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Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients with RAG1/2 Mutations: First Cases Series from Mexico and Description of Two Novel Mutations

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Abstract

Mutations in recombinase activating genes 1 and 2 (RAG1/2) result in human severe combined immunodeficiency (SCID). The products of these genes are essential for V(D)J rearrangement of the antigen receptors during lymphocyte development. Mutations resulting in null-recombination activity in RAG1 or RAG2 are associated with the most severe clinical and immunological phenotypes, whereas patients with hypomorphic mutations may develop leaky SCID, including Omenn syndrome (OS). A group of previously unrecognized clinical phenotypes associated with granulomata and/or autoimmunity have been described as a consequence of hypomorphic mutations. Here, we present six patients from unrelated families with missense variants in RAG1 or RAG2. Phenotypes observed in these patients ranged from OS to severe mycobacterial infections and granulomatous disease. Moreover, we report the first evidence of two variants that had not been associated with immunodeficiency. This study represents the first case series of RAG1- or RAG2-deficient patients from Mexico and Latin America.

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References

  1. Sponzilli I, Notarangelo LD. Severe combined immunodeficiency (SCID): from molecular basis to clinical management. Acta Biomed. 2011;82(1):5–13.

    CAS  PubMed  Google Scholar 

  2. Fischer A. Severe combined immunodeficiencies (SCID). Clin Exp Immunol. 2000;122(2):143–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Tangye SG, Al-Herz W, Bousfiha A, Chatila T, Cunningham-Rundles C, Etzioni A, et al. Human inborn errors of immunity: 2019 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol. 2020;40(1):24–64.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Notarangelo LD, Kim MS, Walter JE, Lee YN. Human RAG mutations: biochemistry and clinical implications. Nat Rev Immunol. 2016;16(4):234–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Dvorak CC, Haddad E, Buckley RH, Cowan MJ, Logan B, Griffith LM, et al. The genetic landscape of severe combined immunodeficiency in the United States and Canada in the current era (2010–2018). J Allergy Clin Immunol. 2019;143(1):405–7.

    Article  PubMed  Google Scholar 

  6. Schwarz K, Gauss GH, Ludwig L, Pannicke U, Li Z, Lindner D, et al. RAG mutations in human B cell-negative SCID. Science. 1996;274(5284):97–9.

    Article  CAS  PubMed  Google Scholar 

  7. Delmonte OM, Schuetz C, Notarangelo LD. RAG deficiency: two genes, many diseases. J Clin Immunol. 2018;38(6):646–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. De Ravin SS, Cowen EW, Zarember KA, Whiting-Theobald NL, Kuhns DB, Sandler NG, et al. Hypomorphic Rag mutations can cause destructive midline granulomatous disease. Blood. 2010;116(8):1263–71.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  9. Patiroglu T, Akar HH, Gilmour K, Ozdemir MA, Bibi S, Henriquez F, et al. Atypical severe combined immunodeficiency caused by a novel homozygous mutation in Rag1 gene in a girl who presented with pyoderma gangrenosum: a case report and literature review. J Clin Immunol. 2014;34(7):792–5.

    Article  PubMed  Google Scholar 

  10. Schuetz C, Huck K, Gudowius S, Megahed M, Feyen O, Hubner B, et al. An immunodeficiency disease with RAG mutations and granulomas. N Engl J Med. 2008;358(19):2030–8.

