Analysis of antibodies from HCV elite neutralizers identifies genetic determinants of broad neutralization

Creators: Weber, Timm; Potthoff, Julian; Bizu, Sven; Labuhn, Maurice; Dold, Leona; Schoofs, Till; Horning, Marcel; Ercanoglu, Meryem S.; Kreer, Christoph; Gieselmann, Lutz; Vanshylla, Kanika; Langhans, Bettina; Janicki, Hanna; Ströh, Luisa J.; Knops, Elena; Nierhoff, Dirk; Spengler, Ulrich; Kaiser, Rolf; Bjorkman, Pamela J.; Krey, Thomas; Bankwitz, Dorothea; Pfeifer, Nico; Pietschmann, Thomas; Flyak, Andrew I.; Klein, Florian

Abstract

The high genetic diversity of hepatitis C virus (HCV) complicates effective vaccine development. We screened a cohort of 435 HCV-infected individuals and found that 2%–5% demonstrated outstanding HCV-neutralizing activity. From four of these patients, we isolated 310 HCV antibodies, including neutralizing antibodies with exceptional breadth and potency. High neutralizing activity was enabled by the use of the VH1-69 heavy-chain gene segment, somatic mutations within CDRH1, and CDRH2 hydrophobicity. Structural and mutational analyses revealed an important role for mutations replacing the serines at positions 30 and 31, as well as the presence of neutral and hydrophobic residues at the tip of the CDRH3. Based on these characteristics, we computationally created a de novo antibody with a fully synthetic VH1-69 heavy chain that efficiently neutralized multiple HCV genotypes. Our findings provide a deep understanding of the generation of broadly HCV-neutralizing antibodies that can guide the design of effective vaccine candidates.

Additional Information

© 2021 Elsevier. Received 16 July 2021, Revised 21 October 2021, Accepted 6 December 2021, Available online 5 January 2022. We thank all study participants who devoted time to our research; members of the Klein, Pietschmann, Pfeifer, Krey, and Bjorkman Laboratories for continuous support and helpful discussions, Maike Schlotz and Carola Ruping for help with sample processing, and Henning Gruell for valuable discussions. We thank the Caltech Protein Expression Center for help with protein expression and the Caltech Molecular Observatory for assistance with structural studies. This work was funded by grants from the European Research Council (ERC-STG-639961 to F.K.), the German Center for Infection Research (DZIF TTU 05.817 and TTU 05.821 to F.K., T.P., T.K., and T.W.) and the German Research Foundation (DFG) (CRC 1310 to F.K.). T.P. and T.K. are funded by the DFG under Germany's Excellence Strategy (EXC 2155 "RESIST"—project ID 39087428). This research was also supported by the U.S. National Institutes of Health (NIH) (NIH grant R01 AI127469 to P.J.B.) and (NIH grant K99 AI153465 to A.I.F.) (content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH) and the Molecular Observatory at Caltech supported by the Gordon and Betty Moore Foundation. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences (contract no DE-AC02-76SF00515). The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by NIHGMS (P41GM103393). Author contributions: Conceptualization, T.W., T.P., A.I.F., and F.K.; methodology, T.W., J.P., S.B., M.L., L.D., T.S., M.H., M.S.E., C.K., L.G., K.V., P.J.B., T.K., D.B., N.P., T.P., A.I.F., and F.K.; investigation, T.W., J.P., S.B., M.L., L.D., T.S., M.H., M.S.E., C.K., L.G., K.V., H.J., D.B., and A.I.F.; software, S.B., C.K., and N.P.; formal analysis, T.W., J.P., L.D., T.S., M.H., C.K., N.P., A.I.F., and F.K.; resources, B.L., L.S., E.K., D.N., U.S., R.K., P.J.B., T.K., T.P., and F.K.; writing–original draft, T.W., J.P., A.I.F., and F.K.; supervision, P.J.B., T.K., N.P., T.P., and F.K. Declaration of interests: Reported antibodies are in the process of being patented. Data and code availability: Nucleotide sequences of all antibodies have been deposited at Genbank. NGS data have been deposited at the Sequence Read Archive (SRA). Coordinates for atomic models have been deposited at the Protein Data Bank (PDB). The data are publicly available as of the date of publication and accession numbers are listed in the key resources table. All original code has been deposited at Zenodo and is publicly available as of the date of publication. The Digital Object Identifier (DOI) is listed in the key resources table. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

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