Abstract
The interpatient variability of tumor proteomes has been investigated on a large scale but many tumors display also intratumoral heterogeneity regarding morphological and genetic features. It remains largely unknown to what extent the local proteome of tumors intrinsically differs. Here, we used hepatocellular carcinoma as a model system to quantify both inter- and intratumor heterogeneity across human patient specimens with spatial resolution. We defined proteomic features that distinguish neoplastic from the directly adjacent nonneoplastic tissue, such as decreased abundance of NADH dehydrogenase complex I. We then demonstrated the existence of intratumoral variations in protein abundance that re-occur across different patient samples, and affect clinically relevant proteins, even in the absence of obvious morphological differences or genetic alterations. Our work demonstrates the suitability and the benefits of using mass spectrometry-based proteomics to analyze diagnostic tumor specimens with spatial resolution. Data are available via ProteomeXchange with identifier PXD007052.
Highlights
Try-based proteomics to analyze diagnostic tumor specimens with spatial resolution
A Protocol That Allows the Quantitative Analysis of intratumor heterogeneity (ITH) in Microdissected Formalin-fixed and paraffin-embedded (FFPE) Specimens With Comprehensive Proteomic Coverage—We developed a novel strategy for efficient proteome analysis of microdissected FFPE material
We combined a strategy based on heatinduced reversing of formalin fixation with a ultrasensitive and rapid protocol that uses paramagnetic bead technology named SP3 and allows for the removal of multiple mass spectrometry noncompatible reagents, such as for example highly concentrated SDS [9, 33]
Summary
Try-based proteomics to analyze diagnostic tumor specimens with spatial resolution. Data are available via ProteomeXchange with identifier PXD007052. Routine diagnostics of tumors involves evaluation of histomorphological features by conventional microscopy It is often combined with immunohistochemical staining (IHC) of marker proteins, the number of proteins that can be quantitatively analyzed by IHC is rather limited by the availability of suitable antibodies and the experimental throughput. Mass spectrometry-based proteomics has been already used to study FFPE cancer tissue specimens [4, 5], but rarely in combination with spatial resolution (6 – 8), because the amount of material that can be obtained from a specific region of an FFPE specimen limits the comprehensiveness, i.e. number of identified and quantified proteins. The great advantage of excellent spatial preservation of FFPE material has not yet been exploited to systematically and jointly analyze interand intratumoral heterogeneity across multiple specimens
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