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.

蛋白质-蛋白质相互作用（Protein–protein interactions, PPIs）是解析生命系统的核心基础，因为蛋白质复合物是执行细胞功能的关键活性分子模块。功能异常的PPIs与包括癌症在内的多种疾病密切相关。系统层面的PPI分析不仅能够揭示疾病病理机制，更可作为筛选潜在治疗靶点的研究范式。近年来，交联质谱（cross-linking mass spectrometry, XL-MS）已成为绘制细胞网络中内源性PPIs的有力工具。尽管已有研究在细胞裂解液、完整细胞及组织中开展了蛋白质组范围的XL-MS分析，但该技术在临床样本中的应用尚未见报道。本研究采用基于DSBSO的体内XL-MS平台，对两株乳腺癌患者来源的异种移植模型（patient-derived xenograft, PDX）的相互作用组图谱进行了绘制。最终，我们构建了包含2557个人类蛋白质的PDX相互作用网络，并鉴定出乳腺癌亚型特异性的相互作用。有趣的是，观测到的多数PPI差异与基于串联质量标签（Tandem Mass Tags, TMT）的蛋白质组定量所得的蛋白质丰度变化具有良好相关性。综上，本研究证实了XL-MS分析应用于临床样本的可行性，并建立了适用于组织交联的分析流程，该流程未来可推广用于患者样本的PPIs绘制，以解析疾病相关的细胞网络。