High-throughput sequencing reveals an altered T cell repertoire in X-linked agammaglobulinemia

• Published in: Clinical immunology (Orlando, Fla.) Vol. 161; no. 2; pp. 190 - 196
• Main Authors: Ramesh, Manish, Simchoni, Noa, Hamm, David, Cunningham-Rundles, Charlotte
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2015
• Subjects: Adolescent; Adult; Agammaglobulinemia - genetics; Allergy and Immunology; Amino acid sequence; B-Lymphocytes - metabolism; Case-Control Studies; Child; Child, Preschool; DNA - genetics; Genetic Diseases, X-Linked - genetics; High throughput sequencing; High-Throughput Nucleotide Sequencing - methods; Humans; Immunoglobulin Variable Region - genetics; Infant; Junctional diversity; Male; Middle Aged; Receptor-CD3 Complex, Antigen, T-Cell - genetics; Receptors, Antigen, T-Cell - genetics; T cell receptor; T-Lymphocytes - metabolism; XLA; Young Adult; Amino acid sequence; Junctional diversity; T cell receptor; High throughput sequencing; XLA
• ISSN: 1521-6616; 1521-7035
• DOI: 10.1016/j.clim.2015.09.002

To examine the T cell receptor structure in the absence of B cells, the TCR β CDR3 was sequenced from DNA of 15 X-linked agammaglobulinemia (XLA) subjects and 18 male controls, using the Illumina HiSeq platform and the ImmunoSEQ analyzer. V gene usage and the V–J combinations, derived from both productive and non-productive sequences, were significantly different between XLA samples and controls. Although the CDR3 length was similar for XLA and control samples, the CDR3 region of the XLA T cell receptor contained significantly fewer deletions and insertions in V, D, and J gene segments, differences intrinsic to the V(D)J recombination process and not due to peripheral T cell selection. XLA CDR3s demonstrated fewer charged amino acid residues, more sharing of CDR3 sequences, and almost completely lacked a population of highly modified Vβ gene segments found in control DNA, suggesting both a skewed and contracted T cell repertoire in XLA. •XLA subjects have fewer n-nucleotide insertions and lack T cells with >12 insertions.•There is altered Vβ usage in productive and non-productive sequences.•CDR3 amino acid usage and hydrophilicity in XLA differ from controls.•Significant increase in sharing of sequences amongst XLA subjects.