Review 1: "LRRC15 suppresses SARS-CoV-2 infection and controls collagen production"

Shengya Cao

doi:doi:10.1162/2e3983f5.04c43aa8

LRRC15 suppresses SARS-CoV-2 infection and controls collagen production

by Lipin Loo, Matthew A. Waller, Alexander J. Cole, Alberto Ospina Stella, Cesar L. Moreno, Christopher E. Denes, Zina Hamoudi, Felicity Chung, Anupriya Aggarwal, Jason K. K. Low, Karishma Patel, Rezwan Siddique, Joel Mackay, Stuart Turville, Daniel Hesselson, and G. Gregory Neely

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dx.doi.org

Description

SummaryAlthough ACE2 is the primary receptor for SARS-CoV-2 infection, a systematic assessment of factors controlling SARS-CoV-2 host interactions has not been described. Here we used whole genome CRISPR activation to identify host factors controlling SARS-CoV-2 Spike binding. The top hit was a Toll-like receptor-related cell surface receptor called leucine-rich repeat-containing protein 15 (LRRC15). LRRC15 expression was sufficient to promote SARS-CoV-2 Spike binding where it forms a cell surface complex with LRRC15 but does not support infection. Instead, LRRC15 functioned as a negative receptor suppressing both pseudotyped and live SARS-CoV-2 infection. LRRC15 is expressed in collagen-producing lung myofibroblasts where it can sequester virus and reduce infection in trans. Mechanistically LRRC15 is regulated by TGF-β, where moderate LRRC15 expression drives collagen production but high levels suppress it, revealing a novel lung fibrosis feedback circuit. Overall, LRRC15 is a master regulator of SARS-CoV-2, suppressing infection and controlling collagen production associated with “long-haul” COVID-19.In BriefUsing pooled whole genome CRISPR activation screening, we identify the TLR relative LRRC15 as a novel SARS-CoV-2 Spike interacting protein. LRRC15 is not a SARS-CoV-2 entry receptor, but instead can suppress SARS-CoV-2 infection. LRRC15 is expressed by lung fibroblasts and regulates both collagen production and infection of ACE2-expressing target cells. This may provide a direct link between SARS-CoV-2 particles and lung fibrosis seen in “long-haul” COVID-19 patients.HighlightsWhole genome CRISPR activation screening implicates the TLR relative LRRC15 in SARS-CoV-2 Spike bindingLRRC15 suppresses live SARS-CoV-2 virus infectionLRRC15 is expressed in lung fibroblasts and sequesters virus while controlling collagen productionLRRC15 can act as a master regulator of infection and fibrosis, potentially controlling SARS-CoV-2 infection outcomes and “long-haul” COVID-19

RR:C19 Evidence Scale rating by reviewer:

Reliable. The main study claims are generally justified by its methods and data. The results and conclusions are likely to be similar to the hypothetical ideal study. There are some minor caveats or limitations, but they would/do not change the major claims of the study. The study provides sufficient strength of evidence on its own that its main claims should be considered actionable, with some room for future revision.

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Review:

Based on the “In Brief”, “Highlights”, and “Summary” sections, the authors appear to be making four claims.

Claim 1: LRRC15 interacts with the SARS-CoV-2 spike protein. Overall, this work provides strong evidence that the interaction exists. The authors identified LRRC15 using an unbiased method and performed several follow-up studies to validate the finding. Interestingly, while the FACS-based studies are clear, the microscopy-based and immunoprecipitation-based studies may suggest complexities beyond a simple protein-protein interaction. Despite that, these studies are still consistent with the overall claim. The claim is further strengthened by the existence of two independent reports^1,2 which identify the same interaction using different cell lines and spike protein forms.

Claim 2: LRRC15 expression suppresses SARS-CoV-2 infection both when co-expressed with the known entry receptor, ACE2, and when expressed on neighboring cells. The authors present strong evidence for LRRC15 expression suppressing pseudovirus infection in HEK293T cells. However, the effect is much weaker when using the D614G live strain of SARS-CoV-2, and there is no effect with the Delta variant. In contrast, one of the independent reports reported that co-expressing LRRC15 in a lung cell line, CaLu-3, enhanced infection². Additionally, the authors reanalyzed published data and found that LRRC15 and ACE2 were expressed on different cell types in human lungs. Therefore, they also tested co-culturing ACE2 expressing cells with LRRC15-expressing fibroblasts. The authors reported that co-culturing resulted in less infection of the ACE2 cells, though it appears to be in the context of overexpressing LRRC15 on top of endogenous LRRC15 in a lung fibroblast cell line. It is unclear whether this reflects expression in human lungs and whether this inhibition would hold in a real-world infection context. However, the data presented appears reliable, and the suppression of infection in a cell line context is corroborated by one of the independent reports¹. Overall, it seems likely that LRRC15 expression can affect SARS-CoV-2 infection though the exact effect in an intact organism remains to be seen. While stating that LRRC15 is a “master regulator” of infection seems to veer towards hyperbole, this work is an important advance for understanding the role of LRRC15 in SARS-CoV-2 infection.

Claim 3: LRRC15 regulates collagen production. The authors reanalyzed published data and found that LRRC15 was expressed in lung fibroblasts. From this, they hypothesized that LRRC15 may regulate collagen production. Using these datasets, they found a positive correlation between LRRC15 expression and expression of different collagens proteins. To test the hypothesis, they transfected different amounts of LRRC15 DNA to achieve high or low expression. They found that COL1A1 expression increased in cells with low, but not high, LRRC15 expression. While this is an interesting observation, more work would be needed to deem LRRC15 a “master regulator” of fibrosis.

Claim 4: LRRC15 connects SARS-CoV-2 infection to collagen production associated with “long-haul” COVID-19. It is unclear if the authors intended this to be a claim, but it can come across as such. While this is an interesting model that can be postulated from findings in this work, the manuscript provides little evidence to support this claim.

Overall, while the exact role of LRRC15 in a real-world infection remains unclear, it seems clear that LRRC15 can bind the SARS-CoV-2 spike protein, is present in human lungs, and can regulate infection in human cell lines.

Song, J. et al. LRRC15 is an inhibitory receptor blocking SARS-CoV-2 spike-mediated entry in trans. bioRxiv 2021.11.23.469714 (2021) doi:10.1101/2021.11.23.469714.
Shilts, J. et al. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein. bioRxiv 2021.09.25.461776 (2021) doi:10.1101/2021.09.25.461776.