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Research Article

Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit

View ORCID ProfileYunxiao Zhang, View ORCID ProfileWan-Jin Lu, David P. Bulkley, Jiahao Liang, Arthur Ralko, Shuo Han, Kelsey J. Roberts, Anping Li, Wonhwa Cho, Yifan Cheng, View ORCID ProfileAashish Manglik, and Philip A. Beachy
PNAS November 17, 2020 117 (46) 28838-28846; first published November 2, 2020; https://doi.org/10.1073/pnas.2011560117
Yunxiao Zhang
aInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305;
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  • ORCID record for Yunxiao Zhang
Wan-Jin Lu
aInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305;
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David P. Bulkley
bDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158;
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Jiahao Liang
cDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
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Arthur Ralko
dDepartment of Chemistry, University of Illinois at Chicago, Chicago, IL 60607;
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Shuo Han
aInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305;
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Kelsey J. Roberts
eDepartment of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
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Anping Li
aInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305;
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Wonhwa Cho
dDepartment of Chemistry, University of Illinois at Chicago, Chicago, IL 60607;
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Yifan Cheng
bDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158;
fHoward Hughes Medical Institute, University of California, San Francisco, CA 94158;
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Aashish Manglik
cDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158;
gDepartment of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158;
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  • For correspondence: aashish.manglik@ucsf.edu pbeachy@stanford.edu
Philip A. Beachy
aInstitute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305;
eDepartment of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
hDepartment of Urology, Stanford University School of Medicine, Stanford, CA 94305;
iDepartment of Chemical and Systems Biology (by courtesy), Stanford University School of Medicine, Stanford, 94305
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  • For correspondence: aashish.manglik@ucsf.edu pbeachy@stanford.edu
  1. Contributed by Philip A. Beachy, September 23, 2020 (sent for review June 5, 2020; reviewed by James Briscoe and Volodymyr M. Korkhov)

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Significance

Precise manipulation of Hedgehog pathway activity holds great value for biological research and clinical applications, but pathway agonists amenable to engineering have been lacking. We selected a nanobody that potentially targets the conformational changes of the Hedgehog receptor Patched1 and demonstrated that this nanobody potently activates the pathway in vivo. This nanobody can serve as the basis for mechanistic studies of Hedgehog pathway activation and for potential therapeutic applications. Our method may further apply to the investigation of other related transporters in the Resistance-Nodulation-Division superfamily.

Abstract

Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental, and agents amenable to tissue targeting for therapeutic application have been lacking. We have developed an agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1 (PTCH1). This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 “switch helix,” as revealed by our cryogenic electron microscopy structure. Nanobody-binding likely traps Patched in one stage of its transport cycle, thus preventing substrate movement through the Patched1 sterol conduit. Unlike the native Hedgehog ligand, this nanobody does not require lipid modifications for its activity, facilitating mechanistic studies of Hedgehog pathway activation and the engineering of pathway activating agents for therapeutic use. Our conformation-selective nanobody approach may be generally applicable to the study of other PTCH1 homologs.

  • hedgehog
  • cryo-EM
  • nanobody
  • Patched
  • transporter

Footnotes

  • ↵1Present address: Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037.

  • ↵2To whom correspondence may be addressed. Email: aashish.manglik{at}ucsf.edu or pbeachy{at}stanford.edu.
  • Author contributions: Y.Z., W.C., Y.C., A.M., and P.A.B. designed research; Y.Z., W.-J.L., D.P.B., J.L., A.R., S.H., K.J.R., A.L., and A.M. performed research; Y.Z., W.-J.L., D.P.B., and P.A.B. analyzed data; and Y.Z. and P.A.B. wrote the paper.

  • Reviewers: J.B., The Francis Crick Institute; and V.M.K., Paul Scherrer Institute.

  • The authors declare no competing interest.

  • This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2011560117/-/DCSupplemental.

Data Availability.

Structure data have been deposited in the Protein Data Bank (accession code 7K65) and Electron Microscope Data Bank (accession code EMD-22689) (51). All study data are included in the article and supporting information.

Published under the PNAS license.

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Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit
Yunxiao Zhang, Wan-Jin Lu, David P. Bulkley, Jiahao Liang, Arthur Ralko, Shuo Han, Kelsey J. Roberts, Anping Li, Wonhwa Cho, Yifan Cheng, Aashish Manglik, Philip A. Beachy
Proceedings of the National Academy of Sciences Nov 2020, 117 (46) 28838-28846; DOI: 10.1073/pnas.2011560117

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Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit
Yunxiao Zhang, Wan-Jin Lu, David P. Bulkley, Jiahao Liang, Arthur Ralko, Shuo Han, Kelsey J. Roberts, Anping Li, Wonhwa Cho, Yifan Cheng, Aashish Manglik, Philip A. Beachy
Proceedings of the National Academy of Sciences Nov 2020, 117 (46) 28838-28846; DOI: 10.1073/pnas.2011560117
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