RESEARCH

From Retrovirus Biology to Viral Vectors and Genome Editing

We strive to understand how retroviruses evolve and what makes some (like HIV-1) highly pathogenic to humans. The overarching goal is to comprehend how various cellular processes control retrovirus replication at [i] protein levels and [ii] RNA levels and how this knowledge can be translated into [iii] developing efficient gene delivery vehicles and gene regulatory circuits.    

[i] Host-Virus interactions

The outcome of virus infection is often determined by cellular pathways and their interaction with viral proteins. Retroviruses vastly hijack the host cell machinery for replication, during which they encounter cellular defenses that have to be overcome by the viruses. The mechanisms of inhibition of retroviruses by the SERINC family of transmembrane proteins are of particular interest. SERINC5 is a host-encoded restriction factor that is incorporated into nef-deficient HIV-1 to impair the particle infectivity in susceptible target cells. HIV-1 and other unrelated retroviruses encode anti-SERINC5 factors, suggesting a fundamental role for this protein in retrovirus propagation. We are currently investigating comprehensive roles undertaken by SERINCs during infection and the consequences of pathways triggered by host proteins. 

[ii] Circular RNAs in viral pathogenesis 

Circular RNAs (circRNAs) are formed by back-splicing events that occur in both coding and non-coding linear transcripts. The back-splice junction connects two ends and distinguishes circRNAs from their linear counterpart. CircRNAs are abundant in immune cells, and several of them have been found to be deregulated during immunological signaling, inflammation, and viral infection. However, only a few circRNAs have been functionally characterized in the context of viral infection. During pathogenic conditions, circRNAs appear to assert a complex interplay between the host and the viruses. We employ high-throughput and modern sequencing technologies to explore the roles of circRNAs during HIV-1 infection. Our studies identified a significant role for a host-encoded circRNA that is hijacked by the virus for successful transmission. 

[iii] Lentivirus-mediated gene delivery and CRISPR 

Viruses like HIV have thus far defied vaccine development efforts. HIV’s success derives from its facile adaptation to the intracellular environment, and the ability to deposit its genome into the host effectively allows the virus to persist. Molecular virologists have developed gene delivery tools inspired by the primate lentiviruses like HIV. These so-called Lentiviral Vectors (LV) have proven so safe in expressing genes for restoring or augmenting the gene function that clinicians use them to treat patients these days. One of the significant limitations of LV is poor gene delivery into primary cells, particularly in immune cells. This is because LV lacks the needed genes (possessed otherwise by HIV when infecting immune cells) to counter the antiviral mechanisms. We address this imperfection of LV by identifying mechanisms that restrict LV transduction in such cell types. The inspiration is used to develop effective ways to enhance gene delivery to human cells for a variety of applications ranging from basic to applied biomedical research. As a proof-of-concept, the contemporary gene-editing platform like CRISPR/Cas9 can be effectively combined with LV for gene editing in human primary cells to make them resistant to HIV-1 infection. The LVs are also useful reporters when coated with different envelope glycoproteins (Like SARS CoV-2 spike) to evaluate viral entry inhibitors and offer a robust high-throughput platform for serodiagnosis and drug discovery.

                                  Funding: IISER Bhopal, India Alliance, DBT, EMBO.