z, Dengjel, J, & Klionsky, DJ (2019). The transcription factor Spt4-Spt5 complex regulates the expression of ATG8 and ATG41. Autophagy:1-14.

Zimmermann, A, Kainz, K, Hofer, SJ, Bauer, MA, Schroeder, S, Dengjel, J, Pietrocola, F, Kepp, O, Ruckenstuhl, C, Eisenberg, T, Sigrist, SJ, Madeo, F, Carmona-Gutierrez, D, & Kroemer, G (2019). 4,4'Dimethoxychalcone: a natural flavonoid that promotes health through autophagy-dependent and -independent effects. Autophagy 15:1662-1664.

Carmona-Gutierrez, D, Zimmermann, A, Kainz, K, Pietrocola, F, Chen, G, Maglioni, S, Schiavi, A, Nah, J, Mertel, S, Beuschel, CB, Castoldi, F, Sica, V, Trausinger, G, Raml, R, Sommer, C, Schroeder, S, Hofer, SJ, Bauer, MA, Pendl, T, Tadic, J, Dammbrueck, C, Hu, Z, Ruckenstuhl, C, Eisenberg, T, Durand, S, Bossut, N, Aprahamian, F, Abdellatif, M, Sedej, S, Enot, DP, Wolinski, H, Dengjel, J, Kepp, O, Magnes, C, Sinner, F, Pieber, TR, Sadoshima, J, Ventura, N, Sigrist, SJ, Kroemer, G, & Madeo, F (2019). The flavonoid 4,4'-dimethoxychalcone promotes autophagy-dependent longevity across species. Nat Commun 10:651.

Gerber, H, Mosser, S, Boury-Jamot, B, Stumpe, M, Piersigilli, A, Goepfert, C, Dengjel, J, Albrecht, U, Magara, F, & Fraering, PC (2019). The APMAP interactome reveals new modulators of APP processing and beta-amyloid production that are altered in Alzheimer's disease. Acta Neuropathol Commun 7:13.

Mitchell, R, Mellows, B, Sheard, J, Antonioli, M, Kretz, O, Chambers, D, Zeuner, MT, Tomkins, JE, Denecke, B, Musante, L, Joch, B, Debacq-Chainiaux, F, Holthofer, H, Ray, S, Huber, TB, Dengjel, J, De Coppi, P, Widera, D, & Patel, K (2019). Secretome of adipose-derived mesenchymal stem cells promotes skeletal muscle regeneration through synergistic action of extracellular vesicle cargo and soluble proteins. Stem Cell Res Ther 10:116.

Sonder, SL, Boye, TL, Tolle, R, Dengjel, J, Maeda, K, Jaattela, M, Simonsen, AC, Jaiswal, JK, & Nylandsted, J (2019). Annexin A7 is required for ESCRT III-mediated plasma membrane repair. Sci Rep 9:6726.

Sporrer, M, Prochnicki, A, Tolle, RC, Nystrom, A, Esser, PR, Homberg, M, Athanasiou, I, Zingkou, E, Schilling, A, Gerum, R, Thievessen, I, Winter, L, Bruckner-Tuderman, L, Fabry, B, Magin, TM, Dengjel, J, Schroder, R, & Kiritsi, D (2019). Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders. EBioMedicine.

Tolle, RC & Dengjel, J (2019). Effects of the Extracellular Matrix on the Proteome of Primary Skin Fibroblasts. Methods Mol Biol 1993:193-204.

Zimmermann, A, Kainz, K, Hofer, SJ, Bauer, MA, Schroeder, S, Dengjel, J, Pietrocola, F, Kepp, O, Ruckenstuhl, C, Eisenberg, T, Sigrist, SJ, Madeo, F, Kroemer, G, & Carmona-Gutierrez, D (2019). Targeting GATA transcription factors - a novel strategy for anti-aging interventions? Microb Cell 6:212-216.

Habich, M, Salscheider, SL, Murschall, LM, Hoehne, MN, Fischer, M, Schorn, F, Petrungaro, C, Ali, M, Erdogan, AJ, Abou-Eid, S, Kashkar, H, Dengjel, J, & Riemer, J (2019). Vectorial Import via a Metastable Disulfide-Linked Complex Allows for a Quality Control Step and Import by the Mitochondrial Disulfide Relay. Cell Rep 26:759-774 e755.

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

Hatakeyama, R, Péli-Gulli, MP, Hu, Z, Jaquenoud, M, Garcia Osuna, GM, Sardu, A, Dengjel, J, De Virgilio C (2019). Spatially Distinct Pools of TORC1 Balance Protein Homeostasis. Mol Cell 73:1–14.  pdf 

2018

He, Y, Thriene, K, Boerries, M, Hausser, I, Franzke, CW, Busch, H, Dengjel, J, & Has, C (2018). Constitutional absence of epithelial integrin alpha3 impacts the composition of the cellular microenvironment of ILNEB keratinocytes. Matrix Biol 74:62-76.

