Improved methods for detecting selection by mutation analysis of Ig V region sequences

International Immunology

Volumn 20, Issue 5, 2008, Pages 683-694

  Hershberg, Uri ^a   Uduman, Mohamed ^b   Shlomchik, Mark J ^a   Kleinstein, Steven H ^a,b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Adaptive immunity; Affinity maturation; B cells; Cancer; Germinal center

Indexed keywords

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; B LYMPHOCYTE; BINOMIAL DISTRIBUTION; COMPUTER MODEL; COMPUTER SIMULATION; FALSE POSITIVE RESULT; GENE SEQUENCE; GENETIC SELECTION; IMMUNOGLOBULIN VARIABLE REGION; IN VIVO STUDY; LARGE CELL LYMPHOMA; MATHEMATICAL COMPUTING; MOUSE; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SOMATIC HYPERMUTATION; STATISTICAL ANALYSIS; TRANSGENIC MOUSE;

ANIMALS; B-LYMPHOCYTES; DNA MUTATIONAL ANALYSIS; FACTOR ANALYSIS, STATISTICAL; GENE REARRANGEMENT, B-LYMPHOCYTE; GENES, IMMUNOGLOBULIN; IMMUNOGLOBULIN VARIABLE REGION; LYMPHOMA, LARGE B-CELL, DIFFUSE; MICE; MUTATION; SENSITIVITY AND SPECIFICITY;

EID: 42949103482     PISSN: 09538178     EISSN: 14602377     Source Type: Journal    
DOI: 10.1093/intimm/dxn026     Document Type: Article

References (41)

