Recombinase-mediated cassette exchange as a novel method to study somatic hypermutation in ramos cells

mBio

Volumn 2, Issue 5, 2011, Pages

  Baughn, Linda B ^a,b   Kalis, Susan L ^a   MacCarthy, Thomas ^a   Wei, Lirong ^a   Fan, Manxia ^a   Bergman, Aviv ^a   Scharff, Matthew D ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN ANTIBODY; IMMUNOGLOBULIN G ANTIBODY; IMMUNOGLOBULIN M ANTIBODY; RECOMBINASE;

AMINO ACID SEQUENCE; ANTIBODY AFFINITY; ANTIBODY SPECIFICITY; ARTICLE; BINDING AFFINITY; CELL MANIPULATION; CONTROLLED STUDY; DNA FLANKING REGION; ENZYME ACTIVATION; ENZYME ANALYSIS; GENE CASSETTE; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; HUMAN; HUMAN CELL; IN VITRO STUDY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN MODIFICATION; PROTEIN MOTIF; PROTEIN STRUCTURE; PROTEIN TARGETING; RECOMBINASE MEDIATED CASSETTE EXCHANGE; REGULATORY MECHANISM; SOMATIC HYPERMUTATION; TARGET CELL; WILD TYPE;

EID: 80455129758     PISSN: None     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00186-11     Document Type: Article

References (66)

