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PUBLICATIONS

2025

 

Aghapour, M., & Herhaus, L. (2025). Extract to lyse bacterial pathogens. Nature microbiology, 10(5), 1036–1037. https://doi.org/10.1038/s41564-025-01995-9

Babic, R., Brenneisen, J., Wilfling, F., & Kraft, C. (2025). Autophagy regulation by phase separation, avidity, and wetting. Trends in biochemical sciences, S0968-0004(25)00244-0. Advance online publication. https://doi.org/10.1016/j.tibs.2025.10.003

 

Baeken, M. W., Christ, M., Schmitt, D., Trein, W., Nagel, H., Clement, A. M., Körschgen, H., & Behl, C. (2025). Conserved LIR-specific interaction of Sigma-1 receptor and GABARAP. iScience, 28(9), 113287. https://doi.org/10.1016/j.isci.2025.113287

 

Baeken, M. W., Borlepawar, A., Kötzner, P., Richly, H., Behl, C., Moosmann, B., & Hajieva, P. (2025). Epigenetic regulation of the respiratory chain by a mitochondrial distress-related redox signal. Frontiers in cell and developmental biology, 13, 1608400. https://doi.org/10.3389/fcell.2025.1608400

Bailey, H. J., Eisert, J., Kazi, R., Gerhartz, J., Pieńkowska, D. E., Dressel, I., Vollrath, J., Kondratov, I., Matviyuk, T., Tolmachova, N., Shah, V. J., Giuliani, G., Mosler, T., Geiger, T. M., Esteves, A. M., Santos, S. P., Sousa, R. L., Bandeiras, T. M., Leibrock, E. M., Bauer, U., … Dikic, I. (2025). An engineered cereblon optimized for high-throughput screening and molecular glue discovery. Cell chemical biology, 32(2), 363–376.e10. https://doi.org/10.1016/j.chembiol.2024.11.002

 

Bhattacharya, D., da Silva-Buttkus, P., Nalbach, K., Cheng, L., Garrett, L., Irmler, M., Kislinger, G., Werner, G., Rodde, R., Lengger, C., Beckers, J., Zimprich, A., Hölter, S. M., Gailus-Durner, V., Fuchs, H., Hrabe de Angelis, M., Wefers, B., Wurst, W., Brill, M. S., Schifferer, M., … Behrends, C. (2025). Neuropathy-associated Tecpr2 mutation knock-in mice reveal endolysosomal loss of function phenotypes in neurons and microglia. Cell death & disease, 16(1), 775. https://doi.org/10.1038/s41419-025-08168-w

Bock, A., Schurig, M., Willoughby, M., Mirecki, A., Seemann, E., Lohachova, K., Katona, I., Mittag, S., Liebmann, L., Franzka, P., Heidari Horestani, M., Khundadze, M., Mosler, T., Louie, T., de Visser, M., Weterman, M. A. J., Kiehntopf, M., Beetz, C., Nietzsche, S., Huber, O., … Hübner, C. A. (2025). REEP1 Accumulation Disrupts ER Integrity and Drives Spinal Motoneuron Degeneration in Distal Hereditary Motor Neuropathy. Advanced science (Weinheim, Baden-Wurttemberg, Germany), e11483. Advance online publication. https://doi.org/10.1002/advs.202511483

Buonomo, V., Lohachova, K., Reggio, A., Cano-Franco, S., Cillo, M., Santorelli, L., Venditti, R., Polishchuk, E., Peluso, I., Brunello, L., Cirillo, C., Petrosino, S., Silva, M., De Cegli, R., Di Bartolomeo, S., Gargioli, C., Swuec, P., Cortese, M., Stolz, A., Bhaskara, R. M., … Grumati, P. (2025). Two FAM134B isoforms differentially regulate ER dynamics during myogenesis. The EMBO journal, 44(4), 1039–1073. https://doi.org/10.1038/s44318-024-00356-2

Fitzgerald, J. C., & Bremm, A. (2025). A structural switch reveals how to disarm USP30 and unlock mitophagy. Nature structural & molecular biology, 32(9), 1586–1588. https://doi.org/10.1038/s41594-025-01640-3

Haydo, A., Schmidt, J., Crider, A., Kögler, T., Ertl, J., Hehlgans, S., Hoffmann, M. E., Rathore, R., Güllülü, Ö., Wang, Y., Zhang, X., Herold-Mende, C., Pampaloni, F., Tegeder, I., Dikic, I., Dai, M., Rödel, F., Kögel, D., & Linder, B. (2025). BRAT1 - a new therapeutic target for glioblastoma. Cellular and molecular life sciences : CMLS, 82(1), 52. https://doi.org/10.1007/s00018-024-05553-0

Ho-Xuan, H., Bruckmann, A., Natali, L., Prieto-Garcia, C., Stuke, J. F. M., Brunello, L., Vicente, A., Pfab, A., Wesseling, H., Cano-Franco, S., Khatri, A., Larivera, S., Sanz-Martinez, P., de la Cruz-Thea, B., Jacomin, A. C., Prochazka, J., Feederle, R., Dötsch, V., Sedlacek, R., Hummer, G., … Stolz, A. (2025). YTHDF proteins and m6A-RNA clients undergo autophagic turnover during contact inhibition. Cell reports, 44(9), 116188. https://doi.org/10.1016/j.celrep.2025.116188

 

Huber, L. S., Merline, R., Zeng-Brouwers, J., Vutukuri, R., Kraus, N., Ortiz, C., Guenther, S., Buhl, E. M., Hahnefeld, L., Gurke, R., Bein, J., Karimova, M., Wurzel, P., Boor, P., Welsch, C., Wild, P., Pfeilschifter, J., Kögel, D., Wygrecka, M., Trebicka, J., … Schaefer, L. (2025). Deletion of ABIN1-LIR motifs impairs hepatic lipid homeostasis and mitophagy via AMPK-TFEB axis in mice. American journal of physiology. Cell physiology, 329(5), C1360–C1379. https://doi.org/10.1152/ajpcell.00544.2025

Kumari, R., Nath, T., Pflaum, J., R, I., Vinay, S., Wilfling, F., & Manjithaya, R. (2025). The autophagy-specific exocyst subcomplex contributes to phagophore assembly site integrity by promoting phagophore expansion. Proceedings of the National Academy of Sciences of the United States of America, 122(41), e2426476122. https://doi.org/10.1073/pnas.2426476122

