Abstract
Host cellular receptors play key roles in the determination of virus tropism and pathogenesis. However, little is known about SARS-CoV-2 host receptors with the exception of ACE2. Furthermore, ACE2 alone cannot explain the multi-organ tropism of SARS-CoV-2 nor the clinical differences between SARS-CoV-2 and SARS-CoV, suggesting the involvement of other receptor(s). Here, we performed genomic receptor profiling to screen 5054 human membrane proteins individually for interaction with the SARS-CoV-2 capsid spike (S) protein. Twelve proteins, including ACE2, ASGR1, and KREMEN1, were identified with diverse S-binding affinities and patterns. ASGR1 or KREMEN1 is sufficient for the entry of SARS-CoV-2 but not SARS-CoV in vitro and in vivo. SARS-CoV-2 utilizes distinct ACE2/ASGR1/KREMEN1 (ASK) receptor combinations to enter different cell types, and the expression of ASK together displays a markedly stronger correlation with virus susceptibility than that of any individual receptor at both the cell and tissue levels. The cocktail of ASK-related neutralizing antibodies provides the most substantial blockage of SARS-CoV-2 infection in human lung organoids when compared to individual antibodies. Our study revealed an interacting host receptome of SARS-CoV-2, and identified ASGR1 and KREMEN1 as alternative functional receptors that play essential roles in ACE2-independent virus entry, providing insight into SARS-CoV-2 tropism and pathogenesis, as well as a community resource and potential therapeutic strategies for further COVID-19 investigations.
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Data availability
The receptor expression levels in each tissue were obtained from the Human Protein Atlas (https://www.proteinatlas.org/). The receptor expression levels in PBMC populations were obtained from the Human Protein Atlas (https://www.proteinatlas.org/) and Human Cell Atlas (http://immunecellatlas.net/). The receptor expression levels in stable cell lines were obtained from Cancer Cell Line Encyclopedia (https://portals.broadinstitute.org/ccle/). ScRNA-seq profiles of the upper airway tract of patients with COVID-19 and metadata were obtained from the Magellan COVID-19 Data Explorer at https://digital.bihealth.org. ScRNA-seq profiles of SARS-CoV-2 infected human bronchial epithelial cells (HBECs) in vitro were from NCBI GEO dataset GSE166766. All data supporting the findings of this study are available within the paper or in the supplementary information.
Change history
01 April 2022
A Correction to this paper has been published: https://doi.org/10.1038/s41422-022-00654-6
References
Zhu, N. et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733 (2020).
Huang, C., Wang, Y. & Li, X. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China (vol 395, pg 497, 2020). Lancet 395, 496–496 (2020).
Hoffmann, M. et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 181, 271–280 e278 (2020).
Li, W. H. et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature 426, 450–454 (2003).
Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–27 (2020).
Puelles, V. G. et al. Multiorgan and Renal Tropism of SARS-CoV-2. N. Engl. J. Med. 383, 590–592 (2020).
Gupta, A. et al. Extrapulmonary manifestations of COVID-19. Nat. Med. 26, 1017–1032 (2020).
Schneider-Schaulies, J. Cellular receptors for viruses: links to tropism and pathogenesis. J. Gen. Virol. 81, 1413–1429 (2000).
Milone, M. C. & Fitzgerald-Bocarsly, P. The mannose receptor mediates induction of IFN-alpha in peripheral blood dendritic cells by enveloped RNA and DNA viruses. J. Immunol. 161, 2391–2399 (1998).
Tseng, C. T., Perrone, L. A., Zhu, H., Makino, S. & Peters, C. J. Severe acute respiratory syndrome and the innate immune responses: modulation of effector cell function without productive infection. J. Immunol. 174, 7977–7985 (2005).
Tay, M. Z., Poh, C. M., Renia, L., MacAry, P. A. & Ng, L. F. P. The trinity of COVID-19: immunity, inflammation and intervention. Nat. Rev. Immunol. 20, 363–374 (2020).
Lukassen, S. et al. SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells. EMBO J 39, e105114 (2020).
Chu, H. et al. Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study. Lancet Microbe 1, e14–e23 (2020).
Zou, L. et al. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N. Engl. J. Med. 382, 1177–1179 (2020).
