Feasibility of amino acid profiling in long-term stored formalin-fixed paraffin-embedded colorectal neoplasia tissue

TL;DR

This study shows that amino acid profiling can be done on long-stored formalin-fixed paraffin-embedded tissue, which is commonly available for colorectal cancer research.

Contribution

The study demonstrates the feasibility of amino acid profiling in FFPE tissue, which is more accessible than fresh frozen samples.

Findings

Fourteen amino acids were successfully detected in FFPE tissue.

Proline levels were significantly higher in colorectal carcinoma compared to both advanced and non-advanced adenomas.

Amino acid profiling in FFPE tissue is feasible despite analytical challenges.

Abstract

Metabolic processes play a role in cancer development, with faecal amino acids emerging as potential biomarkers for colorectal neoplasia. While fresh frozen tissue is preferred for metabolomic analysis, formalin-fixed paraffin-embedded (FFPE) tissue is more widely available.

We aimed to evaluate amino acid profiles in FFPE tissue across different stages of the adenoma-carcinoma sequence.

A panel of 20 amino acids was measured using liquid chromatography–tandem mass spectrometry.

Fourteen amino acids were detected, with proline elevated in colorectal carcinoma versus advanced (FC 2.33, p = 0.04) and non-advanced adenomas (FC 2.42, p = 0.02).

Despite analytical challenges, amino acid profiling in FFPE tissue is feasible.

The online version contains supplementary material available at 10.1007/s11306-025-02301-8.

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