Burnand, D, Milosevic, A, Balog, S, Spuch-Calvar, M, Rothen-Rutishauser, B, Dengjel, J, Kinnear, C, Moore, TL, Petri-Fink, A (2018) . Beyond Global Charge: Role of Amine Bulkiness and Protein Fingerprint on Nanoparticle-Cell Interaction. Small doi: 10.1002/smll.201802088.  pdf

Di Rita, A, Peschiaroli, A, D Acunzo, P, Strobbe, D, Hu, Z, Gruber, J, Nygaard, M, Lambrughi, M, Melino, G, Papaleo, E, Dengjel, J, El Alaoui, S, Campanella, M, Dötsch, V, Rogov, VV, Strappazzon, F, Cecconi, F (2018). HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα. Nat Commun 9:3755.

Schell, C, Sabass, B, Helmstaedter, M, Geist, F, Abed, A, Yasuda-Yamahara, M, Siglek A, Maier, JI, Grahammer, F, Siegerist, F, Artelt, N, Endlich, N, Kerjaschki, D, Arnold, HH, Dengjel, J, Rogg, M, Huber TB. (2018). ARP3 controls the podocyte architecture at the kidney filtration barrier. Dev Cell 47:741-757.e8.

Hiebert, P, Wietecha, MS, Cangkrama, M, Haertel, E, Mavrogonatou, E, Stumpe, M, Steenbock, H, Grossi, S, Beer, HD, Angel, P, Brinckmann, J, Kletsas, D, Dengjel, J, Werner S.(2018). Nrf2-Mediated Fibroblast Reprogramming Drives Cellular Senescence by Targeting the Matrisome. Dev Cell 46:145-161.e10.

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

Carmona-Gutierrez, D, et al. (2018). Guidelines and recommendations on yeast cell death nomenclature. Microb Cell 5:4-31.

Jimenez-Orgaz, A, Kvainickas, A, Nagele, H, Denner, J, Eimer, S, Dengjel, J, & Steinberg, F (2018). Control of RAB7 activity and localization through the retromer-TBC1D5 complex enables RAB7-dependent mitophagy. EMBO J 37:235-254.

Mathew, NR, et al. (2018). Sorafenib promotes graft-versus-leukemia activity in mice and humans through IL-15 production in FLT3-ITD-mutant leukemia cells. Nat Med 24:282-291.

Nystrom, A, Bornert, O, Kuhl, T, Gretzmeier, C, Thriene, K, Dengjel, J, Pfister-Wartha, A, Kiritsi, D, & Bruckner-Tuderman, L (2018). Impaired lymphoid extracellular matrix impedes antibacterial immunity in epidermolysis bullosa. Proc Natl Acad Sci U S A 115:E705-E714.

Rinschen, MM, Godel, M, Grahammer, F, Zschiedrich, S, Helmstadter, M, Kretz, O, Zarei, M, Braun, DA, Dittrich, S, Pahmeyer, C, Schroder, P, Teetzen, C, Gee, H, Daouk, G, Pohl, M, Kuhn, E, Schermer, B, Kuttner, V, Boerries, M, Busch, H, Schiffer, M, Bergmann, C, Kruger, M, Hildebrandt, F, Dengjel, J, Benzing, T, & Huber, TB (2018). A Multi-layered Quantitative In Vivo Expression Atlas of the Podocyte Unravels Kidney Disease Candidate Genes. Cell Rep 23:2495-2508.

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

Viau, A, Bienaime, F, Lukas, K, Todkar, AP, Knoll, M, Yakulov, TA, Hofherr, A, Kretz, O, Helmstadter, M, Reichardt, W, Braeg, S, Aschman, T, Merkle, A, Pfeifer, D, Dumit, VI, Gubler, MC, Nitschke, R, Huber, TB, Terzi, F, Dengjel, J, Grahammer, F, Kottgen, M, Busch, H, Boerries, M, Walz, G, Triantafyllopoulou, A, & Kuehn, EW (2018). Cilia-localized LKB1 regulates chemokine signaling, macrophage recruitment, and tissue homeostasis in the kidney. EMBO J.

2017

Antonioli, M, Ciccosanti, F, Dengjel, J, & Fimia, GM (2017). Methods to Study the BECN1 Interactome in the Course of Autophagic Responses. Methods Enzymol 587:429-445.

Dengjel, J & Abeliovich, H (2017). Roles of mitophagy in cellular physiology and development. Cell Tissue Res 367:95-109.  pdf

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.

