Executive Summary : | Transcriptional silence offers a formidable hindrance for the functional cure of HIV-1. Anti-retroviral treatment fails to eradicate the virus because HIV-1 establishes a latent infection. Vaccines and other therapeutic strategies suffer from the same limitation that they cannot eliminate the latent virus. Therefore, understanding the molecular mechanisms controlling latency and finding an effective HIV latency reversal strategy are the highest global research priorities currently. We recently showed the crucial role Tat, the ‘master regulator, plays in controlling HIV latency, thus offering fresh and vital leads (Chakraborty S et al., J Virol, 2020). Furthermore, we show a high magnitude of TFBS variation emerging in HIV-1C in India (Bhange D et al., https://www.biorxiv.org/content/10.1101/2021.04.28.441760v3). HIV-1C evolution appears to be moving towards gaining stronger viral promoters, which seems paradoxical. Paradoxical because HIV-1 uses transcriptional silence as a powerful tool to evade immune surveillance of the host. How can a viral strain establish and maintain latency when endowed with a stronger promoter? Of note, why only in HIV-1C we find this, not in any other HIV-1 genetic family? Through the present work, we will address three critical aspects associated with HIV-1 latency, especially in the context of HIV-1C of India. (1) Tat-PTM and latency: We will examine the molecular mechanisms regulating HIV-1 latency – especially the roles of Tat and Tat PTM. (2) Latent reservoir characteristics: We will study the viral reservoir properties (size and activation qualities) in clinical samples of at least three emerging viral variant strains. (3) Epigenetic landscape: We will evaluate the landscape of epigenetic modifications, including nucleosome positioning and the histone code that play a critical role in viral gene silencing. To this end, we will construct several panels of reporter viruses (both sub-genomic and replication-competent viruses), engineer target cell lines (T-cell lines, cell lines of monocytes, microglia, and primary CD4 cells), use state-of-art molecular technologies, and humanized mouse models. We will take advantage of the largest pediatric HIV cohort maintained at IGICH. Three different laboratories, renowned for their work in HIV disease management, HIV molecular biology, and host epigenetic modifications, and with a proven track record of long-term collaborations will come together through this project. Notably, the team is well-positioned, given the complementary expertise, skills, and resources. The various latency-reversing agents (LRA) reported thus far lack targeting specificity and efficiency. Only a small proportion of latent virus can be activated using these LRA. The knowledge gained through this work will help devise improved HTS assays to detect LRA specifically targeting the HIV master transcription regulatory circuit and identify LRA with superior latency reversing property. |