 

Licheva, M., Babic, R., Pflaum, J., Mancilla, H., Wilfling, F., & Kraft, C. (2025). To degrade or not to degrade: how phase separation modulates selective autophagy. Autophagy, 21(11), 2518–2520. https://doi.org/10.1080/15548627.2025.2476025

 

Licheva, M., Pflaum, J., Babic, R., Mancilla, H., Elsässer, J., Boyle, E., Hollenstein, D. M., Jimenez-Niebla, J., Pleyer, J., Heinrich, M., Wieland, F. G., Brenneisen, J., Eickhorst, C., Brenner, J., Jiang, S., Hartl, M., Welsch, S., Hunte, C., Timmer, J., Wilfling, F., … Kraft, C. (2025). Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy. Nature cell biology, 27(2), 283–297. https://doi.org/10.1038/s41556-024-01572-y

Mukherjee, R., Bhattacharya, A., Tomaskovic, I., Mello-Vieira, J., Brunstein, M. E., Başoğlu, M., Veenendaal, T., Bailey, H., Colby, T., Misra, M., Eimer, S., Klumperman, J., Münch, C., Matic, I., & Dikic, I. (2025). Phosphoribosyl ubiquitination of SNARE proteins regulates autophagy during Legionella infection. The EMBO journal, 44(15), 4252–4279. https://doi.org/10.1038/s44318-025-00483-4

 

Mukherjee, R., Bhattacharya, A., Mello-Vieira, J., Kuncha, S. K., Hoffmann, M., Gonzalez, A., Rathore, R., Chadha, A., Shin, D., Colby, T., Matic, I., Mukherjee, S., Misra, M., & Dikic, I. (2025). Serine ubiquitination of SQSTM1 regulates NFE2L2-dependent redox homeostasis. Autophagy, 21(2), 407–423. https://doi.org/10.1080/15548627.2024.2404375

Mukhopadhyay, U., Levantovsky, S., Behrends, C., & Bhogaraju, S. (2025). Ub-POD: A Ubiquitin-Specific Proximity-Dependent Labeling Technique to Identify E3 Ubiquitin Ligase Substrates in Human Cells. Bio-protocol, 15(12), e5351. https://doi.org/10.21769/BioProtoc.5351

Orth, B., Pohl, P., Aust, F., Ji, Y., Seenivasan, A., Dybkov, O., Liang, X. J., Bock, L., Leidner, F., Levantovsky, S., Schardey, P., Sander, P., Disch, N. J., Trautz, M. L., Mizi, A., Papantonis, A., Lenz, C., Grubmüller, H., Steinchen, W., Behrends, C., … Lorenz, S. (2025). Selective ubiquitination of drug-like small molecules by the ubiquitin ligase HUWE1. Nature communications, 16(1), 8182. https://doi.org/10.1038/s41467-025-63442-x

Pham, T. N. M., & Behl, C. (2025). Cellular models of stress resistance may pave ways to fight neurodegenerative diseases. Neural regeneration research, 20(9), 2579–2580. https://doi.org/10.4103/NRR.NRR-D-24-00476

Poveda-Cuevas, S. A., Lohachova, K., Markusic, B., Dikic, I., Hummer, G., & M Bhaskara, R. (2025). Janus-like behavior of intrinsically disordered regions in reticulophagy. Autophagy, 21(3), 681–683. https://doi.org/10.1080/15548627.2024.2437652

Reinders, M., Kravic, B., Gahlot, P., Koska, S., van den Boom, J., Schulze, N., Levantovsky, S., Kleine, S., Kaiser, M., Kulathu, Y., Behrends, C., & Meyer, H. (2025). ATXN3 regulates lysosome regeneration after damage by targeting K48-K63-branched ubiquitin chains. The EMBO journal, 44(18), 5086–5111. https://doi.org/10.1038/s44318-025-00517-x

Sanz-Martinez, P., Berkane, R., & Stolz, A. (2025). Function of CSNK2/CK2 selectively affects the endoplasmic reticulum and the Golgi apparatus in mtor-mediated autophagy induction. Autophagy, 21(2), 480–486. https://doi.org/10.1080/15548627.2024.2395725

Stein, A., Vo, S., Freese, C., Kluge, J., Maus, J., Koziollek-Drechsler, I., Silva, B., Behl, C., & Clement, A. M. (2025). The Parkinson Disease-Associated Mutant DNAJC13(N855S) Leads to Its Accelerated Degradation and Negatively Affects Macroautophagy and Retromer Complex-Mediated Dynamics. Journal of cellular physiology, 240(7), e70074. https://doi.org/10.1002/jcp.70074

Vicente, A. M., Hencel, K., Schicktanz, J., Hammann, C., Akay, A., & Kaiser, S. (2025). NAIL-MS Elucidates Crucial tRNA U34 Modifications in Response to Heat Stress across Eukaryotes and Prokaryotes. Journal of molecular biology, 437(16), 169228. https://doi.org/10.1016/j.jmb.2025.169228

 

Zein, L., Dietrich, M., Balta, D., Bader, V., Scheuer, C., Zellner, S., Weinelt, N., Vandrey, J., Mari, M. C., Behrends, C., Zunke, F., Winklhofer, K. F., & Van Wijk, S. J. L. (2025). Linear ubiquitination at damaged lysosomes induces local NFKB activation and controls cell survival. Autophagy, 21(5), 1075–1095. https://doi.org/10.1080/15548627.2024.2443945

2024

Balakrishnan, A., Glogger, M., & Heilemann, M. (2024). Quantitative Super-Resolution Imaging of ER-Phagy Initiation in Cells. Methods in molecular biology (Clifton, N.J.), 2845, 127–140. https://doi.org/10.1007/978-1-0716-4067-8_10

Bajdzienko, J., & Bremm, A. (2024). Mammalian pexophagy at a glance. Journal of cell science, 137(9), jcs259775. https://doi.org/10.1242/jcs.259775

 

