title: Human syndromes of immunodeficiency and dysregulation are characterized by distinct defects in T-cell receptor repertoire development.
abstract: BACKGROUND
  Human immunodeficiencies characterized by hypomorphic mutations in critical developmental and signaling pathway genes allow for the dissection of the role of these genes in the development of the T-cell receptor (TCR) repertoire and the correlation of alterations of the TCR repertoire with diverse clinical phenotypes.
  
  
  OBJECTIVE
  The presence of T cells in patients with Omenn syndrome (OS) and patients with atypical presentations of severe combined immunodeficiency gene mutations presents an opportunity to study the effects of the causal genes on TCR repertoires and provides a window into the clinical heterogeneity observed.
  
  
  METHODS
  We performed deep sequencing of TCRβ complementarity-determining region 3 (CDR3) regions in subjects with a series of immune dysregulatory conditions caused by mutations in recombination activating gene 1/2 (RAG 1/2), IL-2 receptor γ (IL2RG), and ζ chain-associated protein kinase 70 (ZAP70); a patient with atypical DiGeorge syndrome; and healthy control subjects.
  
  
  RESULTS
  We found that patients with OS had marked reductions in TCRβ diversity compared with control subjects, as expected. Patients with atypical presentations of RAG or IL2RG mutations associated with autoimmunity and granulomatous disease did not have altered overall diversity but instead had skewed V-J pairing and skewed CDR3 amino acid use. Although germline TCRs were more abundant and clonally expanded in patients with OS, nongermline sequences were expanded as well. TCRβ from patients with RAG mutations had less junctional diversity and smaller CDR3s than patients with OS caused by other gene mutations and healthy control subjects but relatively similar CDR3 amino acid use.
  
  
  CONCLUSIONS
  High-throughput TCR sequencing of rare immune disorders has demonstrated that quantitative TCR diversity can appear normal despite qualitative changes in repertoire and strongly suggests that in human subjects RAG enzymatic function might be necessary for normal CDR3 junctional diversity.
authors.affiliation: Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Yu
authors.affiliation: Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
authors.forename: Jorge R
authors.initials: JR
authors.lastname: Almeida
authors.affiliation: Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
authors.forename: Sam
authors.initials: S
authors.lastname: Darko
authors.affiliation: Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
authors.forename: Mirjam
authors.initials: M
authors.lastname: van der Burg
authors.affiliation: Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
authors.forename: Suk See
authors.initials: SS
authors.lastname: DeRavin
authors.affiliation: Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
authors.forename: Harry
authors.initials: H
authors.lastname: Malech
authors.affiliation: Department of Paediatric Immunology, Newcastle University, Newcastle upon Tyne, United Kingdom; Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.
authors.forename: Andrew
authors.initials: A
authors.lastname: Gennery
authors.affiliation: Department of Pediatrics, Division of Allergy and Immunology, Duke University Medical Center, Durham, NC.
authors.forename: Ivan
authors.initials: I
authors.lastname: Chinn
authors.affiliation: Department of Pediatrics, Division of Allergy and Immunology, Duke University Medical Center, Durham, NC; Department of Immunology, Duke University Medical Center, Durham, NC.
authors.forename: Mary Louise
authors.initials: ML
authors.lastname: Markert
authors.affiliation: Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md. Electronic address: ddouek@mail.nih.gov.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Douek
authors.affiliation: Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md. Electronic address: jdmilner@niaid.nih.gov.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Milner
mesh_terms: D019943:Amino Acid Substitution; D016022:Case-Control Studies; D002648:Child; D002675:Child, Preschool; D022801:Complementarity Determining Regions / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics* / Q000276:immunology; D007223:Infant; D053631:Interleukin Receptor Common gamma Subunit / Q000235:genetics; D008297:Male; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics; D017422:Sequence Analysis, DNA; D016511:Severe Combined Immunodeficiency / Q000235:genetics; D016176:T-Lymphocyte Subsets / Q000276:immunology / Q000378:metabolism; D051746:ZAP-70 Protein-Tyrosine Kinase / Q000235:genetics
chemical_list: D022801:Complementarity Determining Regions; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D053631:Interleukin Receptor Common gamma Subunit; D009687:Nuclear Proteins; C499311:RAG2 protein, human; D011948:Receptors, Antigen, T-Cell; D016693:Receptors, Antigen, T-Cell, alpha-beta; C064658:RAG-1 protein; D051746:ZAP-70 Protein-Tyrosine Kinase
keywords: Omenn syndrome; T-cell receptor; T-cell receptor sequencing; recombination activating gene