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Waman VP, Ashford P, Lam SD, Sen N, Abbasian M, Woodridge L, Goldtzvik Y, Bordin N, Wu J, Sillitoe I, Orengo CA. Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics. Sci Rep 2024; 14:14208. [PMID: 38902252 PMCID: PMC11190248 DOI: 10.1038/s41598-024-61541-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 06/22/2024] Open
Abstract
The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19. In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and their human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed the impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities for the human viral protein complexes. We predicted a total of 26 affinity-enhancing variants from 13 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed. Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.
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Affiliation(s)
- Vaishali P Waman
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Neeladri Sen
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Mahnaz Abbasian
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Laurel Woodridge
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Yonathan Goldtzvik
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Jiaxin Wu
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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Quirion L, Robert A, Boulais J, Huang S, Bernal Astrain G, Strakhova R, Jo CH, Kherdjemil Y, Thibault MP, Faubert D, Kmita M, Baskin JM, Gingras AC, Smith MJ, Cote JF. Mapping the global interactome of the ARF family reveals spatial organization in cellular signaling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.01.530598. [PMID: 36909472 PMCID: PMC10002736 DOI: 10.1101/2023.03.01.530598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The ADP-ribosylation factors (ARFs) and ARF-like (ARLs) GTPases serve as essential molecular switches governing a wide array of cellular processes. In this study, we utilized proximity-dependent biotin identification (BioID) to comprehensively map the interactome of 28 out of 29 ARF and ARL proteins in two cellular models. Through this approach, we identified ~3000 high-confidence proximal interactors, enabling us to assign subcellular localizations to the family members. Notably, we uncovered previously undefined localizations for ARL4D and ARL10. Clustering analyses further exposed the distinctiveness of the interactors identified with these two GTPases. We also reveal that the expression of the understudied member ARL14 is confined to the stomach and intestines. We identified phospholipase D1 (PLD1) and the ESCPE-1 complex, more precisely SNX1, as proximity interactors. Functional assays demonstrated that ARL14 can activate PLD1 in cellulo and is involved in cargo trafficking via the ESCPE-1 complex. Overall, the BioID data generated in this study provide a valuable resource for dissecting the complexities of ARF and ARL spatial organization and signaling.
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