Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

• Published in: Nature communications Vol. 14; no. 1; p. 8397
• Main Authors: Pardons, Marion, Cole, Basiel, Lambrechts, Laurens, van Snippenberg, Willem, Rutsaert, Sofie, Noppe, Ytse, De Langhe, Nele, Dhondt, Annemieke, Vega, Jerel, Eyassu, Filmon, Nijs, Erik, Van Gulck, Ellen, Boden, Daniel, Vandekerckhove, Linos
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.12.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 1-Phosphatidylinositol 3-kinase; 13/31; 38/77; 38/91; 631/208/514/1949; 631/326/596/2564; 692/699/255/1901; AKT protein; Antiretroviral agents; Antiretroviral therapy; CD4 antigen; Cell activation; HIV; Human immunodeficiency virus; Humanities and Social Sciences; Ionomycin; Latency; Latent infection; Lipids; Lymphocytes; Lymphocytes T; multidisciplinary; Nanoparticles; Proteins; Proteomes; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Tat protein; Transcriptomes; Transcriptomics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-44020-5

The development of latency reversing agents that potently reactivate HIV without inducing global T cell activation would benefit the field of HIV reservoir research and could pave the way to a functional cure. Here, we explore the reactivation capacity of a lipid nanoparticle containing Tat mRNA (Tat-LNP) in CD4 T cells from people living with HIV undergoing antiretroviral therapy (ART). When combined with panobinostat, Tat-LNP induces latency reversal in a significantly higher proportion of latently infected cells compared to PMA/ionomycin (≈ 4-fold higher). We demonstrate that Tat-LNP does not alter the transcriptome of CD4 T cells, enabling the characterization of latently infected cells in their near-native state. Upon latency reversal, we identify transcriptomic differences between infected cells carrying an inducible provirus and non-infected cells (e.g. LINC02964 , GZMA , CCL5 ). We confirm the transcriptomic differences at the protein level and provide evidence that the long non-coding RNA LINC02964 plays a role in active HIV infection. Furthermore, p24+ cells exhibit heightened PI3K/Akt signaling, along with downregulation of protein translation, suggesting that HIV-infected cells display distinct signatures facilitating their long-term persistence. Tat-LNP represents a valuable research tool for in vitro reservoir studies as it greatly facilitates the in-depth characterization of HIV reservoir cells’ transcriptome and proteome profiles. Reactivating latent HIV reservoirs could be beneficial towards a functional cure. Here, the authors show that Tat-LNP effectively reactivates HIV while preserving the cell transcriptome. Upon reactivation, p24+ cells exhibit distinct genes and pathways potentially contributing to their persistence.