Models for antigen receptor gene rearrangement: CDR3 length

Immunology and Cell Biology

Volumn 85, Issue 4, 2007, Pages 323-332

  Saada, Ravit ^a   Weinberger, Moran ^a,b   Shahaf, Gitit ^a   Mehr, Ramit ^a  

^a BAR ILAN UNIVERSITY   (Israel)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

B lymphocytes; Complementarity determining region 3 length; Computer simulation; Immunoglobulin gene rearrangement; Mathematical model; T lymphocytes

Indexed keywords

B LYMPHOCYTE RECEPTOR; LYMPHOCYTE ANTIGEN RECEPTOR; NUCLEOTIDE; T LYMPHOCYTE RECEPTOR BETA CHAIN;

ARTICLE; CALCULATION; CLONING; COMPLEMENTARITY DETERMINING REGION; DNA MODIFICATION; EVOLUTION; GENE REARRANGEMENT; HEAVY CHAIN; HUMAN; MATHEMATICAL MODEL; NORMAL DISTRIBUTION; PROBABILITY; SIMULATION;

B-LYMPHOCYTES; COMPLEMENTARITY DETERMINING REGIONS; COMPUTER SIMULATION; GENE REARRANGEMENT, B-LYMPHOCYTE, HEAVY CHAIN; GENE REARRANGEMENT, BETA-CHAIN T-CELL ANTIGEN RECEPTOR; HUMANS; MODELS, GENETIC; NORMAL DISTRIBUTION; PROBABILITY THEORY; RECEPTORS, ANTIGEN, B-CELL; T-LYMPHOCYTES;

EID: 34249950996     PISSN: 08189641     EISSN: 14401711     Source Type: Journal    
DOI: 10.1038/sj.icb.7100055     Document Type: Article

References (64)