Eisenberg, T, Abdellatif, M, Zimmermann, A, Schroeder, S, Pendl, T, Harger, A, Stekovic, S, Schipke, J, Magnes, C, Schmidt, A, Ruckenstuhl, C, Dammbrueck, C, Gross, AS, Herbst, V, Carmona-Gutierrez, D, Pietrocola, F, Pieber, TR, Sigrist, SJ, Linke, WA, Muhlfeld, C, Sadoshima, J, Dengjel, J, Kiechl, S, Kroemer, G, Sedej, S, & Madeo, F (2017). Dietary spermidine for lowering high blood pressure. Autophagy 13:767-769.

Giese, S, Ciminski, K, Bolte, H, Moreira, EA, Lakdawala, S, Hu, Z, David, Q, Kolesnikova, L, Gotz, V, Zhao, Y, Dengjel, J, Chin, YE, Xu, K, & Schwemmle, M (2017). Role of influenza A virus NP acetylation on viral growth and replication. Nat Commun 8:1259.

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.

Jank, T, Belyi, Y, Wirth, C, Rospert, S, Hu, Z, Dengjel, J, Tzivelekidis, T, Andersen, GR, Hunte, C, Schlosser, A, & Aktories, K (2017). Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A. J Biol Chem 292:16014-16023.

Kvainickas, A, Orgaz, AJ, Nagele, H, Diedrich, B, Heesom, KJ, Dengjel, J, Cullen, PJ, & Steinberg, F (2017). Retromer- and WASH-dependent sorting of nutrient transporters requires a multivalent interaction network with ANKRD50. J Cell Sci 130:382-395.

Kvainickas, A, Jimenez-Orgaz, A, Nagele, H, Hu, Z, Dengjel, J, & Steinberg, F (2017). Cargo-selective SNX-BAR proteins mediate retromer trimer independent retrograde transport. J Cell Biol 216:3677-3693.

Mellows, B, Mitchell, R, Antonioli, M, Kretz, O, Chambers, D, Zeuner, MT, Denecke, B, Musante, L, Ramachandra, DL, Debacq-Chainiaux, F, Holthofer, H, Joch, B, Ray, S, Widera, D, David, AL, Huber, TB, Dengjel, J, De Coppi, P, & Patel, K (2017). Protein and Molecular Characterization of a Clinically Compliant Amniotic Fluid Stem Cell-Derived Extracellular Vesicle Fraction Capable of Accelerating Muscle Regeneration Through Enhancement of Angiogenesis. Stem Cells Dev 26:1316-1333.

Mellows, B, Mitchell, R, Antonioli, M, Kretz, O, Chamber, D, Zeuner, MT, Denecke, B, Musante, L, Ramachandra, D, Debacq-Chainiaux, F, Holthofer, H, Joch, B, Ray, S, Widera, D, David, AL, Huber, TB, Dengjel, J, De Coppi, P, & Patel, K (2017). Protein and molecular characterisation of a clinically compliant amniotic fluid stem cell derived extracellular vesicle fraction capable of accelerating muscle regeneration through the enhancement of angiogenesis. Stem Cells Dev.

Peli-Gulli, MP, Raucci, S, Hu, Z, Dengjel, J, & De Virgilio, C (2017). Feedback Inhibition of the Rag GTPase GAP Complex Lst4-Lst7 Safeguards TORC1 from Hyperactivation by Amino Acid Signals. Cell Rep 20:281-288.

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

Schell, C, Rogg, M, Suhm, M, Helmstadter, M, Sellung, D, Yasuda-Yamahara, M, Kretz, O, Kuttner, V, Suleiman, H, Kollipara, L, Zahedi, RP, Sickmann, A, Eimer, S, Shaw, AS, Kramer-Zucker, A, Hirano-Kobayashi, M, Abe, T, Aizawa, S, Grahammer, F, Hartleben, B, Dengjel, J, & Huber, TB (2017). The FERM protein EPB41L5 regulates actomyosin contractility and focal adhesion formation to maintain the kidney filtration barrier. Proc Natl Acad Sci U S A 114:E4621-E4630.

Stork, B & Dengjel, J (2017). Study of ULK1 Catalytic Activity and Its Regulation. Methods Enzymol 587:391-404.

Weinberg, F, Reischmann, N, Fauth, L, Taromi, S, Mastroianni, J, Kohler, M, Halbach, S, Becker, AC, Deng, N, Schmitz, T, Uhl, FM, Herbener, N, Riedel, B, Beier, F, Swarbrick, A, Lassmann, S, Dengjel, J, Zeiser, R, & Brummer, T (2017). The Atypical Kinase RIOK1 Promotes Tumor Growth and Invasive Behavior. EBioMedicine 20:79-97.

2016

Abeliovich, H & Dengjel, J (2016). Mitophagy as a stress response in mammalian cells and in respiring S. cerevisiae. Biochem Soc Trans 44:541-545.

