In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire

• Published in: Nature medicine Vol. 21; no. 1; pp. 86 - 91
• Main Authors: DeKosky, Brandon J, Kojima, Takaaki, Rodin, Alexa, Charab, Wissam, Ippolito, Gregory C, Ellington, Andrew D, Georgiou, George
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.01.2015; Nature Publishing Group
• Subjects: 13/1; 38; 38/77; 38/91; 631/250/2152; 631/61/514/2254; Adaptive Immunity; Antibodies; Antibodies - genetics; Antibodies - immunology; Antibodies - isolation & purification; Autoantibodies - genetics; Autoantibodies - immunology; Autoantibodies - isolation & purification; Autoimmunity; B-Lymphocytes - immunology; Biomedicine; Cancer Research; DNA sequencing; Emulsions; Genetic aspects; High-Throughput Nucleotide Sequencing; HIV-1 - genetics; HIV-1 - immunology; Humans; Immune system; Immunoglobulin Heavy Chains - genetics; Immunoglobulin Heavy Chains - immunology; Immunoglobulin Light Chains - genetics; Immunoglobulin Light Chains - immunology; Immunoglobulin Variable Region - genetics; Immunoglobulins; Infectious Diseases; Metabolic Diseases; Molecular Medicine; Neurosciences; Nucleotide sequencing; Physiological aspects; RNA, Messenger - genetics; RNA, Messenger - immunology; technical-report; Vaccination; Viral antibodies; United States
• ISSN: 1078-8956; 1546-170X
• DOI: 10.1038/nm.3743

Georgiou and colleagues describe a single-cell, emulsion-based approach for the high-throughput determination of the paired antibody variable heavy and light chain (VH-VL) repertoire encoded by the more than 2 × 10 6 B cells in human peripheral blood samples. High-throughput immune repertoire sequencing has emerged as a critical step in the understanding of adaptive responses following infection or vaccination or in autoimmunity. However, determination of native antibody variable heavy-light pairs (VH-VL pairs) remains a major challenge, and no technologies exist to adequately interrogate the >1 × 10 6 B cells in typical specimens. We developed a low-cost, single-cell, emulsion-based technology for sequencing antibody VH-VL repertoires from >2 × 10 6 B cells per experiment with demonstrated pairing precision >97%. A simple flow-focusing apparatus was used to sequester single B cells into emulsion droplets containing lysis buffer and magnetic beads for mRNA capture; subsequent emulsion RT-PCR generated VH-VL amplicons for next-generation sequencing. Massive VH-VL repertoire analyses of three human donors provided new immunological insights including (i) the identity, frequency and pairing propensity of shared, or 'public', VL genes, (ii) the detection of allelic inclusion (an implicated autoimmune mechanism) in healthy individuals and (iii) the occurrence of antibodies with features, in terms of gene usage and CDR3 length, associated with broadly neutralizing antibodies to rapidly evolving viruses such as HIV-1 and influenza.