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TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry

TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry
TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry
SARS-CoV-2 is associated with broad tissue tropism, a characteristic often determined by the availability of entry receptors on host cells. Here, we show that TMEM106B, a lysosomal transmembrane protein, can serve as an alternative receptor for SARS-CoV-2 entry into angiotensin-converting enzyme 2 (ACE2)-negative cells. Spike substitution E484D increased TMEM106B binding, thereby enhancing TMEM106B-mediated entry. TMEM106B-specific monoclonal antibodies blocked SARS-CoV-2 infection, demonstrating a role of TMEM106B in viral entry. Using X-ray crystallography, cryogenic electron microscopy (cryo-EM), and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we show that the luminal domain (LD) of TMEM106B engages the receptor-binding motif of SARS-CoV-2 spike. Finally, we show that TMEM106B promotes spike-mediated syncytium formation, suggesting a role of TMEM106B in viral fusion. Together, our findings identify an ACE2-independent SARS-CoV-2 infection mechanism that involves cooperative interactions with the receptors heparan sulfate and TMEM106B.
ACE2-independent entry, SARS-CoV-2, TMEM106B, TMEM106B crystal structure, antibody neutralization, coronavirus, cryo-EM, entry receptor
0092-8674
3427-3442.e22
Baggen, Jim
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Jacquemyn, Maarten
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Persoons, Leentje
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Vanstreels, Els
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Pye, Valerie E
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Calvaresi, Valeria
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Wrobel, Antoni G
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Martin, Stephen R
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Roustan, Chloë
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Cronin, Nora B
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Reading, Eamonn
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Thibaut, Hendrik Jan
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Vercruysse, Thomas
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Maes, Piet
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De Smet, Frederik
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Yee, Angie
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Roell, Marina
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Franco-Hernandez, Natalia
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Rhinn, Herve
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Mamchak, Alusha Andre
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Ah Young-Chapon, Maxime
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Brown, Eric
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Cherepanov, Peter
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Daelemans, Dirk
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et al.
Baggen, Jim
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Jacquemyn, Maarten
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Persoons, Leentje
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Vanstreels, Els
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Pye, Valerie E
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Calvaresi, Valeria
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Wrobel, Antoni G
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Martin, Stephen R
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Roustan, Chloë
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Cronin, Nora B
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Reading, Eamonn
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Thibaut, Hendrik Jan
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Vercruysse, Thomas
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Maes, Piet
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De Smet, Frederik
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Yee, Angie
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Nivitchanyong, Toey
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Roell, Marina
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Franco-Hernandez, Natalia
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Rhinn, Herve
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Mamchak, Alusha Andre
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Ah Young-Chapon, Maxime
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Brown, Eric
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Cherepanov, Peter
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Daelemans, Dirk
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Baggen, Jim, Jacquemyn, Maarten, Persoons, Leentje and Reading, Eamonn , et al. (2023) TMEM106B is a receptor mediating ACE2-independent SARS-CoV-2 cell entry. Cell, 186 (16), 3427-3442.e22. (doi:10.1016/j.cell.2023.06.005).

Record type: Article

Abstract

SARS-CoV-2 is associated with broad tissue tropism, a characteristic often determined by the availability of entry receptors on host cells. Here, we show that TMEM106B, a lysosomal transmembrane protein, can serve as an alternative receptor for SARS-CoV-2 entry into angiotensin-converting enzyme 2 (ACE2)-negative cells. Spike substitution E484D increased TMEM106B binding, thereby enhancing TMEM106B-mediated entry. TMEM106B-specific monoclonal antibodies blocked SARS-CoV-2 infection, demonstrating a role of TMEM106B in viral entry. Using X-ray crystallography, cryogenic electron microscopy (cryo-EM), and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we show that the luminal domain (LD) of TMEM106B engages the receptor-binding motif of SARS-CoV-2 spike. Finally, we show that TMEM106B promotes spike-mediated syncytium formation, suggesting a role of TMEM106B in viral fusion. Together, our findings identify an ACE2-independent SARS-CoV-2 infection mechanism that involves cooperative interactions with the receptors heparan sulfate and TMEM106B.

