MHC class II (MHC-II) molecules play a pivotal role in the development, activation, and homeostasis of CD4⁺ T_H cells in the thymus. The absence of MHC-II molecules causes severe T-cell immunodeficiency.

We sought to study thymic function, including T-cell receptor excision circle (TREC) quantification, in patients with MHC-II deficiency.

Eight MHC-II–deficient patients underwent a thorough T-cell immunologic work-up, including thymic activity, which was estimated based on TREC levels and T-cell receptor (TCR) genes, as well as analysis of several sequential human TCR gene rearrangements.

In vitro responses to mitogens were normal or only slightly reduced, and flow cytometric evaluations of the TCR-Vβ repertoires of total CD3⁺ lymphocytes were normal in all patients. However, both the flow cytometric evaluation of the TCR-Vβ repertoire on CD4⁺ cells and spectratyping evaluation of the TCR-Vγ repertoire on total CD3⁺ lymphocytes showed clonal abnormalities. TRECs were present in all patients in both total lymphocytes and sorted CD4⁺ cells. Additionally, TRECs were detected in genomic DNA obtained from Guthrie cards with dried blood spots. Quantitative RT-PCR assessment of different TCR gene rearrangement events revealed lower levels in MHC-II–deficient patients compared with levels seen in healthy control subjects. This was irrespective of the total lymphocyte numbers, suggesting a reduced global thymic activity.

Our report highlights potential pitfalls in diagnosing MHC-II deficiency and emphasizes the probable importance of MHC-II molecules in the normal thymic maturation process of T cells. Patients with MHC-II deficiency have detectable TRECs and might therefore be missed by a TREC-based newborn screening program.