PT - JOURNAL ARTICLE AU - Yi Zhu AU - Tobias Weiss AU - Qiushi Zhang AU - Rui Sun AU - Bo Wang AU - Zhicheng Wu AU - Qing Zhong AU - Xiao Yi AU - Huanhuan Gao AU - Xue Cai AU - Guan Ruan AU - Tiansheng Zhu AU - Chao Xu AU - Sai Lou AU - Xiaoyan Yu AU - Ludovic Gillet AU - Peter Blattmann AU - Karim Saba AU - Christian D. Fankhauser AU - Michael B. Schmid AU - Dorothea Rutishauser AU - Jelena Ljubicic AU - Ailsa Christiansen AU - Christine Fritz AU - Niels J. Rupp AU - Cedric Poyet AU - Elisabeth Rushing AU - Michael Weller AU - Patrick Roth AU - Eugenia Haralambieva AU - Silvia Hofer AU - Chen Chen AU - Wolfram Jochum AU - Xiaofei Gao AU - Xiaodong Teng AU - Lirong Chen AU - Peter J. Wild AU - Ruedi Aebersold AU - Tiannan Guo TI - High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification AID - 10.1101/667394 DP - 2019 Jan 01 TA - bioRxiv PG - 667394 4099 - http://biorxiv.org/content/early/2019/06/11/667394.short 4100 - http://biorxiv.org/content/early/2019/06/11/667394.full AB - Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between one to 15 years in a biobank and show a high degree of the proteome pattern similarity between two types histological region of small FFPE samples, i.e. punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of certain degree of biological variations. Applying the method to two independent DLBCL cohorts we identified myeloperoxidase (MPO), a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.