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More information

e-pub ahead of print date: 3 July 2023
Published date: 3 August 2023
Additional Information: Funding Information: We thank Niels Willems, Yanicka Smolders, Joni Punjwani, Nathalie van Winkel, Lotte Bral, Jitte Mollekens, and Kristien Minner for performing infections, qPCR, immunofluorescence, cloning, and cell line production and thank Katharina Coun, Jolien Timmermans, and Nathalie Thys for making pseudoviruses. We thank Elisabeth Heylen, Steven Carmans, and Dominique Schols for organizing central lab facilities. We thank John Skehel and David Bauer for suggestions to improve the manuscript; Kai Dallmeier and Johan Neyts for providing hamster anti-SARS-CoV-2 serum; Phil Walker and Andrew Purkiss (Francis Crick Institute) for computer, software, and synchrotron access support; and the staff of beamline I24 of the Diamond Light Source (Oxfordshire, UK) for assistance with data collection. The D.D. laboratory was supported by the Research Foundation – Flanders (FWO; G067423N), Alector LCC, and patent income. The P.C. laboratory and the Structural Biology of Disease Processes Laboratory (lead by Steve Gamblin) were supported by the Francis Crick Institute, funded by Cancer Research UK (FC001061 and FC001078), the UK Medical Research Council (FC001061 and FC001078), and the Wellcome Trust (FC001061 and FC001078). V.C. was supported by a post-doctoral position funded by King's College London, and E.R. was supported by a UKRI Future Leaders fellowship (MR/S015426/1). Cryo-EM data were collected at the London Consortium Electron Microscopy Facility at the Francis Crick Institute funded by the Wellcome Trust (206175/Z/17/Z to Prof. X. Zhang). J.B. L.P. and E.V. conducted infection assays. M.J. made DNA constructs and genetically modified cell lines. P.C. and C.R. produced recombinant proteins. V.E.P. and P.C. crystallized TMEM106BLD. V.E.P. performed X-ray crystallography and prepared cryo-EM samples. N.B.C. and P.C. acquired cryo-EM data. P.C. processed cryo-EM data. V.C. and E.R. conducted HDX-MS. A.G.W. and S.R.M. conducted biolayer interferometry. T.V. made pseudoviruses, which was supervised by H.J.T. P.M. isolated and sequenced SARS-CoV-2 strains. F.D.S. provided patient-derived glioblastoma cells. A.Y. T.N. and E.B. made anti-TMEM106B antibodies. A.Y. M.R. and N.F.-H. characterized anti-TMEM106B antibodies. H.R. A.A.M. M.A.Y.-C. and E.B. conceptualized and designed anti-TMEM106B antibody production and characterization. J.B. M.J. L.P. E.V. P.C. and D.D. designed the project. J.B. P.C. and D.D. wrote initial text drafts. M.J. L.P. E.V. V.E.P. A.G.W. V.C. H.J.T. A.Y. M.R. A.A.M. M.A.Y.-C. and E.B. reviewed and edited the manuscript. P.C. and D.D. supervised the project. A.A.M. A.Y. E.B. M.R. M.A.Y.-C. N.F.-H. and T.N. are employees of Alector LLC, and H.R. was an Alector employee at the time of manuscript conception and may have an equity interest in Alector, Inc. Several authors have patents related to TMEM106B-specific antibodies. Work in the D.D. laboratory was partially funded by Alector LCC. Funding Information: We thank Niels Willems, Yanicka Smolders, Joni Punjwani, Nathalie van Winkel, Lotte Bral, Jitte Mollekens, and Kristien Minner for performing infections, qPCR, immunofluorescence, cloning, and cell line production and thank Katharina Coun, Jolien Timmermans, and Nathalie Thys for making pseudoviruses. We thank Elisabeth Heylen, Steven Carmans, and Dominique Schols for organizing central lab facilities. We thank John Skehel and David Bauer for suggestions to improve the manuscript; Kai Dallmeier and Johan Neyts for providing hamster anti- SARS-CoV-2 serum; Phil Walker and Andrew Purkiss (Francis Crick Institute) for computer, software, and synchrotron access support; and the staff of beamline I24 of the Diamond Light Source (Oxfordshire, UK) for assistance with data collection. The D.D. laboratory was supported by the Research Foundation – Flanders ( FWO ; G067423N ), Alector LCC , and patent income. The P.C. laboratory and the Structural Biology of Disease Processes Laboratory (lead by Steve Gamblin) were supported by the Francis Crick Institute , funded by Cancer Research UK ( FC001061 and FC001078 ), the UK Medical Research Council ( FC001061 and FC001078 ), and the Wellcome Trust ( FC001061 and FC001078 ). V.C. was supported by a post-doctoral position funded by King’s College London , and E.R. was supported by a UKRI Future Leaders fellowship ( MR/S015426/1 ). Cryo-EM data were collected at the London Consortium Electron Microscopy Facility at the Francis Crick Institute funded by the Wellcome Trust ( 206175/Z/17/Z to Prof. X. Zhang). Publisher Copyright: © 2023 The Author(s)
Keywords: ACE2-independent entry, SARS-CoV-2, TMEM106B, TMEM106B crystal structure, antibody neutralization, coronavirus, cryo-EM, entry receptor

Identifiers

Local EPrints ID: 479995
URI: http://eprints.soton.ac.uk/id/eprint/479995
ISSN: 0092-8674
PURE UUID: 32ae4b31-5253-49fb-b3ee-656c79b22e11
ORCID for Eamonn Reading: ORCID iD orcid.org/0000-0001-8219-0052

Catalogue record

Date deposited: 31 Jul 2023 17:09
Last modified: 06 Jun 2024 02:17

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Contributors

Author: Jim Baggen
Author: Maarten Jacquemyn
Author: Leentje Persoons
Author: Els Vanstreels
Author: Valerie E Pye
Author: Valeria Calvaresi
Author: Antoni G Wrobel
Author: Stephen R Martin
Author: Chloë Roustan
Author: Nora B Cronin
Author: Eamonn Reading ORCID iD
Author: Hendrik Jan Thibaut
Author: Thomas Vercruysse
Author: Piet Maes
Author: Frederik De Smet
Author: Angie Yee
Author: Toey Nivitchanyong
Author: Marina Roell
Author: Natalia Franco-Hernandez
Author: Herve Rhinn
Author: Alusha Andre Mamchak
Author: Maxime Ah Young-Chapon
Author: Eric Brown
Author: Peter Cherepanov
Author: Dirk Daelemans
Corporate Author: et al.

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