Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes

Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization. We anticipate broad applicability of our method for providing insights into adaptive immune responses associated with various diseases, vaccinations, and cancer immunotherapies.

[1]  M. Egholm,et al.  Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing , 2009, Science Translational Medicine.

[2]  Irina Czogiel,et al.  Single‐cell based high‐throughput sequencing of full‐length immunoglobulin heavy and light chain genes , 2014, European journal of immunology.

[3]  Veronica Sanchez-Freire,et al.  Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns , 2012, Nature Protocols.

[4]  S. Quake,et al.  The promise and challenge of high-throughput sequencing of the antibody repertoire , 2014, Nature Biotechnology.

[5]  P. Wilson,et al.  Tools to therapeutically harness the human antibody response , 2012, Nature Reviews Immunology.

[6]  Zuhong Lu,et al.  Emulsion PCR-based method to detect Y chromosome microdeletions. , 2007, Analytical biochemistry.

[7]  George Georgiou,et al.  In-depth determination and analysis of the human paired heavy- and light-chain antibody repertoire , 2014, Nature Medicine.

[8]  C. Luschnig,et al.  Maximum yields of microsomal-type membranes from small amounts of plant material without requiring ultracentrifugation , 2010, Analytical biochemistry.

[9]  P. Lipsky,et al.  Secondary Immunization Generates Clonally Related Antigen-Specific Plasma Cells and Memory B Cells , 2010, The Journal of Immunology.

[10]  Sai T Reddy,et al.  Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting , 2016, Science Advances.

[11]  F. Sallusto,et al.  Human monoclonal antibodies by immortalization of memory B cells , 2007, Current Opinion in Biotechnology.

[12]  J. Galson,et al.  Studying the antibody repertoire after vaccination: practical applications. , 2014, Trends in immunology.

[13]  Seung Hyun Kang,et al.  Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells , 2010, Nature Biotechnology.

[14]  R. Emerson,et al.  High-throughput pairing of T cell receptor alpha and beta sequences (TECH2P.930) , 2015, The Journal of Immunology.

[15]  Marie-Paule Lefranc,et al.  IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF , 2009, Nucleic Acids Res..

[16]  W. M. Collinson Practical Applications , 2021, Royal Society of Health journal.

[17]  George Georgiou,et al.  High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire , 2013, Nature Biotechnology.

[18]  John McCafferty,et al.  Beyond natural antibodies: the power of in vitro display technologies , 2011, Nature Biotechnology.

[19]  Mikhail Shugay,et al.  Pairing of T‐cell receptor chains via emulsion PCR , 2013, European journal of immunology.

[20]  Jeffrey J. Gray,et al.  Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires , 2016, Proceedings of the National Academy of Sciences.

[21]  H. Wardemann,et al.  Expression cloning of human B cell immunoglobulins. , 2013, Methods in molecular biology.

[22]  J. Thèze,et al.  Analysis of human VH gene repertoire expression in peripheral CD19+ B cells , 2004, Immunogenetics.

[23]  George Georgiou,et al.  Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes , 2016, Nature Protocols.

[24]  Tilman Schneider-Poetsch,et al.  Inhibition of Eukaryotic Translation Elongation by Cycloheximide and Lactimidomycin , 2010, Nature chemical biology.

[25]  Johannes Trück,et al.  Identification of Antigen-Specific B Cell Receptor Sequences Using Public Repertoire Analysis , 2015, The Journal of Immunology.

[26]  Michael J. Osborn,et al.  Antigen-specific single B cell sorting and expression-cloning from immunoglobulin humanized rats: a rapid and versatile method for the generation of high affinity and discriminative human monoclonal antibodies , 2017, BMC Biotechnology.

[27]  Samuel Aparicio,et al.  High-throughput microfluidic single-cell RT-qPCR , 2011, Proceedings of the National Academy of Sciences.

[28]  Michael W. McCormick,et al.  Shaping of Human Germline IgH Repertoires Revealed by Deep Sequencing , 2012, The Journal of Immunology.

[29]  Anchi Cheng,et al.  Automated molecular microscopy: the new Leginon system. , 2005, Journal of structural biology.

[30]  Mikhail Shugay,et al.  MiXCR: software for comprehensive adaptive immunity profiling , 2015, Nature Methods.

[31]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[32]  Harry B. Greenberg,et al.  Erratum: Lineage structure of the human antibody repertoire in response to influenza vaccination (Science Translational Medicine (2013) 5 (193er8)) , 2013 .

[33]  Grace X. Y. Zheng,et al.  Massively parallel digital transcriptional profiling of single cells , 2016, Nature Communications.

[34]  Andrew D. Ellington,et al.  Identification and characterization of the constituent human serum antibodies elicited by vaccination , 2014, Proceedings of the National Academy of Sciences.

[35]  Enkelejda Miho,et al.  Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires. , 2015, Trends in immunology.

[36]  Steven H. Kleinstein,et al.  Tumor-infiltrating immune repertoires captured by single-cell barcoding in emulsion , 2017, bioRxiv.

[37]  V. Erdmann,et al.  A streamlined protocol for emulsion polymerase chain reaction and subsequent purification. , 2011, Analytical biochemistry.

[38]  Scott D Boyd,et al.  Convergent antibody signatures in human dengue. , 2013, Cell host & microbe.

[39]  H. Diao,et al.  Current status and recent advances of next generation sequencing techniques in immunological repertoire , 2016, Genes and Immunity.

[40]  H. Lehrach,et al.  Onset of Immune Senescence Defined by Unbiased Pyrosequencing of Human Immunoglobulin mRNA Repertoires , 2012, PloS one.

[41]  C. Nicchitta,et al.  Partitioning and translation of mRNAs encoding soluble proteins on membrane-bound ribosomes. , 2003, RNA.

[42]  R. White,et al.  High-Throughput Sequencing of the Zebrafish Antibody Repertoire , 2009, Science.

[43]  R. Emerson,et al.  High-throughput pairing of T cell receptor α and β sequences , 2015, Science Translational Medicine.

[44]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[45]  G. Dranoff,et al.  Ex vivo characterization and isolation of rare memory B cells with antigen tetramers. , 2011, Blood.

[46]  Y. Louzoun,et al.  Rep‐Seq: uncovering the immunological repertoire through next‐generation sequencing , 2012, Immunology.

[47]  Mark M. Davis,et al.  Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination , 2013, Science Translational Medicine.