Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions

Antibody variable regions are composed of a heavy and a light chain, and in humans, there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain complementarity-determining region (CDR)-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains and probed the Protein Data Bank to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda, and heavy chain gene rearrangements are correlated within donors but can differ between donors. This indicates that terminal deoxynucleotidyl transferase may work with differing efficiencies between different people but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response.

[1]  Patrice Duroux,et al.  IMGT/HIGHV-QUEST: THE IMGT® WEB PORTAL FOR IMMUNOGLOBULIN (IG) OR ANTIBODY AND T CELL RECEPTOR (TR) ANALYSIS FROM NGS HIGH THROUGHPUT AND DEEP SEQUENCING , 2012 .

[2]  M. Radic,et al.  Editors and editing of anti-DNA receptors. , 2001, Immunity.

[3]  Peter Dalgaard,et al.  R Development Core Team (2010): R: A language and environment for statistical computing , 2010 .

[4]  Valérie Barbié,et al.  Protein Displays of the Human Immunoglobulin Heavy, Kappa and Lambda Variable and Joining Regions , 1999, Experimental and Clinical Immunogenetics.

[5]  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.

[6]  D. Rossi,et al.  Selective influences in the expressed immunoglobulin heavy and light chain gene repertoire in hairy cell leukemia , 2008, Haematologica.

[7]  T. Waldmann,et al.  Human immunoglobulin kappa light-chain genes are deleted or rearranged in lambda-producing B cells. , 1981, Nature.

[8]  H. Scheraga,et al.  Statistical analysis of the physical properties of the 20 naturally occurring amino acids , 1985 .

[9]  H. G. Boman,et al.  Antibacterial peptides: basic facts and emerging concepts , 2003, Journal of internal medicine.

[10]  J. Erikson,et al.  Assignment of the genes for human lambda immunoglobulin chains to chromosome 22. , 1981, Nature.

[11]  F. Redegeld,et al.  Antigen Binding Characteristics of Immunoglobulin Free Light Chains: Crosslinking by Antigen is Essential to Induce Allergic Inflammation , 2012, PloS one.

[12]  S. Morrison,et al.  Influence of the Isotype of the Light Chain on the Properties of IgG1 , 2002, The Journal of Immunology.

[13]  M. Radic,et al.  Light chain editors of anti-DNA receptors in human B cells , 2014, The Journal of experimental medicine.

[14]  Jinsong Zhang,et al.  Cloning, sequencing and analyzing of the heavy chain V region genes of human polyreactive antibodies , 1994, Cell Research.

[15]  T. Waldmann,et al.  Human immunoglobulin κ light-chain genes are deleted or rearranged in λ-producing B cells , 1981, Nature.

[16]  Sabyasachi Das,et al.  Evolutionary Genomics of Immunoglobulin-Encoding Loci in Vertebrates , 2012, Current genomics.

[17]  R. Redfield,et al.  λ Light Chain Bias Associated With Enhanced Binding and Function of Anti-HIV Env Glycoprotein Antibodies. , 2016, The Journal of infectious diseases.

[18]  M. Béné,et al.  Light chains of immunoglobulins in human secretions. , 1994, Clinica chimica acta; international journal of clinical chemistry.

[19]  A. Lesk,et al.  Canonical structures for the hypervariable regions of immunoglobulins. , 1987, Journal of molecular biology.

[20]  K. Rajewsky,et al.  Regulation of immunoglobulin light chain gene rearrangements during early B cell development in the human , 2001, European journal of immunology.

[21]  G. Mostoslavsky,et al.  The efficiency of B cell receptor (BCR) editing is dependent on BCR light chain rearrangement status , 2002, European journal of immunology.

[22]  D. Kipling,et al.  Assessment of B Cell Repertoire in Humans. , 2015, Methods in molecular biology.

[23]  S H Chui,et al.  Light-chain ratios of immunoglobulins G, A, and M determined by enzyme immunoassay. , 1990, Clinical chemistry.

[24]  R. Markus,et al.  Glia-Pinealocyte Network: The Paracrine Modulation of Melatonin Synthesis by Tumor Necrosis Factor (TNF) , 2012, PloS one.