Bhattacharya, A., Torggler, R., Reiter, W., Romanov, N., Licheva, M., Ciftci, A., Mari, M., Kolb, L., Kaiser, D., Reggiori, F., Ammerer, G., Hollenstein, D. M., & Kraft, C. (2024). Decoding the function of Atg13 phosphorylation reveals a role of Atg11 in bulk autophagy initiation. EMBO reports, 25(2), 813–831. https://doi.org/10.1038/s44319-023-00055-9

Bozkurt, S., Parmar, B. S., & Münch, C. (2024). Quantifying mitochondrial protein import by mePRODmt proteomics. Methods in enzymology, 706, 449–474. https://doi.org/10.1016/bs.mie.2024.07.017

Cristiani, A., Dutta, A., Poveda-Cuevas, S. A., Kern, A., & Bhaskara, R. M. (2024). Identification of potential selective autophagy receptors from protein-content profiling of autophagosomes. Journal of cellular biochemistry, 125(11), e30405. https://doi.org/10.1002/jcb.30405

Eickhorst, C., Babic, R., Rush-Kittle, J., Lucya, L., Imam, F. L., Sánchez-Martín, P., Hollenstein, D. M., Michaelis, J., Münch, C., Meisinger, C., Slade, D., Gámez-Díaz, L., & Kraft, C. (2024). FIP200 Phosphorylation Regulates Late Steps in Mitophagy. Journal of molecular biology, 436(15), 168631. https://doi.org/10.1016/j.jmb.2024.168631

Herhaus, L., Gestal-Mato, U., Eapen, V. V., Mačinković, I., Bailey, H. J., Prieto-Garcia, C., Misra, M., Jacomin, A. C., Ammanath, A. V., Bagarić, I., Michaelis, J., Vollrath, J., Bhaskara, R. M., Bündgen, G., Covarrubias-Pinto, A., Husnjak, K., Zöller, J., Gikandi, A., Ribičić, S., Bopp, T., … Dikic, I. (2024). IRGQ-mediated autophagy in MHC class I quality control promotes tumor immune evasion. Cell, 187(25), 7285–7302.e29. https://doi.org/10.1016/j.cell.2024.09.048

Hoffmann, M. E., Jacomin, A. C., Popovic, D., Kalina, D., Covarrubias-Pinto, A., & Dikic, I. (2024). TBC1D2B undergoes phase separation and mediates autophagy initiation. Journal of cellular biochemistry, 125(8), e30481. https://doi.org/10.1002/jcb.30481

Isigkeit, L., Schallmayer, E., Busch, R., Brunello, L., Menge, A., Elson, L., Müller, S., Knapp, S., Stolz, A., Marschner, J. A., & Merk, D. (2024). Chemogenomics for NR1 nuclear hormone receptors. Nature communications, 15(1), 5201. https://doi.org/10.1038/s41467-024-49493-6

Kessler, L. F., Balakrishnan, A., Menche, T., Wang, D., Li, Y., Mantel, M., Glogger, M., Dietz, M. S., & Heilemann, M. (2024). Self-Quenched Fluorophore-DNA Labels for Super-Resolution Fluorescence Microscopy. The journal of physical chemistry. B, 128(28), 6751–6759. https://doi.org/10.1021/acs.jpcb.4c02065

Kew, C., Prieto-Garcia, C., Bhattacharya, A., Tietgen, M., MacNair, C. R., Carfrae, L. A., Mello-Vieira, J., Klatt, S., Cheng, Y. L., Rathore, R., Gradhand, E., Fleming, I., Tan, M. W., Göttig, S., Kempf, V. A. J., & Dikic, I. (2024). The aryl hydrocarbon receptor and FOS mediate cytotoxicity induced by Acinetobacter baumannii. Nature communications, 15(1), 7939. https://doi.org/10.1038/s41467-024-52118-7

Gestal-Mato, U., & Herhaus, L. (2024). Autophagy-dependent regulation of MHC-I molecule presentation. Journal of cellular biochemistry, 125(11), e30416. https://doi.org/10.1002/jcb.30416

Krämer, N., Mato, U. G., Krauter, S., Büscher, N., Afifi, A., Herhaus, L., Florin, L., Plachter, B., & Zimmermann, C. (2024). The Autophagy Receptor SQSTM1/p62 Is a Restriction Factor of HCMV Infection. Viruses, 16(9), 1440. https://doi.org/10.3390/v16091440

Körschgen, H., & Behl, C. (2024). Aggresome-aggrephagy transition process: getting closer to the functional roles of HDAC6 and BAG3. Neural regeneration research, 19(6), 1181–1182. https://doi.org/10.4103/1673-5374.386407

Lizarrondo, J., & Wilfling, F. (2024). Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken?. Journal of molecular biology, 436(15), 168574. https://doi.org/10.1016/j.jmb.2024.168574

 

Mukhopadhyay, U., Levantovsky, S., Carusone, T. M., Gharbi, S., Stein, F., Behrends, C., & Bhogaraju, S. (2024). A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates. Science advances, 10(32), eadp3000. https://doi.org/10.1126/sciadv.adp3000

 

Pastor-Maldonado, C. J., & Proikas-Cezanne, T. (2024). Ferritinophagy: Assessing the Selective Degradation of Iron by Autophagy in Human Fibroblasts. Journal of visualized experiments : JoVE, (204), 10.3791/65110. https://doi.org/10.3791/65110

 

Prieto-Garcia, C., Matkovic, V., Mosler, T., Li, C., Liang, J., Oo, J. A., Haidle, F., Mačinković, I., Cabrera-Orefice, A., Berkane, R., Giuliani, G., Xu, F., Jacomin, A. C., Tomaskovic, I., Basoglu, M., Hoffmann, M. E., Rathore, R., Cetin, R., Boutguetait, D., Bozkurt, S., … Dikic, I. (2024). Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy. Science (New York, N.Y.), 386(6723), 768–776. https://doi.org/10.1126/science.adi5295

 

Poveda-Cuevas, S. A., Lohachova, K., Markusic, B., Dikic, I., Hummer, G., & Bhaskara, R. M. (2024). Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy. Proceedings of the National Academy of Sciences of the United States of America, 121(44), e2408071121. https://doi.org/10.1073/pnas.2408071121

 

