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Liu Y, Sundah NR, Ho NRY, Shen WX, Xu Y, Natalia A, Yu Z, Seet JE, Chan CW, Loh TP, Lim BY, Shao H. Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells. Nat Biomed Eng 2024:10.1038/s41551-024-01225-3. [PMID: 38898172 DOI: 10.1038/s41551-024-01225-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/05/2024] [Indexed: 06/21/2024]
Abstract
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.
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Affiliation(s)
- Yu Liu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Noah R Sundah
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Nicholas R Y Ho
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Wan Xiang Shen
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yun Xu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Auginia Natalia
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Zhonglang Yu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Ju Ee Seet
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Ching Wan Chan
- Department of Surgery, National University Hospital, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tze Ping Loh
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Brian Y Lim
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Department of Computer Science, School of Computing, National University of Singapore, Singapore, Singapore.
| | - Huilin Shao
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.
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Mulhall EM, Ward A, Yang D, Koussa MA, Corey DP, Wong WP. Single-molecule force spectroscopy reveals the dynamic strength of the hair-cell tip-link connection. Nat Commun 2021; 12:849. [PMID: 33558532 PMCID: PMC7870652 DOI: 10.1038/s41467-021-21033-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023] Open
Abstract
The conversion of auditory and vestibular stimuli into electrical signals is initiated by force transmitted to a mechanotransduction channel through the tip link, a double stranded protein filament held together by two adhesion bonds in the middle. Although thought to form a relatively static structure, the dynamics of the tip-link connection has not been measured. Here, we biophysically characterize the strength of the tip-link connection at single-molecule resolution. We show that a single tip-link bond is more mechanically stable relative to classic cadherins, and our data indicate that the double stranded tip-link connection is stabilized by single strand rebinding facilitated by strong cis-dimerization domains. The measured lifetime of seconds suggests the tip-link is far more dynamic than previously thought. We also show how Ca2+ alters tip-link lifetime through elastic modulation and reveal the mechanical phenotype of a hereditary deafness mutation. Together, these data show how the tip link is likely to function during mechanical stimuli.
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Affiliation(s)
- Eric M Mulhall
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Program in Neuroscience, Harvard University, Cambridge, MA, USA
| | - Andrew Ward
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Mounir A Koussa
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Program in Neuroscience, Harvard University, Cambridge, MA, USA
| | - David P Corey
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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DeRosa JR, Moyer BS, Lumen E, Wolfe AJ, Sleeper MB, Bianchi AH, Crawford A, McGuigan C, Wortel D, Fisher C, Moody KJ, Blanden AR. RPtag as an Orally Bioavailable, Hyperstable Epitope Tag and Generalizable Protein Binding Scaffold. Biochemistry 2018; 57:3036-3049. [PMID: 29722979 DOI: 10.1021/acs.biochem.8b00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibodies are the most prolific biologics in research and clinical environments because of their ability to bind targets with high affinity and specificity. However, antibodies also carry liabilities. A significant portion of the life-science reproducibility crisis is driven by inconsistent performance of research-grade antibodies, and clinical antibodies are often unstable and require costly cold-chain management to reach their destinations in active form. In biotechnology, antibodies are also limited by difficulty integrating them in many recombinant systems due to their size and structural complexity. A switch to small, stable, sequence-verified binding scaffolds may overcome these barriers. Here we present such a scaffold, RPtag, based on a ribose-binding protein (RBP) from extremophile Caldanaerobacter subterraneus. RPtag binds an optimized peptide with pM affinity, is stable to extreme temperature, pH, and protease treatment, readily refolds after denaturation, is effective in common laboratory applications, was rationally engineered to bind bioactive PDGF-β, and was formulated as a gut-stable orally bioavailable preparation.
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Affiliation(s)
- Jennifer R DeRosa
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Brandon S Moyer
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ellie Lumen
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Aaron J Wolfe
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Meegan B Sleeper
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Anthony H Bianchi
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ashleigh Crawford
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Connor McGuigan
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Danique Wortel
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Cheyanne Fisher
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Kelsey J Moody
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Adam R Blanden
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
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