An outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has caused a pandemic associated with a severe acute pulmonary disease named COVID-19 (coronavirus disease 2019) (
1). A related coronavirus, SARS-CoV, led to a much smaller outbreak in 2003, possibly due to infection occurring predominantly in the lower respiratory system, whereas SARS-CoV-2 spreads rapidly through active pharyngeal viral shedding (
2). Despite these differences, uptake of both viruses is mediated by the same cellular receptor: angiotensin-converting enzyme 2 (ACE2) (
3–
5). One hypothesis to explain the enhanced spreading of SARS-CoV-2 is the presence of a polybasic furin-type cleavage site, RRAR^S, at the S1-S2 junction in the SARS-CoV-2 spike (S) protein that is absent in SARS-CoV (
6). Similar sequences are found in the S proteins of many other pathogenic human viruses, including Ebola, HIV-1, and highly virulent strains of avian influenza (
6,
7). The presence of the polybasic cleavage site in SARS-CoV-2 results in enhanced pathogenicity by priming the fusion activity (
8) and could potentially create additional cell surface receptor binding sites. Proteolytic cleavage of RRAR^S by furin exposes a conserved C-terminal motif, RXXR
OH [where R is arginine and X is any amino acid; R can be substituted by lysine (K)], in the S protein. Such C-terminal sequences that conform to the C-end rule (CendR) are known to bind to and activate neuropilin (NRP1 and NRP2) receptors at the cell surface (
9). Recent cryo–electron microscopy structures of the SARS-CoV-2 S protein demonstrated that the S1-S2 junction is part of a solvent-exposed loop and is therefore accessible for receptor interactions (
10,
11).
To determine whether SARS-CoV-2 can use NRP1 for virus entry and infectivity, we generated lentiviral particles pseudotyped with the SARS-CoV-2 S protein. Pseudoviruses are well suited for virus entry assays, as they allow viral entry to be distinguished from other virus life-cycle steps. Human embryonic kidney 293 T (HEK-293T) cells, which have almost no detectable
ACE2 and
NRP1 transcripts (fig. S1), were transfected with plasmids that encode the two established host factors (
4), human ACE2 and the transmembrane protease serine 2 (TMPRSS2), or NRP1. When expressed alone, ACE2 rendered cells susceptible to infection (
Fig. 1A). Although NRP1 did not promote infection in HEK-293T cells, its coexpression with ACE2 and TMPRSS2 markedly enhanced infection (
Fig. 1, A and B). NRP1 expression increased infection in Caco-2 cells, which endogenously express ACE2 (
12) (
Fig. 1C and fig. S1D), showing that NRP1 can potentiate infection in the presence of other host factors. To test the specificity of NRP1-dependent virus entry, we developed monoclonal antibodies (mAbs) that were designed to functionally block the extracellular b1b2 domain of NRP1, which is known to mediate binding to CendR peptides (
13). The mAb3 was observed to bind to the recombinant b1b2 domain of wild-type (WT) NRP1 but not to the triple-mutant b1b2 domain (S346A, E348A, and T349A in the CendR binding pocket) (fig. S2A). The potency of the mAbs in preventing cellular binding and internalization of NRP ligands was tested using 80-nm silver nanoparticles (AgNP) coated with the prototypic NRP1-binding CendR peptide RPARPAR
OH (
9) (fig. S2B). mAb3 efficiently blocked AgNP-CendR binding (fig. S2C) and internalization (fig. S2, D and E), whereas another monoclonal antibody, mAb2, had no effect and was used as a control in further experiments. Treatment of HEK-293T with mAb3 significantly reduced infection by SARS-CoV-2 pseudoviruses in cells expressing ACE2, TMPRSS2, and NRP1 (
Fig. 1D), but not in cells expressing ACE2 and TMPRSS2 only (fig. S2F). When SARS-CoV-2 pseudovirus was preincubated with recombinant, soluble extracellular b1b2 domain of NRP1, the wild type significantly reduced infection compared with the triple mutant (
Fig. 1E and fig. S2G).
