A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency

Journal of Allergy and Clinical Immunology

Volumn 133, Issue 4, 2014, Pages

  Lee, Yu Nee ^a   Frugoni, Francesco ^a   Dobbs, Kerry ^a   Walter, Jolan E ^a,b   Giliani, Silvia ^c   Gennery, Andrew R ^d   Al Herz, Waleed ^e   Haddad, Elie ^f   Ledeist, Francoise ^f   Bleesing, Jack H ^g   Henderson, Lauren A ^a   Pai, Sung Yun ^a   Nelson, Robert P ^h   El Ghoneimy, Dalia H ⁱ   El Feky, Reem A ⁱ   Reda, Shereen M ⁱ   Hossny, Elham ⁱ   Soler Palacin, Pere ^j   Fuleihan, Ramsay L ^k   Patel, Niraj C ^l   Massaad, Michel J ^a   Geha, Raif S ^a   Puck, Jennifer M ^m   Palma, Paolo ⁿ   Cancrini, Caterina ⁿ   Chen, Karin ^o   Vihinen, Mauno ^p   Alt, Frederick W ^a   Notarangelo, Luigi D ^a   more..

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c UNIVERSITY OF BRESCIA   (Italy)

^d NEWCASTLE UPON TYNE HOSPITALS NHS FOUNDATION TRUST   (United Kingdom)

^e KUWAIT UNIVERSITY   (Kuwait)

^f UNIVERSITY OF MONTREAL   (Canada)

^g CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^h INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ Ain Shams University   (Egypt)

^j HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

^k NORTHWESTERN UNIVERSITY   (United States)

^l CAROLINAS MEDICAL CENTER   (United States)

^m UNIVERSITY OF CALIFORNIA   (United States)

ⁿ UNIVERSITY OF ROME TOR VERGATA   (Italy)

^o UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^p LUND UNIVERSITY   (Sweden)

more..

Author keywords

autoimmunity; genotype phenotype correlation; immune repertoire; Omenn syndrome; Recombination activating gene 1; severe combined immune deficiency; V(D)J recombination

Indexed keywords

GREEN FLUORESCENT PROTEIN; IMMUNOGLOBULIN E; MUTANT PROTEIN; RAG1 PROTEIN;

ANIMAL CELL; ARTICLE; AUTOIMMUNITY; B LYMPHOCYTE; CELL CYCLE G0 PHASE; CELL CYCLE G1 PHASE; CONTROLLED STUDY; EOSINOPHIL; FLOW CYTOMETRY; GENE LOCUS; GENETIC ANALYSIS; GENETIC DISORDER; GENOTYPE PHENOTYPE CORRELATION; HUMAN; HUMAN CELL; MAJOR CLINICAL STUDY; MISSENSE MUTATION; MOUSE; NONHUMAN; PATHOGENICITY; PHENOTYPIC VARIATION; PRE B LYMPHOCYTE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RECOMBINATION ACTIVATING GENE 1 DEFICIENCY; RECOMBINATION ACTIVITY; T LYMPHOCYTE; VDJ RECOMBINATION;

AUTOIMMUNITY; GENOTYPE-PHENOTYPE CORRELATION; IMMUNE REPERTOIRE; OMENN SYNDROME; RECOMBINATION-ACTIVATING GENE 1; SEVERE COMBINED IMMUNE DEFICIENCY; V(D)J RECOMBINATION;

ALLELES; B-LYMPHOCYTES; CHILD; CHILD, PRESCHOOL; GENE ORDER; GENE REARRANGEMENT; GENETIC ASSOCIATION STUDIES; HOMEODOMAIN PROTEINS; HUMANS; IMMUNOGLOBULIN HEAVY CHAINS; INFANT; INFANT, NEWBORN; MUTATION; PHENOTYPE; SEVERE COMBINED IMMUNODEFICIENCY; T-LYMPHOCYTES; V(D)J RECOMBINATION;

EID: 84897389616     PISSN: 00916749     EISSN: 10976825     Source Type: Journal    
DOI: 10.1016/j.jaci.2013.10.007     Document Type: Article

References (43)

