About This Project

Epstein-Barr virus (EBV) infects 9 out of 10 people and can lead to cancers such as Hodgkin's, Burkitt's, and AIDS-related lymphomas. This project will explore molecular structure in EBV as a potential source of its cancer-causing properties, which are not well understood currently. Additionally, this work will help in the development of new cancer drugs that can target EBV molecular structures.

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What is the context of this research?

This project will determine the structures of molecules made by Epstein-Barr virus (EBV) that have important implications to cancer.

EBV causes lifelong infections in more than 9 out of 10 people. In ways that are not yet known infection can increase one's chances of developing cancers such as Hodgkin's, Burkitt's, and AIDS-related lymphomas. During infection the virus "hides" within white blood cells and produces various biological molecules to manipulate cells to maintain infection. It is believed that this manipulation is what increases the risk of cancer.

One type of molecule produced by the virus is ribonucleic acid (RNA). RNA is similar to DNA, but can fold back on itself to form complex 3D structures that can mediate many important biological functions. My previous work at Yale was focused on using powerful computational approaches to identify RNAs likely to form functional structures: this work was recently published in the journals BMC Genomics and RNA Biology.

Of particular interest, I discovered two new EBV RNA molecules that are produced in very high abundance during an especially active type of EBV infection. Both RNAs are predicted to fold into complex structures that I believe are involved in important interactions with host cells. What is required now are data to experimentally determine these structures. This information will allow us to make better hypotheses about the functions of these RNAs. This information will also help in the design of new cancer therapeutics that target (by binding to) RNA structures to inhibit function.

What is the significance of this project?

This work has great potential for not only increasing our knowledge of a virus of very high medical importance, but also in the treatment of cancer. EBV-associated cancers are of serious concern globally. EBV is related to a common cancer known as Hodgkin's lymphoma, which disproportionately affects the young (ages 15 - 35) and people in their early middle ages (55+). In the developing world EBV is more commonly associated with another blood cancer known as Burkitt's lymphoma. Sadly, Burkitt's lymphomas occur most commonly in children - indeed, Burkitt's lymphomas are the leading cause of cancer in African children. In immune-compromised adults (e.g. transplant patients, or HIV positive individuals) EBV is also implicated in various other cancers (lymphoproliferative disorders).

This research will experimentally determine the molecular structures of RNA molecules produced by EBV in an especially aggressive type of infection. Knowledge of these structures provides a basis for future studies to better understand their functions and, importantly, in the targeting of these structures with drug molecules. RNA as a therapeutic target is an emerging, cutting-edge field in biomedicine. The functional structures I will determine in EBV will provide excellent candidates for drug targets.

What are the goals of the project?

The goal of this project is to perform biochemical structure mapping on EBV RNA structures that have importance to viral infection and cancer. Specifically, I need the requested funding to buy reagents to perform these experiments and to analyze the results.
In this approach I will:

1. Expose EBV RNAs to structure-sensitive chemicals (DMS and SHAPE). These chemicals modify parts of RNA depending on whether or not that region is buried in structure.
2. Analyze which parts of the RNA are reactive to these chemicals. After chemical modification, the parts of the RNA that react with chemicals can be determined using RNA sequencing.
3. Use the pattern of chemical reactivity to determine the functional structure of the RNA. The parts of the RNA that react strongly with chemicals are unlikely to be buried in structure. This knowledge can be used as a constraint in building a model of this RNA's structure.

I will focus attention on the new RNAs that I discovered, which I strongly suspect have important roles in cancer.

Stretch Goal: After these structural analyses I will be in a better position to make functional hypotheses regarding these new EBV RNAs. To help determine these possible functions I will perform knockdowns on the EBV RNAs using antisense DNA (small bits of DNA that can bind the RNA and lead to molecular degradation). I will perform high-throughput RNA sequencing (RNA-Seq) comparing untreated EBV-infected cells to EBV RNA-knockdown cells. RNA-Seq will allow me to quantify host gene expression in untreated and knockdowns cells (lacking the EBV RNAs). Changes in expression between the samples will show which host genes are affected by the EBV RNAs and may shed light on the genetic pathways affected by EBV that may give rise to cancer.