Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry
Open accessPublished version of a preprint
Abstract
Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)–protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.
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- Authors
- Yazaki, J., Yamanashi, T., Nemoto, S., Kobayashi, A., Han, Y.-W., Hasegawa, T., Iwase, A., Ishikawa, M., Konno, R., Imami, K., Kawashima, Y., & Seita, J.
- Affiliations
- Setsunan University (JP)
- University of Tsukuba (JP)
- RIKEN Center for Integrative Medical Sciences (JP)
- RIKEN Center for Sustainable Resource Science (JP)
- Kazusa DNA Research Institute (JP)
- Corresponding author
- Yazaki, Junshi
- ORCID
- Venue
- Biology Methods and Protocols
- Publisher
- Oxford University Press (OUP)
- Published
- 2024
- Volume
- 9
- Issue
- 1
- Pages
- bpae039-bpae039
- ISSN
- 2396-8923 (ISSN-L)
- PMC
- PMC11180226
- OpenAlex
- W4399117958
- Cited by
- 2
- References
- 9
- Citations by year
- 2026: 1 · 2025: 1
- FWCI
- 0.25
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Biology Methods and Protocols (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- SSRN Electronic Journal (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Ministry of Education, Science, Sports, and Culture
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- HaloTag, protein-protein interaction, protein complex stoichiometry, adipogenesis, transcriptional regulatory networks
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