1. D.G. Schatz, and P.C. Swanson V(D)J recombination: mechanisms of initiation Annu Rev Genet 45 2011 167 202
2. F.W. Alt, Y. Zhang, F.L. Meng, C. Guo, and B. Schwer Mechanisms of programmed DNA lesions and genomic instability in the immune system Cell 152 2013 417 429
3. K. Schwarz, G.H. Gauss, L. Ludwig, U. Pannicke, Z. Li, and D. Lindner et al. RAG mutations in human B cell-negative SCID Science 274 1996 97 99
4. A. Villa, S. Santagata, F. Bozzi, S. Giliani, A. Frattini, and L. Imberti et al. Partial V(D)J recombination activity leads to Omenn syndrome Cell 93 1998 885 896
5. - severe combined immune deficiency or Omenn syndrome Blood 97 2001 2772 2776
6. C. Sobacchi, V. Marrella, F. Rucci, P. Vezzoni, and A. Villa RAG-dependent primary immunodeficiencies Hum Mutat 27 2006 1174 1184
7. S. Pasic, S. Djuricic, G. Ristic, and B. Slavkovic Recombinase-activating gene 1 immunodeficiency: different immunological phenotypes in three siblings Acta Paediatr 98 2009 1062 1064
8. I. Dalal, D. Tasher, R. Somech, A. Etzioni, B.Z. Garti, and D. Lev et al. Novel mutations in RAG1/2 and ADA genes in Israeli patients presenting with T-B-SCID or Omenn syndrome Clin Immunol 140 2011 284 290
9. B. Cassani, P.L. Poliani, D. Moratto, C. Sobacchi, V. Marrella, and L. Imperatori et al. Defect of regulatory T cells in patients with Omenn syndrome J Allergy Clin Immunol 125 2010 209 216
10. A. Villa, C. Sobacchi, L.D. Notarangelo, F. Bozzi, M. Abinun, and T.G. Abrahamsen et al. V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations Blood 97 2001 81 88
11. J.P. de Villartay, A. Lim, H. Al-Mousa, S. Dupont, J. Dechanet-Merville, and E. Coumau-Gatbois et al. A novel immunodeficiency associated with hypomorphic RAG1 mutations and CMV infection J Clin Invest 115 2005 3291 3299
12. S. Ehl, K. Schwarz, A. Enders, U. Duffner, U. Pannicke, and J. Kuhr et al. A variant of SCID with specific immune responses and predominance of gamma delta T cells J Clin Invest 115 2005 3140 3148
13. C. Schuetz, K. Huck, S. Gudowius, M. Megahed, O. Feyen, and B. Hubner et al. An immunodeficiency disease with RAG mutations and granulomas N Engl J Med 358 2008 2030 2038
14. S.S. De Ravin, E.W. Cowen, K.A. Zarember, N.L. Whiting-Theobald, D.B. Kuhns, and N.G. Sandler et al. Hypomorphic Rag mutations can cause destructive midline granulomatous disease Blood 116 2010 1263 1271
15. L.A. Henderson, F. Frugoni, G. Hopkins, H. de Boer, S.Y. Pai, and Y.N. Lee et al. Expanding the spectrum of recombination-activating gene 1 deficiency: a family with early-onset autoimmunity J Allergy Clin Immunol 132 2013 969 971.e2
16. T.W. Kuijpers, H. Ijspeert, E.M. van Leeuwen, M.H. Jansen, M.D. Hazenberg, and K.C. Weijer et al. Idiopathic CD4+ T lymphopenia without autoimmunity or granulomatous disease in the slipstream of RAG mutations Blood 117 2011 5892 5896
17. M.R. Lieber, J.E. Hesse, S. Lewis, G.C. Bosma, N. Rosenberg, and K. Mizuuchi et al. The defect in murine severe combined immune deficiency: joining of signal sequences but not coding segments in V(D)J recombination Cell 55 1988 7 16
18. C. Couedel, C. Roman, A. Jones, P. Vezzoni, A. Villa, and P. Cortes Analysis of mutations from SCID and Omenn syndrome patients reveals the central role of the Rag2 PHD domain in regulating V(D)J recombination J Clin Invest 120 2010 1337 1344
19. A.L. Bredemeyer, G.G. Sharma, C.Y. Huang, B.A. Helmink, L.M. Walker, and K.C. Khor et al. ATM stabilizes DNA double-strand-break complexes during V(D)J recombination Nature 442 2006 466 470
20. C. Wang, C.M. Sanders, Q. Yang, H.W. Schroeder Jr., E. Wang, and F. Babrzadeh et al. High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets Proc Natl Acad Sci U S A 107 2010 1518 1523
21. E. Alamyar, V. Giudicelli, S. Li, P. Duroux, and M.P. Lefranc IMGT/HighV-QUEST: the IMGT(R) web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing Immunome Res 8 2012 26
22. T. Rogosch, S. Kerzel, K.H. Hoi, Z. Zhang, R.F. Maier, and G.C. Ippolito et al. Immunoglobulin analysis tool: a novel tool for the analysis of human and mouse heavy and light chain transcripts Front Immunol 3 2012 176
