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Li K, Chatterjee A, Qian C, Lagree K, Wang Y, Becker CA, Freeman MR, Murali R, Yang W, Underhill DM. Profiling phagosome proteins identifies PD-L1 as a fungal-binding receptor. Nature 2024:10.1038/s41586-024-07499-6. [PMID: 38839956 DOI: 10.1038/s41586-024-07499-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
Phagocytosis is the process by which myeloid phagocytes bind to and internalize potentially dangerous microorganisms1. During phagocytosis, innate immune receptors and associated signalling proteins are localized to the maturing phagosome compartment, forming an immune information processing hub brimming with microorganism-sensing features2-8. Here we developed proximity labelling of phagosomal contents (PhagoPL) to identify proteins localizing to phagosomes containing model yeast and bacteria. By comparing the protein composition of phagosomes containing evolutionarily and biochemically distinct microorganisms, we unexpectedly identified programmed death-ligand 1 (PD-L1) as a protein that specifically enriches in phagosomes containing yeast. We found that PD-L1 directly binds to yeast upon processing in phagosomes. By surface display library screening, we identified the ribosomal protein Rpl20b as a fungal protein ligand for PD-L1. Using an auxin-inducible depletion system, we found that detection of Rpl20b by macrophages cross-regulates production of distinct cytokines including interleukin-10 (IL-10) induced by the activation of other innate immune receptors. Thus, this study establishes PhagoPL as a useful approach to quantifying the collection of proteins enriched in phagosomes during host-microorganism interactions, exemplified by identifying PD-L1 as a receptor that binds to fungi.
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Affiliation(s)
- Kai Li
- Department of Biomedical Sciences, Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Avradip Chatterjee
- Department of Biomedical Sciences, Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chen Qian
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katherine Lagree
- Department of Biomedical Sciences, Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yang Wang
- Department of Biomedical Sciences, Division Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Courtney A Becker
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael R Freeman
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Division Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wei Yang
- Department of Biomedical Sciences, Division Cancer Biology and Therapeutics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David M Underhill
- Department of Biomedical Sciences, Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Medicine, Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Dong TN, Brogden G, Gerold G, Khosla M. A multitask transfer learning framework for the prediction of virus-human protein-protein interactions. BMC Bioinformatics 2021; 22:572. [PMID: 34837942 PMCID: PMC8626732 DOI: 10.1186/s12859-021-04484-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection and pathogenesis. This could further help in prevention and treatment of virus-related diseases. However, the task of predicting protein-protein interactions between a new virus and human cells is extremely challenging due to scarce data on virus-human interactions and fast mutation rates of most viruses. RESULTS We developed a multitask transfer learning approach that exploits the information of around 24 million protein sequences and the interaction patterns from the human interactome to counter the problem of small training datasets. Instead of using hand-crafted protein features, we utilize statistically rich protein representations learned by a deep language modeling approach from a massive source of protein sequences. Additionally, we employ an additional objective which aims to maximize the probability of observing human protein-protein interactions. This additional task objective acts as a regularizer and also allows to incorporate domain knowledge to inform the virus-human protein-protein interaction prediction model. CONCLUSIONS Our approach achieved competitive results on 13 benchmark datasets and the case study for the SARS-COV-2 virus receptor. Experimental results show that our proposed model works effectively for both virus-human and bacteria-human protein-protein interaction prediction tasks. We share our code for reproducibility and future research at https://git.l3s.uni-hannover.de/dong/multitask-transfer .
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Affiliation(s)
- Thi Ngan Dong
- L3S Research Center, Leibniz University Hannover, Hannover, Germany.
| | - Graham Brogden
- Institute for Biochemistry, University of Veterinary Medicine, Hannover, Germany.,Institute of Experimental Virology, TWINCORE, Center for Experimental and Clinical Infection Research Hannover, Hannover, Germany
| | - Gisa Gerold
- Institute for Biochemistry, University of Veterinary Medicine, Hannover, Germany.,Institute of Experimental Virology, TWINCORE, Center for Experimental and Clinical Infection Research Hannover, Hannover, Germany.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Megha Khosla
- L3S Research Center, Leibniz University Hannover, Hannover, Germany
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