Evaluating predictive markers for viral rebound and safety assessment in blood and lumbar fluid during HIV-1 treatment interruption

Abstract

Background: Validated biomarkers to evaluate HIV-1 cure strategies are currently lacking, therefore requiring analytical treatment interruption (ATI) in study participants. Little is known about the safety of ATI and its long-term impact on patient health.

Objectives: ATI safety was assessed and potential biomarkers predicting viral rebound were evaluated.

Methods: PBMCs, plasma and CSF were collected from 11 HIV-1-positive individuals at four different timepoints during ATI (NCT02641756). Total and integrated HIV-1 DNA, cell-associated (CA) HIV-1 RNA transcripts and restriction factor (RF) expression were measured by PCR-based assays. Markers of neuroinflammation and neuronal injury [neurofilament light chain (NFL) and YKL-40 protein] were measured in CSF. Additionally, neopterin, tryptophan and kynurenine were measured, both in plasma and CSF, as markers of immune activation.

Results: Total HIV-1 DNA, integrated HIV-1 DNA and CA viral RNA transcripts did not differ pre- and post-ATI. Similarly, no significant NFL or YKL-40 increases in CSF were observed between baseline and viral rebound. Furthermore, markers of immune activation did not increase during ATI. Interestingly, the RFs SLFN11 and APOBEC3G increased after ATI before viral rebound. Similarly, Tat-Rev transcripts were increased preceding viral rebound after interruption.

Conclusions: ATI did not increase viral reservoir size and it did not reveal signs of increased neuronal injury or inflammation, suggesting that these well-monitored ATIs are safe. Elevation of Tat-Rev transcription and induced expression of the RFs SLFN11 and APOBEC3G after ATI, prior to viral rebound, indicates that these factors could be used as potential biomarkers predicting viral rebound.

© The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Figures

Figure 1.

Schematic overview of the study set-up. PBMCs were collected at four different timepoints (T1, T2, T3 and T4). CSF was collected at two timepoints (T1 and T3). T1 represents the sampling under cART (baseline; undetectable VL). ATI occurs at Day 0. T2 represents 7–15 days after ATI (undetectable VL). At T3, viral rebound occurs (detectable VL). T4 represents a timepoint after cART restart (approximately 3 months; undetectable VL).

Figure 2.

Viral reservoir size quantification at the four different timepoints during ATI. Levels of total HIV-1 DNA (a) and integrated HIV-1 DNA (b) at T1, T2, T3 and T4. Levels for the different transcripts (TAR, long LTR, polyA, Pol and Tat-Rev) of CA HIV-1 RNA (c) at T1, T2, T3 and T4. Friedman statistical analysis with post hoc Dunn test was performed. Significant P values are indicated in red. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.

Figure 3.

Inflammation marker levels in CSF and plasma during ATI. (a) Levels of NFL and YKL-40 in CSF at T1 and T3. (b) Levels of immune activation markers neopterin, kynurenine and kynurenine/tryptophan in CSF at T1 and T3. (c) Levels of neopterin, kynurenine and kynurenine/tryptophan in plasma at T1, T2, T3 and T4. Statistical Wilcoxon signed rank (a and b) and Friedman test with post hoc Dunn analysis (c) were performed. Significant P values are indicated in red. Kyn/Trp, kynurenine/tryptophan. (d) Maximum-likelihood phylogenetic trees representing CSF and plasma sequences at T1 and T3 for five participants from whom we obtained CSF sequences. The coloured strip represents sampling origin for each sequence as indicated by the legend. The trees are drawn to scale and the grey circles represent the branch length from the root expressed as the number of substitutions per site. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.

Figure 4.

ISG, RF and HIV-1 dependency factor expression levels at four timepoints during ATI. Normalized relative quantity levels at T1, T2, T3 and T4 for: (a) MX1 and IFIT1; (b) MX2, TRIM5 and BST2; (c) SAMHD1 and PAF1; and (d) NLRX1 and PSIP1. Friedman statistical analysis with post hoc Dunn test was performed. Significant P values are indicated in red. NRQ, normalized relative quantity. This figure appears in colour in the online version of JAC and in black and white in the print version of JAC.