    Article  CAS  PubMed  Google Scholar 

  11. Villa A, Notarangelo LD. RAG gene defects at the verge of immunodeficiency and immune dysregulation. Immunol Rev. 2019;287(1):73–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Boutboul D, Kuehn HS, Van de Wyngaert Z, Niemela JE, Callebaut I, Stoddard J, et al. Dominant-negative IKZF1 mutations cause a T, B, and myeloid cell combined immunodeficiency. J Clin Invest. 2018;128(7):3071–87.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res. 2000;28(1):235–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kim MS, Lapkouski M, Yang W, Gellert M. Crystal structure of the V(D)J recombinase RAG1-RAG2. Nature. 2015;518(7540):507–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, et al. Cracking the DNA code for V(D)J recombination. Mol Cell. 2018;70(2):358-70 e4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Chen X, Cui Y, Best RB, Wang H, Zhou ZH, Yang W, et al. Cutting antiparallel DNA strands in a single active site. Nat Struct Mol Biol. 2020;27(2):119–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Chen X, Cui Y, Wang H, Zhou ZH, Gellert M, Yang W. How mouse RAG recombinase avoids DNA transposition. Nat Struct Mol Biol. 2020;27(2):127–33.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Ru H, Chambers MG, Fu TM, Tong AB, Liao M, Wu H. Molecular mechanism of V(D)J recombination from synaptic RAG1-RAG2 complex structures. Cell. 2015;163(5):1138–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, et al. DNA melting initiates the RAG catalytic pathway. Nat Struct Mol Biol. 2018;25(8):732–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell JD, et al. Transposon molecular domestication and the evolution of the RAG recombinase. Nature. 2019;569(7754):79–84.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14(1):33–8 (27-8).

    Article  CAS  PubMed  Google Scholar 

  22. Russell RB, Barton GJ. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins. 1992;14(2):309–23.

    Article  CAS  PubMed  Google Scholar 

  23. Roberts E, Eargle J, Wright D, Luthey-Schulten Z. MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics. 2006;7:382.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Bertoni M, Kiefer F, Biasini M, Bordoli L, Schwede T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Sci Rep. 2017;7(1):10480.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Ramon-Maiques S, Kuo AJ, Carney D, Matthews AG, Oettinger MA, Gozani O, et al. The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc Natl Acad Sci U S A. 2007;104(48):18993–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Jo S, Kim T, Iyer VG, Im W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem. 2008;29(11):1859–65.

    Article  CAS  PubMed  Google Scholar 

  27. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30(10):1545–614.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, et al. CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J Chem Theory Comput. 2016;12(1):405–13.

    Article  CAS  PubMed  Google Scholar 

  29. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, et al. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins. 2003;50(3):437–50.

    Article  CAS  PubMed  Google Scholar 

  30. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.

    Article  PubMed  PubMed Central  Google Scholar 

  31. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 2012;40(Web Server issue):W452-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, et al. PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Comput Biol. 2014;10(1):e1003440.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Laskowski RA, Stephenson JD, Sillitoe I, Orengo CA, Thornton JM. VarSite: Disease variants and protein structure. Protein Sci. 2020;29(1):111–9.

    Article  CAS  PubMed  Google Scholar 

  35. Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am J Hum Genet. 2016;99(4):877–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Niroula A, Urolagin S, Vihinen M. PON-P2: prediction method for fast and reliable identification of harmful variants. PLoS ONE. 2015;10(2):e0117380.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Banerjee A, Mitra P. Estimating the effect of single-point mutations on protein thermodynamic stability and analyzing the mutation landscape of the p53 protein. J Chem Inf Model. 2020;60(6):3315–23.

    Article  CAS  PubMed  Google Scholar 

  38. Ittisoponpisan S, Islam SA, Khanna T, Alhuzimi E, David A, Sternberg MJE. Can predicted protein 3D structures provide reliable insights into whether missense variants are disease associated? J Mol Biol. 2019;431(11):2197–212.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Meshaal SS, El Hawary RE, AbdElaziz DS, Eldash A, Alkady R, Lotfy S, et al. Phenotypical heterogeneity in RAG-deficient patients from a highly consanguineous population. Clin Exp Immunol. 2019;195(2):202–12.

    Article  CAS  PubMed  Google Scholar 

  40. Lev A, Simon AJ, Trakhtenbrot L, Goldstein I, Nagar M, Stepensky P, et al. Characterizing T cells in SCID patients presenting with reactive or residual T lymphocytes. Clin Dev Immunol. 2012;2012:261470.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Sobacchi C, Marrella V, Rucci F, Vezzoni P, Villa A. RAG-dependent primary immunodeficiencies. Hum Mutat. 2006;27(12):1174–84.