1. Rajewsky K, Förster I, Cumano A. 1987. Evolutionary and somatic selection of the antibody repertoire in the mouse. Science 238:1088-1094.
2. Peled JU, et al. 2008. The biochemistry of somatic hypermutation. Annu. Rev. Immunol. 26:481-511.
3. Muramatsu M, et al. 2000. Class switch recombination and hypermuta-tion require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102:553-563.
4. Revy P, et al. 2000. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell 102:565-575.
5. Maul RW, Gearhart PJ. 2010. AID and somatic hypermutation. Adv. Immunol. 105:159-191.
6. Stavnezer J. 2011. Complex regulation and function of activation-induced cytidine deaminase. Trends Immunol. 32:194-201.
7. Jolly CJ, et al. 1996. The targeting of somatic hypermutation. Semin. Immunol. 8:159-168.
8. Pham P, Bransteitter R, Petruska J, Goodman MF. 2003. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 424:103-107.
9. Rogozin IB, Diaz M. 2004. Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process. J. Immunol. 172:3382-3384.
10. Ohm-Laursen L, Barington T. 2007. Analysis of 6912 unselected somatic hypermutations in human VDJ rearrangements reveals lack of strand specificity and correlation between phaseIIsubstitution rates and distance to the nearest 3' activation-induced cytidine deaminase target. J. Immunol. 178:4322-4334.
11. Longerich S, Tanaka A, Bozek G, Nicolae D, Storb U. 2005. The very 5' end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions. J. Exp. Med. 202:1443-1454.
12. Rada C, Milstein C. 2001. The intrinsic hypermutability of antibody heavy and light chain genes decays exponentially. EMBOJ.20:4570-4576.
13. Liu M, et al. 2008. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451:841-845.
14. Batrak V, Blagodatski A, Buerstedde JM. 2011. Understanding the im-munoglobulin locus specificity of hypermutation. Methods Mol. Biol. 745:311-326.
15. Tanaka A, Shen HM, Ratnam S, Kodgire P, Storb U. 2010. Attracting AID to targets of somatic hypermutation. J. Exp. Med. 207:405-415.
16. Bachl J, Caldwell RB, Buerstedde JM. 2007. Biotechnology and the chicken B cell line DT40. Cytogenet. Genome Res. 117:189-194.
17. Sale JE, Calandrini DM, Takata M, Takeda S, Neuberger MS. 2001. Ablation of XRCC2/3 transforms immunoglobulin V gene conversion into somatic hypermutation. Nature 412:921-926.
18. Magari M, et al. 2009. Enhancement of antibody production from a chicken B cell line DT40 by reducing Pax5 expression. J. Biosci. Bioeng. 107:206-209.
19. Kajita M, et al. 2010. Efficient affinity maturation of antibodies in an engineered chicken B cell line DT40-SW by increasing point mutation. J. Biosci. Bioeng. 110:351-358.
20. Bachl J, Ertongur I, Jungnickel B. 2006. Involvement of Rad18 in somatic hypermutation. Proc. Natl. Acad. Sci. U. S. A. 103:12081-12086.
21. Arakawa H, et al. 2006. A role for PCNA ubiquitination in immunoglob-ulin hypermutation. PLoS Biol. 4:e366.
22. Aoufouchi S, et al. 2008. Proteasomal degradation restricts the nuclear lifespan of AID. J. Exp. Med. 205:1357-1368.
23. Feng YQ, et al. 1999. Site-specific chromosomal integration in mammalian cells: highly efficient CRE recombinase-mediated cassette exchange. J. Mol. Biol. 292:779-785.
24. Toledo F, Liu CW, Lee CJ, Wahl GM. 2006. RMCE-ASAP: a gene targeting method for ES and somatic cells to accelerate phenotype analyses. Nucleic Acids Res. 34:e92.
25. Wong ET, et al. 2005. Reproducible doxycycline-inducible transgene expression at specific loci generated by Cre-recombinase mediated cassette exchange. Nucleic Acids Res. 33:e147.
26. Han L, Masani S, Yu K. 2011. Overlapping activation-induced cytidine deaminase hotspot motifs in Ig class-switch recombination. Proc. Natl. Acad. Sci. U. S. A. 108:11584-11589.
27. Sale JE, et al. 2001. In vivo and in vitro studies of immunoglobulin gene somatic hypermutation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 356: 21-28.
28. Harris RS, Croom-Carter DS, Rickinson AB, Neuberger MS. 2001. Epstein-Barr virus and the somatic hypermutation of immunoglobulin genes in Burkitt's lymphoma cells. J. Virol. 75:10488-10492.
29. Martin A, et al. 2002. Activation-induced cytidine deaminase turns on somatic hypermutation in hybridomas. Nature 415:802-806.
30. Zhang W, et al. 2001. Clonal instability of V region hypermutation in the Ramos Burkitt's lymphoma cell line. Int. Immunol. 13:1175-1184.
31. Cumbers SJ, et al. 2002. Generation and iterative affinity maturation of antibodies in vitro using hypermutating B-cell lines. Nat. Biotechnol. 20: 1129-1134.
32. Green NS, Lin MM, Scharff MD. 1998. Ig hypermutation in cultured cells. Immunol. Rev. 162:77-87.
33. Martin A, Scharff MD. 2002. Somatic hypermutation of the AID trans-gene in B and non-B cells. Proc. Natl. Acad. Sci. U. S. A. 99:12304-12308.
34. Yang SY, Schatz DG. 2007. Targeting of AID-mediated sequence diversification by cis-acting determinants. Adv. Immunol. 94:109-125.
35. Maquat LE. 2004. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat. Rev. Mol. Cell Biol. 5:89-99.
36. Woo CJ, Martin A, Scharff MD. 2003. Induction of somatic hypermu-tationisassociated with modificationsin immunoglobulin variable region chromatin. Immunity 19:479-489.