Duteil, D, Tosic, M, Lausecker, F, Nenseth, HZ, Muller, JM, Urban, S, Willmann, D, Petroll, K, Messaddeq, N, Arrigoni, L, Manke, T, Kornfeld, JW, Bruning, JC, Zagoriy, V, Meret, M, Dengjel, J, Kanouni, T, & Schule, R (2016). Lsd1 Ablation Triggers Metabolic Reprogramming of Brown Adipose Tissue. Cell Rep 17:1008-1021.

Eisenberg, T, Abdellatif, M, Schroeder, S, Primessnig, U, Stekovic, S, Pendl, T, Harger, A, Schipke, J, Zimmermann, A, Schmidt, A, Tong, M, Ruckenstuhl, C, Dammbrueck, C, Gross, AS, Herbst, V, Magnes, C, Trausinger, G, Narath, S, Meinitzer, A, Hu, Z, Kirsch, A, Eller, K, Carmona-Gutierrez, D, Buttner, S, Pietrocola, F, Knittelfelder, O, Schrepfer, E, Rockenfeller, P, Simonini, C, Rahn, A, Horsch, M, Moreth, K, Beckers, J, Fuchs, H, Gailus-Durner, V, Neff, F, Janik, D, Rathkolb, B, Rozman, J, de Angelis, MH, Moustafa, T, Haemmerle, G, Mayr, M, Willeit, P, von Frieling-Salewsky, M, Pieske, B, Scorrano, L, Pieber, T, Pechlaner, R, Willeit, J, Sigrist, SJ, Linke, WA, Muhlfeld, C, Sadoshima, J, Dengjel, J, Kiechl, S, Kroemer, G, Sedej, S, & Madeo, F (2016). Cardioprotection and lifespan extension by the natural polyamine spermidine. Nat Med 22:1428-1438.

Eisenhardt, AE, Sprenger, A, Roring, M, Herr, R, Weinberg, F, Kohler, M, Braun, S, Orth, J, Diedrich, B, Lanner, U, Tscherwinski, N, Schuster, S, Dumaz, N, Schmidt, E, Baumeister, R, Schlosser, A, Dengjel, J, & Brummer, T (2016). Phospho-proteomic analyses of B-Raf protein complexes reveal new regulatory principles. Oncotarget 7:26628-26652.

Erbil, S, Oral, O, Mitou, G, Kig, C, Durmaz-Timucin, E, Guven-Maiorov, E, Gulacti, F, Gokce, G, Dengjel, J, Sezerman, OU, & Gozuacik, D (2016). RACK1 Is an Interaction Partner of ATG5 and a Novel Regulator of Autophagy. J Biol Chem 291:16753-16765.

Groll, N, Petrikat, T, Vetter, S, Wenz, C, Dengjel, J, Gretzmeier, C, Weiss, F, Poetz, O, Joos, TO, Schwarz, M, & Braeuning, A (2016). Inhibition of beta-catenin signaling by phenobarbital in hepatoma cells in vitro. Toxicology 370:94-105.

Gupta, VK, Pech, U, Bhukel, A, Fulterer, A, Ender, A, Mauermann, SF, Andlauer, TF, Antwi-Adjei, E, Beuschel, C, Thriene, K, Maglione, M, Quentin, C, Bushow, R, Schwarzel, M, Mielke, T, Madeo, F, Dengjel, J, Fiala, A, & Sigrist, SJ (2016). Spermidine Suppresses Age-Associated Memory Impairment by Preventing Adverse Increase of Presynaptic Active Zone Size and Release. PLoS Biol 14:e1002563.

Halbach, S, Hu, Z, Gretzmeier, C, Ellermann, J, Wohrle, FU, Dengjel, J, & Brummer, T (2016). Axitinib and sorafenib are potent in tyrosine kinase inhibitor resistant chronic myeloid leukemia cells. Cell Commun Signal 14:6.

Halbach, S, Dengjel, J, & Brummer, T (2016). Quantitative Proteomics Analysis of Leukemia Cells. Methods Mol Biol 1465:139-148.

Klionsky, DJ, et al. (2016). Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy 12:1-222.

Loi, M, Muller, A, Steinbach, K, Niven, J, Barreira da Silva, R, Paul, P, Ligeon, LA, Caruso, A, Albrecht, RA, Becker, AC, Annaheim, N, Nowag, H, Dengjel, J, Garcia-Sastre, A, Merkler, D, Munz, C, & Gannage, M (2016). Macroautophagy Proteins Control MHC Class I Levels on Dendritic Cells and Shape Anti-viral CD8(+) T Cell Responses. Cell Rep 15:1076-1087.

Maier, K, He, Y, Esser, PR, Thriene, K, Sarca, D, Kohlhase, J, Dengjel, J, Martin, L, & Has, C (2016). Single Amino Acid Deletion in Kindlin-1 Results in Partial Protein Degradation Which Can Be Rescued by Chaperone Treatment. J Invest Dermatol 136:920-929.

