Professor of Internal Medicine and Adjunct Professor of Microbiology and Immunology
Chief of Infectious Diseases
Virology, Immunology, Epigenetics
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:
- 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.
- 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.
- 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.
- 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.
References (Selected Peer-Reviewed Publications)
- Verma D, Mel Church T, Swaminathan S. Epstein-Barr virus lytic replication induces ACE2 expression and enhances SARS CoV-2 pseudotyped virus entry in epithelial cells. J. Virol. 2021, 95(13):e0019221. doi: 10.1128/JVI.00192-21. Epub 2021 Jun 10.PMID: 33853968.
- Verma D, Church TM, Swaminathan S. Epstein-Barr virus co-opts TFIIH component XPB to specifically activate essential viral lytic promoters. Proc Natl Acad. Sci. USA. 2020, 117 (23) 13044-13055; https://doi.org/10.1073/pnas.2000625117
- Martin RM, Burke K, Verma D, Xie H, Langer J, Schlaberg R, Swaminathan S, Hanson KE. Contact Transmission of Vaccinia to an Infant Diagnosed by Viral Culture and Metagenomic Sequencing. Open Forum Infect. Dis. 2020, 7(4): https://doi.org/10.1093/ofid/ofaa111.
- Swaminathan S, Schlaberg R, Lewis J, Hanson KE, Couturier MR. Fatal Zika Virus Infection with Secondary Nonsexual Transmission. N Engl J Med. 2016, 375(19):1907-1909. Epub 2016 Sep 28. PubMed PMID: 27681699.
- Church, TM, Verma, D, Swaminathan, S.Efficient translation of EBV DNA polymerase contributes to the enhanced lytic replication phenotype of M81 EBV. J Virol. 2018, 92(6). pii: e01794-17. doi: 10.1128/JVI.01794-17. Print 2018 Mar 15
- Li D, Fu W, Swaminathan S. Continuous DNA replication is required for late gene transcription and maintenance of replication compartments in gammaherpesviruses. PLOS Pathogens. 2018, 14(5):e1007070. doi: 10.1371/journal.ppat.1007070.
- Fu W, Verma D, Burton A, Swaminathan S. EBV SM protein binds the cellular RNA helicase DHX9 and counteracts its antiviral activity. J Virol. 2019, 93(4). pii: e01244-18. doi: 10.1128/JVI.01244-18. Print 2019 Feb 15. PMID:30541834
- Li D and Swaminathan, S. Human IFIT proteins inhibit lytic replication of KSHV: a new feed-forward loop in the innate immune system. PLOS Pathogens. 2019, e1007609. https://doi.org/10.1371/journal.ppat.1007609
- Verma D, Thompson J, and Swaminathan S. Spironolactone blocks Epstein-Barr virus production by inhibiting EBV SM protein function. Proc Natl Acad Sci U S A. 2016, 113(13): 3609-14.
- Baglio SR, van Eijndhoven MA, Koppers-Lalic D, Berenguer J, Lougheed SM, Gibbs S, Léveillé N, Rinkel RN, Hopmans ES, Swaminathan S, Verkuijlen SA, Scheffer GL, van Kuppeveld FJ, de Gruijl TD, Bultink IE, Jordanova ES, Hackenberg M, Piersma SR, Knol JC, Voskuyl AE, Wurdinger T, Jiménez CR, Middeldorp JM, and Pegtel DM. Sensing of latent EBV infection through exosomal transfer of 5'pppRNA. Proc Natl Acad Sci U S A. 2016, 113(5): E587-96.
- Verma D, Li DJ, Krueger B, Renne R, and Swaminathan, S. Identification of the physiological gene targets of the essential lytic replicative KSHV ORF57 protein. J Virol. 2015, 89(3): 1688-702.
- Thompson J, Verma D, Li D, Mosbruger T, and Swaminathan S. Identification and Characterization of the Physiological Gene Targets of the Essential Lytic Replicative Epstein-Barr Virus SM Protein. J Virol. 2015, 90(3): 1206-21.