37. Sale JE, Neuberger MS. 1998. TdT-accessible breaks are scattered over the immunoglobulin V domain in a constitutively hypermutating B cell line. Immunity 9:859-869.
38. Di Noia JM, Neuberger MS. 2007. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 76:1-22.
39. Zarrin AA, et al. 2004. An evolutionarily conserved target motif for immunoglobulin class-switch recombination. Nat. Immunol. 5:1275-1281.
40. Beale RC, et al. 2004. Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo. J. Mol. Biol. 337:585-596.
41. Martomo SA, Yang WW, Gearhart PJ. 2004. A role for Msh6 but not Msh3 in somatic hypermutation and class switch recombination. J. Exp. Med. 200:61-68.
42. Martomo SA, et al. 2005. Different mutation signatures in DNA poly-merase eta- and MSH6-deficient mice suggest separate roles in antibody diversification. Proc. Natl. Acad. Sci. U. S. A. 102:8656-8661.
43. Min IM, Rothlein LR, Schrader CE, Stavnezer J, Selsing E. 2005. Shifts in targetingofclass switch recombination sitesin mice that lack mu switch region tandem repeats or Msh2. J. Exp. Med. 201:1885-1890.
44. Manis JP, Tian M, Alt FW. 2002. Mechanism and control of class-switch recombination. Trends Immunol. 23:31-39.
45. Wang L, Jackson WC, Steinbach PA, Tsien RY. 2004. Evolution of new nonantibody proteins via iterative somatic hypermutation. Proc. Natl. Acad. Sci. U. S. A. 101:16745-16749.
46. Basu U, et al. 2005. The AID antibody diversification enzyme is regulated by protein kinase A phosphorylation. Nature 438:508-511.
47. Cheng HL, et al. 2009. Integrity of the AID serine-38 phosphorylation site is critical for class switch recombination and somatic hypermutation in mice. Proc. Natl. Acad. Sci. U. S. A. 106:2717-2722.
48. Yamane A, et al. 2011. Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes. Nat. Immunol. 12:62-69.
49. Chaudhuri J, Khuong C, Alt FW. 2004. Replication protein A interacts with AID to promote deamination of somatic hypermutation targets. Nature 430:992-998.
50. Bransteitter R, Pham P, Calabrese P, Goodman MF. 2004. Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase. J. Biol. Chem. 279:51612-51621.
51. Michael N, et al. 2003. The E box motif CAGGTG enhances somatic hypermutation without enhancing transcription. Immunity 19:235-242.
52. Carpenter MA, Rajagurubandara E, Wijesinghe P, Bhagwat AS. 2010. Determinants of sequence-specificity within human AID and APOBEC3G. DNA Repair (Amst.) 9:579-587.
53. Kohli RM, et al. 2009. A portable hot spot recognition loop transfers sequence preferences from APOBEC family members to activation-induced cytidine deaminase. J. Biol. Chem. 284:22898-22904.
54. Wang M, Rada C, Neuberger MS. 2010. Altering the spectrum of immu-noglobulin V gene somatic hypermutation by modifying the active site of AID. J. Exp. Med. 207:141-153.
55. Wang M, Yang Z, Rada C, Neuberger MS. 2009. AID upmutants isolated using a high-throughput screen highlight the immunity/cancer balance limiting DNA deaminase activity. Nat. Struct. Mol. Biol. 16:769-776.
56. Milstein C, Neuberger MS, Staden R. 1998. Both DNA strands of antibody genes are hypermutation targets. Proc. Natl. Acad. Sci. U. S. A. 95: 8791-8794.
57. Frey S, et al. 1998. Mismatch repair deficiency interferes with the accumulation of mutations in chronically stimulated B cells and not with the hypermutation process. Immunity 9:127-134.
58. Rada C, Ehrenstein MR, Neuberger MS, Milstein C. 1998. Hot spot focusing of somatic hypermutation in MSH2-deficient mice suggests two stages of mutational targeting. Immunity 9:135-141.
59. Wagner SD, Elvin JG, Norris P, McGregor JM, Neuberger MS. 1996. Somatic hypermutation of Ig genes in patients with xeroderma pigmen-tosum (XP-D). Int. Immunol. 8:701-705.
60. Larijani M, et al. 2007. AID associates with single-stranded DNA with high affinity andalong complex half-lifein asequence-independent manner. Mol. Cell. Biol. 27: 20-30.
61. Pham P, Calabrese P, Park SJ, Goodman MF. 2011. Analysis of a single-stranded DNA-scanning process in which activation-induced de-oxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity. J. Biol. Chem. 286:24931-24942.
62. Ta VT, et al. 2003. AID mutant analyses indicate requirement for class-switch-specific cofactors. Nat. Immunol. 4:843-848.
63. Dickerson SK, Market E, Besmer E, Papavasiliou FN. 2003. AID mediates hypermutation by deaminating single stranded DNA. J. Exp. Med. 197:1291-1296.
64. Chelico L, Pham P, Petruska J, Goodman MF. 2009. Biochemical basis of immunological and retroviral responses to DNA-targeted cytosine deamination by activation-induced cytidine deaminase and APOBEC3G. J. Biol. Chem. 284:27761-27765.
65. Ford GS, Yin CH, Barnhart B, Sztam K, Covey LR. 1998. CD40 ligand exerts differential effects on the expression of I gamma transcripts in subclones of an IgM+ human B cell lymphoma line. J. Immunol. 160: 595-605.
66. Bookout AL, Cummins CL, Mangelsdorf DJ, Pesola JM, Kramer MF. 2006. High-throughput real-time quantitative reverse transcription PCR. Curr. Protoc. Mol. Biol. Chapter 15:Unit 15.8.