Metzger, E, Willmann, D, McMillan, J, Forne, I, Metzger, P, Gerhardt, S, Petroll, K, von Maessenhausen, A, Urban, S, Schott, AK, Espejo, A, Eberlin, A, Wohlwend, D, Schule, KM, Schleicher, M, Perner, S, Bedford, MT, Jung, M, Dengjel, J, Flaig, R, Imhof, A, Einsle, O, & Schule, R (2016). Assembly of methylated KDM1A and CHD1 drives androgen receptor-dependent transcription and translocation. Nat Struct Mol Biol 23:132-139.

Schlicher, L, Wissler, M, Preiss, F, Brauns-Schubert, P, Jakob, C, Dumit, V, Borner, C, Dengjel, J, & Maurer, U (2016). SPATA2 promotes CYLD activity and regulates TNF-induced NF-kappaB signaling and cell death. EMBO Rep 17:1485-1497.

Weber, A, Heinlein, M, Dengjel, J, Alber, C, Singh, PK, & Hacker, G (2016). The deubiquitinase Usp27x stabilizes the BH3-only protein Bim and enhances apoptosis. EMBO Rep 17:724-738.

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.

Bohrer, C, Pfurr, S, Mammadzada, K, Schildge, S, Plappert, L, Hils, M, Pous, L, Rauch, KS, Dumit, VI, Pfeifer, D, Dengjel, J, Kirsch, M, Schachtrup, K, & Schachtrup, C (2015). The balance of Id3 and E47 determines neural stem/precursor cell differentiation into astrocytes. EMBO J 34:2804-2819.

2015

Braun, RJ, Sommer, C, Leibiger, C, Gentier, RJ, Dumit, VI, Paduch, K, Eisenberg, T, Habernig, L, Trausinger, G, Magnes, C, Pieber, T, Sinner, F, Dengjel, J, van Leeuwen, FW, Kroemer, G, & Madeo, F (2015). Accumulation of Basic Amino Acids at Mitochondria Dictates the Cytotoxicity of Aberrant Ubiquitin. Cell Rep.

Braun, RJ, Sommer, C, Leibiger, C, Gentier, RJ, Dumit, VI, Paduch, K, Eisenberg, T, Habernig, L, Trausinger, G, Magnes, C, Pieber, T, Sinner, F, Dengjel, J, Leeuwen, FW, Kroemer, G, & Madeo, F (2015). Modeling non-hereditary mechanisms of Alzheimer disease during apoptosis in yeast. Microb Cell 2:136-138.

Cianfanelli, V, Fuoco, C, Lorente, M, Salazar, M, Quondamatteo, F, Gherardini, PF, De Zio, D, Nazio, F, Antonioli, M, D'Orazio, M, Skobo, T, Bordi, M, Rohde, M, Dalla Valle, L, Helmer-Citterich, M, Gretzmeier, C, Dengjel, J, Fimia, GM, Piacentini, M, Di Bartolomeo, S, Velasco, G, & Cecconi, F (2015). AMBRA1 links autophagy to cell proliferation and tumorigenesis by promoting c-Myc dephosphorylation and degradation. Nat Cell Biol 17:706.

Fiala, GJ, Janowska, I, Prutek, F, Hobeika, E, Satapathy, A, Sprenger, A, Plum, T, Seidl, M, Dengjel, J, Reth, M, Cesca, F, Brummer, T, Minguet, S, & Schamel, WW (2015). Kidins220/ARMS binds to the B cell antigen receptor and regulates B cell development and activation. J Exp Med 212:1693-1708.

Frank, DO, Dengjel, J, Wilfling, F, Kozjak-Pavlovic, V, Hacker, G, & Weber, A (2015). The pro-apoptotic BH3-only protein Bim interacts with components of the translocase of the outer mitochondrial membrane (TOM). PLoS One 10:e0123341.

Funk, MC, Bera, AN, Menchen, T, Kuales, G, Thriene, K, Lienkamp, SS, Dengjel, J, Omran, H, Frank, M, & Arnold, SJ (2015). Cyclin O (Ccno) functions during deuterosome-mediated centriole amplification of multiciliated cells. EMBO J 34:1078-1089.

Haug, S, Schnerch, D, Halbach, S, Mastroianni, J, Dumit, VI, Follo, M, Hasenburg, A, Kohler, M, Dierbach, H, Herzog, S, Proske, A, Werner, M, Dengjel, J, Brummer, T, Lassmann, S, Wasch, R, & Zeiser, R (2015). Metadherin exon 11 skipping variant enhances metastatic spread of ovarian cancer. Int J Cancer 136:2328-2340.

Hieke, N, Loffler, AS, Kaizuka, T, Berleth, N, Bohler, P, Driessen, S, Stuhldreier, F, Friesen, O, Assani, K, Schmitz, K, Peter, C, Diedrich, B, Dengjel, J, Holland, P, Simonsen, A, Wesselborg, S, Mizushima, N, & Stork, B (2015). Expression of a ULK1/2 binding-deficient ATG13 variant can partially restore autophagic activity in ATG13-deficient cells. Autophagy 11:1471-1483.