- Li DJ, Verma D, Mosbruger T, and Swaminathan, S. CTCF and Rad21 act as host cell restriction factors for Kaposi's sarcoma-associated herpesvirus (KSHV) lytic replication by modulating viral gene transcription. PLoS Pathog. 2014, 10(1): e1003880.
- Verma D, Kim EA, and Swaminathan, S. Cell-based screening assay for antiviral compounds targeting the ability of herpesvirus posttranscriptional regulatory proteins to stabilize viral mRNAs. J Virol. 2013, 87(19): 10742-51.
- Li DJ, Verma D, and Swaminathan S. Binding of cellular export factor REF/Aly by Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 protein is not required for efficient KSHV lytic replication J Virol. 2012, 86(18): 9866-74.
- Verma D, Bais S, Gaillard M, and Swaminathan S. Epstein-Barr virus SM protein utilizes cellular splicing factor SRp20 to mediate alternative splicing. J. Virol. 2010, 84(22): 11781-9.
- Han Z, Verma D, Hilscher C, Dittmer DP, and Swaminathan S. General and target-specific RNA binding properties of Epstein Barr virus SM post-transcriptional regulatory protein. J Virol. 2009, 83(22): 11635-11644.
- Verma D, Ling C, Johannsen E, Nagaraja T, and Swaminathan S. Negative autoregulation of EBV replicative gene expression by EBV SM protein. J. Virol. 2009 Aug; 83(16): 8041-50.
- Verma D and Swaminathan S. Epstein-Barr virus SM protein functions as an alternative splicing factor. J Virol. 2008, 82(14): 7180-8.
- Swaminathan S. Oncogenic herpesvirus noncoding RNAs. J. Cell. Physiol. 2008, 216(2): 321-6.
- Nekorchuk M, Han Z, Hsieh T, and Swaminathan S. Kaposi's sarcoma-associated herpesvirus ORF 57 protein enhances nuclear mRNA accumulation independent of effects on RNA export. J Virol. 2007, 81:(18): 9990-9998.
- Han Z, Marendy E, Wang Y-D, Yuan J, Sample JT, and Swaminathan S. Multiple roles of Epstein Barr virus SM protein in lytic replication. J. Virol. 2007, 81(8): 4058-69.
- Han Z and Swaminathan S. The KSHV lytic gene ORF57 is essential for infectious virion production. J Virol. 2006, Jun; 80(11): 5251-60.
- Swaminathan S. Post-transcriptional gene regulation in gamma-herpesviruses. J. Cell. Biochem. 2005, 95(4): 698-711.
- Nicewonger J, Suck G, Bloch D, and Swaminathan S. Epstein Barr virus SM protein induces and recruits cellular Sp110b to stabilize mRNAs and enhance EBV lytic gene expression. J. Virol. 2004, 78(17): 9412-22.
- Ruvolo V, Sun L, Howard K, Sung S, Delecluse H-J, Hammerschmidt W, and Swaminathan S. Functional analysis of Epstein-Barr virus SM protein: identification of amino acids essential for structure, transactivation, splicing inhibition and virion production. J. Virol. 2004, 78(1): 340-352.
- Ruvolo V, Navarro L, Sample C, David M, Seung S, and Swaminathan S. The Epstein-Barr Virus SM protein induces STAT1 and interferon stimulated gene expression. J. Virol. 2003, 77(6): 3690-701.
- Ruvolo V, Gupta AK, and Swaminathan S. Epstein-Barr virus SM protein interacts with messenger RNA in vivo and mediates a gene-specific increase in cytoplasmic mRNA. J. Virol. 2001, 75: 6033-6041.
- Ruvolo V, Wang E, Boyle S, and Swaminathan S. The Epstein-Barr virus nuclear protein SM is both a posttranscriptional inhibitor and activator of gene expression. Proc. Natl. Acad. Sci. 1998; 95: 8852-8857.