Deep sequencing and Circos analyses of antibody libraries reveal antigen-driven selection of Ig VH genes during HIV-1 infection

Experimental and Molecular Pathology

Volumn 95, Issue 3, 2013, Pages 357-363

  Xiao, Madelyne ^a,b,c   Prabakaran, Ponraj ^b,c   Chen, Weizao ^b   Kessing, Bailey ^c   Dimitrov, Dimiter S ^b  

^a Urbana High School   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

Author keywords

454 sequencing; Antibody repertoire; Antibodyome; HIV 1; Human monoclonal antibody; VDJ analysis

Indexed keywords

IMMUNOGLOBULIN; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M; ANTIBODY; IMMUNOGLOBULIN F(AB) FRAGMENT; IMMUNOGLOBULIN HEAVY CHAIN; IMMUNOGLOBULIN VARIABLE REGION;

ADAPTIVE IMMUNITY; ANTIBODY LIBRARY; ARTICLE; COMBINATORIAL LIBRARY; GENE SEQUENCE; GENETIC VARIABILITY; HEAVY CHAIN; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE RESPONSE; IMMUNE SYSTEM; NONHUMAN; ADULT; BLOOD; COMPUTER PROGRAM; DNA SEQUENCE; FETUS BLOOD; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNOGLOBULIN HEAVY CHAIN GENE; IMMUNOGLOBULIN VARIABLE REGION; IMMUNOLOGY; NEWBORN; VDJ RECOMBINATION; VIROLOGY;

ADULT; ANTIBODIES; FETAL BLOOD; GENES, IMMUNOGLOBULIN HEAVY CHAIN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HIV INFECTIONS; HIV-1; HUMANS; IMMUNOGLOBULIN FAB FRAGMENTS; IMMUNOGLOBULIN HEAVY CHAINS; IMMUNOGLOBULIN M; IMMUNOGLOBULIN VARIABLE REGION; INFANT, NEWBORN; SEQUENCE ANALYSIS, DNA; SOFTWARE; V(D)J RECOMBINATION;

EID: 84887560765     PISSN: 00144800     EISSN: 10960945     Source Type: Journal    
DOI: 10.1016/j.yexmp.2013.10.004     Document Type: Article

References (24)

1. Agrawal A., et al. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998, 394:744-751.
2. Arnaout R., et al. High-resolution description of antibody heavy-chain repertoires in humans. PLoS ONE 2011, 6:e22365.
3. Bonsignori M., et al. Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors. J. Virol. 2011, 85:9998-10009.
4. Boyd S.D., et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel V-D-J pyrosequencing. Sci. Transl. Med. 2009, 1.
5. Boyd S.D., et al. Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci. Transl. Med. 2009, 1:12-23.
6. Breden F., et al. Comparison of antibody repertoires produced by HIV-1 infection, other chronic and acute infections, and systemic autoimmune disease. PLoS ONE 2011, 6:e16857.
7. Briney B.S., et al. High-throughput antibody sequencing reveals genetic evidence of global regulation of the naive and memory repertoires that extends across individuals. Genes Immun. 2012, 13:469-473.
8. Chapal N., et al. Thyroid peroxidase autoantibodies obtained from random single chain Fv libraries contain the same heavy/light chain combinations as occur in vivo. Endocrinology 2001, 142:4740-4750.
9. Chen W., et al. Cross-reactive human IgM-derived monoclonal antibodies that bind to HIV-1 envelope glycoproteins. Viruses 2010, 2:547-565.
10. Chen W., et al. Characterization of human IgG repertoires in an acute HIV-1 infection. Exp. Mol. Pathol. 2012, 93:399-407.
11. Dimitrov D.S. Therapeutic antibodies, vaccines and antibodyomes. Mabs 2010, 2:347-356.
12. Glanville J., et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:20216-20221.
13. Jiang N., et al. Determinism and stochasticity during maturation of the zebrafish antibody repertoire. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:5348-5353.
14. Kidd M.J., et al. The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements. J. Immunol. 2012, 188:1333-1340.
15. Lefranc M.P., et al. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 2009, 37:D1006-D1012.
16. Li L., et al. Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:4148-4153.
17. Lloyd C., et al. Modelling the human immune response: performance of a 1011 human antibody repertoire against a broad panel of therapeutically relevant antigens. Protein Eng. Des. Sel. 2009, 22:159-168.
18. Owens G.P., et al. VH4 gene segments dominate the intrathecal humoral immune response in multiple sclerosis. J. Immunol. 2007, 179:6343-6351.
19. Prabakaran P., et al. Expressed antibody repertoires in human cord blood cells: 454 sequencing and IMGT/HighV-QUEST analysis of germline gene usage, junctional diversity, and somatic mutations. Immunogenetics 2012, 64:337-350.
20. Prabakaran P., et al. Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing. Front. Microbiol. 2012, 3:277.
21. Ravn U., et al. By-passing in vitro screening - next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res. 2010, 38:e193.
22. Weinstein J.A., et al. High-throughput sequencing of the zebrafish antibody repertoire. Science 2009, 324:807-810.
23. Wu X., et al. Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science 2011, 333:1593-1602.
24. Zhu Z., Dimitrov D.S. Construction of a large naive human phage-displayed Fab library through one-step cloning. Methods Mol. Biol. 2009, 525:129-142. (xv).