Hou, Y. J. et al. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell 182, 429–446 e414 (2020).
Hikmet, F. et al. The protein expression profile of ACE2 in human tissues. Mol. Syst. Biol. 16, e9610 (2020).
Sungnak, W. et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat. Med. 26, 681–687 (2020).
Chua, R. L. et al. COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis. Nat. Biotechnol. 38, 970–979 (2020).
Ren, X. et al. COVID-19 immune features revealed by a large-scale single cell transcriptome atlas. Cell 184, 1895–1913 (2021).
Deng, M. et al. A motif in LILRB2 critical for Angptl2 binding and activation. Blood 124, 924–935 (2014).
Deng, M. et al. LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration. Nature 562, 605–609 (2018).
Zheng, J. et al. Inhibitory receptors bind ANGPTLs and support blood stem cells and leukaemia development. Nature 485, 656–660 (2012).
Jeffers, S. A. et al. CD209L (L-SIGN) is a receptor for severe acute respiratory syndrome coronavirus. Proc. Natl. Acad. Sci. USA 101, 15748–15753 (2004).
Wrapp, D. et al. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science 367, 1260–1263 (2020).
Letko, M., Marzi, A. & Munster, V. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nat. Microbiol. 5, 562–569 (2020).
Wu, L. et al. Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2. Cell Discov 6, 68 (2020).
Bao, L. et al. The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature 583, 830–833 (2020).
Sun, J. et al. Generation of a Broadly Useful Model for COVID-19 Pathogenesis, Vaccination, and Treatment. Cell 182, 734–743 e735 (2020).
Liu, L. et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature 584, 450–456 (2020).
Chi, X. et al. A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science 369, 650–655 (2020).
Lu, G., Wang, Q. & Gao, G. F. Bat-to-human: spike features determining ‘host jump’ of coronaviruses SARS-CoV, MERSCoV, and beyond. Trends Microbiol 23, 468–478 (2015).
Wang, N. et al. Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD. Cell Rep 28, 3395–3405 e3396 (2019).
Mao, B. et al. Kremen proteins are Dickkopf receptors that regulate Wnt/beta-catenin signalling. Nature 417, 664–667 (2002).
Staring, J. et al. KREMEN1 Is a Host Entry Receptor for a Major Group of Enteroviruses. Cell Host Microbe 23, 636–643 e635 (2018).
Seidah, N. G., Chretien, M. & Mbikay, M. The ever-expanding saga of the proprotein convertases and their roles in body homeostasis: emphasis on novel proprotein convertase subtilisin kexin number 9 functions and regulation. Curr. Opin. Lipidol. 29, 144–150 (2018).
Saunier, B. et al. Role of the asialoglycoprotein receptor in binding and entry of hepatitis C virus structural proteins in cultured human hepatocytes. J. Virol. 77, 546–559 (2003).
Xiao, F. et al. Evidence for Gastrointestinal Infection of SARS-CoV-2. Gastroenterology 158, 1831–1833 e1833 (2020).
Phipps, M. M. et al. Acute Liver Injury in COVID-19: Prevalence and Association with Clinical Outcomes in a Large US Cohort. Hepatology 72, 807–817 (2020).
Wan, J. et al. Human-IgG-Neutralizing Monoclonal Antibodies Block the SARS-CoV-2 Infection. Cell Rep 32, 107918 (2020).
Ravindra, N. G. et al. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS Biol 19, e3001143 (2021).
Han, Y. et al. Identification of SARS-CoV-2 inhibitors using lung and colonic organoids. Nature 589, 270–275 (2021).
Jacob, F. et al. Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium. Cell Stem Cell 27, 937–950 e939 (2020).
Salahudeen, A. A. et al. Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Nature 588, 670–675 (2020).
Yang, L. et al. A Human Pluripotent Stem Cell-based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids. Cell Stem Cell 27, 125–136 e127 (2020).
Zhou, J. et al. Infection of bat and human intestinal organoids by SARS-CoV-2. Nat. Med. 26, 1077–1083 (2020).
Daniloski, Z. et al. Identification of required host factors for SARS-CoV-2 infection in human cells. Cell 184, 92–105 e116 (2021).
Schneider, W. M. et al. Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks. Cell 184, 120–132 e114 (2021).
