Proximity proteomics reveals UCH-L1 as an essential regulator of NLRP3-mediated IL-1β production in human macrophages and microglia

Zhu Liang; Andreas Damianou; Iolanda Vendrell; Edward Jenkins; Frederik H Lassen; Sam J Washer; Athina Grigoriou; Guihai Liu; Gangshun Yi; Hantao Lou; Fangyuan Cao; Xiaonan Zheng; Ricardo A Fernandes; Tao Dong; Edward W Tate; Elena Di Daniel; Benedikt M Kessler

doi:10.1016/j.celrep.2024.114152

Proximity proteomics reveals UCH-L1 as an essential regulator of NLRP3-mediated IL-1β production in human macrophages and microglia

Cell Rep. 2024 Apr 25;43(5):114152. doi: 10.1016/j.celrep.2024.114152. Online ahead of print.

Authors

Zhu Liang¹, Andreas Damianou², Iolanda Vendrell², Edward Jenkins³, Frederik H Lassen⁴, Sam J Washer⁵, Athina Grigoriou², Guihai Liu⁶, Gangshun Yi⁷, Hantao Lou⁸, Fangyuan Cao⁹, Xiaonan Zheng⁶, Ricardo A Fernandes⁶, Tao Dong⁶, Edward W Tate⁹, Elena Di Daniel¹⁰, Benedikt M Kessler¹¹

Affiliations

¹ Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK. Electronic address: zhu.liang@ndm.ox.ac.uk.
² Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
³ Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK.
⁴ Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK.
⁵ James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.
⁶ Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
⁷ Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
⁸ Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK.
⁹ Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
¹⁰ Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
¹¹ Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK. Electronic address: benedikt.kessler@ndm.ox.ac.uk.

PMID: 38669140
DOI: 10.1016/j.celrep.2024.114152

Abstract

Activation of the NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome complex is an essential innate immune signaling mechanism. To reveal how human NLRP3 inflammasome assembly and activation are controlled, in particular by components of the ubiquitin system, proximity labeling, affinity purification, and RNAi screening approaches were performed. Our study provides an intricate time-resolved molecular map of different phases of NLRP3 inflammasome activation. Also, we show that ubiquitin C-terminal hydrolase 1 (UCH-L1) interacts with the NACHT domain of NLRP3. Downregulation of UCH-L1 decreases pro-interleukin-1β (IL-1β) levels. UCH-L1 chemical inhibition with small molecules interfered with NLRP3 puncta formation and ASC oligomerization, leading to altered IL-1β cleavage and secretion, particularly in microglia cells, which exhibited elevated UCH-L1 expression as compared to monocytes/macrophages. Altogether, we profiled NLRP3 inflammasome activation dynamics and highlight UCH-L1 as an important modulator of NLRP3-mediated IL-1β production, suggesting that a pharmacological inhibitor of UCH-L1 may decrease inflammation-associated pathologies.

Keywords: CP: Immunology; DUB; IL-1β; NLRP3; UCH-L1; deubiquitylase; inflammasome; macrophages; microglia; monocytes; protease inhibitor; ubiquitin; ubiquitin C-terminal hydrolase.