23. Hammer ∅, Harper DAT, Ryan PD. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 2001;4:1-9.
24. E.M. Avila, G. Uzel, A. Hsu, J.D. Milner, M.L. Turner, and S. Pittaluga et al. Highly variable clinical phenotypes of hypomorphic RAG1 mutations Pediatrics 126 2010 e1248 e1252
25. J. Zhang, L. Quintal, A. Atkinson, B. Williams, E. Grunebaum, and C.M. Roifman Novel RAG1 mutation in a case of severe combined immunodeficiency Pediatrics 116 2005 e445 e449
26. E. Asai, T. Wada, Y. Sakakibara, A. Toga, T. Toma, and T. Shimizu et al. Analysis of mutations and recombination activity in RAG-deficient patients Clin Immunol 138 2011 172 177
27. K. Felgentreff, R. Perez-Becker, C. Speckmann, K. Schwarz, K. Kalwak, and G. Markelj et al. Clinical and immunological manifestations of patients with atypical severe combined immunodeficiency Clin Immunol 141 2011 73 82
28. S. Safaei, Z. Pourpak, M. Moin, and M. Houshmand IL7R and RAG1/2 genes mutations/polymorphisms in patients with SCID Iran J Allergy Asthma Immunol 10 2011 129 132
29. S.A. Muljo, and M.S. Schlissel A small molecule Abl kinase inhibitor induces differentiation of Abelson virus-transformed pre-B cell lines Nat Immunol 4 2003 31 37
30. A. Olatubosun, J. Valiaho, J. Harkonen, J. Thusberg, and M. Vihinen PON-P: integrated predictor for pathogenicity of missense variants Hum Mutat 33 2012 1166 1174
31. F.F. Yin, S. Bailey, C.A. Innis, M. Ciubotaru, S. Kamtekar, and T.A. Steitz et al. Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis Nat Struct Mol Biol 16 2009 499 508
32. C. Guo, H.S. Yoon, A. Franklin, S. Jain, A. Ebert, and H.L. Cheng et al. CTCF-binding elements mediate control of V(D)J recombination Nature 477 2011 424 430
33. I.I. Ivanov, R.L. Schelonka, Y. Zhuang, G.L. Gartland, M. Zemlin, and H.W. Schroeder Jr. 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 174 2005 7773 7780
34. M.Z. Radic, and M. Weigert Genetic and structural evidence for antigen selection of anti-DNA antibodies Annu Rev Immunol 12 1994 487 520
35. H. Wardemann, S. Yurasov, A. Schaefer, J.W. Young, E. Meffre, and M.C. Nussenzweig Predominant autoantibody production by early human B cell precursors Science 301 2003 1374 1377
36. S. Tsukada, H. Sugiyama, Y. Oka, and S. Kishimoto Estimation of D segment usage in initial D to JH joinings in a murine immature B cell line. Preferential usage of DFL16.1, the most 5' D segment and DQ52, the most JH-proximal D segment J Immunol 144 1990 4053 4059
37. W. Giblin, M. Chatterji, G. Westfield, T. Masud, B. Theisen, and H.L. Cheng et al. Leaky severe combined immunodeficiency and aberrant DNA rearrangements due to a hypomorphic RAG1 mutation Blood 113 2009 2965 2975
38. S.Y. Wong, C.P. Lu, and D.B. Roth A RAG1 mutation found in Omenn syndrome causes coding flank hypersensitivity: a novel mechanism for antigen receptor repertoire restriction J Immunol 181 2008 4124 4130
39. M. Zemlin, G.C. Ippolito, C. Zemlin, J. Link, M. Monestier, and H.W. Schroeder Jr. Adult lupus-prone MRL/MpJ2+ mice express a primary antibody repertoire that differs in CDR-H3 length distribution and hydrophobicity from that expressed in the C3H parental strain Mol Immunol 42 2005 789 798
40. X. Yu, J. Almeida, S. Darko, M. van der Burg, S.S. DeRavin, and H. Malech et al. Human syndromes of immune deficiency and dysregulation are characterized by distinct defects in T-cell receptor repertoire development J Allergy Clin Immunol 133 2014 1109 1115
41. H.E. Liang, L.Y. Hsu, D. Cado, L.G. Cowell, G. Kelsoe, and M.S. Schlissel The "dispensable" portion of RAG2 is necessary for efficient to-DJ rearrangement during B and T cell development Immunity 17 2002 639 651
42. C.A. Mainville, K. Parmar, I. Unnikrishnan, L. Gong, G.D. Raffel, and N. Rosenberg Temperature-sensitive transformation by an Abelson virus mutant encoding an altered SH2 domain J Virol 75 2001 1816 1823
43. C.A. Schneider, W.S. Rasband, and K.W. Eliceiri NIH Image to ImageJ: 25 years of image analysis Nat Methods 9 2012 671 675