Rahm, J. V., Balakrishnan, A., Wehrheim, M., Kaminer, A., Glogger, M., Kessler, L. F., Kaschube, M., Barth, H. D., & Heilemann, M. (2024). Fast and Long-Term Super-Resolution Imaging of Endoplasmic Reticulum Nano-structural Dynamics in Living Cells Using a Neural Network. Small science, 5(1), 2400385. https://doi.org/10.1002/smsc.202400385

Roth, C., Paulini, L., Hoffmann, M. E., Mosler, T., Dikic, I., Brunschweiger, A., Körschgen, H., Behl, C., Linder, B., & Kögel, D. (2024). BAG3 regulates cilia homeostasis of glioblastoma via its WW domain. BioFactors (Oxford, England), 50(6), 1113–1133. https://doi.org/10.1002/biof.2060

Sanz-Martinez, P., Tascher, G., Cano-Franco, S., Cabrerizo-Poveda, P., Münch, C., Homan, E. J., & Stolz, A. (2024). GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention. Journal of molecular biology, 436(15), 168643. https://doi.org/10.1016/j.jmb.2024.168643

 

Stolz A. (2024). CSNK2/CK2 regulates selective autophagy of the endoplasmic reticulum. Autophagy, 20(7), 1694–1695. https://doi.org/10.1080/15548627.2024.2330037

Weigert, A., & Herhaus, L. (2024). Immune modulation through secretory autophagy. Journal of cellular biochemistry, 125(11), e30427. https://doi.org/10.1002/jcb.30427

2023

 

Berkane, R., Ho-Xuan, H., Glogger, M., Sanz-Martinez, P., Brunello, L., Glaesner, T., Kuncha, S. K., Holzhüter, K., Cano-Franco, S., Buonomo, V., Cabrerizo-Poveda, P., Balakrishnan, A., Tascher, G., Husnjak, K., Juretschke, T., Misra, M., González, A., Dötsch, V., Grumati, P., Heilemann, M., … Stolz, A. (2023). The function of ER-phagy receptors is regulated through phosphorylation-dependent ubiquitination pathways. Nature communications, 14(1), 8364. https://doi.org/10.1038/s41467-023-44101-5

Cano-Franco, S., Ho-Xuan, H., Brunello, L., & Stolz, A. (2023). Live-Cell High-Throughput Screen for Monitoring Autophagy Flux. Methods in molecular biology (Clifton, N.J.), 2706, 215–224. https://doi.org/10.1007/978-1-0716-3397-7_16

Dönig, J., Mende, H., Davila Gallesio, J., Wagner, K., Hotz, P., Schunck, K., Piller, T., Hölper, S., Uhan, S., Kaulich, M., Wirth, M., Keller, U., Tascher, G., Bohnsack, K. E., & Müller, S. (2023). Characterization of nucleolar SUMO isopeptidases unveils a general p53-independent checkpoint of impaired ribosome biogenesis. Nature communications, 14(1), 8121. https://doi.org/10.1038/s41467-023-43751-9

González, A., Covarrubias-Pinto, A., Bhaskara, R. M., Glogger, M., Kuncha, S. K., Xavier, A., Seemann, E., Misra, M., Hoffmann, M. E., Bräuning, B., Balakrishnan, A., Qualmann, B., Dötsch, V., Schulman, B. A., Kessels, M. M., Hübner, C. A., Heilemann, M., Hummer, G., & Dikić, I. (2023). Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature, 618(7964), 394–401. https://doi.org/10.1038/s41586-023-06089-2

 

Haydo, A., Wehle, A., Herold-Mende, C., Kögel, D., Pampaloni, F., & Linder, B. (2023). Combining organotypic tissue culture with light-sheet microscopy (OTCxLSFM) to study glioma invasion. EMBO reports, 24(12), e56964. https://doi.org/10.15252/embr.202356964

 

Hertel, A., Eimer, S., & Bremm, A. (2023). LAMTOR1 ubiquitination restricts its interaction with the vacuolar-type H+-ATPase, promotes autophagy and is controlled by USP32. Autophagy, 19(8), 2406–2407. https://doi.org/10.1080/15548627.2023.2184958

Kessler, L. F., Balakrishnan, A., Deußner-Helfmann, N. S., Li, Y., Mantel, M., Glogger, M., Barth, H. D., Dietz, M. S., & Heilemann, M. (2023). Self-quenched Fluorophore Dimers for DNA-PAINT and STED Microscopy. Angewandte Chemie (International ed. in English), 62(39), e202307538. https://doi.org/10.1002/anie.202307538

Körschgen, H., Baeken, M., Schmitt, D., Nagel, H., & Behl, C. (2023). Co-chaperone BAG3 enters autophagic pathway via its interaction with microtubule associated protein 1 light chain 3 beta. Traffic (Copenhagen, Denmark), 24(12), 564–575. https://doi.org/10.1111/tra.12916

 

Körschgen H, Behl C. Aggresome-aggrephagy transition process: getting closer to the functional roles of HDAC6 and  BAG3. Neural Regeneration Research. 2024 June; 19(6):p 1181-1182. doi:  10.4103/1673-5374.386407

Mende, H., Khatri, A., Lange, C., Poveda-Cuevas, S. A., Tascher, G., Covarrubias-Pinto, A., Löhr, F., Koschade, S. E., Dikic, I., Münch, C., Bremm, A., Brunetti, L., Brandts, C. H., Uckelmann, H., Dötsch, V., Rogov, V. V., Bhaskara, R. M., & Müller, S. (2023). An atypical GABARAP binding module drives the pro-autophagic potential of the AML-associated NPM1c variant. Cell reports, 42(12), 113484. https://doi.org/10.1016/j.celrep.2023.113484

Meyer, L. M., Koschade, S. E., Vischedyk, J. B., Thoelken, M., Gubas, A., Wegner, M., Basoglu, M., Knapp, S., Kaulich, M., Eimer, S., Shaid, S., & Brandts, C. H. (2023). Deciphering the mitophagy receptor network identifies a crucial role for OPTN (optineurin) in acute myeloid leukemia. Autophagy, 19(11), 2982–2996. https://doi.org/10.1080/15548627.2023.2230839

Nalbach, K., Schifferer, M., Bhattacharya, D., Ho-Xuan, H., Tseng, W., Williams, L. A., Stolz, A., Lichtenthaler, S. F., Elazar, Z., & Behrends, C. (2023). Spatial proteomics reveals secretory pathway disturbances caused by neuropathy-associated TECPR2. Nature communications, 14(1), 870. https://doi.org/10.1038/s41467-023-36553-6