Next, we explored the role of NRP1 using SARS-CoV-2 isolated from COVID-19 patients from the Helsinki University Hospital. We used WT SARS-CoV-2 and a cleavage-impaired SARS-CoV-2 mutant that was isolated from Vero-E6 cells, which rapidly accumulate mutations at the furin cleavage site of the S protein during passaging (
Fig. 2, A and B) (
14). First, we confirmed that furin cleaved the WT, but not the mutant, SARS-CoV-2 S protein by analyzing S protein processing in Chinese hamster ovary cells with functional (parental) or deficient (FD11) furin enzyme (fig. S3) (
15). Next, we validated that exogenous ACE2 expression rendered HEK-293T cells susceptible to infection with SARS-CoV-2 (
Fig. 2, C and D). NRP1 expression alone caused lower levels of infection, which were detectable only with increasing virus titer (
Fig. 2, C and D). We then compared the ability of WT and mutant SARS-CoV-2 to infect HEK-293T that stably express ACE2; ACE2 and TMPRSS2; or ACE2, TMPRSS2, and NRP1. Infection of these cell lines by the WT, but not the mutant, virus increased in the presence of NRP1, providing further evidence that NRP1 requires a furin-cleaved substrate for its effects (
Fig. 2, E and F). We studied the effect of the NRP1-blocking antibody, mAb3, on infection of Caco-2 cells by WT and mutant SARS-CoV-2 and found that preincubation with NRP1-blocking antibody reduced WT virus infection by ~40%, whereas the control mAb2 had no effect (
Fig. 2, G and H). NRP1-blocking antibody had no effect on the infection by the mutated virus (
Fig. 2, G and H).
Cleavage of SARS-CoV-2 S protein at the S1-S2 site generates the C-terminal end sequence TQTNSPRRAR
OH. To determine whether this specific sequence can function as a substrate for NRP1, we used AgNPs coated with TQTNSPRRAR
OH peptide or different control peptides, including one with a terminal amide group (TQTNSPRRAR
NH2), which reduces NRP1 binding (
9) (
Fig. 3A). We found that AgNP-TQTNSPRRAR
OH, but not control AgNPs, were efficiently taken up by HEK-293T cells expressing NRP1 (
Fig. 3, B and C). Next, we determined whether AgNP-TQTNSPRRAR
OH particles were also internalized into cells in vivo. We chose to study nanoparticle entry in the mouse olfactory epithelium, owing to the known expression of NRP1 in the olfactory system (
16), including olfactory neuronal cells of the epithelium (fig. S4). AgNPs-TQTNSPRRAR
OH and control AgNP-TQTNSPRRAR
NH2 were administered into the nose of anesthetized adult mice. Six hours after administration, we observed a significantly larger uptake of AgNP-TQTNSPRRAR
OH than of AgNP-TQTNSPRRAR
NH2 into the olfactory epithelium (
Fig. 3, D and E) and, unexpectedly, into neurons and blood vessels of the cortex (
Fig. 3, F and G). Similar results were obtained for AgNPs coated with the prototypic NRP1-binding CendR peptide RPARPAR
OH (fig. S5).
Having obtained evidence for a role of NRP1 in cell entry of SARS-CoV-2, we examined whether NRP1 expression correlated with the detection of virus RNA in single-cell transcriptomes. For these analyses, we used published single-cell RNA sequencing (scRNA-seq) datasets of cultured experimentally infected human bronchial epithelial cells and cells isolated from bronchoalveolar lavage fluid (BALF) of severely affected COVID-19 patients (
17). Among the proposed entry and amplification factors,
NRP1,
FURIN, and
TMPRSS11A were enriched in SARS-CoV-2–infected cells compared with noninfected cells (fig. S6). We also detected increased expression of these proteins after infection (fig. S6). In addition, RNA expression of
NRP1 and its homolog
NRP2 was elevated in SARS-CoV-2–positive cells compared with adjacent cells in the BALF of severely affected COVID-19 patients (fig. S7).