    Article  CAS  PubMed  Google Scholar 

  42. Tabori U, Mark Z, Amariglio N, Etzioni A, Golan H, Biloray B, et al. Detection of RAG mutations and prenatal diagnosis in families presenting with either T-B- severe combined immunodeficiency or Omenn’s syndrome. Clin Genet. 2004;65(4):322–6.

    Article  CAS  PubMed  Google Scholar 

  43. Corneo B, Moshous D, Gungor T, Wulffraat N, Philippet P, Le Deist FL, et al. Identical mutations in RAG1 or RAG2 genes leading to defective V(D)J recombinase activity can cause either T-B-severe combined immune deficiency or Omenn syndrome. Blood. 2001;97(9):2772–6.

    Article  CAS  PubMed  Google Scholar 

  44. Corneo B, Moshous D, Callebaut I, de Chasseval R, Fischer A, de Villartay JP. Three-dimensional clustering of human RAG2 gene mutations in severe combined immune deficiency. J Biol Chem. 2000;275(17):12672–5.

    Article  CAS  PubMed  Google Scholar 

  45. Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581(7809):434–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29(1):308–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Cooper DN, Ball EV, Krawczak M. The human gene mutation database. Nucleic Acids Res. 1998;26(1):285–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Luk ADW, Lee PP, Mao H, Chan KW, Chen XY, Chen TX, et al. Family history of early infant death correlates with earlier age at diagnosis but not shorter time to diagnosis for severe combined immunodeficiency. Front Immunol. 2017;8:808.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  49. Al-Mousa H, Abouelhoda M, Monies DM, Al-Tassan N, Al-Ghonaium A, Al-Saud B, et al. Unbiased targeted next-generation sequencing molecular approach for primary immunodeficiency diseases. J Allergy Clin Immunol. 2016;137(6):1780–7.

    Article  CAS  PubMed  Google Scholar 

  50. Schuetz C, Neven B, Dvorak CC, Leroy S, Ege MJ, Pannicke U, et al. SCID patients with ARTEMIS vs RAG deficiencies following HCT: increased risk of late toxicity in ARTEMIS-deficient SCID. Blood. 2014;123(2):281–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Safaei S, Pourpak Z, Moin M, Houshmand M. IL7R and RAG1/2 genes mutations/polymorphisms in patients with SCID. Iran J Allergy Asthma Immunol. 2011;10(2):129–32.

    CAS  PubMed  Google Scholar 

  52. Villa A, Sobacchi C, Notarangelo LD, Bozzi F, Abinun M, Abrahamsen TG, et al. V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood. 2001;97(1):81–8.

    Article  CAS  PubMed  Google Scholar 

  53. Gomez CA, Ptaszek LM, Villa A, Bozzi F, Sobacchi C, Brooks EG, et al. Mutations in conserved regions of the predicted RAG2 kelch repeats block initiation of V(D)J recombination and result in primary immunodeficiencies. Mol Cell Biol. 2000;20(15):5653–64.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Noordzij JG, de Bruin-Versteeg S, Verkaik NS, Vossen JM, de Groot R, Bernatowska E, et al. The immunophenotypic and immunogenotypic B-cell differentiation arrest in bone marrow of RAG-deficient SCID patients corresponds to residual recombination activities of mutated RAG proteins. Blood. 2002;100(6):2145–52.

    CAS  PubMed  Google Scholar 

  55. Ireland SM, Martin ACR. ZincBind-the database of zinc binding sites. Database (Oxford). 2019;2019:baz006.

    Article  CAS  Google Scholar 

  56. Krezel A, Maret W. The biological inorganic chemistry of zinc ions. Arch Biochem Biophys. 2016;611:3–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Soni K, Martinez-Lumbreras S, Sattler M. Conformational dynamics from ambiguous zinc coordination in the RanBP2-type zinc finger of RBM5. J Mol Biol. 2020;432(14):4127–38.

    Article  CAS  PubMed  Google Scholar 

  58. Lee YN, Frugoni F, Dobbs K, Walter JE, Giliani S, Gennery AR, et al. A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency. J Allergy Clin Immunol. 2014;133(4):1099–108.