Pham, T. N. M., Perumal, N., Manicam, C., Basoglu, M., Eimer, S., Fuhrmann, D. C., Pietrzik, C. U., Clement, A. M., Körschgen, H., Schepers, J., & Behl, C. (2023). Adaptive responses of neuronal cells to chronic endoplasmic reticulum (ER) stress. Redox biology, 67, 102943. https://doi.org/10.1016/j.redox.2023.102943

Proikas-Cezanne, T., Haas, M. L., Pastor-Maldonado, C. J., & Schüssele, D. S. (2024). Human WIPI β-propeller function in autophagy and neurodegeneration. FEBS letters, 598(1), 127–139. https://doi.org/10.1002/1873-3468.14782

 

Reisbeck L, Linder B, Tascher G, Bozkurt S, Weber KJ, Herold-Mende C, van Wijk SJL, Marschalek R, Schaefer L, Münch C, Kögel D.(2023) The iron chelator and OXPHOS inhibitor VLX600 induces mitophagy and an autophagy-dependent type of cell death in glioblastoma cells. Am J Physiol Cell Physiol. 325(6):C1451-C1469. doi: 10.1152/ajpcell.00293.2023

Rogov, V. V., Nezis, I. P., Tsapras, P., Zhang, H., Dagdas, Y., Noda, N. N., Nakatogawa, H., Wirth, M., Mouilleron, S., McEwan, D. G., Behrends, C., Deretic, V., Elazar, Z., Tooze, S. A., Dikic, I., Lamark, T., & Johansen, T. (2023). Atg8 family proteins, LIR/AIM motifs and other interaction modes. Autophagy reports, 2(1), 2188523. https://doi.org/10.1080/27694127.2023.2188523

Sanchez-Martin, P., Kriegenburg, F., Alves, L., Adam, J., Elsaesser, J., Babic, R., Mancilla, H., Licheva, M., Tascher, G., Munch, C., Eimer, S., & Kraft, C. (2023). ULK1-mediated phosphorylation regulates the conserved role of YKT6 in autophagy. J Cell Sci. https://doi.org/10.1242/jcs.260546

Schmitt, D., Bozkurt, S., Henning-Domres, P., Huesmann, H., Eimer, S., Bindila, L., Behrends, C., Boyle, E., Wilfling, F., Tascher, G., Münch, C., Behl, C., & Kern, A. (2023). FACS-mediated isolation of native autophagic vesicles. Autophagy, 19(7), 2146–2147. https://doi.org/10.1080/15548627.2022.2151188

 

Schüssele, D. S., Haller, P. K., Haas, M. L., Hunter, C., Sporbeck, K., & Proikas-Cezanne, T. (2023). Autophagy profiling in single cells with open source CellProfiler-based image analysis. Autophagy, 19(1), 338–351. https://doi.org/10.1080/15548627.2022.2065617

Sutandy, F.X.R., Goessner, I., Tascher, G., Münch, C. (2023). A cytosolic surveillance mechanism activates the mitochondrial UPR. Nature (accepted)


 

2022

 

Baeken, M. W., & Behl, C. (2022). On the origin of BAG(3) and its consequences for an expansion of BAG3’s role in protein homeostasis. Journal of cellular biochemistry, 123(1), 102–114. https://doi.org/10.1002/jcb.29925

 

Bata, N., Chaikuad, A., Bakas, N. A., Limpert, A. S., Lambert, L. J., Sheffler, D. J., Berger, L. M., Liu, G., Yuan, C., Wang, L., Peng, Y., Dong, J., Celeridad, M., Layng, F., Knapp, S., & Cosford, N. D. P. (2022). Inhibitors of the Hippo Pathway Kinases STK3/MST2 and STK4/MST1 Have Utility for the Treatment of Acute Myeloid Leukemia. Journal of medicinal chemistry, 65(2), 1352–1369. https://doi.org/10.1021/acs.jmedchem.1c00804

 

Bieber, A., Capitanio, C., Erdmann, PS., Fiedler, F., Beck, F., Lee, CW., Li, D., Hummer, G., Schulman, BA., Baumeister, W., Wilfling, F. (2022). In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proc. Natl. Acad. Sci. U.S.A. 119, e2209823119. https://doi.org/10.1073/pnas.2209823119

 

Denk, D., Petrocelli, V., Conche, C., Drachsler, M., Ziegler, P. K., Braun, A., Kress, A., Nicolas, A. M., Mohs, K., Becker, C., Neurath, M. F., Farin, H. F., Buchholz, C. J., Andreux, P. A., Rinsch, C., & Greten, F. R. (2022). Expansion of T memory stem cells with superior anti-tumor immunity by Urolithin A-induced mitophagy. Immunity, 55(11), 2059–2073.e8. https://doi.org/10.1016/j.immuni.2022.09.014

 

Denk, D., & Greten, F. R. (2022). Inflammation: the incubator of the tumor microenvironment. Trends in cancer, 8(11), 901–914. https://doi.org/10.1016/j.trecan.2022.07.002

 

Di Lorenzo, G., G., Iavarone, F., Maddaluno, M., Plata-Gómez, A. B., Aureli, S., Quezada Meza, C. P., Cinque, L., Palma, A., Reggio, A., Cirillo, C., Sacco, F., Stolz, A., Napolitano, G., Marin, O., Pinna, L. A., Ruzzene, M., Limongelli, V., Efeyan, A., Grumati, P., & Settembre, C. (2022). Phosphorylation of FAM134C by CK2 controls starvation-induced ER-phagy. Science Advances, 8 (35). Doi: 10.1126/sciadv.abo1215

 

Glogger, M., Wang, D., Kompa, J., Balakrishnan, A., Hiblot, J., Barth, H. D., Johnsson, K., & Heilemann, M. (2022). Synergizing Exchangeable Fluorophore Labels for Multitarget STED Microscopy. ACS nano, 16(11), 17991–17997. https://doi.org/10.1021/acsnano.2c07212

 

