UPLC‑MS/MS‑based metabolomic characterization and comparison of pancreatic adenocarcinoma tissues using formalin‑fixed, paraffin‑embedded and optimal cutting temperature‑embedded materials

Abstract

The purpose of the present study was to compare metabolites from formalin-fixed and paraffin-embedded (FFPE) pancreatic tissue blocks with those identified in optimal cutting temperature (OCT)-embedded pancreatic tissue blocks. Thus, ultra-performance liquid chromatograph-mass spectrometry/mass spectrometry-based metabolic profiling was performed in paired frozen (n=13) and FFPE (n=13) human pancreatic adenocarcinoma tissue samples, in addition to their benign counterparts. A total of 206 metabolites were identified in both OCT-embedded and FFPE tissue samples. The method feasibility was confirmed through reproducibility and a consistency assessment. Partial least-squares discriminant analysis and heatmap analysis reliably distinguished tumor and normal tissue phenotypes. The expression of 10 compounds, including N-acetylaspartate and creatinine, was significantly different in both OCT-embedded and FFPE tumor samples. These ten compounds may be viable candidate biomarkers of malignant pancreatic tissues. The super-categories to which they belonged exhibited no significant differences between FFPE and OCT-embedded samples. Furthermore, purine, arginine and proline, and pyrimidine metabolism used a shared pathway found in both OCT-embedded and FFPE tissue samples. These results supported the notion that metabolomic data acquired from FFPE pancreatic cancer specimens are reliable for use in retrospective and clinical studies.

Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC–MS/MS technologies

“…Previous studies demonstrated that lipids in fixed tissue differed from those in fresh‐frozen tissue based on ultraperformance liquid chromatography–mass spectrometry (UPLC–MS), gas chromatography–mass spectrometry (GC–MS), and MALDI‐IMS technologies 22,32,34,44–50 . Of these three technologies, MALDI‐IMS exhibited the maximal overlap of ions observed in PFA‐fixed and fresh‐frozen tissue 22–27 .…”

Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies

“…23,43 Previous studies demonstrated that lipids in fixed tissue differed from those in fresh-frozen tissue based on UPLC-MS, GC-MS, and MALDI-IMS technologies. 22,32,34,[44][45][46][47][48][49][50] Of these three technologies, MALDI-IMS exhibited the maximal overlap of ions observed in paraformaldehyde-fixed and fresh-frozen tissue. [22][23][24][25][26][27] Regarding studies of retina, Ly et al 23 developed and compared lipid imaging by applying MALDI-IMS in fresh-frozen vs fixed mammalian (porcine) retina.…”

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“…In particular, formalin-fixed paraffin-embedded (FFPE) ovarian cancer tissue should be used for metabolomics testing because recurrent ascites are usually produced after surgical resection of the cancer tissue. FFPE tissue is not a routine metabolomics sample, but it has been reported that significant differential metabolites have been obtained from them (Arima et al, 2010;Feng et al, 2019).…”