Hoffmann, H. H. et al. Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors. Cell Host Microbe 29, 267–280 e265 (2021).
Cantuti-Castelvetri, L. et al. Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science 370, 856–860 (2020).
Daly, J. L. et al. Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science 370, 861–865 (2020).
Wang, K. et al. CD147-spike protein is a novel route for SARS-CoV-2 infection to host cells. Signal Transduct. Target Ther 5, 283 (2020).
Wang, S. et al. AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells. Cell Res 31, 126–140 (2021).
Liao, M. et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat. Med. 26, 842–844 (2020).
Zhou, Y. G. et al. Pathogenic T-cells and inflammatory monocytes incite inflammatory storms in severe COVID-19 patients. Natl. Sci. Rev. 7, 998–1002 (2020).
Schoeman, D. & Fielding, B. C. Coronavirus envelope protein: current knowledge. Virol. J. 16, 69 (2019).
Lontok, E., Corse, E. & Machamer, C. E. Intracellular targeting signals contribute to localization of coronavirus spike proteins near the virus assembly site. J. Virol. 78, 5913–5922 (2004).
Gordon, D. E. et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459–468 (2020).
Gaillard, D. et al. beta-catenin is required for taste bud cell renewal and behavioral taste perception in adult mice. PLoS Genet 13, e1006990 (2017).
Liu, F. et al. Wnt-beta-catenin signaling initiates taste papilla development. Nat. Genet. 39, 106–112 (2007).
Kurimoto, A. et al. The absence of core fucose up-regulates GnT-III and Wnt target genes: a possible mechanism for an adaptive response in terms of glycan function. J. Biol. Chem. 289, 11704–11714 (2014).
Menni, C. et al. Real-time tracking of self-reported symptoms to predict potential COVID-19. Nat. Med. 26, 1037–1040 (2020).
Xydakis, M. S. et al. Smell and taste dysfunction in patients with COVID-19. Lancet Infect. Dis. 20, 1015–1016 (2020).
Schmidt, F. et al. Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses. J. Exp. Med. 217, e20201181 (2020).
Acknowledgements
We thank Cheng Cheng Zhang of UT Southwestern Medical Center and Guy Riddihough of Life Science Editors for the discussions on and revision of the paper and the staff at the BSL3 Laboratory of Fudan University for helping with the experiments. We thank Aihua Zheng of Institute of Zoology, Chinese Academy of Science, for providing replication-competent rVSV-GFP/SARS-CoV-2 S chimeric virions. This study was funded by the National Natural Science Foundation of China (81873438, 81873922, 81971921, 81830054 and 81772723, 32125013), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16020905), the Basic Frontier Science Research Program of Chinese Academy of Sciences (No. ZDBS-LY-SM015), the National Key R&D Program of China (2020YFA0509002 and 2017YFA0505500), and the National Key Project for Infectious Diseases of China (2018ZX10301208 and 2018ZX10302207-004-002).
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Z.L., M.L., Y.X., Yun Z. and D.G. conceived the project. Y.G., XY.Z. and J.C., with help from J.Z., X.J., J.W., J.Y., X.Z., and Yun Z., performed the receptor profiling studies and the characterization of receptor-ligand interactions. M.L., H.G., J.X., X.J. and J.W. assessed the virus sensitivity of cell lines. J.C., J.H. and D.G. performed the organoid experiments. J.C., H.G. and Y.W., with help from G.S., X.J., F.L., G.H., Yuanfei Z., S.D., Yunkai Z., R.Z. and D.Q., performed the virus-related experiments. Z.L., M.L., Y.G., J.C., H.G. and Y.W. performed the bioinformatics analysis and analyzed the data. Z.L., M.L., Y.X., G.X., Yun Z. and D.G. wrote the paper.
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M.L., Z.L., Yun Z., H.G. and Y.X. are listed as inventors on a pending patent application for the newly identified S receptors described in this paper. The other authors declare no competing interests.
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Gu, Y., Cao, J., Zhang, X. et al. Receptome profiling identifies KREMEN1 and ASGR1 as alternative functional receptors of SARS-CoV-2. Cell Res 32, 24–37 (2022). https://doi.org/10.1038/s41422-021-00595-6
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DOI: https://doi.org/10.1038/s41422-021-00595-6
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