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

Area of Science:

• Biochemistry
• Proteomics
• Cancer Research

Background:

• Formalin-fixed, paraffin-embedded (FFPE) tissues are crucial for clinical research.
• Analyzing FFPE tissue proteomes presents unique challenges.

Purpose of the Study:

• To develop and validate a proteomic workflow for FFPE tissues.
• To compare FFPE and fresh-frozen (FF) tissue proteomes.
• To discover novel biomarkers for prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL).

Main Methods:

• Pressure cycling technology (PCT)-SWATH mass spectrometry workflow.
• Analysis of FFPE and FF tissue samples from PCa and DLBCL cohorts.
• Assessment of proteome stability and similarity in FFPE samples.

Main Results:

• High proteome similarity between FFPE and FF PCa samples.
• Consistent protein regulation in PCa tissues confirmed.
• Temporal stability of FFPE proteome patterns demonstrated (1-15 years).
• High similarity between FFPE biopsy and section proteomes.
• Myeloperoxidase identified as a novel prognostic marker for DLBCL.

Conclusions:

• PCT-SWATH is a robust method for FFPE tissue proteomic analysis.
• FFPE tissues are practical and superior to FF tissues for proteome biomarker discovery.
• Novel biomarker candidates for PCa and DLBCL were identified.