Gubas, A., & Dikic, I. (2022a). A guide to the regulation of selective autophagy receptors. FEBS Journal, 289(1), 75–89. https://doi.org/10.1111/febs.15824

 

Gubas, A., & Dikic, I. (2022b). ER remodeling via ER-phagy. In Molecular Cell (Vol. 82, Issue 8, pp. 1492–1500). Mol Cell. https://doi.org/10.1016/j.molcel.2022.02.018

 

Hertel, A., Alves, L. M., Dutz, H., Tascher, G., Bonn, F., Kaulich, M., Dikic, I., Eimer, S., Steinberg, F., & Bremm, A. (2022). USP32-regulated LAMTOR1 ubiquitination impacts mTORC1 activation and autophagy induction. Cell reports, 41(10), 111653. https://doi.org/10.1016/j.celrep.2022.111653

Jandl, K., Mutgan, A. C., Eller, K., Schaefer, L., & Kwapiszewska, G. (2022). The basement membrane in the cross-roads between the lung and kidney. Matrix Biol, 105, 31-52. https://doi.org/10.1016/j.matbio.2021.11.003

 

Koschade, S. E., Tascher, G., Parmar, B. S., Brandts, C. H., & Münch, C. (2022). SpinTip: A Simple, Robust, and Versatile Preanalytical Method for Microscale Suspension Cell Proteomics. Journal of proteome research, 21(11), 2827–2835. https://doi.org/10.1021/acs.jproteome.2c00478

Koschade, S. E., Klann, K., Shaid, S., Vick, B., Stratmann, J. A., Thölken, M., Meyer, L. M., Nguyen, T. D., Campe, J., Moser, L. M., Hock, S., Baker, F., Meyer, C. T., Wempe, F., Serve, H., Ullrich, E., Jeremias, I., Münch, C., & Brandts, C. H. (2022). Translatome proteomics identifies autophagy as a resistance mechanism to on-target FLT3 inhibitors in acute myeloid leukemia. Leukemia, 36(10), 2396–2407. https://doi.org/10.1038/s41375-022-01678-y

 

Merline, R., Rodig, H., Zeng-Brouwers, J., Poluzzi, C., Tascher, G., Michaelis, J., Lopez-Mosqueda, J., Rhiner, A., Huber, L. S., Diehl, V., Dikic, I., Kogel, D., Munch, C., Wygrecka, M., & Schaefer, L. (2022). A20 binding and inhibitor of nuclear factor kappa B (NF-kappaB)-1 (ABIN-1) - a novel modulator of mitochondrial autophagy. Am J Physiol Cell Physiol. https://doi.org/10.1152/ajpcell.00493.2022

Michaelis, J. B., Brunstein, M. E., Bozkurt, S., Alves, L., Wegner, M., Kaulich, M., Pohl, C., & Münch, C. (2022). Protein import motor complex reacts to mitochondrial misfolding by reducing protein import and activating mitophagy. Nature communications, 13(1), 5164. https://doi.org/10.1038/s41467-022-32564-x

 

Mukherjee, R., & Dikic, I. (2022). Regulation of Host-Pathogen Interactions via the Ubiquitin System. In Annual review of microbiology (Vol. 76, pp. 211–233). Annu Rev Microbiol. https://doi.org/10.1146/annurev-micro-041020-025803

 

Remy, J., Linder, B., Weirauch, U., Day, B. W., Stringer, B. W., Herold-Mende, C., Aigner, A., Krohn, K., & Kogel, D. (2022). STAT3 Enhances Sensitivity of Glioblastoma to Drug-Induced Autophagy-Dependent Cell Death. Cancers (Basel), 14(2). https://doi.org/10.3390/cancers14020339

 

Schäfer, J. A., Bozkurt, S., Michaelis, J. B., Klann, K., & Münch, C. (2022). Global mitochondrial protein import proteomics reveal distinct regulation by translation and translocation machinery. Molecular cell, 82(2), 435–446.e7. https://doi.org/10.1016/j.molcel.2021.11.004

 

Schmitt, D., Bozkurt, S., Henning-Domres, P., Huesmann, H., Eimer, S., Bindila, L., Behrends, C., Boyle, E., Wilfling, F., Tascher, G., Münch, C., Behl, C., & Kern, A. (2022). FACS-mediated isolation of native autophagic vesicles. Autophagy. https://doi.org/10.1080/15548627.2022.2151188

 

Schmitt, D., Bozkurt, S., Henning-Domres, P., Huesmann, H., Eimer, S., Bindila, L., Behrends, C., Boyle, E., Wilfling, F., Tascher, G., Münch, C., Behl, C., & Kern, A. (2022). Lipid and protein content profiling of isolated native autophagic vesicles. EMBO Rep, 23(12): e53065. https://doi.org/10.15252/embr.202153065

 

Schürmanns, L., Hamann, A., Osiewacz, H.D. (2022). Lifespan increase of Podospora anserina by oleic acid is linked to alterations in energy metabolism, membrane trafficking and autophagy. Cells, 11 (3), 519. doi: 10.3390/cells11030519

 

Seibert M, Kurrle N, Stolp V, Nuernberger H, Tzschentke S, Boerner L, Wempe F, Serve H, Schnuetgen F (2022) Selection-free endogenous tagging of cell lines by bicistronic co-expression of the surface antigen NGFR. MethodsX. 9:101929. https://doi.org/10.1016/j.mex.2022.101929

 

Siebert, A., Gattringer, V., Weishaupt, J. H., & Behrends, C. (2022). ALS-linked loss of Cyclin-F function affects HSP90. Life science alliance, 5(12), e202101359. https://doi.org/10.26508/lsa.202101359.

