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Decade-Resolved Proteomic Profiling of Gastric Cancer FFPE Archives: Evaluating Storage-Associated Shifts and Signal Stability Over 50 Years
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DOI：10.1002/pmic.70161.png)
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Abstract
En 中文
Archival formalin-fixed, paraffin-embedded (FFPE) tissues are invaluable for retrospective clinical research, yet the impact of multi-decade storage on quantitative proteomic fidelity remains poorly understood. We conducted a systematic, decade-resolved proteomic assessment using data-independent acquisition (DIA) LC–MS/MS to evaluate FFPE specimens spanning 50 years. This study included 33 gastric cancer cases collected at approximately 10-year intervals from 1972 to 2022. From each case, tumor tissue, matched non-tumorous mucosa, and muscle layer were macrodissected and processed simultaneously using a standardized workflow to minimize technical bias. Longitudinal analysis across five decades demonstrated that a substantial portion of the detectable proteome remains quantitatively stable. While storage- and archival-era-associated factors contributed to measurable variance, tissue-specific biological signatures were the dominant drivers of proteomic profiles. The muscle layer exhibited the highest stability, serving as a structural reference for evaluating archival ageing. Differential expression analysis between tumor and nontumorous mucosa identified robust pathological signatures that persisted even in 50-year-old specimens. Although we observed era-specific variations in protein detectability, a core set of differentially expressed proteins and their associated functional pathways—including cell cycle and metabolic remodeling—were consistently preserved across the evaluable year groups. Notably, the treatment-naïve 1972 cohort provided high-depth biological insights comparable to contemporary samples. Our findings establish that long-term archival storage does not preclude biologically interpretable proteomic profiles, although storage- and archival-era-associated shifts should be explicitly accounted for in analysis and interpretation.
Keywords:
archival stability
biomarker discovery
data-independent acquisition (DIA)
FFPE (formalin-fixed paraffin-embedded)
gastric cancer
long-term storage
mass spectrometry-based proteomics
muscle layer
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