Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.

捕获蛋白质相互作用组中不同层次相互作用的全部复杂性具有挑战性。在这里，我们报告了一种 DNA 条形码方法，用于对成对和高阶蛋白质相互作用及其在细胞内的动态进行多重映射。该方法利用与条形码 DNA 链缀合的抗体，这些抗体可以双向杂交和共价连接，以线性化单个 3D 蛋白质复合物内紧密间隔的相互作用，编码和解码蛋白质成分及其之间的相互作用。通过绘制癌细胞和正常细胞中蛋白质相互作用的图谱，我们发现肿瘤细胞表现出更大的多样性和丰富的具有高阶相互作用的蛋白质复合物。在人类乳腺癌组织的活检中，该方法准确地识别了癌症亚型，并揭示了高阶蛋白质相互作用与癌症侵袭性相关。