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

•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.

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.