High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification

  • 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 (PC a) and diffuse large B‐cell lymphoma (DLBCL ) samples. We show that the proteome patterns of FFPE PC a tissue samples and their analogous fresh‐frozen (FF ) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PC a tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, 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 PC a and DLBCL have been discovered.

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Author:Yi ZhuORCiD, Tobias WeissORCiDGND, Qiushi ZhangORCiD, Rui SunORCiD, Bo Wang, Xiao YiORCiD, Zhicheng Wu, Huanhuan GaoORCiD, Xue CaiORCiD, Guan RuanORCiD, Tiansheng ZhuORCiD, Chao Xu, Sai Lou, Xiaoyan Yu, Ludovic GilletORCiDGND, Peter BlattmannORCiDGND, Karim SabaORCiDGND, Christian D. FankhauserORCiD, Michael B. Schmid, Dorothea RutishauserORCiD, Jelena Ljubicic, Ailsa Christiansen, Christine Fritz, Niels Jan Felix RuppORCiDGND, Cedric PoyetORCiD, Elisabeth Rushing, Michael WellerORCiDGND, Patrick Roth, Eugenia Haralambieva, Silvia Hofer, Chen Chen, Wolfram Jochum, Xiaofei Gao, Xiaodong Teng, Lirong Chen, Qing ZhongORCiD, Peter Johannes WildORCiDGND, Ruedi AebersoldORCiDGND, Tiannan GuoORCiDGND
Pubmed Id:https://pubmed.ncbi.nlm.nih.gov/31495056
Parent Title (English):Molecular oncology
Publisher:John Wiley & Sons, Inc
Place of publication:Hoboken, NJ
Document Type:Article
Date of Publication (online):2019/09/18
Date of first Publication:2019/09/18
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2020/06/21
Tag:FFPE; SWATH; biomarker; pressure cycling technology; proteome; tumor
Page Number:24
First Page:2305
Last Page:2328
Institutes:Medizin / Medizin
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Licence (German):License LogoCreative Commons - Namensnennung 4.0