Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.
Yu LiuNoah R SundahNicholas R Y HoWan Xiang ShenYun XuAuginia NataliaZhonglang YuJu Ee SeetChing Wan ChanTze Ping LohBrian Y LimHuilin ShaoPublished in: Nature biomedical engineering (2024)
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.
Keyphrases
- induced apoptosis
- protein protein
- cell cycle arrest
- high resolution
- amino acid
- binding protein
- squamous cell carcinoma
- gene expression
- mass spectrometry
- papillary thyroid
- dna methylation
- cell death
- single molecule
- genome wide
- cell free
- antiretroviral therapy
- circulating tumor cells
- hepatitis c virus
- hiv infected
- squamous cell
- pi k akt
- wastewater treatment
- ultrasound guided