Nystrom, A, Thriene, K, Mittapalli, V, Kern, JS, Kiritsi, D, Dengjel, J, & Bruckner-Tuderman, L (2015). Losartan ameliorates dystrophic epidermolysis bullosa and uncovers new disease mechanisms. EMBO Mol Med 7:1211-1228.

Petrungaro, C, Zimmermann, KM, Kuttner, V, Fischer, M, Dengjel, J, Bogeski, I, & Riemer, J (2015). The Ca(2+)-Dependent Release of the Mia40-Induced MICU1-MICU2 Dimer from MCU Regulates Mitochondrial Ca(2+) Uptake. Cell Metab 22:721-733.

Ramachandran, H, Engel, C, Muller, B, Dengjel, J, Walz, G, & Yakulov, TA (2015). Anks3 alters the sub-cellular localization of the Nek7 kinase. Biochem Biophys Res Commun 464:901-907.

Schwarz, JJ, Wiese, H, Tolle, RC, Zarei, M, Dengjel, J, Warscheid, B, & Thedieck, K (2015). Functional Proteomics Identifies Acinus L as a Direct Insulin- and Amino Acid-Dependent Mammalian Target of Rapamycin Complex 1 (mTORC1) Substrate. Mol Cell Proteomics 14:2042-2055.

Yakulov, TA, Yasunaga, T, Ramachandran, H, Engel, C, Muller, B, Hoff, S, Dengjel, J, Lienkamp, SS, & Walz, G (2015). Anks3 interacts with nephronophthisis proteins and is required for normal renal development. Kidney Int 87:1191-1200.

2014

Antonioli, M, Albiero, F, Nazio, F, Vescovo, T, Perdomo, AB, Corazzari, M, Marsella, C, Piselli, P, Gretzmeier, C, Dengjel, J, Cecconi, F, Piacentini, M, & Fimia, GM (2014). AMBRA1 interplay with cullin E3 ubiquitin ligases regulates autophagy dynamics. Dev Cell 31:734-746.

Becker, AC & Dengjel, J (2014). Autophagosomal proteome analysis by protein correlation profiling-SILAC. Methods Mol Biol 1188:271-279.

Chylek, LA, Akimov, V, Dengjel, J, Rigbolt, KT, Hu, B, Hlavacek, WS, & Blagoev, B (2014). Phosphorylation site dynamics of early T-cell receptor signaling. PLoS One 9:e104240.

Dengjel, J & Abeliovich, H (2014). Musical chairs during mitophagy. Autophagy 10:706-707.

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.

Eisenberg, T, Schroeder, S, Andryushkova, A, Pendl, T, Kuttner, V, Bhukel, A, Marino, G, Pietrocola, F, Harger, A, Zimmermann, A, Moustafa, T, Sprenger, A, Jany, E, Buttner, S, Carmona-Gutierrez, D, Ruckenstuhl, C, Ring, J, Reichelt, W, Schimmel, K, Leeb, T, Moser, C, Schatz, S, Kamolz, LP, Magnes, C, Sinner, F, Sedej, S, Frohlich, KU, Juhasz, G, Pieber, TR, Dengjel, J, Sigrist, SJ, Kroemer, G, & Madeo, F (2014). Nucleocytosolic depletion of the energy metabolite acetyl-coenzyme a stimulates autophagy and prolongs lifespan. Cell Metab 19:431-444.

Eisenberg, T, Schroeder, S, Buttner, S, Carmona-Gutierrez, D, Pendl, T, Andryushkova, A, Marino, G, Pietrocola, F, Harger, A, Zimmermann, A, Magnes, C, Sinner, F, Sedej, S, Pieber, TR, Dengjel, J, Sigrist, S, Kroemer, G, & Madeo, F (2014). A histone point mutation that switches on autophagy. Autophagy 10:1143-1145.

Engelke, R, Riede, J, Hegermann, J, Wuerch, A, Eimer, S, Dengjel, J, & Mittler, G (2014). The quantitative nuclear matrix proteome as a biochemical snapshot of nuclear organization. J Proteome Res 13:3940-3956.

He, Y, Sonnenwald, T, Sprenger, A, Hansen, U, Dengjel, J, Bruckner-Tuderman, L, Schmidt, G, & Has, C (2014). RhoA activation by CNFy restores cell-cell adhesion in kindlin-2-deficient keratinocytes. J Pathol 233:269-280.

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.

Nowag, H, Guhl, B, Thriene, K, Romao, S, Ziegler, U, Dengjel, J, & Munz, C (2014). Macroautophagy Proteins Assist Epstein Barr Virus Production and Get Incorporated Into the Virus Particles. EBioMedicine 1:116-125.

