Protein-protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.
Keyphrases
- mass spectrometry
- liquid chromatography
- ms ms
- multiple sclerosis
- high performance liquid chromatography
- high resolution
- protein protein
- gas chromatography
- capillary electrophoresis
- gene expression
- endothelial cells
- amino acid
- tandem mass spectrometry
- stem cells
- current status
- microbial community
- young adults
- simultaneous determination
- climate change
- cell death
- mesenchymal stem cells
- wastewater treatment
- papillary thyroid
- childhood cancer
- single molecule
- cell therapy
- signaling pathway
- antibiotic resistance genes
- anaerobic digestion