High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

Ian Setliff; Andrea R Shiakolas; Kelsey A Pilewski; Amyn A Murji; Rutendo E Mapengo; Katarzyna Janowska; Simone Richardson; Charissa Oosthuysen; Nagarajan Raju; Larance Ronsard; Masaru Kanekiyo; Juliana S Qin; Kevin J Kramer; Allison R Greenplate; Wyatt J McDonnell; Barney S Graham; Mark Connors; Daniel Lingwood; Priyamvada Acharya; Lynn Morris; Ivelin S Georgiev

doi:10.1016/j.cell.2019.11.003

High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

Cell. 2019 Dec 12;179(7):1636-1646.e15. doi: 10.1016/j.cell.2019.11.003. Epub 2019 Nov 28.

Authors

Ian Setliff¹, Andrea R Shiakolas², Kelsey A Pilewski², Amyn A Murji², Rutendo E Mapengo³, Katarzyna Janowska⁴, Simone Richardson⁵, Charissa Oosthuysen⁵, Nagarajan Raju², Larance Ronsard⁶, Masaru Kanekiyo⁷, Juliana S Qin⁸, Kevin J Kramer², Allison R Greenplate⁸, Wyatt J McDonnell⁹, Barney S Graham⁷, Mark Connors¹⁰, Daniel Lingwood⁶, Priyamvada Acharya¹¹, Lynn Morris¹², Ivelin S Georgiev¹³

Affiliations

¹ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
² Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
³ National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa.
⁴ Division of Structural Biology, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
⁵ National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa.
⁶ Ragon Institute of Massachusetts General Hospital, Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁷ Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
⁸ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
⁹ Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Translational and Clinical Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
¹⁰ National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
¹¹ Division of Structural Biology, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
¹² National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4041, South Africa.
¹³ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA. Electronic address: ivelin.georgiev@vanderbilt.edu.

Abstract

B cell receptor (BCR) sequencing is a powerful tool for interrogating immune responses to infection and vaccination, but it provides limited information about the antigen specificity of the sequenced BCRs. Here, we present LIBRA-seq (linking B cell receptor to antigen specificity through sequencing), a technology for high-throughput mapping of paired heavy- and light-chain BCR sequences to their cognate antigen specificities. B cells are mixed with a panel of DNA-barcoded antigens so that both the antigen barcode(s) and BCR sequence are recovered via single-cell next-generation sequencing. Using LIBRA-seq, we mapped the antigen specificity of thousands of B cells from two HIV-infected subjects. The predicted specificities were confirmed for a number of HIV- and influenza-specific antibodies, including known and novel broadly neutralizing antibodies. LIBRA-seq will be an integral tool for antibody discovery and vaccine development efforts against a wide range of antigen targets.

Keywords: B cells; HIV; antibodies; antibody discovery; antibody repertoire; broadly neutralizing antibody; influenza; single cell immunology; systems immunology.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't

MeSH terms

Antibodies, Neutralizing / chemistry
Antibodies, Neutralizing / immunology
Antigens / chemistry
Antigens / immunology
Cells, Cultured
Epitope Mapping / methods*
Epitopes / chemistry*
Epitopes / immunology
HEK293 Cells
HIV Antibodies / chemistry
HIV Antibodies / immunology
High-Throughput Nucleotide Sequencing / methods
High-Throughput Screening Assays / methods
Humans
Receptors, Antigen, B-Cell / chemistry*
Receptors, Antigen, B-Cell / immunology
Sequence Analysis, DNA / methods*
Single-Cell Analysis / methods*
THP-1 Cells

Substances

Antibodies, Neutralizing
Antigens
Epitopes
HIV Antibodies
Receptors, Antigen, B-Cell

Abstract

Publication types

MeSH terms

Substances

Grants and funding