Abstract
Although re-sequencing of gene panels and mRNA expression profiling are now firmly established in clinical laboratories, in-depth proteome analysis has remained a niche technology, better suited for studying model systems rather than challenging materials such as clinical trial samples. To address this limitation, we have developed a novel and optimized platform called SP3-Clinical Tissue Proteomics (SP3-CTP) for in-depth proteome profiling of practical quantities of tumour tissues, including formalin fixed and paraffin embedded (FFPE). Using single 10 μm scrolls of clinical tumour blocks, we performed in-depth quantitative analyses of individual sections from ovarian tumours covering the high-grade serous, clear cell, and endometrioid histotypes. This examination enabled the generation of a novel high-resolution proteome map of ovarian cancer histotypes from clinical tissues. Comparison of the obtained proteome data with large-scale genome and transcriptome analyses validated the observed proteome biology for previously validated hallmarks of this disease, and also identified novel protein features. A tissue microarray analysis validated cystathionine gamma-lyase (CTH) as a novel clear cell carcinoma feature with potential clinical relevance. In addition to providing a milestone in the understanding of ovarian cancer biology, these results show that in-depth proteomic analysis of clinically annotated FFPE materials can be effectively used as a biomarker discovery tool and perhaps ultimately as a diagnostic approach.
Highlights
Re-sequencing of gene panels and mRNA expression profiling are firmly established in clinical laboratories, in-depth proteome analysis has remained a niche technology, better suited for studying model systems rather than challenging materials such as clinical trial samples
We evaluated the abundance of cystathionine gamma-lyase (CTH) and LEFTY1 that were both enriched in CCC compared to HGSC and ENOC in the proteomics data (Supplemental Fig. 10) and across all public repositories (Fig. 4a–c)
In this work we have presented an improvement and novel application of the SP3 proteomics methodology that enabled high quality quantitative analysis of clinical formalin fixed and paraffin embedded (FFPE) tumour sections
Summary
Re-sequencing of gene panels and mRNA expression profiling are firmly established in clinical laboratories, in-depth proteome analysis has remained a niche technology, better suited for studying model systems rather than challenging materials such as clinical trial samples To address this limitation, we have developed a novel and optimized platform called SP3-Clinical Tissue Proteomics (SP3-CTP) for in-depth proteome profiling of practical quantities of tumour tissues, including formalin fixed and paraffin embedded (FFPE). The limited adoption of proteomics in these areas stems primarily from the poor performance of standard MS based approaches to work efficiently with practical quantities of formalin fixed paraffin embedded (FFPE) samples that are the standard media for clinical diagnostics[1,2] Despite these challenges, recent research efforts have successfully obtained high quantitative coverage of the proteome from FFPE tissues using MS3–7. A high-sensitivity MS-based analysis of ovarian cancer histotypes can potentially build upon gene expression and immunohistochemistry (IHC) data to identify targetable proteins that drive different clinical phenotypes
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