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.

Schroeder, S, Pendl, T, Zimmermann, A, Eisenberg, T, Carmona-Gutierrez, D, Ruckenstuhl, C, Marino, G, Pietrocola, F, Harger, A, Magnes, C, Sinner, F, Pieber, TR, Dengjel, J, Sigrist, SJ, Kroemer, G, & Madeo, F (2014). Acetyl-coenzyme A: a metabolic master regulator of autophagy and longevity. Autophagy 10:1335-1337.

2013

Abeliovich, H, Zarei, M, Rigbolt, KT, Youle, RJ, & Dengjel, J (2013). Involvement of mitochondrial dynamics in the segregation of mitochondrial matrix proteins during stationary phase mitophagy. Nat Commun 4:2789.

Boerries, M, Grahammer, F, Eiselein, S, Buck, M, Meyer, C, Goedel, M, Bechtel, W, Zschiedrich, S, Pfeifer, D, Laloe, D, Arrondel, C, Goncalves, S, Kruger, M, Harvey, SJ, Busch, H, Dengjel, J, & Huber, TB (2013). Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks. Kidney Int 83:1052-1064.

Buttner, S, Habernig, L, Broeskamp, F, Ruli, D, Vogtle, FN, Vlachos, M, Macchi, F, Kuttner, V, Carmona-Gutierrez, D, Eisenberg, T, Ring, J, Markaki, M, Taskin, AA, Benke, S, Ruckenstuhl, C, Braun, R, Van den Haute, C, Bammens, T, van der Perren, A, Frohlich, KU, Winderickx, J, Kroemer, G, Baekelandt, V, Tavernarakis, N, Kovacs, GG, Dengjel, J, Meisinger, C, Sigrist, SJ, & Madeo, F (2013). Endonuclease G mediates alpha-synuclein cytotoxicity during Parkinson's disease. EMBO J 32:3041-3054.

Fischer, M, Horn, S, Belkacemi, A, Kojer, K, Petrungaro, C, Habich, M, Ali, M, Kuttner, V, Bien, M, Kauff, F, Dengjel, J, Herrmann, JM, & Riemer, J (2013). Protein import and oxidative folding in the mitochondrial intermembrane space of intact mammalian cells. Mol Biol Cell 24:2160-2170.

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.

Nazio, F, Strappazzon, F, Antonioli, M, Bielli, P, Cianfanelli, V, Bordi, M, Gretzmeier, C, Dengjel, J, Piacentini, M, Fimia, GM, & Cecconi, F (2013). mTOR inhibits autophagy by controlling ULK1 ubiquitylation, self-association and function through AMBRA1 and TRAF6. Nat Cell Biol 15:406-416.

Romao, S, Gasser, N, Becker, AC, Guhl, B, Bajagic, M, Vanoaica, D, Ziegler, U, Roesler, J, Dengjel, J, Reichenbach, J, & Munz, C (2013). Autophagy proteins stabilize pathogen-containing phagosomes for prolonged MHC II antigen processing. J Cell Biol 203:757-766.

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

Akkad, N, Schatz, M, Dengjel, J, Tenzer, S, & Schild, H (2012). Census of cytosolic aminopeptidase activity reveals two novel cytosolic aminopeptidases. Med Microbiol Immunol 201:463-473.

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.

Bozzacco, L, Yu, H, Dengjel, J, Trumpfheller, C, Zebroski, HA, 3rd, Zhang, N, Kuttner, V, Ueberheide, BM, Deng, H, Chait, BT, Steinman, RM, Mojsov, S, & Fenyo, D (2012). Strategy for identifying dendritic cell-processed CD4+ T cell epitopes from the HIV gag p24 protein. PLoS One 7:e41897.

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.

Fuellen, G, Dengjel, J, Hoeflich, A, Hoeijemakers, J, Kestler, HA, Kowald, A, Priebe, S, Rebholz-Schuhmann, D, Schmeck, B, Schmitz, U, Stolzing, A, Suhnel, J, Wuttke, D, & Vera, J (2012). Systems biology and bioinformatics in aging research: a workshop report. Rejuvenation Res 15:631-641.

Klionsky, DJ, et al. (2012). Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8:445-544.

Preuss, B, Berg, C, Dengjel, J, Stevanovic, S, & Klein, R (2012). Relevance of the inner mitochondrial membrane enzyme F1F0-ATPase as an autoantigen in autoimmune liver disorders. Liver Int 32:249-257.

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

Bozzacco, L, Yu, H, Zebroski, HA, Dengjel, J, Deng, H, Mojsov, S, & Steinman, RM (2011). Mass spectrometry analysis and quantitation of peptides presented on the MHC II molecules of mouse spleen dendritic cells. J Proteome Res 10:5016-5030.

