In close collaboration with the virology department of the university clinic here in Frankfurt we were able to measure the first quantitative proteomics dataset of human cells infected with SARS-CoV-2. We applied multi-layered proteomics to quantify the dynamic changes of protein synthesis, PTMs and total protein levels over the infection course. We analysed the changes to the host cell proteome to identify pathways important for viral replication. By the identification of these pathways we detected vulnerabilities of the viral replication process that can be targeted by already exisiting drugs. Repurposing these drugs we were able to block the proliferation of the virus in vitro and lay a molecular groundwork for future clincal research.

Bojkova, D., Klann, K., Koch, B. et al. Nature 2020. 583, 469–472
Klann K, Bojkova D et al. Mol Cell 2020. 80 (1) 164-174.e4
Kohli A et al. Life Sci Alliance 2022 Feb 2;5(5):e202201371.

Modification profiling

Protein Dynamics

Image: National Cancer Institute

Cancer cells exhibit critical rearrangements of the proteome. The changes of total protein levels, PTM patterns and protein dynamics finally lead to the diverse disease phenotypes. Profiling the alterations on a system-wide scale and on different layers provides an essential groundwork for translational research. The recently founded Frankfurt Cancer Institute partners scientists from a broad spectrum of disciplines, ranging from basic research to all clinical aspects of cancer. Embedded in this great scientific environment we are currently studying the proteome changes during cancer progression to understand disease mechanisms. Therefore, we are applying a wide range of mass-spectrometry powered proteomics ranging from interaction proteomics over PTM profiling to protein dynamics measurements. Tailoring these assays to different models and scientific questions will drive research of many aspects of cancer.

Nguyen et al. Blood 2019, 133(2), 168-179
Koschade SE et al. Leukemia 2022

Modification profiling

Protein-Protein Interactions

Protein Dynamics

Cells can adapt rapidly to changing environments. These responses are often shaped by alterations in the translational landscape of the cell. Quantifying these changes in an unbiased way provides with new insights to translational regulation and molecular mechanisms. To facilitate faithful translation quantification and to overcome technical limitations we developed multiplexed enhanced Protein Dynamics (mePROD) mass spectrometry. The combination of Tandem Mass Tags and SILAC pulse labeling together with a carrier or booster signal enables us to profile translatome wide changes in the range of minutes without loosing depth of anaylsis. mePROD is able to accurately measure the translation of thousands of proteins, even under conditions where global translation rates are effected (e.g. stress responses). We successfully appied mePROD to diverse disease scenarios, such as viral infection. We are currently integrating functional translation proteomics into a wide range of applications to spark new ideas in disease biology.

Klann et al. Molecular Cell 2020, 77(4), 913-925.e4
Klann et al. Analytical Chemistry 2020, 92, 12, 8041-8045
Bojkova, Klann, Koch et al. Nature 2020, 583, 469-472
Schäfer JA, Bozkurt S, Michaelis JB et al. Molecular Cell 2022, 82(2), 435-446

A detailed protocol can be found here: Klann and Münch, Methods Mol Biol 2022,2428:75-87.

Protein Dynamics

Protein-Protein interactions are essential for cellular function. Upon changing environments proteins can immediately change their interaction partners to fulfill new functions or modulate activities. These changes in activity often cannot be detected at the level of total protein amounts, but contain crucial information about cellular processes. To profile these interaction networks we mainly apply the TurboID system, developed by the Ting lab in Stanford. We are applying this powerful tool to examine how protein-protein interaction networks dynamically change upon stress conditions.