Journal Article

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

Boden, Daniel, Van Gulck, Ellen, Dhondt, Annemieke, Rutsaert, Sofie, Eyassu, Filmon, Nijs, Erik, Pardons, Marion, van Snippenberg, Willem, Noppe, Ytse, Vega, Jerel, Lambrechts, Laurens, De Langhe, Nele, Vandekerckhove, Linos, Cole, Basiel

2023

Overview

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.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 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 drugs / Antiretroviral therapy / Antiretroviral Therapy, Highly Active / CD4 antigen / CD4 Antigens - genetics / CD4 Antigens - metabolism / CD4-Positive T-Lymphocytes - drug effects / CD4-Positive T-Lymphocytes - virology / Cell activation / Cells, Cultured / Gene Products, tat - genetics / Gene Products, tat - metabolism / HIV / HIV Core Protein p24 - genetics / HIV Core Protein p24 - metabolism / HIV Infections - drug therapy / HIV Infections - genetics / HIV Infections - virology / HIV-1 - drug effects / HIV-1 - genetics / Human immunodeficiency virus / Humanities and Social Sciences / Humans / Ionomycin / Ionomycin - pharmacology / Latency / Latent infection / Lipids / Lymphocytes / Lymphocytes T / multidisciplinary / Nanoparticles / Nanoparticles - administration & dosage / Nanoparticles - chemistry / Panobinostat - pharmacology / Proteins / Proteomes / Proviruses - drug effects / Proviruses - genetics / Ribonucleic acid / RNA / RNA, Long Noncoding - metabolism / RNA, Viral - administration & dosage / RNA, Viral - genetics / RNA, Viral - metabolism / Science / Science (multidisciplinary) / Single-Cell Gene Expression Analysis / Tat protein / Transcriptomes / Transcriptomics / Virus Latency - drug effects / Virus Latency - genetics