    Article  CAS  PubMed  Google Scholar 

  59. Alsmadi O, Al-Ghonaium A, Al-Muhsen S, Arnaout R, Al-Dhekri H, Al-Saud B, et al. Molecular analysis of T-B-NK+ severe combined immunodeficiency and Omenn syndrome cases in Saudi Arabia. BMC Med Genet. 2009;10:116.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  60. Farmer JR, Foldvari Z, Ujhazi B, De Ravin SS, Chen K, Bleesing JJH, et al. Outcomes and treatment strategies for autoimmunity and hyperinflammation in patients with RAG deficiency. J Allergy Clin Immunol Pract. 2019;7(6):1970-85 e4.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Lawless D, Geier CB, Farmer JR, Lango Allen H, Thwaites D, Atschekzei F, et al. Prevalence and clinical challenges among adults with primary immunodeficiency and recombination-activating gene deficiency. J Allergy Clin Immunol. 2018;141(6):2303–6.

    Article  PubMed  PubMed Central  Google Scholar 

  62. Baumann U, Routes JM, Soler-Palacin P, Jolles S. The lung in primary immunodeficiencies: new concepts in infection and inflammation. Front Immunol. 2018;9:1837.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Kutukculer N, Gulez N, Karaca NE, Aksu G, Berdeli A. Novel mutations and diverse clinical phenotypes in recombinase-activating gene 1 deficiency. Ital J Pediatr. 2012;38:8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Perelygina L, Icenogle J, Sullivan KE. Rubella virus-associated chronic inflammation in primary immunodeficiency diseases. Curr Opin Allergy Clin Immunol. 2020;20(6):574–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Dorna MB, Barbosa PFA, Rangel-Santos A, Csomos K, Ujhazi B, Dasso JF, et al. Combined immunodeficiency with late-onset progressive hypogammaglobulinemia and normal B cell count in a patient with RAG2 deficiency. Front Pediatr. 2019;7:122.

    Article  PubMed  PubMed Central  Google Scholar 

  66. Carmona LM, Fugmann SD, Schatz DG. Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination. Genes Dev. 2016;30(8):909–17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Oudinet C, Braikia FZ, Dauba A, Khamlichi AA. Recombination may occur in the absence of transcription in the immunoglobulin heavy chain recombination centre. Nucleic Acids Res. 2020;48(7):3553–66.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Shimazaki N, Tsai AG, Lieber MR. H3K4me3 stimulates the V(D)J RAG complex for both nicking and hairpinning in trans in addition to tethering in cis: implications for translocations. Mol Cell. 2009;34(5):535–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors would like to thank the patients and their families for participating in this study.

Funding

MECM is supported by Consejo Nacional de Ciencia y Tecnología (CONACYT 281854).

LDN is supported by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.

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MECM and SEP conceived the study. MECM, SORL, and NP wrote the manuscript. SORL, JN, SDR, and LDN performed, analyzed, and interpreted the genetics. NP performed and analyzed the protein modeling. EGS and LBR performed proliferation assays and provided flow cytometry data. CAV, CMG, LLFL, and KCS provided the in silico analysis and classification of RAG1/2 variants. MAYN, SSM, GW, MENN, APMR, ATSB, and EVM took care of the patients and provided clinical data. PG and JAY performed genetic studies. IMD provided their expertise on congenital disorders. All authors critically reviewed the manuscript and approved the final version.

Corresponding authors

Correspondence to Sara Espinosa-Padilla or Mario Ernesto Cruz-Munoz.

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The original online version of this article was revised: Had typos in the last names of two authors.

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Lugo-Reyes, S.O., Pastor, N., González-Serrano, E. et al. Clinical Manifestations, Mutational Analysis, and Immunological Phenotype in Patients with RAG1/2 Mutations: First Cases Series from Mexico and Description of Two Novel Mutations. J Clin Immunol 41, 1291–1302 (2021). https://doi.org/10.1007/s10875-021-01052-0

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