 

Stelzl, LS., Pietrek, LM., Holla, A., Oroz, J., Sikora, M., Köfinger, J., Schuler, B., Zweckstetter, M., Hummer, G. (2022). Global structure of the intrinsically disordered protein tau emerges from its local structure. JACS Au 2: 673-686. https://doi.org/10.1021/jacsau.1c00536

 

Strohm, L., Hu, Z., Suk, Y., Rühmkorf, 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., & Behrends, C. (2022). Multi-omics profiling identifies a deregulated FUS-MAP1B axis in ALS/FTD-associated UBQLN2 mutants. Life science alliance, 5(11), e202101327. https://doi.org/10.26508/lsa.202101327

 

Tomaskovic, I., Gonzalez, A. & Dikic, I. (2022). Ubiquitin and Legionella: From bench to bedside. Seminars in Cell and Developmental Biology. https://doi.org/10.1016/J.SEMCDB.2022.02.008

 

Tiku, V., Kew, C., Kofoed, E. M., Peng, Y., Dikic, I. & Tan, M. W. (2022). Acinetobacter baumannii Secretes a Bioactive Lipid That Triggers Inflammatory Signaling and Cell Death. Frontiers in Microbiology, 13. https://doi.org/10.3389/FMICB.2022.870101/FULL

 

Warnsmann, V., Marschall, L. M., Meeßen, A. C., Wolters, M., Schürmanns, L., Basoglu, M., Eimer, S., & Osiewacz, H. D. (2022). Disruption of the MICOS complex leads to an aberrant cristae structure and an unexpected, pronounced lifespan extension in Podospora anserina. Journal of cellular biochemistry, 123(8), 1306–1326. https://doi.org/10.1002/jcb.30278

 

Zhou, D., Borsa, M., Puleston, D. J., Zellner, S., Capera, J., Sanderson, S., Schifferer, M., Hester, S. S., Ge, X., Fischer, R., Jostins, L., Behrends, C., Alsaleh, G., & Simon, A. K. (2022). Mapping autophagosome contents identifies interleukin-7 receptor-α as a key cargo modulating CD4+ T cell proliferation. Nature communications, 13(1), 5174. https://doi.org/10.1038/s41467-022-32718-x

Heinz D, Krotova E, Hamann A, Osiewacz HD. 2021. Simultaneous Ablation of the Catalytic AMPK α-Subunit SNF1 and Mitochondrial Matrix Protease CLPP Results in Pronounced Lifespan Extension. Front Cell Dev Biol. vol.9, 259. https://doi.org/10.3389/fcell.2021.616520

2021

Baker, F., Polat, I. H., Abou-El-Ardat, K., Alshamleh, I., Thoelken, M., Hymon, D., Gubas, A., Koschade, S. E., Vischedyk, J. B., Kaulich, M., Schwalbe, H., Shaid, S., & Brandts, C. H. (2021). Metabolic Rewiring Is Essential for AML Cell Survival to Overcome Autophagy Inhibition by Loss of ATG3. Cancers, 13(23), 6142. https://doi.org/10.3390/cancers13236142

 

Basic, M., Hertel, A., Bajdzienko, J., Bonn, F., Tellechea, M., Stolz, A., Kern, A., Behl, C., & Bremm, A. (2021). The deubiquitinase USP11 is a versatile and conserved regulator of autophagy. The Journal of biological chemistry, 297(5), 101263. https://doi.org/10.1016/j.jbc.2021.101263

 

Diehl, V., Wegner, M., Grumati, P., Husnjak, K., Schaubeck, S., Gubas, A., Shah, V. J., Polat, I. H., Langschied, F., Prieto-Garcia, C., Müller, K., Kalousi, A., Ebersberger, I., Brandts, C. H., Dikic, I., & Kaulich, M. (2021). Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. Nucleic acids research, 49(10), 5684–5704. https://doi.org/10.1093/nar/gkab309

 

Glogger, M., Spahn, C., Enderlein, J., & Heilemann, M. (2021). Multi-Color, Bleaching-Resistant Super-Resolution Optical Fluctuation Imaging with Oligonucleotide-Based Exchangeable Fluorophores. Angewandte Chemie (International ed. In English), 60(12), 6310–6313. https://doi.org/10.1002/anie.202013166

 

Hahn, M., Covarrubias-Pinto, A., Herhaus, L., Satpathy, S., Klann, K., Boyle, K. B., Münch, C., Rajalingam, K., Randow, F., Choudhary, C., & Dikic, I. (2021). SIK2 orchestrates actin-dependent host response upon Salmonella infection. Proceedings of the National Academy of Sciences, 118(19). https://doi.org/10.1073/pnas.2024144118

 

Herhaus L. (2021). TBK1 (TANK-binding kinase 1)-mediated regulation of autophagy in health and disease. Matrix biology : journal of the International Society for Matrix Biology, 100-101, 84–98. https://doi.org/10.1016/j.matbio.2021.01.004

 

Heinz, D., Krotova, E., Hamann, A., Osiewacz, H.D. (2021). Simultaneous ablation of the catalytic AMPK -subunit SNF1 and mitochondrial matrix protease CLPP results in pronounced lifespan extension. Front Cell Dev Biol, 9, 259. doi: 10.3389/fcell.2021.616520

 

Ho, N.T., Siggel, M., Camacho, K.V., Bhaskara, R.M., Hicks, J.M., Yao, Y., Zhang, Y., Köfinger, J., Hummer, G., & Noy, A. (2021). Membrane fusion and drug delivery with carbon nanotube porins. Proc Natl Acad Sci USA,118(19): e2016974118. https://doi.org/10.1073/pnas.2016974118

 

Juretschke, T., & Beli, P. (2021). Causes and consequences of DNA damage-induced autophagy. Matrix biology : journal of the International Society for Matrix Biology, 100-101, 39–53. https://doi.org/10.1016/j.matbio.2021.02.004.

 

Liu, Y., Mukherjee, R., Bonn, F., Colby, T., Matic, I., Glogger, M., Heilemann, M., & Dikic, I. (2021). Serine-ubiquitination regulates Golgi morphology and the secretory pathway upon Legionella infection. Cell Death and Differentiation, 28(10), 2957–2969. https://doi.org/10.1038/s41418-021-00830-y

 

Meyer, N., Henkel, L., Linder, B., Zielke, S., Tascher, G., Trautmann, S., Geisslinger, G., Munch, C., Fulda, S., Tegeder, I., & Kogel, D. (2021). Autophagy activation, lipotoxicity and lysosomal membrane permeabilization synergize to promote pimozide- and loperamide-induced glioma cell death. Autophagy, 17(11), 3424-3443. https://doi.org/10.1080/15548627.2021.1874208

 

 

Osiewacz, H.D., Schürmanns, L. (2021). A network of pathways controlling cellular homeostasis affects the onset of senescence in Podospora anserina. J Fungi, 7, 263. doi: 10.3390/jof7040263.