[25]  Jiye Shi,et al.  SAbDab: the structural antibody database , 2013, Nucleic Acids Res..

[26]  S Rackovsky,et al.  On the Information Content of Protein Sequences , 2011, Journal of biomolecular structure & dynamics.

[27]  D. Schatz,et al.  The RAG proteins and V(D)J recombination: complexes, ends, and transposition. , 2000, Annual review of immunology.

[28]  Uri Hershberg,et al.  Differences in potential for amino acid change after mutation reveals distinct strategies for kappa and lambda light-chain variation. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Narayan Jayaram,et al.  Germline VH/VL pairing in antibodies. , 2012, Protein engineering, design & selection : PEDS.

[30]  David Kipling,et al.  High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations. , 2010, Blood.

[31]  M. Flajnik,et al.  Isolation of a shark immunoglobulin light chain cDNA clone encoding a protein resembling mammalian kappa light chains: implications for the evolution of light chains. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Akinori Kidera,et al.  Relation between sequence similarity and structural similarity in proteins. Role of important properties of amino acids , 1985 .

[33]  R. Pelanda,et al.  Receptor editing is the main mechanism of B cell tolerance toward membrane antigens , 2004, Nature Immunology.

[34]  Joseph M. Volpe,et al.  Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains , 2009, Immunome research.

[35]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[36]  A. Tramontano,et al.  Structural repertoire of immunoglobulin λ light chains , 2011, Proteins.

[37]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[38]  S. Muyldermans,et al.  Naturally occurring antibodies devoid of light chains , 1993, Nature.

[39]  A Ikai,et al.  Thermostability and aliphatic index of globular proteins. , 1980, Journal of biochemistry.

[40]  M. Ferguson-Smith,et al.  Localization of human immunoglobulin kappa light chain variable region genes to the short arm of chromosome 2 by in situ hybridization. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[41]  K. Rajewsky,et al.  Forced usage of positively charged amino acids in immunoglobulin CDR-H3 impairs B cell development and antibody production , 2006, The Journal of experimental medicine.

[42]  A. Zemla,et al.  Antibody elbow angles are influenced by their light chain class. , 2006, Journal of molecular biology.

[43]  Guoli Wang,et al.  PISCES: a protein sequence culling server , 2003, Bioinform..

[44]  Véronique Giudicelli,et al.  The Human Immunoglobulin Lambda Variable (IGLV) Genes and Joining (IGLJ) Segments , 1998, Experimental and Clinical Immunogenetics.

[45]  I. Sanz,et al.  Human Ig heavy chain CDR3 regions in adult bone marrow pre-B cells display an adult phenotype of diversity: evidence for structural selection of DH amino acid sequences. , 1997, International immunology.

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

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

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

[49]  Uri Hershberg,et al.  Differences in potential for amino acid change after mutation reveals distinct strategies for κ and λ light-chain variation , 2006, Proceedings of the National Academy of Sciences.

[50]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[51]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[52]  Jan Berka,et al.  Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire , 2009, Proceedings of the National Academy of Sciences.

[53]  L. Wyns,et al.  Camel heavy‐chain antibodies: diverse germline VHH and specific mechanisms enlarge the antigen‐binding repertoire , 2000, The EMBO journal.

[54]  M. Nussenzweig,et al.  Human Autoantibody Silencing by Immunoglobulin Light Chains , 2004, The Journal of experimental medicine.

[55]  A. Lesk,et al.  Standard conformations for the canonical structures of immunoglobulins. , 1997, Journal of molecular biology.

[56]  M. Nei,et al.  Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers , 2008, Proceedings of the National Academy of Sciences.

[57]  J. Xu,et al.  Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities. , 2000, Immunity.

[58]  M. Nussenzweig,et al.  Predominant Autoantibody Production by Early Human B Cell Precursors , 2003, Science.

[59]  Valérie Barbié,et al.  The Human Immunoglobulin Kappa Variable (IGKV) Genes and Joining (IGKJ) Segments , 1998, Experimental and Clinical Immunogenetics.