DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples

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.