TY  - JOUR
A1  - Zhu, Yi
A1  - Weiss, Tobias
A1  - Zhang, Qiushi
A1  - Sun, Rui
A1  - Wang, Bo
A1  - Yi, Xiao
A1  - Wu, Zhicheng
A1  - Gao, Huanhuan
A1  - Cai, Xue
A1  - Ruan, Guan
A1  - Zhu, Tiansheng
A1  - Xu, Chao
A1  - Lou, Sai
A1  - Yu, Xiaoyan
A1  - Gillet, Ludovic
A1  - Blattmann, Peter
A1  - Saba, Karim
A1  - Fankhauser, Christian D.
A1  - Schmid, Michael B.
A1  - Rutishauser, Dorothea
A1  - Ljubicic, Jelena
A1  - Christiansen, Ailsa
A1  - Fritz, Christine
A1  - Rupp, Niels Jan Felix
A1  - Poyet, Cedric
A1  - Rushing, Elisabeth
A1  - Weller, Michael
A1  - Roth, Patrick
A1  - Haralambieva, Eugenia
A1  - Hofer, Silvia
A1  - Chen, Chen
A1  - Jochum, Wolfram
A1  - Gao, Xiaofei
A1  - Teng, Xiaodong
A1  - Chen, Lirong
A1  - Zhong, Qing
A1  - Wild, Peter Johannes
A1  - Aebersold, Ruedi
A1  - Guo, Tiannan
T1  - High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification
T2  - Molecular oncology
N2  - 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.
KW  - biomarker
KW  - FFPE
KW  - pressure cycling technology
KW  - proteome
KW  - SWATH
KW  - tumor
Y1  - 2019
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/54948
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-549488
SN  - 1878-0261
VL  - 13
SP  - 2305
EP  - 2328
PB  - John Wiley & Sons, Inc
CY  - Hoboken, NJ
ER  -