1. Gauss GH, Lieber MR. Mechanistic constraints on diversity in human V(D)J recombination. Mol Cell Biol 1995; 16: 258-269.
2. Gellert M. Recent advances in understanding V(D)J recombination. Adv Immunol 1997; 64: 39-64.
3. Gellert M. DNA double-strand break and hairpin in V(D)J recombination. Semin Immunol 1994; 6: 125-130.
4. Hesslein D, Schatz DG. Factors and forces controlling V(D)J recombination. Adv Immunol 2001; 78: 169-232.
5. Hofle M, Linthicum DS, Ioerger T. Analysis of diversity of nucleotide and amino acid distribution in the VD and DJ joining regions in Ig heavy chain. Mol Immunol 2000; 37: 827-835.
6. Janeway CA, Travers P, Walport M, Capra JD. Immunobiology, 4th ed. 1999. Chapters 3, 6 and 7 Garland Publishing: New York.
7. Livak F, Petrie HT. Somatic generation of antigen receptor diversity: a reprise. Trends Immunol 2001; 22: 608-612.
8. Sadofsky MJ. The RAG proteins in V(D)J recombination: more than just a nuclease. Nucl Acids Res 2001; 29: 1399-1409.
9. Schlissel MS. Structure of non hairpin coding-end DNA breaks in cells undergoing V(D)J recombination. Mol Cell Biol 1998; 18: 2029-2037.
10. Schlissel MS. Does artemis end the hunt for the hairpin-opening activity in V(D)J recombination. Cell 2002; 109: 1-4.
11. Smider V, Chu G. The end-joining reaction in V(D)J recombination. Semin Immunol 1997; 9: 189-197.
12. Pannetier C, Even J, Kourilsky P. T-cell repertoire diversity and clonal expansions in normal and clinical samples. Immunol Today 1995; 16: 176-181.
13. Rock EP, Sibbald PR, Davis MM, Chien YH. CDR3 length in antigen-specific human receptors. J Exp Med 1994; 179: 323-328.
14. Zemlin M, Klinger M, Link J, Zemlin C, Bauer K, Engler JA et al. Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures. J Mol Biol 2003; 334: 733-749.
15. Edwards BM, Barash SC, Main SH, Choi GH, Minter R, Ullrich S et al. The remarkable flexibility of the human antibody repertoire: isolation of over one thousand different antibodies to a single protein BLyS. J Mol Biol 2003; 334: 103-118.
16. Nikolich-ugich J, Slifka MK, Messaoudi I. The many important facets of T-cell repertoire diversity. Nat Rev Immunol 2004; 4: 123-132.
17. Mehr R, Shannon M, Litwin S. Models for antigen receptor gene rearrangement. I. Biased receptor editing in B cells: implications for allelic exclusion. J Immunol 1999; 163: 1793-1798.
18. Piper H, Litwin S, Mehr R. Models for antigen receptor gene rearrangement. II. T cell receptor editing: allelic exclusion or inclusion? J Immunol 1999; 163: 1799-1808.
19. Kalmanovich G, Mehr R. Models for antigen receptor gene rearrangement. III. Heavy and light chain allelic exclusion. J Immunol 2003; 170: 182-193.
20. Kouskoff V, Nemazee D. Role of receptor editing and revision in shaping the B and T lymphocyte repertoire. Life Sci 2001; 69: 1105-1113.
21. Kocks C, Rajewsky K. Stepwise intraclonal maturation of antibody affinity through somatic hypermutation. Proc Natl Acad Sci 1988; 85: 8206-8210.
22. Manser T. Evolution of antibody structure during the immune response. J Exp Med 1989; 170: 1211-1230.
23. Jacob J, Kelsoe G, Rajewsky K, Weiss U. Intraclonal generation of antibody mutants in germinal centers. Nature 1991; 354: 389-392.
24. Jacob J, Kelsoe G. In situ studies of the primary immune response to (4-hydroxy-3-nitrophenyl) acetyl. II. A common clonal origin for periarteriolar lymphoid sheath-associated foci and germinal centers. J Exp Med 1992; 176: 679-687.
25. Jacob J, Przylepa J, Miller C, Kelsoe G. In situ studies of the primary immune response to (4-hydroxy-3- nitrophenyl) acetyl. III. The kinetics of V region mutation and selection in germinal centre B cells. J Exp Med 1993; 178: 1293-1307.
26. Vora KA, Tumas-Brundage K, Manser T. Contrasting the in situ behaviour of a memory B cell clone during primary and secondary immune responses. J Immunol 1999; 163: 4315-4327.
27. Dunn-Walters DK, Boursier L, Ciclitira PJ, Spencer J. Immunoglobulin genes from human duodenal and colonic plasma cells are mutated. Biochem Soc Trans 1997a; 25: 324S.
28. Dunn-Walters DK, Isaacson PG, Spencer J. Sequence analysis of human IgVH genes indicates that ileal lamina propria plasma cells are derived from Peyer's patches. Eur J Immunol 1997b; 27: 463-467.
29. Schiaffella E, Sehgal D, Anderson AO, Mage RG. Gene conversion and hypermutation during diversification of VH sequences in developing splenic germinal centers of immunized rabbits. J Immunol 1999; 162: 3984-3995.
30. Sehgal D, Schiaffella E, Anderson AO, Mage RG. Analysis of single B cells by PCR reveals rearranged VH with germline sequences in spleen of immunized rabbits: implications for B cell repertoire maintenance and renewal. J Immunol 1998; 161: 5347-5356.
31. Sehgal D, Schiaffella E, Anderson AO, Mage RG. Generation of heterogeneous rabbit anti-DNP antibodies by gene conversion and hypermutation of rearranged VL and VH genes during clonal expansion of B cells in splenic germinal centers. Eur J Immunol 2000; 30: 3634-3644.
32. Sehgal D, Obiakor H, Mage RG. Distinct clonal diversification patterns in young appendix compared to antigen specific splenic clones. J Immunol 2002; 168: 5424-5433.
33. Sims GP, Shiono H, Willcox N, Stott DI. Somatic hypermutation and selection of B cells in thymic germinal centers responding to acetylcholine receptor in Myasthenia Gravis. J Immunol 2001; 167: 1935-1944.
34. Stott DI, Hiepe F, Hummel M, Steinhauser G, Berek C. Antigen-driven proliferation of B cells within the target tissue of an autoimmune disease. The salivary glands of patients with Sjogren's syndrome. J Clin Invest 1998; 102: 938-946.
