Research Projects

Despite having anti-retroviral therapy (ART), HIV/AIDS still remains a major global public health problem. According to the WHO reports, currently 38 million people are living with HIV worldwide. The current treatment drug regimen ART fails to eliminate latently infected CD4 T cells that act as a viral reservoir. Thus there is an urgent need to understand the silencing and reactivation mechanisms of latently residing provirus in CD4+ T cells. Human endogenous retroviruses (HERV), a class of Long terminal repeat retrotransposons, that occupy 8% of the genome are silenced in normal somatic cells but are activated in myriad of human pathologies. HIV and HERVs share genomic similarities; both are remnant of ancient retroviruses, replicate through reverse transcription and activate cytosolic sensors that recognise nucleic acids leading to the activation of innate immune programs. Therefore, understanding the silencing mechanisms that operate to repress LTR based retrotransposons HERVs would provide us a novel strategy to completely silence and eradicate latently infected cells. HERV silencing involves action of around 400 different KRAB-Zinc Finger Proteins (KZFPs) that promote the recruitment of heterochromatin by promoting repressive histone marks like H3K9me3 and methylation of CpG DNA repeats. The central theme of this study is to identify highly active KZFPs in CD4+ T cells that effectively repress HERVs and then target these KZFPs for latent HIV silencing. Our preliminary data from transcriptomic studies led to the identification of HERV family members such as HERVI, LTR16, LTR34 that mimic HIV re-activation and latency. We also identified the members of other HERV families that are active in T cells, though remain repressed in latently infected cells, but remain unresponsive or are further down regulated when HIV is reactivated. We further aim to employ CRISPRi techniques to knockdown KZFps and investigate the behaviour of these identified LTR transposons in context of re-activation and durable repression of HIV during latency. Objectives: 1. Identifying KRAB-Zinc Finger Proteins (KZFPs) targeting HERVs in Jurkat T cells using Chromatin immunoprecipitation. 2. To compare chromatin factors bound to HERV and HIV LTRs using proteomics of isolated chromatin segments (PICh) in latently infected human CD4 T cells 3. Validation of the repressive effects of the identified repressors of HERVs on proviruses under reactivating and latency conditions. Novel approaches to eliminate the survival of HIV provirus of HIV are urgently needed. In this proposal, we aim to develop a novel strategy to completely silence latent HIV infections, ‘not to re-activate the latent virus but to deeply silence the virus’. Our strategy is fundamentally different and novel from the previously tested strategies to cure HIV infections.