Next-generation protein analysis in the pathology department

Abstract

<jats:p>Traditionally, immunohistochemistry (IHC) is used by pathologists to localise specific proteins or peptides in tissue slides. In the era of personalised medicine, however, molecular tissue analysis becomes indispensable for correct diagnosis, prognosis and therapeutic decision, not only on the DNA or mRNA level but also on the protein level. Combining molecular information with imaging presents many advantages. Therefore, matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) is a promising technique to be added to the armamentarium of the pathologist. Here, we focus on the workflow, advantages and drawbacks of both MALDI IMS and IHC. We also briefly discuss a few other protein imaging modalities and give examples of applications.</jats:p>

Unbiased spatial proteomics with single-cell resolution in tissues

“…As a first step, surface proteins are digested in situ to produce a peptide representation of the proteome. This technology has recently been applied to various states of disease, including cancer, to discover diagnostic, predictive and survival markers (Ahmed et al, 2020). While the laser spot could probably be focused to enable single-cell resolution for MALDI, the digestion of proteins into peptides in slides can lead to analyte delocalization.…”

Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment

“…[ 30 ] As proteomic‐driven, it is widely compatible with frozen and FFPE samples with a theoretical detectability of 50–100 peptides at a time. [ 31 ] It is a quantitative antibody‐free approach without tissue destruction, making it compatible with downstream applications such as digital PCR. [ 32 ] Highlights of MALDI‐IMS in multiple solid tumors have demonstrated in resolving the complexity of spatial patterns of proteins in heterogenous tissue specimen, most of which focused on tumor typing, grading, and sub‐histological classification.…”

“…Besides, obtaining higher resolutions for TME still proves to be difficult due to its untargeted detection nature and sub‐optimal quantification capability. [ 31 ] The latter defect was partially overcome by multiplexed ion beam imaging (MIBI). MIBI uses a mixture of elemental isotope‐labeled primary antibodies to react with tissues mounted on conductive substrates.…”

Multicenter Evaluation of Tissue Classification by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

“…The ability to differentiate histomorphologically ambiguous conditions and conduct accurate diagnoses is a pressing concern in this age where precise subtyping is crucial for subsequent selection of treatment strategies. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) has been identified as a potentially powerful tool in pathology by allowing the determination of tissue- or clinically specific molecular profiles. − This technique consists of spatially resolved mass spectrometry conducted from intact tissue sections mounted on conductive glass slides and has been used to investigate a variety of compounds such as proteins, tryptic peptides, N- glycans, extracellular matrix components, and endogenous metabolites. − The lack of labels allows not only for an untargeted discovery approach, for example examining metabolite or lipid differences between different samples and structures, but also for the possibility to conduct molecular phenotyping and predict the type of tissue based on its mass spectrometric pattern (also known as tissue typing) …”