Identification of ITK deficiency as a novel genetic cause of idiopathic CD4⁺ T-cell lymphopenia

To the editor:

Idiopathic CD4 lymphopenia represents a heterogeneous group of combined primary immunodeficiencies with markedly reduced CD4⁺ T-cell counts. Although several genetic etiologies including MHC class II deficiency¹  or mutations in RAG1,² MST1,³  or LCK⁴  have been reported, the majority of patients remain genetically undetermined.

Here we describe a 17-year-old male Turkish patient of consanguineous background, referred to the hospital at 7 years of age. He suffered from recurrent pulmonary infections causing progressive immune reaction and bronchiectasia. Immunological analysis at the age of 10 showed persistently low CD4⁺ T-cell counts (range: 8% to 16%; 286-714/µL) and increased CD8⁺ T-cell counts (range: 50% to 59%; 1404-2950/µL, Figure 1A). T-cell proliferation responses to CD3/CD28 stimulation were reduced (not shown), whereas PHA stimulation led to normal proliferation of T-cells. B-cell counts and immunoglobulin levels were unremarkable (not shown); however, the patient showed reduced antipneumococcal antibody response.

To elucidate the underlying genetic cause, we combined homozygosity mapping (Figure 1B) and exome sequencing as previously reported, with minor modifications.⁵  Unexpectedly, we identified a homozygous nonsense mutation located within the first exon of the Interleukin-2-inducible T-cell kinase (ITK) gene (c.C49T:p.Q17X) likely leading to nonsense-mediated decay of the corresponding gene product. The mutation was validated using capillary sequencing and showed perfect segregation under the assumption of autosomal-recessive inheritance (Figure 1C). ITK is a tyrosine kinase comprising 2 Src homology and a pleckstrin homology domain, respectively, acting downstream of the T-cell receptor complex and playing a critical role during thymic CD4⁺/CD8⁺ selection.⁶ Itk^−/− mice have reduced iNKT-cells and show an activated phenotype of peripheral CD4⁺ T-cells.⁷ 

All ITK-deficient patients reported to date developed EBV-associated B-cell lymphoproliferation accompanied by hepato- and splenomegaly or Hodgkin lymphoma.^8-10  Decreased numbers of iNKT-cells are a hallmark feature of the disease.^8-11 

Surprisingly, this patient remained at sero-negative EBV status until the age of 17, although PCR-based copy-number analysis indicated borderline detectable EBV virus load (1000-2000 copies/mL). As all previously reported ITK-deficient patients were analyzed when they showed EBV-induced lymphoproliferation, we here had the unique opportunity to dissect EBV-dependent and EBV-independent ITK deficiency phenotypes. Consistent with previous findings in mouse⁷  and human,^8-11  flow cytometry indicated an absence of iNKT-cells (Figure 1D), illustrating that the absence of iNKT-cells is a primary phenotype of ITK deficiency. Although CD4 lymphopenia has already been described in other ITK-deficient patients suffering from lymphoproliferative disease,^9,11  we here show that combined immunodeficiency with CD4 deficiency can be the predominant disease manifestation. Furthermore, defective T-cell proliferation has not been described in ITK-deficient patients, although it is concordant with the findings in Itk^−/− mice. Of note, at the most recent follow-up, the patient presented with leiomyoma (not shown) and a high titer for EBV (23 × 10⁶ copies/mL), in line with the characteristic, marked vulnerability to EBV infection in human ITK deficiency.^8-11 

In conclusion, in this case we identify ITK deficiency as a novel cause of idiopathic CD4 lymphopenia. Our analysis also sheds light on the immunophenotype of ITK deficiency in the absence of EBV-associated lymphoproliferation. Genetic assessment of patients with combined immunodeficiencies, in particular with predominant CD4 lymphophenia, should include mutational analysis of ITK even in the absence of EBV lymphoproliferation.