CP04 | Proteomic dissection of cell death-mediated protein release and proteolysis
Prof. Dr. Pitter Huesgen
Institute of Biology II, University of Freiburg
Contact: pitter.huesgen(at)biologie.uni-freiburg(dot)de
For more information visit: Huesgen lab
Prof. Dr. Felix Meissner
Institute for Innate Immunity, University Bonn
Contact: felix.meissner(at)uni-bonn(dot)de
For more information visit: Meissner lab
Abstract
This project is funded within the 2nd funding period of the SFB 1403, starting from 2024
This core project aims to i) develops tailored mass spectrometry-based approaches for the comprehensive analysis of cell death released proteins and protease substrates in both mammalian and plant systems and ii) advise all interested CRC members on experimental design and execution of proteomics experiments, including sample preparation, measurement and initial data analysis, and contribute to data interpretation and dissemination. Thus, this core project will provide essential tools and expertise to decipher the mechanisms underlying the cross-talk between dying and bystander cells.
Recent Publications
2026
Project CP04 Publications 2nd Funding Period 2024 -2027
2025
Mantz M, Dewes P, Huesgen PF. Terminomics for plant protease substrate discovery: Achievements, challenges and new opportunities. J Exp Bot. 2025 May 4:eraf173. doi: 10.1093/jxb/eraf173. Epub ahead of print. PMID: 40319448.
Tamilselvan R, Dewes P, Cosenza-Contreras M, Huesgen PF. Hunter-Dia: An updated protocol for enrichment and mass spectrometry-based identification of protein N-terminal peptides. Methods Enzymol. 2025;719:25-42. doi: 10.1016/bs.mie.2025.06.025. Epub 2025 Jul 25. PMID: 40992842.
2024
Weiss FD, Alvarez Y, Shakeri F, Sahu A, Leka P, Dernst A, Rollheiser J, Vasconcelos M, Geraci A, Duthie F, Stahl R, Lee HE, Gellner AK, Buness A, Latz E, Meissner F. Retention of ES cell-derived 129S genome drives NLRP1 hypersensitivity and transcriptional deregulation in Nlrp3tm1Flv mice. Cell Death Differ. 2024 Sep 17. doi: 10.1038/s41418-024-01379-2. Epub ahead of print. PMID: 39289506.
Mooney BC, Doorly CM, Mantz M, García P, Huesgen PF, Graciet E. Hypoxia represses pattern-triggered immune responses in Arabidopsis. Plant Physiol. 2024 Aug 19:kiae432. doi: 10.1093/plphys/kiae432. Epub ahead of print. PMID: 39158089.
van Midden KP, Mantz M, Fonovič M, Gazvoda M, Svete J, Huesgen PF, van der Hoorn RAL, Klemenčič M. Mechanistic insights into CrCEP1: A dual-function cysteine protease with endo- and transpeptidase activity. Int J Biol Macromol. 2024 Jun;271(Pt 1):132505. doi: 10.1016/j.ijbiomac.2024.132505. Epub 2024 May 18. PMID: 38768911.
Project related Publications
2017 - 2022
Meissner, F., Geddes-McAlister, J., Mann, M., Bantscheff, M. (2022). The emerging role of mass spectrometry-based proteomics in drug discovery. Nat Rev Drug Discov. 21, 637-654.
Demir, F., Kizhakkedathu, J.N., Rinschen, M.M., Huesgen, P.F. (2021). MANTI: Automated Annotation of Protein N-Termini for Rapid Interpretation of N-Terminome Data Sets. Anal Chem 93, 5596-5605.
Phulphagar, K., Kühn, L.I., Ebner, S., Frauenstein, A., Swietlik, J.J., Rieckmann, J., Meissner, F. (2021). Proteomics reveals distinct mechanisms regulating the release of cytokines and alarmins during pyroptosis. Cell Rep. 34, 108826.
Passarge, A., Demir, F., Green, K., Depotter, J.R.L., Scott, B., Huesgen, P.F., Doehlemann, G., and Misas-Villamil, J.C. (2021). Host apoplastic cysteine protease activity is suppressed during the mutualistic association of Lolium perenne and Epichloe festucae. J Exp Bot 72, 3410-3426.
Tanzer, M.C., Frauenstein, A., Stafford, C.A., Phulphagar, K., Mann, M., and Meissner, F. (2020). Quantitative and Dynamic Catalogs of Proteins Released during Apoptotic and Necroptotic Cell Death. Cell Rep. 30, 1260-1270.e5.
Misas Villamil,J., Mueller, A., Demir, F., Meyer, U., Ökmen, B., Schulze Hüynck, J., Breuer, M., Dauben, H., Win, J., Huesgen, P.F., and Doehlemann, G. (2019). A fungal substrate mimicking molecule suppresses plant immunity via an inter-kingdom conserved motif. Nat Commun10, 1576.
Weng, S.S.H., Demir, F., Ergin, E.K., Dirnberger, S., Uzozie, A., Tuscher, D., Nierves, L., Tsui, J., Huesgen, P.F., and Lange, P.F. (2019). Sensitive determination of proteolytic proteoforms in limited microscale proteome samples. Mol Cell Proteomics 18, 2335-2347
Winter, S.V., Meier, F., Wichmann, C., Cox, J., Mann, M., and Meissner, F. (2018). EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification. Nat Methods 15, 527-530.
Rieckmann, J.C., Geiger, R., Hornburg, D., Wolf, T., Kveler, K., Jarrossay, D., Sallusto, F., Shen-Orr, S.S., Lanzavecchia, A., Mann, M., and Meissner, F. (2017). Social network architecture of human immune cells unveiled by quantitative proteomics. Nat Immunol. 18, 583-593.