Because the availability of virus receptors and entry cofactors on the surface of host cells determines infectivity, we compared the expression patterns of
ACE2 and
NRP1 in published scRNA-seq datasets of human lung tissue (
18) and human olfactory epithelium (
19). Whereas
ACE2 was detected at very low levels, both
NRP1 and
NRP2 were abundantly expressed in almost all pulmonary and olfactory cells, with the highest levels of expression in endothelial cells (figs. S8 and S9). We confirmed these results by examining NRP1 immunoreactivity in human autopsy tissue and detected NRP1 in the epithelial surface layer of the human respiratory and olfactory epithelium (fig. S10A). ACE2 was hardly detectable in these tissues (fig. S10B). Within the olfactory epithelium, NRP1 was also observed in cells positive for oligodendrocyte transcription factor 2 (OLIG2), which is mostly expressed by olfactory neuronal progenitors (fig. S10C).
In light of the widely reported disturbance of olfaction in a large fraction of COVID-19 patients (
20,
21) and the enrichment of NRPs in the olfactory epithelium, we analyzed a series of autopsies from six COVID-19 patients and eight noninfected control patients to determine whether SARS-CoV-2 could infect NRP1-positive cells (
Fig. 4 and table S1). Using antibodies against the S protein, we detected infection of the olfactory epithelium in five of six COVID-19 patients. The infected olfactory epithelial cells showed high expression of NRP1 (
Fig. 4, A and B). Additional costaining indicated infection of cells positive for OLIG2 (
Fig. 4B and fig. S11).
There is limited knowledge about the virus–host interactions that determine cellular entry of SARS-CoV-2. Viruses display considerable redundancy and flexibility because they can exploit weak multivalent interactions to enhance affinity. To date, studies of SARS-CoV-2 entry have focused almost entirely on ACE2, which is expressed at very low protein levels in respiratory and olfactory epithelial cells (
22). This raises the possibility that cofactors are required to facilitate virus–host cell interactions in cells with low ACE2 expression. NRP1 could represent such an ACE2 potentiating factor by promoting the interaction of the virus with ACE2. The reason a number of viruses (
23–
26) use NRPs as entry factors may be their high expression on epithelia facing the external environment and their function in enabling cell, vascular, and tissue penetration (
9,
13).
Acknowledgments
We thank R. Müller, K. Schulz, and U. Scheidt for expert technical assistance; S. Osborne for proofreading the manuscript, and the DNA Dream Lab facility and K. Kogan for design and cloning of plasmids.
Funding: The work in Munich and Göttingen was supported by grants from the German Research Foundation (SPP2191, TRR128-2, TRR274-1, SyNergy Excellence Cluster, EXC2145, Projekt ID390857198, EXC 2067/1- 390729940, and STA 1389/5-1), the ERC (Consolidator Grant to M.S.), and the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation. The work at the University of Helsinki was supported by the University of Helsinki and by donations from Finnish colleagues to whom we are very grateful. The Academy of Finland supported G.B. (318434), O.V. (336490), S.J.B. (315950 and 336471), and J.H. (1308613 and 1314119). O.V. was supported by Jane and Aatos Erkko Foundation, EU Horizon 2020 program VEO (874735), and Helsinki University Hospital Funds (TYH2018322). S.J.B. was supported by the Swedish Research Foundation and M.A. by the Marie Sklodowska-Curie Actions (799929). M.J. is supported by The Australian Research Council’s Discovery Early Career Researcher Award (DE190100565). F.A.M. is supported by an Australian National Health and Medical Research Council Senior Research Fellowship (GNT1155794). T.T. and A.T. are supported by the European Regional Development Fund (project 2014-2020.4.01.15-0012), Wellcome Trust International Fellowship WT095077MA, European Research Council grant GLIOGUIDE, and the Estonian Research Council (grants PRG230 and EAG79 to T.T.).
Author contributions: G.B., M.S., and A.H. conceived the project. L.C.C., R.O., L.D.P., M.D., J.F., S.K., F.v.d.M., K.K., M.A., and L.S. designed and carried out experiments. A.T., T.T., L.L., O.V., J.H., O.G., H.K.K., P.O., and M.J., developed and provided tools. L.C.C., R.O., L.D.P., M.D., J.F., S.K., T.K., C.S., T.S., M.J., F.A.M., S.J.B., J.H., and O.V. analyzed the data or supervised data acquisition. L.C.C., R.O., L.D.P., M.D., J.F., S.K., T.K., and O.G. visualized the data. T.K. and O.G. performed the scRNA-seq data analysis. M.S.W., B.M., C.S., and H.K.K. provided human samples. G.B. and M.S. wrote the manuscript. G.B. and M.S. supervised the project.
