The importance of taking ART appropriately in children and adolescents with HIV-1 to reach the highest capacity of immune function later in life

Abstract

Current antiretroviral therapy (ART) guidelines recommend treating all children with HIV-1 infection. This has changed from the broader use of ART to treat children to improve morbidity and minimise mortality. However, prior to current recommendations, not everyone with HIV-1 received timely treatment. What happens to the paediatric immune system when HIV-1 replication is not appropriately supressed remains unclear. 11 samples from adolescents with HIV-1 on ART and uninfected controls in the UK, aged 12-25 years, were examined; overall, adolescents with CD4⁺ counts > 500/μl and a viral load < 50 copies/ml were compared with adolescents with CD4⁺ counts < 500/μl and a viral load > 50 copies/ml at time of sampling. Measurements of thymic output were combined with high throughput next generation sequencing and bioinformatics to systematically organize CD4⁺ and CD8⁺ T cell receptor (TCR) repertoires. TCR repertoire diversity, clonal expansions, TCR sequence sharing, and formation of TCR clusters in HIV-1 infected adolescents with successful HIV-1 suppression were compared to adolescents with ineffective HIV-1 suppression. Thymic output and CD4⁺ T cell numbers were decreased in HIV-1 infected adolescents with poor HIV-1 suppression. A strong homeostatic TCR response, driven by the decreased CD4⁺ T cell compartment and reduced thymic output was observed in the virally uncontrolled HIV-1-infected adolescents. Formation of abundant robust TCR clusters and structurally related TCRs were found in the adolescents with effective HIV-1 suppression. Numerous CD4⁺ T cell numbers in the virally controlled adolescents emphasize the importance of high thymic output and formation of robust TCR clusters in the maintenance of HIV-1 suppression. While the profound capacity for immune recovery in children may allow better opportunity to deal with immunological stress, when ART is taken appropriately, this study demonstrates new insights into the unique paediatric immune system and the immunological changes when HIV-1 replication is ongoing.

Keywords: HIV-1; T cell receptor clonal expansions; T cell receptor repertoires; antiretroviral therapy (ART); children; high throughout sequencing; immune reconstitution; thymic output.

Figure 1

Viral load, age-normalised CD4⁺ and CD8⁺ T cell numbers, CXCL8 T cell production, and thymic output in adolescents with HIV-1. (A) Overview of the different groups. (B) Viral load (copies per ml). (C) Age-normalised CD4⁺ T cell counts. (D) Age-normalised CD8⁺ T cell counts. (E) Ki67 production in naïve CD4⁺, CD45RA⁺, CD31⁺ T cells (%). (F) CXCL8 production in naïve CD4⁺, CD45RA⁺, CD31⁺ T cells (%). (G) Thymic output (number of recent thymic emigrants measured by the mathematical model). Black lines: median(IQR). *P ≤ 0.05, **P≤ 0.005.

Figure 2

TCR abundance distribution in CD4⁺ and CD8⁺ T cells in adolescents with different responses to HIV-1 (A) The degree of clonal expansion in the CD4⁺ TCR repertoire measured using the Gini coefficient in TCR alpha (blue) and TCR beta sequences (pink). (B) Individual TCR sequence abundance distribution in the CD4⁺ TCR repertoire. (C) The degree of clonal expansion in the CD8⁺ TCR repertoire measured using the Gini coefficient in TCR alpha (blue) and TCR beta sequences (pink). (D) Individual TCR sequence abundance distribution in the CD8⁺ TCR repertoire. Black lines: median(IQR).

Figure 3

The abundance differences of the public TCR repertoire in children with different responses to HIV-1. The y axis shows the abundance of shared TCRs (dots) between groups. Lines are connecting identical shared TCRs between two groups. (A) CD4⁺ TCR repertoires and (B) CD8⁺ TCR repertoires. (C, D) Shared CDR3s between patients from CD8⁺ T cells are shown with connecting grey lines. Left panels show α chain samples; right panels show β chain samples. The horizontal bar represents a sample, with white space showing the percentage of CDR3s unique to that sample within each panel, and these constitute the majority of each sample. Within each of the six panels, all the CDR3s occurring in more than one sample are coloured and separated by black outlines, thus many CDR3s shared at low frequencies appear black. A broad coloured band indicates that the CDR3 has expanded multiple times. Within each panel, a given colour represents the same CDR3; grey lines overlaid show pairwise shared CDR3s.

Figure 4

T cell receptor clustering in children with different responses to HIV-1 (A) Structurally related CDR3s with the same motifs in their sequences forming network clusters (shown as nodes) in the CD8⁺ T cell population. (B) TCR clusters (nodes) as a proportion of the number of total TCRs being clustered for each sample, showing median (IQR). (C) The distribution of pairwise Hamming distances between CDR3s in the CD8⁺ T cell repertoires.