High frequency of CD8 escape mutations in elite controllers as new obstacle for HIV cure

ABSTRACT

Accumulation of mutations in epitopes of cytolytic-T-lymphocytes immune response (CTL) in HIV-reservoir seems to be one of the reasons for shock-and-kill strategy failure. Ten non-controller patients on successful cART (TX) and seven elite controllers (EC) were included. HIV-Gag gene from purified resting memory CD4+ T-cells was sequenced by Next-Generation-Sequencing. HLA class-I alleles were typed to predict optimal HIV-Gag CTL epitopes. For each subject, the frequency of mutated epitopes in the HIV-Gag gene, the proportion of them considered as CTL-escape variants as well as their effect on antigen recognition by HLA were assessed. The proportion (%) of mutated HIV-Gag CTL epitopes in the reservoir was high and similar in EC and TX (86%[50–100] and 57%[48–82] respectively, p=0.315). Many of them were predicted to negatively impact antigen recognition. Moreover, the proportion of mutated epitopes considered to be CTL-escape variants was also similar in TX and EC (77%[49–92] vs. 50%[33–75] respectively, p=0.117). Thus, the most relevant finding of our study was the high and similar proportions of HIV-Gag CTL-escape mutations in the reservoir of both HIV-noncontroller patients with cART (TX) and patients with spontaneous HIV-control (EC). Our findings suggest that escape mutations of CTL-response may be another obstacle to eliminate the HIV reservoir and constitute a proof of concept that challenges HIV cure strategies focused on the reactivation of reservoirs. Due to the small sample size that could impact the robustness of the study, further studies with larger cohorts of elite controller patients are needed to confirm these results.

KEYWORDS:

• HIV reservoir
• resting memory CD4+ T-cells
• elite controllers
• CTL response
• HIV-Gag proviral DNA
• next generation sequencing (NGS)

Acknowledgments

We especially thank Marcial García for his technical assistance. We would especially like to thank the patients in this study for their participation and the different collaborating centers for the donation of clinical samples employed in this study.

Authors’ contributions

NR and JMB conceived and designed the study. AC and MG contributed to the recruitment and follow-up of patients. NR, J.M.B., and MANN-M carried out the samples collection and Trm cells isolation. MANN-M, AH, JMB, and NR performed HIV-Gag gene amplification by different patients-specific strategies. RR carried out Next-Generation Sequencing (NGS) of HIV-Gag gene experiments. RR, NR, JMB, and MANN-M performed the NGS bioinformatics analysis. MANN-M, JMB, and NR performed the in silico studies. JMB, MAN-M, and NR performed the statistical analysis and interpretation of data. MANN-M, JMB, and NR drafted the manuscript. All authors reviewed and approved the final version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Data that support the findings of this study are available from the corresponding author upon reasonable request.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/21505594.2022.2129353.

Additional information

Funding

This work was supported by project PI16/01769 to N Rallón and project RD16/0025/0013 to JM Benito, integrated into the State Plan for Scientific and Technical Research and Innovation from the General Sub-Directorate for research assessment and promotion, Spanish Carlos III Institute of Health (ISCIII) co-funded by the European Regional Development Fund (ERDF). Maria A Navarrete-Muñoz was funded by the Spanish Directorate General for Research and Technology of the “Comunidad de Madrid” [grant: IND2018/BMD9651]. Norma Rallón is supported by the Miguel Servet program funded by the Spanish Health Institute Carlos III [grant: CPII19/00025].