Ndhlovu, M, Preuss, BE, Dengjel, J, Stevanovic, S, Weiner, SM, & Klein, R (2011). Identification of alpha-tubulin as an autoantigen recognized by sera from patients with neuropsychiatric systemic lupus erythematosus. Brain Behav Immun 25:279-285.

Nylandsted, J, Becker, AC, Bunkenborg, J, Andersen, JS, Dengjel, J, & Jaattela, M (2011). ErbB2-associated changes in the lysosomal proteome. Proteomics 11:2830-2838.

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.

Feuchtinger, M, Christ, S, Preuss, B, Dengjel, J, Duman, S, Stevanovic, S, & Klein, R (2009). Detection of novel non-M2-related antimitochondrial antibodies in patients with anti-M2 negative primary biliary cirrhosis. Gut 58:983-989.

Gannage, M, Dormann, D, Albrecht, R, Dengjel, J, Torossi, T, Ramer, PC, Lee, M, Strowig, T, Arrey, F, Conenello, G, Pypaert, M, Andersen, J, Garcia-Sastre, A, & Munz, C (2009). Matrix protein 2 of influenza A virus blocks autophagosome fusion with lysosomes. Cell Host Microbe 6:367-380.

Wahlstrom, J, Dengjel, J, Winqvist, O, Targoff, I, Persson, B, Duyar, H, Rammensee, HG, Eklund, A, Weissert, R, & Grunewald, J (2009). Autoimmune T cell responses to antigenic peptides presented by bronchoalveolar lavage cell HLA-DR molecules in sarcoidosis. Clin Immunol 133:353-363.

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.

Wahlstrom, J, Dengjel, J, Persson, B, Duyar, H, Rammensee, HG, Stevanovic, S, Eklund, A, Weissert, R, & Grunewald, J (2007). Identification of HLA-DR-bound peptides presented by human bronchoalveolar lavage cells in sarcoidosis. J Clin Invest 117:3576-3582.

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.

Schmid, D, Dengjel, J, Schoor, O, Stevanovic, S, & Munz, C (2006). Autophagy in innate and adaptive immunity against intracellular pathogens. J Mol Med (Berl) 84:194-202.

Trautwein, M, Schindler, C, Gauss, R, Dengjel, J, Hartmann, E, & Spang, A (2006). Arf1p, Chs5p and the ChAPs are required for export of specialized cargo from the Golgi. EMBO J 25:943-954.

2005

Coia, V, Juliger, S, Mordmuller, B, Kreidenweis, A, Stroh, AL, Ortega, C, Vindigni, A, Dengjel, J, Lukyanov, DV, Destro-Bisol, G, Fedorov, A, Podgornaya, OI, & Kun, JF (2005). Analysis of polymorphic sites in the promoter of the nitric oxide synthase 2 gene. Biochem Biophys Res Commun 335:1123-1131.

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.

Duyar, H, Dengjel, J, de Graaf, KL, Wiesmuller, KH, Stevanovic, S, & Weissert, R (2005). Peptide motif for the rat MHC class II molecule RT1.Da: similarities to the multiple sclerosis-associated HLA-DRB1*1501 molecule. Immunogenetics 57:69-76.

Kruger, T, Schoor, O, Lemmel, C, Kraemer, B, Reichle, C, Dengjel, J, Weinschenk, T, Muller, M, Hennenlotter, J, Stenzl, A, Rammensee, HG, & Stevanovic, S (2005). Lessons to be learned from primary renal cell carcinomas: novel tumor antigens and HLA ligands for immunotherapy. Cancer Immunol Immunother 54:826-836.

Stoll, H, Dengjel, J, Nerz, C, & Gotz, F (2005). Staphylococcus aureus deficient in lipidation of prelipoproteins is attenuated in growth and immune activation. Infect Immun 73:2411-2423.

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.

Lemmel, C, Weik, S, Eberle, U, Dengjel, J, Kratt, T, Becker, HD, Rammensee, HG, & Stevanovic, S (2004). Differential quantitative analysis of MHC ligands by mass spectrometry using stable isotope labeling. Nat Biotechnol 22:450-454.

Tenzer, S, Stoltze, L, Schonfisch, B, Dengjel, J, Muller, M, Stevanovic, S, Rammensee, HG, & Schild, H (2004). Quantitative analysis of prion-protein degradation by constitutive and immuno-20S proteasomes indicates differences correlated with disease susceptibility. J Immunol 172:1083-1091.

Trautwein, M, Dengjel, J, Schirle, M, & Spang, A (2004). Arf1p provides an unexpected link between COPI vesicles and mRNA in Saccharomyces cerevisiae. Mol Biol Cell 15:5021-5037.

2003

Sandmann, T, Herrmann, JM, Dengjel, J, Schwarz, H, & Spang, A (2003). Suppression of coatomer mutants by a new protein family with COPI and COPII binding motifs in Saccharomyces cerevisiae. Mol Biol Cell 14:3097-3113.