Project C2
Mapping the fitness landscapes of metastasizing cancers
| 2022 – 2025 | The influence of stroma-metastasis interaction on tumor evolution |
| 2018 – 2021 | Predicting the constrained evolution of tumors |
In this project, we will characterize adaptive processes of a tumor enabling its establishment as a metastasis and predict the seeding probability as a function of the cell’s mutations and the tumor environment. By single-nucleus RNA-sequencing, we will characterize the transcriptomic state of cancer cells, immune cells, and stromal cells of both the primary tumor and the metastasis. Using systems-scale computational modelling, we will infer adaptive responses of cancer cells to their environment and adaptive responses of stromal cells to the tumor.
Publications
Analysis of Limited Proteolysis-Coupled Mass Spectrometry Data
Nagel, L., Grossbach, J., Cappelletti, V., Dörig, C., Picotti, P., & Beyer, A., Molecular & Cellular Proteomics, 24(4), 100934, 07. Mar 2025, 10.1016/j.mcpro.2025.100934
Predicting the next move: Tracking the complexity of lung cancer evolution and metastasis
Lorenz, C., Hillmer, A. M., & Brägelmann, J, Signal Transduction and Targeted Therapy, 8(1), 09. Aug 2023, 10.1038/s41392-023-01567-5
Genetic effects on molecular network states explain complex traits
Weith, M., Großbach, J., Clement-Ziza, M., Gillet, L., Rodríguez-López, M., Marguerat, S., Workman, C. T., Picotti, P., Bähler, J., Aebersold, R., & Beyer, A, Molecular Systems Biology, 19(8), 24. Jul 2023, 10.15252/msb.202211493
Mackmull, M.-T., Nagel, L., Sesterhenn, F., Muntel, J., Grossbach, J., Stalder, P., Bruderer, R., Reiter, L., Van De Berg, W. D. J., De Souza, N., Beyer, A., & Picotti, P., Nature Structural & Molecular Biology, 29(10), 978–989, 12. Oct 2022, 10.1038/s41594-022-00837-0
The impact of genomic variation on protein phosphorylation states and regulatory networks
Grossbach J., Gillet L., Clément-Ziza M., Schmalohr C.L., Schubert O.T., Schütter M., Mawer J.S.P, Barnes C., Bludau I., Weith M., Tessarz P., Graef M., Aebersold R., Beyer A., Molecular Systems Biology, 16. May 2022, 10.15252/msb.202110712
Convergent network effects along the axis of gene expression during prostate cancer progression
Charmpi, K., Guo, T., Zhong, Q. et al., Beyer A., Genome Biol, 21 302, 14. Dec 2020, 10.1186/s13059-020-02188-9
Kamrad S., Grossbach J., Rodríguez‐López M., Mülleder M., Townsend S.J, Cappelletti V., Stojanovski G., Correia‐Melo C., Picotti P., Beyer A., Ralser M., Bähler J., Mol Syst Biol (2020)16:e9270, 01. Apr 2020, 10.15252/msb.20199270
Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers
Guo T., Li L., Zhong Q., Rupp N.J., Charmpi K., Wong C.E., Wagner U., Rueschoff J.H., Jochum W., Fankhauser C.D., Saba K., Poyet C., Wild P.J., Aebersold R., Beyer A., Life Science Alliance, 29. May 2018, 10.26508/lsa.201800042
regNet: an R package for network-based propagation of gene expression alterations
Seifert M., Beyer A., Bioinformatics Volume 34 Issue 2:308–311, 15. Jan 2018, 10.1093/bioinformatics/btx544
Christodoulou E.G., Yang H., Lademann F., Pilarsky C., Beyer A., Schroeder M., Oncotarget 8:34283-34297, 10. March 2017, 10.18632/oncotarget.16079