LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein

Shilts, J.; Crozier, T. M.; Teixeira-Silva, A.; Gabaev, I.; Greenwood, E. J. D.; Watson, S. J.; Ortmann, B. M.; Gawden-Bone, C. M.; Pauzaite, T.; Hoffmann, M.; Nathan, J. A.; Pöhlmann, S.; Lehner, P. J.; Wright, G. J.

doi:10.1101/2021.09.25.461776

bioRxiv · 10.1101/2021.09.25.461776

LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein

Shilts, J.·Crozier, T. M.·Teixeira-Silva, A.·Gabaev, I.·Greenwood, E. J. D.·Watson, S. J.·Ortmann, B. M.·Gawden-Bone, C. M.·Pauzaite, T.·Hoffmann, M.·Nathan, J. A.·Pöhlmann, S.·Lehner, P. J.·Wright, G. J.

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Abstract

The interactions between severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and human host factors enable the virus to propagate infections that lead to COVID-19. The spike protein is the largest structural component of the virus and mediates interactions essential for infection, including with the primary ACE2 receptor. We performed two independent cell-based systematic screens to determine whether there are additional proteins by which the spike protein of SARS-CoV-2 can interact with human cells. We discovered that in addition to ACE2, expression of LRRC15 also causes spike protein binding. This interaction is distinct from other known spike attachment mechanisms such as heparan sulfates or lectin receptors. Measurements of orthologous coronavirus spike proteins implied the interaction was restricted to SARS-CoV-2, suggesting LRRC15 represents a novel class of spike binding interaction. We localized the interaction to the C-terminus of the S1 domain, and showed that LRRC15 shares recognition of the ACE2 receptor binding domain. From analyzing proteomics and single-cell transcriptomics, we identify LRRC15 expression as being common in human lung vasculature cells and fibroblasts. Although infection assays demonstrated that LRRC15 alone is not sufficient to permit viral entry, we present evidence it can modulate infection of human cells. This unexpected interaction merits further investigation to determine how SARS-CoV-2 exploits host LRRC15 and whether it could account for any of the distinctive features of COVID-19. In briefWe present evidence from genome-wide screening that the spike protein of SARS-CoV-2 interacts with human cells expressing LRRC15. The interaction is distinct from previously known classes of spike attachment factors, and appears to have emerged recently within the coronavirus family. Although not sufficient for cell invasion, this interaction can modulate viral infection. Our data point to an unappreciated host factor for SARS-CoV-2, with potential relevance to COVID-19. Highlights- Two systematic cell-based screens for SARS-CoV-2 spike protein binding identify LRRC15 as a human host factor - Interaction with LRRC15 is reproducible in different human cell lines and independent of known glycan or ACE2 binding pathways - The C-terminal S1 domain of SARS-CoV-2 spike binds LRRC15 with sub-micromolar affinity, while related coronavirus spikes do not - LRRC15 is expressed in tissues with high ACE2 levels and may modulate infection

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Shilts, J., Crozier, T. M., Teixeira-Silva, A., Gabaev, I., Greenwood, E. J. D., Watson, S. J., Ortmann, B. M., Gawden-Bone, C. M., Pauzaite, T., Hoffmann, M., Nathan, J. A., Pöhlmann, S., Lehner, P. J., Wright, G. J.. 2021-09-25. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. https://doi.org/10.1101/2021.09.25.461776

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