1. McKean, D., Huppi, K., Bell, M., Staudt, L., Gerhard, W. and Weigert, M. 1984. Generation of antibody diversity in the immune response of BALB/c mice to influenza virus hemagglutinin. Proc. Natl Acad. Sci. USA 81:3180.
2. Siskind, G. W. and Benacerraf, B. 1969. Cell selection by antigen in the immune response. Adv Immunol. 10:1.
3. Shlomchik, M. J., Aucoin, A. H., Pietsky, D. S. and Weigert, M. G. 1987. Structure and function of anti-DNA autoantibodies derived from a single autoimmune mouse. Proc. Natl Acad. Sci. USA. 84:9150.
4. Chang, B. and Casali, P. 1994. The CDR1 sequences of a major proportion of human germline Ig VH genes are inherently susceptible to amino acid replacement. Immunol. Today 15:367.
5. Lossos, I. S., Tibshirani, R., Narasimhan, B. and Levy, R. 2000. The inference of antigen selection on Ig genes. J. Immunol. 165:5122.
6. Bose, B. and Sinha, S. 2005. Problems in using statistical analysis of replacement and silent mutations in antibody genes for determining antigen-driven affinity selection. Immunology 116:172.
7. William, J., Euler, C., Christensen, S. and Shlomchik, M. J. 2002. Evolution of autoantibody responses via somatic hypermutation outside of germinal centers. Science 297:2066.
8. Lossos, I. S., Okada, C. Y., Tibshirani, R. et al. 2000. Molecular analysis of immunoglobulin genes in diffuse large B-cell lymphomas. Blood 95:1797.
9. Bagnara, D., Callea, V, Stelitano, C. et al. 2006. IgV gene intraclonal diversification and clonal evolution in B-cell chronic lymphocytic leukaemia. Br. J. Haematol. 133:50.
10. Flajnik, M. F. 2002. Comperative analyses of Ig genes: Surprises and portents. Nat. Rev. Immunol. 2:688.
11. Dunn-Walters, D. K. and Spencer, J. 1998. Strong intrinsic biases towards mutation and conservation of bases in human IgVH genes during somatic hypermutation prevent statistical analysis of antigen selection. Immunology 95:339.
12. Kleinstein, S. H. and Singh, J. P. 2003. Why are there so few key mutant clones? The influence of stochastic selection and blocking on affinity maturation in the germinal center. Int Immunol. 15:871.
13. Shapiro, G. S., Aviszus, K., Murphy, J. and Wysocki, L. J. 2002. Evolution of Ig DNA sequence to target specific base positions within codons for somatic hypermutation. J. Immunol. 168:2302.
14. Smith, D. S., Creadon, G., Jena, P. K, Portanova, J. P., Kotzin, B. L. and Wysocki, L. J. 1996. Di- and trinucleotide target preferences of somatic mutagenesis in normal and autoreactive B cells. J. Immunol. 156:2642.
15. Cowell, L. G. and Kepler, T. B. 2000. The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation. J. Immunol. 164:1971.
16. Shlomchik, M. J., Watts, P., Weigert, M. G. and Litwin, S. 1998. "Clone": A Monte-Carlo computer simulation of B cell clonal expansion, somatic mutation and antigen-driven selection. Curr Top. Microbiol. Immunol. 229:173.
17. Kleinstein, S. H., Louzoun, Y. and Shlomchik, M. J. 2003. Estimating hypermutation rates from clonal tree data. J. Immunol. 171:4639.
18. Kabat, E. A., Wu, T. T., Reid-Miller, M., Perry, H. and Gottesman, K. 1987. Sequences of Proteins of Immunological Interest, 4th edn: US Government Printing Office, Washington DC. 165.
19. Souto-Carneiro, M. M., Sims, G. P., Girschik, H., Lee, J. and Lipsky, P. E. 2005. Developmental changes in the human heavy chain CDR3. J. Immunol. 175:7425.
20. Parr, T B., Johnson, T. A., Silberstein, L. E. and Kipps, T. J. 1994. Anti-B cell autoantibodies encoded by VH 4-21 genes in human fetal spleen do not require in vivo somatic selection. Eur. J. Immunol. 24:2941.
21. Dorner, T., Brezinschek, H. P., Brezinschek, R. I., Foster, S. J., Domiati-Saad, R. and Lipsky, P. E. 1997. Analysis of the frequency and pattern of somatic mutations within nonproductively rearranged human variable heavy chain genes. J. Immunol. 158:2779.
22. Brezinschek, H. P., Brezinschek, R. I. and Lipsky, P. E. 1995. Analysis of the heavy chain repertoire of human peripheral B cells using single-cell polymerase chain reaction. J. Immunol. 155:190.
23. Volpe, J. M., Cowell, L. G. and Kepler, T. B. 2006. SoDA: Implementation of a 3D alignment algorithm for inference of antigen receptor recombinations. Bioinformatics 22:438.
24. Pocock, M., Down, T. and Hubbard, T. 2000. BioJava: Open source components for bioinformatics. ACM SIGBIO Newsl. 20:10.
25. Taki, S., Meiering, M. and Rajewsky, K. 1993. Targeted insertion of a variable region gene into the immunoglobulin heavy chain locus. Science 262-268.
26. Dal Porto, J. M., Haberman, A. M., Shlomchik, M. J. and Kelsoe, G. 1998. Antigen drives very low affinity B cells to become plasmacytes and enter germinal centers. J. Immunol. 161:5373.
27. Hannum, L. G., Haberman, A. M., Anderson, S. M. and Shlomchik, M. J. 2000. Germinal center initiation, variable gene region hypermutation, and mutant B cell selection without detectable immune complexes on follicular dendritic cells. J. Exp. Med. 192:931.
28. Chen, J., Trounstine, M., Alt, F. W. et al. 1993. Immunoglobulin gene rearrangement in B cell deficient mice generated by tarpeted deletion of the JH locus. Int. Immunol. 5:647.
29. Hershberg, U. and Shlomchik, M. J. 2006. Differences in potential for amino acid change following mutation reveals distinct strategies for κ and λ light chain variation. Proc. Natl Acad. Sci. USA. 103:15963.
30. Lefranc, M. P., Giudicelli, V., Kaas, Q. et al. 2005. IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 593.
31. Shlomchik, M. J., Euler, C. W., Christensen, S. C. and William, J. 2003. Activation of rheumatoid factor (RF) B cells and somatic hypermutation outside of germinal centers in autoimmune-prone MRL/Ipr mice. Ann. N. Y. Acad. Sci. 987:38.
32. Oprea, M., Cowell, L. G. and Kepler, T. B. 2001. The targeting of somatic hypermutation closely resembles that of meiotic mutation. J. Immunol. 166:892.
33. Allen, D., Cumano, A., Dildrop, R. et al. 1987. Timing, genetic requirements and functional consequences of somatic hypermutation during B-cell development. Immunol. Rev. 96:5.
34. Storey, J. D. and Tibshirani, R. 2003. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA. 100:9440.
35. Lenze, D., Berg, E., Volkmer-Engert, R. et al. 2006. Influence of antigen on the development of MALT lymphoma. Blood 107:1141.
36. Volkheimer, A. D., Weinberg, J. B., Beasley, B. E. et al. 2007. Progressive immunoglobulin gene mutations in chronic lymphocytic leukemia: Evidence for antigen-driven intraclonal diversification. Blood 109:1559.
37. Margolin, D. H., Saunders, E. H., Bronfin, B. et al. 2006. Germinal center function in the spleen during simian HIV infection in rhesus monkeys. J. Immunol. 177:1108.
38. Yang, F., Waldbieser, G. C. and Lobb, C. J. 2006. The nucleotide targets of somatic mutation and the role of selection in immunoglobulin heavy chains of a teleost fish. J. Immunol. 176:1655.
39. Ghosh, S. and Huber, B. T. 2007. Clonal diversification in OspA-specific antibodies from peripheral circulation of a chronic Lyme arthritis patient. J. Immunol. Methods 321:121.
40. Odegard, V. H. and Schatz, D. G. 2006. Targeting of somati hypermutation. Nat. Rev. Immunol. 6:573.
41. Unniraman, S. and Schatz, D. G. 2007. Strand-biased spreading of mutations during somatic hypermutation. Science 317:1227.