The supply of naive T cells by the thymus normally requires precursor T cell proliferation within the thymus and would be particularly important in the setting of HIV infection when both naive and memory T cells are progressively depleted. As a robust, quantitative index of intrathymic proliferation, the ratio of different T cell receptor excision circles (TRECs), molecular markers of distinct T cell receptor rearrangements occurring at different stages of thymocyte development, was measured in peripheral blood-mononuclear cells (PBMCs). This ratio has the virtue that it is a "signature" of thymic emigrants throughout their entire life and, thus, can be measured in peripheral cell populations that are easy to obtain. Using the new assay, we evaluated the effect of HIV infection on intrathymic precursor T cell proliferation by longitudinal analysis of PBMCs from recently infected individuals. Our findings reveal a substantial reduction in intrathymic proliferation. The analysis also indicates the existence of a compensatory mechanism acting to sustain the numbers of recent thymic emigrants (RTEs) in the periphery.

Allogeneic hematopoietic stem cell transplantation (AHSCT) leads to a prolonged state of immunodeficiency characterized by low peripheral naive T-cell counts. To identify the mechanisms leading to this defect we quantitatively and qualitatively analyzed thymic function through quantification of T-cell receptor excision circle (TREC) frequencies (both the signal-joint TREC [sjTREC] and 6 different D␤J␤ TRECs, by-products of T-cell receptor [TCR] ␣ and ␤ gene rearrangement, respectively), in conjunction with immunophenotype and spectratype analyses in a cohort of patients sampled from 1 to 10 years following AHSCT. In this cohort, reduced thymic function was associated only with ongoing clinical chronic graft-versushost disease (cGVHD). Nonetheless, the diversity of thymic production remained unchanged irrespective of the patient's cGVHD status. Interestingly, increased homeostatic proliferation was found in the naive T-cell compartment of cGVHD ؊ patients who underwent transplantation. However, reduced expression of both the interleukin-7 receptor ␣ (IL-7R␣) (CD127) chain and the antiapoptotic protein Bcl-2 was observed. Taken together, these data indicate that the inability to reconstitute the naive T-cell compartment for several years after AHSCT, in the absence of cGVHD, is a consequence of impaired naive T-cell survival rather than thymic dysfunction. IntroductionAllogeneic hematopoietic stem cell transplantation (AHSCT) is often the only available treatment for several hematologic disorders such as severe aplastic anemia (SAA), acute lymphocytic/ myelogenous leukemia (ALL, AML), chronic myelogenous leukemia (CML), and multiple myeloma (MM). 1,2 The transplantation procedure/conditioning regimen generally leads to a profound and long-lasting state of immunodeficiency characterized by persisting low levels of naive T cells. 3 Pioneer studies aimed at better understanding the mechanisms responsible for the regeneration of the T-cell compartment demonstrated that T cells can be generated through both thymus-dependent and thymus-independent pathways. [4][5][6][7][8][9] However, adequate broadening of the naive T-cell receptor (TCR) repertoire is ensured by the thymus. 10,11 Nowadays, the magnitude of thymic function is best determined through the peripheral blood quantification of T-cell receptor excision circles (TRECs), by-products of TCR gene rearrangement events that occur during thymocyte ontogeny. 12 TREC molecules are extrachromosomal circular DNA generated during V(D)J recombination that do not replicate themselves during mitosis and are diluted-out upon cellular proliferation. As a consequence of this behavior, peripheral blood signal-joint TREC (sjTREC) frequencies are considered surrogate markers for thymic function. Furthermore, peripheral blood quantification of the TREC molecules generated during T-cell receptor beta-chain variable region chain rearrangements (ie, distinct D␤-J␤ or V␤-D␤J␤ TRECs 13 ) illustrates the assortment of the different gene rearrangement events that occurred in the thymus, ...