Prof. Dr. Oliver Schilling

Proteolysis in Tumorigenesis and Tumor-Stroma Interaction

Proteolysis is an irreversible post-translational modification that affects every protein. The large number of genetically encoded proteases in man (> 560) illustrates the biological importance of proteolysis. Proteolysis plays a crucial role in cellular signalling and pericellular homeostasis as generation of stable cleavage products from precursors leads to neo–proteins with altered, often antagonistic activities. Elevated proteolytic activity is a hallmark of many tumors. Many proteases promote tumor development. However, depending on the tumor context, some proteases, such as prostasin and neprilysin have tumor-suppressing roles.

The most crucial task in present proteolysis research is elucidation of protease substrate repertoires. Most cleavage events have remained elusive for most proteases. This is a serious deficit since proteases alter protein abundance through degradation and protein function by generating stable cleavage products. Recent key inventions in the area of “protease proteomics” now enable elucidation of protease substrate repertoires in vivo or in the cellular context. I have co–invented these techniques. Published in Nature Biotechnology and Nature Methods, these strategies enable a focused analysis of native and proteolytically generated protein N- or C-termini. Through combination with differential protease expression and stable isotope labeling, induced cleavage events are distinguished from background proteolysis and protease–specific substrate repertoires are determined. Protease substrate profiling is performed with loss– and gain–of–function systems in a panel of cancer cell lines together with determination of cellular parameters that mirror tumor aggressiveness, such as proliferation, invasion, and migration.

The combination of N– and C–terminal analysis is pivotal for the analysis of shedding by cell surface proteases irrespective of the transmembrane orientation of the substrate. Processing of selected substrates is studied in detail in order to understand how N– or C–terminal truncations and/or shedding alters key characteristics of a substrate. Examples include chemotactic properties of cytokines or activity status of enzymes. The aim is to understand how individual cleavage events contribute to an (anti)-tumor activity of a given protease. To this end we determine the ratio of native vs. processed substrate in wild–type control samples. In protease-depleted cells (silenced gene expression), we reconstruct this situation by dosable expression of the cleavage product and dosable repression of the intact substrate, followed by cellular characterization. By applying concepts and tools of synthetic biology we reconstruct individual cleavage events in the absence of the executing protease. This interplay of analysis and synthetic reconstruction is a unique opportunity to decipher proteolytic networks involved in cell-cell signaling.

10 selected publications

• Proteome biology of primary colorectal carcinoma and corresponding liver metastases.
  Fahrner M, Bronsert P, Fichtner-Feigl S, Jud A, Schilling O (2021).
  Neoplasia. 23(12):1240-1251
• Accessible and reproducible mass spectrometry imaging data analysis in Galaxy.
  Föll MC, Moritz L, Wollmann T, Stillger MN, Vockert N, Werner M, Bronsert P, Rohr K, Grüning BA, Schilling O (2019).
  Gigascience 8: 1-12
• ADAM9 contributes to vascular invasion in pancreatic ductal adenocarcinoma.
  Oria VO, Lopatta P, Schmitz T, Preca BT, Nyström A, Conrad C, Bartsch JW, Kulemann B, Hoeppner J, Maurer J, Bronsert P, Schilling O (2019).
  Mol Oncol 13: 456-479
• Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance.
  4. Oria VO, Bronsert P, Thomsen AR, Föll MC, Zamboglou C, Hannibal L, Behringer S, Biniossek ML, Schreiber C, Grosu AL, Bolm L, Rades D, Keck T, Werner M, Wellner UF, Schilling O (2018).
  Transl Oncol 11: 1307-1322
• Proteomic distinction of renal oncocytomas and chromophobe renal cell carcinomas.
  Drendel V, Heckelmann B, Schell C, Kook L, Biniossek ML, Werner M, Jilg CA, and Schilling O (2018).
  Clin Proteomics 15: 25
• Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas.
  Föll MC, Fahrner M, Gretzmeier C, Thoma K, Biniossek ML, Kiritsi D, Meiss F, Schilling O§, Nyström A§, and Kern JS (2018).
  Matrix Biol 66: 1-21
  §Shared corresponding author
• OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
  Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, and Kohlbacher O (2016).
  Nat Methods. 13: 741-748
• Formalin-Fixed, Paraffin-Embedded Tissues (FFPE) as a Robust Source for the Profiling of Native and Protease-Generated Protein Amino Termini.
  Lai ZW, Weisser J, Nilse L, Costa F, Keller E, Tholen M, Kizhakkedathu JN, Biniossek M, Bronsert P, and Schilling O (2016).
  Mol Cell Proteomics 15: 2203-2213
• Fibroblast activation protein-α, a stromal cell surface protease, shapes key features of cancer associated fibroblasts through proteome and degradome alterations.
  Koczorowska MM, Tholen S, Bucher F, Lutz L, Kizhakkedathu JN, De Wever O, Wellner UF, Biniossek ML, Stahl A, Lassmann S, and Schilling O (2016).
  Mol Oncol 10: 40-58
• Proteome-wide analysis of protein carboxy termini: C terminomics.
  Schilling O, Barré O, Huesgen PF, and Overall CM (2010).
  Nat Methods. 7: 508-511