Sankar Swaminathan

The major long-term goal of our research studies is to understand the mechanisms by which human cancer-causing herpesviruses interact with the host cell. We study Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated virus (KSHV). EBV has been identified as a cause of Burkitt's lymphoma, Hodgkin's lymphoma, lymphomas in transplant recipients, gastric cancer and nasopharyngeal carcinoma. KSHV causes lymphoma in addition to Kaposi's sarcoma, a malignancy of the blood vessels. Both of these viruses maintain latent infections in their human host but intermittently lead to uncontrolled cellular proliferation that results in cancer. We apply molecular techniques to identify how specific viral gene products modulate cell functions. We introduce targeted genetic changes into the viral DNA, altering or deleting the gene of interest.  We developed techniques which allowed the generation of viable EBV viruses (genetic recombinants) that could be used to determine the role of virtually any EBV gene. We have applied these and other methods to study a unique EBV gene, known as the SM gene, that regulates not only EBV genes, but also those of the host cell. The SM protein acts by pirating components of the host cell to facilitate expression of EBV genes and also modulates host gene expression. This work is currently supported by NIH RO1 funding from the National Cancer Institute and we have been consistently funded by the NIH in the field of gammaherpesvirus research for over 25 years. Our most recent research accomplishments include the following:

1. We have shown why the SM gene is essential for EBV replication by using high throughput RNA sequencing. Specifically, SM is required for efficient expression of several essential EBV proteins, establishing the potential utility of SM as a therapeutic target for novel treatment modalities. We have done analogous studies in KSHV and identified the key targets of the KSHV SM homolog.
2. We have shown that SM affects host cell RNA splicing. This effect of EBV on host cell splicing, by altering the levels of proteins in the interferon pathway, is predicted to have an inhibitory effect on IFN gamma signaling. Thus the EBV protein downregulates the host immune response to virus replication at the level of mRNA processing.
3. We have established a high throughput screening assay to look for compounds active against EBV by targeting the SM protein function. We have used this assay to show that spironolactone, a drug used in heart failure has antiviral properties completely unrelated to its hormone-antagonist functions. This surprising finding is being used as a starting point to develop novel antivirals against EBV and other herpesviruses, such as herpes simplex virus and cytomegalovirus.
4. We have established that two host DNA binding factors, CTCF and the cohesin complex, also bind to specific sites on the EBV and KSHV viral genomes.  We have demonstrated that these act as intrinsic restriction factors by which the cell prevents KSHV and EBV replication and gene expression.

Our current research agenda consists of further discovery of the molecular interactions between EBV and KSHV and the host cell. Specifically, we are performing experiments to determine exactly how these RNA binding proteins recognize their target messenger RNAs. By defining the structure and sequence of the target, we will be able to fully understand how the virus modulates cellular gene expression.

A second major area of research is to understand the role of the proteins produced by the host cell in response to interferon and viral infection (the ISGs). These proteins are the primary response of the cell to infection, yet surprisingly little is known about their function. We are examining how these proteins protect against virus infection. Understanding the mechanism of action of these proteins has the potential to lead to discovery of protective mechanisms against viral infection. We have been studying the expression and activity of these proteins both in vitro and in immunocompromised cancer patients with viral infections.

The third major area of investigation is to discover exactly how CTCF and cohesin inhibit EBV and KSHV replication; whether they prevent DNA replication by topologically interfering with the process of replication and/or by inhibiting viral RNA transcription.  We are using a variety of molecular techniques to explore the regulation of this process and cells from patients with mutations in the cohesin pathway.

We have now launched a drug discovery component to our studies where we are identifying compounds with antiviral activity based on their ability to target the SM protein or its homologs in other herpesviruses. This will allow not only therapeutic drug development but also allow us to probe the mechanism of action of SM and its homologs.