Abstract
Recent advances in mass spectrometry (MS) have enabled extensive analysis of cancer proteomes. Here, we employed quantitative proteomics to profile protein expression across 24 breast cancer patient-derived xenograft (PDX) models. Integrated proteogenomic analysis shows positive correlation between expression measurements from transcriptomic and proteomic analyses; further, gene expression-based intrinsic subtypes are largely re-capitulated using non-stromal protein markers. Proteogenomic analysis also validates a number of predicted genomic targets in multiple receptor tyrosine kinases. However, several protein/phosphoprotein events such as overexpression of AKT proteins and ARAF, BRAF, HSP90AB1 phosphosites are not readily explainable by genomic analysis, suggesting that druggable translational and/or post-translational regulatory events may be uniquely diagnosed by MS. Drug treatment experiments targeting HER2 and components of the PI3K pathway supported proteogenomic response predictions in seven xenograft models. Our study demonstrates that MS-based proteomics can identify therapeutic targets and highlights the potential of PDX drug response evaluation to annotate MS-based pathway activities.
Highlights
Recent advances in mass-spectrometry provide an unprecedented opportunity for antibody-independent proteome profiling with approximately 80% of all proteins in major human tissues quantifiable by this technique[12]
The human patient cohort was composed of 10 basal, 1 claudin-low (CLDN-low), 9 luminal B and 4 HER2enriched (HER2-E) breast tumours based on PAM50 expression subtyping (Supplementary Data 1)
WHIM17 and WHIM46, both harboured BTK and PLCG2 protein overexpression, exhibited overall high phosphorylation of the NFkB signalling pathway (Fig. 4c,d; FDR 1⁄4 6.94e-3, 4.53e-5 respectively). This observation further supports the strong similarity between these two Patient-derived xenografts (PDXs) models based on protein/phosphoprotein clustering (Fig. 3b,c) and their classification as EBV-positive lymphoproliferation. While pathways such as PI3K/AKT/MTOR are known to be activated across the majority of breast tumours[22], our analysis shows that other complementary tumorigenesis-related pathways including RAS/MAPK are activated in a small set of breast tumours due to specific genomic or proteomic alterations, representing alternative treatment opportunities
Summary
Recent advances in mass-spectrometry provide an unprecedented opportunity for antibody-independent proteome profiling with approximately 80% of all proteins in major human tissues quantifiable by this technique[12]. We generated high-coverage proteome and phosphoproteome data for 24 PDX models representing different breast cancer subtypes using both isobaric mass-tag labelling and label-free proteomic methods for cross-validated identification of 12,794 proteins and 56,874 phosphorylation sites. PDX models exhibiting proteomic and/or phosphoproteomic upregulation events of HER2 or the PI3K pathway, we validated the efficacy of targeted inhibitors in suppressing PDX growth. Taken together, these observations show that comprehensive proteogenomic profiling has potential to identify new targets for individualized treatment approaches in cancer
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