High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue

Abstract

Formalin-fixed and paraffin-embedded (FFPE) tissue specimens are the gold standard for histological examination, and they provide valuable molecular information in tissue-based research. Metabolite assessment from archived tissue samples has not been extensively conducted because of a lack of appropriate protocols and concerns about changes in metabolite content or chemical state due to tissue processing. We present a protocol for the in situ analysis of metabolite content from FFPE samples using a high-mass-resolution matrix-assisted laser desorption/ionization fourier-transform ion cyclotron resonance mass spectrometry imaging (MALDI-FT-ICR-MSI) platform. The method involves FFPE tissue sections that undergo deparaffinization and matrix coating by 9-aminoacridine before MALDI-MSI. Using this platform, we previously detected ∼1,500 m/z species in the mass range m/z 50-1,000 in FFPE samples; the overlap compared with fresh frozen samples is 72% of m/z species, indicating that metabolites are largely conserved in FFPE tissue samples. This protocol can be reproducibly performed on FFPE tissues, including small samples such as tissue microarrays and biopsies. The procedure can be completed in a day, depending on the size of the sample measured and raster size used. Advantages of this approach include easy sample handling, reproducibility, high throughput and the ability to demonstrate molecular spatial distributions in situ. The data acquired with this protocol can be used in research and clinical practice.

Breast Cancer: Multiple Subtypes within a Tumor?

“…In the case of FFPE based diagnosis, mass spectrometry based techniques have been employed to spatially unravel molecularly distinct tumor subpopulations with clinically relevant attributes [65, 66]. There is also potential for integration of multiple ‘omics’ platforms, since some of these mass-spectrometric methods are also amenable to parameters such as metabolites [67]. Beyond the ability to tease out the heterogeneity between tumor populations, the distribution and abundance of various stromal populations could also be mapped out concurrently with these methods.…”

Imaging mass spectrometry in drug development and toxicology

“…Commonly used perfusion and fixation strategies are generally not compatible with mass spectrometry, due to interference of the polymeric fixation agents such as paraffin. Solutions to overcome this problem, including in situ trypsinization following paraffin removal or alternatively use of a reactive matrix 2,4-dinitrophenylhydrazine, have been suggested (Lemaire et al 2007; Ly et al 2016). Another elegant workaround was recently presented to delineate spatial protein N-glycosylation patterns (Gustafsson et al 2015).…”

Classification and analysis of human ovarian tissue using full field optical coherence tomography

“…Additionally, only FFPE tissue blocks were used for this preliminary study. Although, some previous spectroscopic imaging studies have indicated that classification of fresh and FFPE tissues produce comparable results [28], however, further compatibility studies need to be conducted between these two tissue groups. Menopausal status of the patients, which was not available for the samples studied, also needs to be considered for more accurate analysis.…”