Tissue-Specific Expressed Antibody Variable Gene Repertoires

Recent developments in genetic technologies allow deep analysis of the sequence diversity of immune repertoires, but little work has been reported on the architecture of immune repertoires in mucosal tissues. Antibodies are the key to prevention of infections at the mucosal surface, but it is currently unclear whether the B cell repertoire at mucosal surfaces reflects the dominant antibodies found in the systemic compartment or whether mucosal tissues harbor unique repertoires. We examined the expressed antibody variable gene repertoires from 10 different human tissues using RNA samples derived from a large number of individuals. The results revealed that mucosal tissues such as stomach, intestine and lung possess unique antibody gene repertoires that differed substantially from those found in lymphoid tissues or peripheral blood. Mutation frequency analysis of mucosal tissue repertoires revealed that they were highly mutated, with little evidence for the presence of naïve B cells, in contrast to blood. Mucosal tissue repertoires possessed longer heavy chain complementarity determining region 3 loops than lymphoid tissue repertoires. We also noted a large increase in frequency of both insertions and deletions in the small intestine antibody repertoire. These data suggest that mucosal immune repertoires are distinct in many ways from the systemic compartment.

[1]  V. Pascual,et al.  Amino acid insertions and deletions contribute to diversify the human Ig repertoire , 1998, Immunological reviews.

[2]  F. Alt,et al.  VDJ recombination. , 1992, Immunology today.

[3]  P. M. Wilson,et al.  Diversity of Immunoglobulin Light Chain Usage in the Human Immune Response to Haemophilus influenzae Type b Capsular Polysaccharide , 1993, Pediatric Research.

[4]  V. Giudicelli,et al.  IMGT(®) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. , 2012, Methods in molecular biology.

[5]  K. Rajewsky,et al.  Regulation of Repertoire Development through Genetic Control of DH Reading Frame Preference1 , 2008, The Journal of Immunology.

[6]  M Hummel,et al.  Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: Report of the BIOMED-2 Concerted Action BMH4-CT98-3936 , 2003, Leukemia.

[7]  H. Ploegh,et al.  Predominant Autoantibody Production by Early Human B Cell Precursors , 2003 .

[8]  James E. Crowe,et al.  Location and length distribution of somatic hypermutation-associated DNA insertions and deletions reveals regions of antibody structural plasticity , 2012, Genes and Immunity.

[9]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[10]  Pham Phung,et al.  Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target , 2009, Science.

[11]  Tasuku Honjo,et al.  Intestinal IgA synthesis: regulation of front-line body defences , 2003, Nature Reviews Immunology.

[12]  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 .

[13]  James E. Crowe,et al.  Human Peripheral Blood Antibodies with Long HCDR3s Are Established Primarily at Original Recombination Using a Limited Subset of Germline Genes , 2012, PloS one.

[14]  T. Martin,et al.  Heavy chain variable region, light chain variable region, and heavy chain CDR3 influences on the mono- and polyreactivity and on the affinity of human monoclonal rheumatoid factors. , 1995, Journal of immunology.

[15]  J. Crowe,et al.  Immunodominance of the VH1–46 Antibody Gene Segment in the Primary Repertoire of Human Rotavirus-Specific B Cells Is Reduced in the Memory Compartment through Somatic Mutation of Nondominant Clones1 , 2008, The Journal of Immunology.

[16]  Mario Roederer,et al.  Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1 , 2010, Science.

[17]  A. Chorny,et al.  Immunoglobulin responses at the mucosal interface. , 2011, Annual review of immunology.

[18]  Keiichiro Suzuki,et al.  The sensing of environmental stimuli by follicular dendritic cells promotes immunoglobulin A generation in the gut. , 2010, Immunity.

[19]  V(D)J Recombination , 2002 .

[20]  W. Caspary,et al.  IgA and IgM V(H) repertoires in human colon: evidence for clonally expanded B cells that are widely disseminated. , 2000, Gastroenterology.

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

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

[23]  W. Carroll,et al.  Restricted Ig H chain V gene usage in the human antibody response to Haemophilus influenzae type b capsular polysaccharide. , 1991, Journal of immunology.

[24]  Andrew D. Ellington,et al.  Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response , 2013, Proceedings of the National Academy of Sciences.

[25]  B A McKinney,et al.  High-throughput antibody sequencing reveals genetic evidence of global regulation of the naïve and memory repertoires that extends across individuals , 2012, Genes and Immunity.

[26]  J. Crowe,et al.  Evidence for preferential Ig gene usage and differential TdT and exonuclease activities in human naïve and memory B cells. , 2007, Molecular immunology.

[27]  Virginia Pascual,et al.  Somatic Hypermutation Introduces Insertions and Deletions into Immunoglobulin V Genes , 1998, The Journal of experimental medicine.

[28]  Renate Kunert,et al.  Cardiolipin Polyspecific Autoreactivity in Two Broadly Neutralizing HIV-1 Antibodies , 2005, Science.

[29]  M. Zouali.  Nonrandom features of the human immunoglobulin variable region gene repertoire expressed in response to HIV-1 , 1996, Applied biochemistry and biotechnology.

[30]  S. Zolla-Pazner,et al.  Preferential use of the VH5-51 gene segment by the human immune response to code for antibodies against the V3 domain of HIV-1. , 2009, Molecular immunology.

[31]  I. Wilson,et al.  An Insertion Mutation That Distorts Antibody Binding Site Architecture Enhances Function of a Human Antibody , 2011, mBio.

[32]  M. Egholm,et al.  Individual Variation in the Germline Ig Gene Repertoire Inferred from Variable Region Gene Rearrangements , 2010, The Journal of Immunology.

[33]  S. Tonegawa,et al.  Somatic generation of antibody diversity. , 1976, Nature.

[34]  C. Milstein,et al.  Maturation of the immune response. , 1996, Advances in protein chemistry.

[35]  I. Aguilera,et al.  Molecular structure of eight human autoreactive monoclonal antibodies , 2001, Immunology.

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

[37]  C. Milstein,et al.  Somatic hypermutation. , 1995, Current opinion in immunology.

[38]  H. Wardemann,et al.  The majority of intestinal IgA+ and IgG+ plasmablasts in the human gut are antigen-specific. , 2011, The Journal of clinical investigation.

[39]  M. Neuberger,et al.  Antibody diversification by somatic mutation: from Burnet onwards , 2008, Immunology and cell biology.

[40]  M. Lefranc.  IMGT, the International ImMunoGeneTics Information System. , 2011, Cold Spring Harbor protocols.

[41]  B. LaFleur,et al.  VH1–46 Is the Dominant Immunoglobulin Heavy Chain Gene Segment in Rotavirus-Specific Memory B Cells Expressing the Intestinal Homing Receptor α4β71 , 2005, The Journal of Immunology.

[42]  C. Nusbaum,et al.  High-Resolution Description of Antibody Heavy-Chain Repertoires in Humans , 2011, PloS one.

[43]  Pham Phung,et al.  Broad neutralization coverage of HIV by multiple highly potent antibodies , 2011, Nature.