Transient Viral Rebound in Children with Perinatally Acquired HIV-1 Induces a Unique Soluble Immunometabolic Signature Associated with Decreased CD4/CD8 Ratio

Abstract

Background: To determine by multi-omic analysis changes in metabolites, lipids, and proteins as a consequence of transient viral rebound (tVR) in children with perinatally acquired HIV-1 (PHIV).

Methods: Plasma samples from children with PHIV and with tVR (first episode of transient RNA-HIV viral load >20 copies/ml followed by suppression) on the time-point immediately before (pre-tVR) and after (post-tVR) the tVR were assessed. Multi-omic analyses were performed using nLC-Orbitrap, GC-qTOF-MS, and LC-qTOF-MS.

Results: Comparing pre- and post-tVR time-points, HIV-1 children with tVR (n = 5) showed a trend to a decrease in ratio CD4/CD8 (p = 0.08) but no significant differences were observed in plasma metabolites, lipids, or proteins. Post-tVR condition was compared with a reference group of children with PHIV with persistent viral control (n = 9), paired by sex, age, and time under antiretroviral treatment. A total of 10 proteins, 8 metabolites, and 2 lipids showed significant differences (p < 0.05): serotransferrin, clusterin, kininogen-1, succinic acid, threonine, 2-hydroxyisovaleric acid, methionine, 2-hydroxyglutaric, triacylglyceride 50:0 (TG50:0), and diacylglyceride 34:1 (DG34:1) were upregulated while alpha-2-macroglobulin, apolipoprotein A-II, carboxylic ester hydrolase, apolipoprotein D, coagulation factor IX, peptidase inhibitor 16, SAA2-SAA4 readthrough, oleic acid, palmitoleic acid, and D-sucrose downregulated on post-tVR time-point compared to the reference group. Ratio CD4/CD8 correlated with apolipoprotein A-II, DG34:1, and methionine (p = 0.004; ρ = 0.71, p = 0.016; ρ = -0.63; and p = 0.032; ρ = -0.57, respectively). Nadir CD4+ correlated inversely with kininogen-1 (p = 0.022; ρ = -0.60) and positively with D-sucrose (p = 0.001; ρ = 0.77).

Conclusions: tVR followed by suppression implies changes in soluble proteins, lipids, and metabolites that correlate with immunological parameters, mainly ratio CD4/CD8, that decreased after tVR. These distinct soluble biomarkers could be considered potential biomarkers of immune progression.

Keywords: omics; ratio CD4/CD8; vertically HIV-1 children; viral rebounds.

Figure 1.

Plasma HIV-RNA viral load and ratio CD4/CD8 over time in children with perinatally acquired HIV-1 who develop transient viral rebounds (tVR). Open cycles represent viral load values above detection limit. Light gray bands are the time-points pre-loss (pre-tVR) and post-loss (post-tVR) selected for plasma multi-omic approaches. Note that, for both time-points, HIV viral load remains under detection limit (>20 copies/ml, but less than 1000 copies/ml) in all participants.

Figure 2.

Multiomic analysis comparing post-tVR and reference group of children with perinatally acquired HIV-1 with persistent viral control. (A) Protein fold change of significantly changed proteins in post-tVR compared to the reference group (persistent viral control). Sparse partial least squares-discriminant analysis (sPLS-DA) plot displays the post-tVR group in red and the reference group with persistent viral control in green. Plot proteins loading graph insert displays key protein differences between groups for sPLS-DA component 1. (B) Metabolite fold change of significantly changed metabolites in post-tVR compared to the reference group (persistent viral control). sPLS-DA plot results on post-tVR and reference group, and plot metabolite loading graph (insert) displaying the key metabolite differences between groups for sPLS-DA component 1. (C) Loading score plots of sPLS-DA and correlation heatmap based on the 115 lipid species identified from the two groups under study. Spearman’s coefficient values are depicted using the color gradient scale. *P value < 0.05, *** P value ≤ 0.001.

Figure 3.

Correlations between proteins, lipids, and metabolites differentially expressed at post-tVR time-point and immunological and clinical parameters compared to the reference group. A total of 14 participants are included in the analysis. TG: triacylglyceride; DG: diacylglycerides; ART: antiretroviral treatment. The Spearman ρ correlation coefficient test was used. Ө 0.1 > P value ≥ 0.05, *P value < 0.05, **P value ≤ 0.01, ***P value ≤ 0.001.