Assessment of molecular differentiation in FFPE colon adenocarcinoma tissues using PCA analysis of MALDI IMS spectral data

Abstract

MALDI IMS datasets comprise huge amounts of spectra and their interpretation requires the use of multivariate statistical methods. MALDI IMS spectral data have been processed using sequential principal component analysis and 2-D peak distribution tests so as to investigate the molecular differentiation of tumor regions in formalin-fixed paraffin-embedded tissue biopsies of colorectal adenocarcinoma. In some of the cases fresh frozen tissue section samples were also analyzed for comparison. Multivariate analysis of spectral data revealed a specific pattern of mass ion peaks in different tumor regions that were distinguishable from the adjacent normal regions within a given specimen. Moreover, similar mass ion peaks could be detected in both FFPE and fresh-frozen tissue section samples. These significant mass ion peaks have been used to generate ion images and visualize the difference between tumor and normal regions. These specific and statistically significant ion peaks may serve as potential biomarkers for colorectal adenocarcinoma.

Applications of MALDI-MS/MS-Based Proteomics in Biomedical Research

“…LC-MALDI-MS/MS and MALDI-MSI investigation was used to compare the molecular profiles of primary tumors and their metastases in regional lymph nodes to emphasize molecular heterogeneity of papillary thyroid cancer stored as formalin-fixed paraffin-embedded (FFPE) samples [ 159 ]. MALDI-MSI coupled with MALDI-ToF/ToF was also used to assess the molecular differentiation in both FFPE and fresh-frozen colon adenocarcinoma tissue samples [ 160 ]. Overexpressed in various tumors, including breast cancer, the epidermal growth factor receptor (EGFR) was detected using an immune tandem mass spectrometry (iMALDI) diagnostic assay based on MALDI-MS to assess the molecular weight of the epitope-containing peptides and MALDI-MS/MS to perform their amino acid sequence [ 161 ].…”