Competing interests: T.T., O.V., and G.B. have a pending patent on the monoclonal antibody 3 (mAb3) against the NRP1 b1 domain for SARS-CoV-2 inhibition.
Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper or the supplementary materials. This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. To view a copy of this license, visit
https://creativecommons.org/licenses/by/4.0/. This license does not apply to figures/photos/artwork or other content included in the article that is credited to a third party; obtain authorization from the rights holder before using such material.
RE: Neuropilins, from cancer to COVID-19
The results obtained by Cantuti-Castelvetri et al. and Daly et al. open up new perspectives in the fight of COVID-19. Indeed, both articles revealed that Neuropilin transmembrane receptors (NRPs) interact with the SARS-CoV-2 virus and potentiate its entry and infectivity. This matters because NRPs are already known in the oncology field, and these discoveries open avenues to promising repurposing therapies.
Both articles (1, 2) focus on the first step of SARS-CoV-2 infection involving the viral Spike (S) protein for host cell attachment and entry and which is cleaved by the host protease furin into two associated polypeptides: S1 and S2. Daly et al. showed that the C-terminus of the S1 protein named CendR binds to NRP, while Cantuti-Castelvetri et al. demonstrated that NRP1 significantly potentiates SARS-CoV-2 infectivity by using a SARS-CoV-2 mutant with an altered furin cleavage site or by blocking the extracellular b1b2-domain of NRP1 known to bind to CendR peptides.
NRPs are transmembrane proteins involved in a number of physiological processes, but have also been associated with growth, invasiveness and poor prognosis in many cancers, and their high expression in tumors, blood vessels and immune cells makes them relevant oncology targets (3). This means that drugs already developed in the context of oncology could be considered as antiviral strategy as they may be able to block SARS-Cov-2 cell entry mechanism mediated by NRP1: for instance a humanized monoclonal antibody specific for extracellular domains b1 and b2 of NRP1 named vesencumab targets precisely the domains which interact with the SARS-CoV-2 and which potentiate virus cell entry and infectivity. The treatment was well tolerated in the dose-escalation trials with premedication including dexamethasone (4).
While this will hopefully deliver positive results in the fight against the pandemic, it also reminds us of the value of multidisciplinarity and integrated research.
Acknowledgements: MDC and AT are very grateful to Fondation ARC pour la Recherche sur le Cancer (COVID202001321).
REFERENCES
AT has served in a consulting/advisory role and or received honoraria for Amgen, Merck, Servier, Mylan and has received travel, accommodations, and expenses from Astra-Zeneca, Pfizer, Sanofi. MDC has no conflicts of interest to declare.1. L. Cantuti-Castelvetri et al., Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science. 370, 856‑860 (2020).
2. J. L. Daly et al., Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science. 370, 861‑865 (2020).
3. A. Dumond, G. Pagès, Neuropilins, as Relevant Oncology Target: Their Role in the Tumoral Microenvironment. Front. Cell Dev. Biol. 8, 662 (2020)
4. C. D. Weekes et al., A phase I study of the human monoclonal anti-NRP1 antibody MNRP1685A in patients with advanced solid tumors. Invest New Drugs. 32, 653‑660 (2014).
NRP-1 ligands as modulators of SARS-CoV2 entry ?
We read with interest the two articles published in the Science Journal (1, 2) showing the role of Neuropilin-1 (NRP-1) in the entry of the SARS-CoV2 virus. Interestingly, we and other have shown that NRP-1 is a co-receptor already used by other viruses such as HTLV-1 (3) and EBV (4), which suggest the phylogenetic importance of this transmembrane protein.
In our laboratory, we are working on the role of NRP-1 in virology and immunology (5). The main feature of this co-receptor is to form complexes with multiple other receptors (6). Hence, there is a competition between receptors to complex with NRP-1, which may determine their abilities both quantitatively and qualitatively to transduce signals (7). It is tempting to hypothesize that the occupancy of NRP-1 with one receptor may thus decrease its availability for virus entry. Recent proteomics work has shown that NRP-1 can form a complex with the α7 nicotinic receptor in mice (8). Both receptors are expressed in the human nasal and pulmonary epitheliums (9–11).
