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Guo T, Li L, Zhong Q, Rupp NJ, Charmpi K, Wong CE, Wagner U, Rueschoff JH, Jochum W, Fankhauser CD, Saba K, Poyet C, Wild PJ, Aebersold R, Beyer A. Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers. Life Sci Alliance 2018; 1. [PMID: 30090875 PMCID: PMC6078179 DOI: 10.26508/lsa.201800042] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Application of pressure cycling technology and Sequential Windowed Acquisition of all THeoretical mass spectrometry allows quantifying the degree of intra-tumor heterogeneity of protein expression in prostate tumors. The data show that protein intra-tumor heterogeneity, if not characterized, may distort protein biomarker suitability in tumor tissues. It remains unclear to what extent tumor heterogeneity impacts on protein biomarker discovery. Here, we quantified proteome intra-tissue heterogeneity (ITH) based on a multi-region analysis of prostate tissues using pressure cycling technology and Sequential Windowed Acquisition of all THeoretical fragment ion mass spectrometry. We quantified 6,873 proteins and analyzed the ITH of 3,700 proteins. The level of ITH varied depending on proteins and tissue types. Benign tissues exhibited more complex ITH patterns than malignant tissues. Spatial variability of 10 prostate biomarkers was validated by immunohistochemistry in an independent cohort (n = 83) using tissue microarrays. Prostate-specific antigen was preferentially variable in benign prostatic hyperplasia, whereas growth/differentiation factor 15 substantially varied in prostate adenocarcinomas. Furthermore, we found that DNA repair pathways exhibited a high degree of variability in tumorous tissues, which may contribute to the genetic heterogeneity of tumors. This study conceptually adds a new perspective to protein biomarker discovery: it suggests that recent technological progress should be exploited to quantify and account for spatial proteome variation to complement biomarker identification and utilization.
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Affiliation(s)
- Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland.,Westlake Institute for Advanced Study, Westlake University, Hangzhou, Zhejiang, China
| | - Li Li
- CECAD, University of Cologne, Cologne, Germany
| | - Qing Zhong
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Cancer Data Science Group, ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | | | - Christine E Wong
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Ulrich Wagner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Jan H Rueschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Wolfram Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | | | - Karim Saba
- Department of Urology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Cedric Poyet
- Department of Urology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Andreas Beyer
- CECAD, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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