35. Kim HJ, Krenn V, Steinhauser G, Berek C. Plasma cell development in synovial germinal centers in patients with rheumatoid and reactive arthritis. J Immunol 1999; 162: 3053-3062.
36. Gause A, Gundlach K, Zdichavsky M, Jacobs G, Koch B, Hopf T et al. The B lymphocyte in rheumatoid arthritis: analysis of rearranged V kappa genes from B cells infiltrating the synovial membrane. Eur J Immunol 1995; 25: 2775-2782.
37. Gellrich S, Rutz S, Borkowski A, Golembowski S, Gromnica-Ihle E, Sterry W et al. Analysis of VH-D-JH gene transcripts in B cells infiltrating the salivary glands and lymph node tissues of patients with Sjögren's syndrome. Arthritis Rheum 1999; 42: 240-247.
38. Jacobi AM, Hansen A, Kaufmann O, Pruss A, Burmester GR, Lipsky PE et al. Analysis of immunoglobulin light chain rearrangements in the salivary gland and blood of a patient with Sjögren's syndrome. Arthritis Res 2002; 4: R4.
39. Miura Y, Chu CC, Dines DM, Asnis SE, Furie RA, Chiorazzi N et al. Diversification of the Ig variable region gene repertoire of synovial B lymphocytes by nucleotide insertion and deletion. Mol Med 2003; 9: 166-174.
40. Manske MK, Zuckerman NS, Timm MM, Maiden S, Edelman H, Shahaf G et al. Analysis of clonal bone marrow CD19+ B cells: use of B cell lineage trees to delineate their role in the pathogenesis of light chain amyloidosis. Clin Immunol 2006; 120: 106-120.
41. Abraham RS, Manske MK, Zuckerman NS, Sohni A, Edelman H, Shahaf G et al. Novel analysis of clonal diversification in blood B cell and bone marrow plasma cell clones in immunoglobulin light chain amyloidosis. J Clin Immunol 2007; 27: 69-87.
42. Dunn-Walters DK, Belelovsky A, Edelman H, Banerjee M, Mehr R. The dynamics of germinal centre selection as measured by graph-theoretical analysis of mutational lineage trees. Dev Immunol 2002; 9: 233-245.
43. Dunn-Walters DK, Edelman H, Mehr R. Immune system learning and memory quantified by graphical analysis of B-lymphocyte phylogenetic trees. BioSystems 2004; 76: 141-155.
44. Banerjee M, Mehr R, Belelovsky A, Spencer J, Dunn-Walters DK. Age and tissue-specific differences in human germinal centre B cell selection. Eur J Immunol 2002; 32: 1947-1957.
45. Dunn-Walters DK, Banerjee M, Mehr R. Effect of age on antibody affinity maturation. Biochem Soc Trans 2003; 31: 447-448.
46. Mehr R, Edelman H, Sehgal D, Mage R. Analysis of mutational lineage trees from sites of primary and Secondary immunoglobulin gene diversification in rabbits and chickens. J Immunol 2004; 172: 4790-4796.
47. Steiman-Shimony A, Edelman H, Barak M, Shahaf G, Dunn-Walters D, Stott DI et al. Immunoglobulin variable-region gene mutational lineage tree analysis: application to autoimmune diseases. Autoimmunity Rev 2006; 5: 242-251.
48. Rosner K, Winter DB, Tarone RE, Skovgaard GL, Bohr VA, Gearhart PJ. Third complementarity-determining region of mutated VH immunoglobulin genes contains shorter V D J P, and N components than non-mutated genes. Immunology 2001; 103: 179-187.
49. Xue W, Luo S, Adler WH, Schulze DH, Berman JE. Immunoglobulin heavy chain junctional diversity in young and aged humans. Hum Immunol 1997; 57: 80-92.
50. Ivanov II, Schelonka RL, Zhuang Y, Gartland GL, Zemlin M, Schroeder Jr HW. Development of the expressed Ig CDR-H3 repertoire is marked by focusing of constraints in length, amino acid use, and charge that are first established in early B cell progenitors. J Immunol 2005; 174: 7773-7780.
51. Corbett SJ, Tomlinson IM, Sonnhammer EL, Buck D, Winter G. Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, 'minor' D segments or D-D recombination. J Mol Biol 1997; 270: 587-597.
52. Nishio J, Suzuki M, Nanki T, Miyasaka N, Kohsaka H. Development of TCRB CDR3 length repertoire of human T lymphocytes. Int Immunol 2004; 16: 423-431.
53. Mehr R, Shahaf G, Sah A, Cancro M. Asynchronous differentiation models explain bone marrow labeling kinetics and predict reflux between the pre- and immature B cell pools. Intl Immunol 2003; 15: 301-312.
54. Matthews RAJ, Stone F. Coincidences: the truth is out there. Teaching Statistics 1997; 20: 17-19.
55. Matthews RAJ, Blackmore SJ. Why are coincidences so impressive? Perceptual motor skill 1995; 80: 1121-1122.
56. Hall MA, Reid JL, Lanchbury JS. The distribution of human TCR junctional region lengths shifts with age in both CD4 and CD8T cell. Int Immunol 1998; 10: 1407-1419.
57. Wang X, Stollar BD. Immunoglobulin VH gene expression in human aging. Clin Immunol 1999; 93: 132-142.
58. Chong Y, Ikematsu H, Yamaji K, Nishimura M, Kashiwagi S, Hayashi J. Age-related accumulation of Ig V H gene somatic mutations in peripheral B cells from aged humans. Clin Exp Immunol 2003; 133: 59-66.
59. MRC center for protein engineering. V Base: the database of human antibody genes. http://vbase.mrc-cpe.cam.ac.uk/. 1997.
60. Jackson KJ, Gaeta B, Sewell W, Collins AM. Exonuclease activity and P nucleotide addition in the generation of the expressed immunoglobulin repertoire. BMC Immunol 2004; 5: 5-19.
61. Lafaille JJ, DeCloux A, Bonneville M, Takagaki Y, Tonegawa S. Junctional sequences of T cell receptor gamma delta genes: implications for gamma delta T cell lineages and for a novel intermediate of V-(D)-J joining. Cell 1989; 59: 859-870.
62. Lewis SM. P nucleotides, hairpin DNA and V(D)J joining: making the connection. Semin Immunol 1994; 6: 131-141.
63. Lieber M. Site-specific recombination in the immune system. FASEB J 1991; 5: 2934-2944.
64. Meier JT, Lewis SM. P nucleotides in V(D)J recombination: a fine-structure analysis. Mol Cell Biol 1993; 13: 1078-1092.