Several independent epidemiological studies have shown that the prevalence of humoral anti- SARS-CoV2 immunity was lower in smokers in homogeneous populations (12–18), whereas recent meta-analyses suggest that infected smokers have an increased COVID-19-related mortality (19, 20) as observed in many respiratory infectious diseases (21).
The link between the low anti-SARS-CoV2 seroprevalence and smoking seems counter-intuitive, especially since smoking is associated with an increase in the expression of ACE2, the main receptor of the SARS-CoV2 virus (22, 23). We hypothesize that the administration of high dose nicotine to the respiratory tract causes a preferential interaction between NRP-1 and the α7 nicotinic receptor (or nicotinic receptor family), inducing a lower availability of NRP-1 to form complex with ACE2 for virus entry. This hypothesis requires, however, experimental validation and may have therapeutic implications.
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2. J. L. Daly, B. Simonetti, K. Klein, K.-E. Chen, M. K. Williamson, C. Antón-Plágaro, D. K. Shoemark, L. Simón-Gracia, M. Bauer, R. Hollandi, U. F. Greber, P. Horvath, R. B. Sessions, A. Helenius, J. A. Hiscox, T. Teesalu, D. A. Matthews, A. D. Davidson, B. M. Collins, P. J. Cullen, Y. Yamauchi, Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science. 370, 861–865 (2020).
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Virus-neuropilin-1 interaction and animal models of SARS-CoV-2 infection
The nice and elegant article by Dr Ludovico Cantuti-Castelvetri and coworkers (1) offers an absolutely reliable basis for deciphering the apparent discrepancies between angiotensin-converting enzyme-2 (ACE2)-expressing cells and tissues, on one side, and Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2) tissue tropism, on the other.
In this respect, the prominent expression of neuropilin-1 (NP1) on behalf of the neuro-olfactory epithelium provides biological plausibility for "anosmia", a sign commonly experienced by SARS-CoV-2-infected patients. Still of interest, endothelial cells - the damage of which is a key feature in the pathogenesis of SARS-CoV-2 infection, with special emphasis on those individuals affected by severe CoronaVirus Disease-2019 (CoViD-19) phenotypes - were reported to express consistent NP1 levels by the same Authors (1), with this finding representing another plausible basis for SARS-CoV-2 dissemination throughout the human host's body.
Nevertheless, while ACE2 is widely expressed also by endothelial cells (2), it should be additionally emphasized that pericytes - perivascular cells playing a key role in the maintenance of microvessel integrity - exhibit, at their turn, very high expression levels of ACE2, with SARS-CoV-2-induced damage (and dysfunction) of pericytes having been suggested as a pathogenetic driver of the severe vasculopathy found in CoViD-19-affected individuals (3).
It would be interesting to investigate, in my opinion, if (and to what extent) human pericytes do also express NP1 and, to this aim, a parallel investigation of the body cells and tissues expressing - either simultaneously, or separately - ACE2 and NP1 in a number of SARS-CoV-2-susceptible species (like macaques, cats, minks, hamsters, etc.) would be also recommendable. By doing so, in fact, the already existing data on the percentage(s) of sequence homology between human and animal ACE2 coronaviral receptors could become accompanied by new, relevant data regarding the percentage(s) of NP1 sequence homology between the aforementioned (and, possibly, other SARS-CoV-2-susceptible) species and the human one.
This could greatly help, among others, in "candidating" a given animal species as a potentially valuable model in the comparative pathogenetic study of human SARS-CoV-2 infection, thereby also contributing to shed light on the "past" and "future" trajectories of the virus, with special reference to its origin as well as to its "spillover and spillback" dynamics from animals to mankind (and viceversa).
References
1) Cantuti-Castelvetri L., et al. (2020) - Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science 20 Oct 2020: eabd2985 (DOI: 10.1126/science.abd2985).
2) Donoghue M. (2000) - A novel angiotensin-converting enzyme-related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1-9. Circulation Research 87:E1-E9.
3) Burel-Vandenbos F., et al. (2020) - Pulmonary vascular pathology in CoViD-19.
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