The γδ T-cell receptor repertoire is reconstituted in HIV patients after prolonged antiretroviral therapy

Abstract

Objective: Determine whether reconstitution of Vγ2Vδ2 T cells in patients with HIV is due to new cell synthesis with recovery of the T-cell receptor repertoire or proliferative expansion of residual cells from the time of treatment initiation.

Design: Perform a cross-sectional analysis of the T-cell receptor complexity of Vγ2 chain in patients treated for HIV, natural virus suppressors who control viremia to undetectable levels, patients with chronic low-level viremia in the absence of therapy, and uninfected controls. Apply quantitative methods for repertoire analysis to assess the degree of Vδ2 repertoire loss or reconstitution.

Methods: T-cell receptor Vγ2 chain DNA clones (up to 300 per patient sample) were sequenced and aligned to enumerate the antigen-reactive subset with Vγ2-Jγ1.2 rearrangements. Predominant shared (public) sequences in each patient were compared to a reference library of public sequences from uninfected controls to assess the extent of similarity. Repertoire comparisons were quantified through bioinformatics testing.

Results: Patients with prolonged virus suppression due to antiretroviral therapy reconstituted the Vγ2 T-cell repertoire to near-normal levels. Natural virus suppressors were similar to the treatment group. Severe defects in the Vγ2 T-cell receptor repertoire were observed in patients with chronic viremia despite the absence of overt disease.

Conclusion: Prolonged HIV suppression with antiretroviral therapy leads to reconstitution of the Vγ2Vδ2 T-cell subset deleted in HIV disease. Direct evidence for repair of the T-cell receptor repertoire supports a view that treatment-associated immune reconstitution is due to new cell synthesis and not to expansion of residual cell populations.

Fig. 1. HIV infection depletes circulating Vγ2-Jγ1.2Vδ2 T cells

(a) The fraction of Vγ2 chains expressing Jγ1.2 segment is lowest for the VIR group. The fraction of chains expressing Jγ1.2 was calculated and plotted for the four groups (mean + SD). On average, approximately 60% of Jγ2 chains expressed the Jγ1.2 segment in healthy controls, whereas only approximately 10% Jγ2 chains were Jγ1.2 in VIR. For NVS and ART groups this number was approximately 30%. (b) The fraction of Vγ2-Jγ1.2 chains expressing public Jγ1.2 clonotype is lowest for the VIR group. Public clonotypes were identified as aa sequences present in more than one patient in the control group, and these sequences were scored for their presence in HIV-positive groups. For control group, approximately 52% of Vγ2-Jγ1.2 chains were found in two or more donors, whereas approximately 20% of Vγ2-Jγ1.2 chains were public for VIR and NVS groups. ART group had approximately 30% public Vγ2-Jγ1.2 chain. For each panel horizontal lines represent mean values. Statistical comparisons used Kruskal–Wallis test; P values less than 0.05 were considered significant. (c) Clonotype and nucleotype abundance for the most common public Vγ2-Jγ1.2 chains in control, ART, NVS, and VIR groups. The eight most common public clonotypes (PubSeq 1–8) are listed along with all their nucleotypes found in this study. Vertical columns are grouped into control, ART, NVS, and VIR groups as described in the text. Each individual column represents sequencing data for an individual patient. A shaded box indicates that nucleotype was present in the set of TCR-Vγ2 sequences from the individual patient or control. ART, antiretroviral therapy; NVS, natural virus suppressor; TCR, T-cell receptor; VIR, viremic and not receiving therapy.

Fig. 2. Similarity analysis between the TCR-Vγ2 repertoires of pairs of individuals within each group

The number of clonotypes (a) or nucleotypes (c) common between individual repertoires and the Morisita-Horn similarity indices for clonotype (b) and nucleotype (d) repertoires were estimated for a sample size of 98 TCR-Vγ2 sequences per individual repertoire. Horizontal lines represent the median similarity values per group and asterisks show P < 0.0005 (***), (P < 0.005 (**), or P < 0.05 (*). Statistical comparisons were made using a Kruskal–Wallis test and Dunn's multiple comparison post-tests. In terms of common nucleotypes (c) or similarity index for nucleotype repertoire (d), control and ART groups were not different at P < 0.05. ART, antiretroviral therapy; TCR, T-cell receptor.