 

Roedig, J., Kowald, L., Juretschke, T., Karlowitz, R., Ahangarian Abhari, B., Roedig, H., Fulda, S., Beli, P., & van Wijk, S. J. (2021). USP22 controls necroptosis by regulating receptor-interacting protein kinase 3 ubiquitination. EMBO reports, 22(2), e50163. https://doi.org/10.15252/embr.202050163

 

Schaefer, L., & Dikic, I. (2021). Autophagy: Instructions from the extracellular matrix. Matrix Biol, 100-101, 1-8. https://doi.org/10.1016/j.matbio.2021.06.002

 

Seibert M, Kurrle N, Schnuetgen F, Serve H (2021) Amino acid sensory complex proteins in mTORC1 and macroautophagy regulation. Matrix Biol. 100-101:65-83. https://doi.org/10.1016/j.matbio.2021.01.001

 

Siggel, M., Bhaskara, RM., Moesser, MK., Dikic, I., Hummer, G. (2021). FAM134B-RHD protein clustering drives spontaneous budding of asymmetric membranes. J. Phys. Chem. Lett. 2021, 12, 1926-1931. https://doi.org/10.1021/acs.jpclett.1c00031

 

Warnsmann, V., Marschall, L-M., Osiewacz, H.D.(2021). Impaired F1Fo-ATP-synthase dimerization leads to the induction of cyclophilin D-mediated autophagy-dependent cell death and accelerated aging. Cells, 10, 757. doi: 10.3390/cells10040757

 

Zellner, S., Schifferer, M., & Behrends, C. (2021). Systematically defining selective autophagy receptor-specific cargo using autophagosome content profiling. Molecular cell, 81(6), 1337–1354.e8. https://doi.org/10.1016/j.molcel.2021.01.009

 

Zein, L., Fulda, S., Kogel, D., & van Wijk, S. J. L. (2021). Organelle-specific mechanisms of drug-induced autophagy-dependent cell death. Matrix Biol, 100-101, 54-64. https://doi.org/10.1016/j.matbio.2020.12.003

 

Zielke, S., Kardo, S., Zein, L., Mari, M., Covarrubias-Pinto, A., Kinzler, M. N., Meyer, N., Stolz, A., Fulda, S., Reggiori, F., Kogel, D., & van Wijk, S. (2021). ATF4 links ER stress with reticulophagy in glioblastoma cells. Autophagy, 17(9), 2432-2448. https://doi.org/10.1080/15548627.2020.1827780

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Barz S, Kriegenburg F, Henning A, Bhattacharya A, Mancilla H, Sánchez-Martín P, & Kraft C. 2020. Atg1 kinase regulates autophagosome-vacuole fusion by controlling SNARE bundling. EMBO reports, 21(12), e51869.

Eickhorst C, Licheva M, Kraft C. 2020. Scaffold proteins in bulk and selective autophagy. Prog Mol Biol Transl Sci. 2020;172:15-35.

Glogger M, Spahn C, Enderlein J, Heilemann M. 2020. Multi-Color, Bleaching-Resistant Super-Resolution Optical Fluctuation Imaging with Oligonucleotide-based Exchangeable Fluorophores. Angew Chem Int Ed Engl. https://doi.org/10.1002/anie.202013166

Henkel V, Schürmanns L, Brunner M, Hamann A, Osiewacz HD. 2020. Role of sorting nexin PaATG24 in autophagy, aging and development of Podospora anserina. Mech Aging Dev, 186:111211

Hollenstein DM, Kraft C. 2020. Autophagosomes are formed at a distinct cellular structure. Curr Opin Cell Biol. 2020;65:50-57.

Kern A, Behl C. 2020. On-demand autophagic network adaptations upon limited lipid availability. Autophagy, 16:7, 1348-1350

Kinzler MN, Zielke S, Kardo S, Meyer N, Kögel D, van Wijk SJL, Fulda S. 2020. STF-62247 and pimozide induce autophagy and autophagic cell death in mouse embryonic fibroblasts. Sci Rep 10, 687

Kögel D, Linder B, Brunschweiger A, Chines S, Behl C. 2020. At the Crossroads of Apoptosis and Autophagy: Multiple Roles of the Co-Chaperone BAG3 in Stress and Therapy Resistance of Cancer. Cells, 9(3), 574.

Steinberg R, Origi A, Natriashvili A, Sarmah P, Licheva M, Walker PM, Kraft C, High S, Luirink J, Shi WQ, Helmstädter M, Ulbrich MH, Koch HG. 2020. Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle. PLoS Biol. 18(9), e3000874.

Wesch N, Kirkin V, Rogov V.V. 2020. Atg8-Family Proteins-Structural Features and Molecular Interactions in Autophagy and Beyond. Cells, 9:9, E2008

Wiechmann S, Maisonneuve P, Grebbin BM, Hoffmeister M, Kaulich M, Clevers H, Rajalingam K, Kurinov I, Farin HF, Sicheri F, Ernst A. 2020. Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids. J Biol Chem. pii: jbc.RA119.011025.

Zein L, Fulda S, Kögel D, & van Wijk S. 2020. Organelle-specific mechanisms of drug-induced autophagy-dependent cell death. Matrix Biol. https://doi.org/10.1016/j.matbio.2020.12.003

Zielke S, Kardo S, Zein L, Mari M, Covarrubias-Pinto A, Kinzler MN, Meyer N, Stolz A, Fulda S, Reggiori F, Kögel D, van Wijk S. 2020. ATF4 links ER stress with reticulophagy in glioblastoma cells. Autophagy, 1-17

Chaikuad A, Koschade SE, Stolz A, Zivkovic K, Pohl C, Shaid S, Ren H, Lambert LJ, Cosford NDP, Brandts CH & Knapp S. 2019. Conservation of structure, function and inhibitor binding in UNC-51-like kinase 1 and 2 (ULK1/2). Biochem J, 476, 875-887.

Chakraborty D, Felzen V, Hiebel C, Stuerner E, Perumal N, Manicam C, Grus F, Wolfrum U, Behl C. 2019. Enhanced autophagic-lysosomal activity and increased BAG3-mediated selective macroautophagy as adaptive response of neuronal cells to chronic oxidative stress. Redox Biol, accepted

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