David Graham of Molecular and Comparative Pathobiology on pioneering viral proteomics:
What is viral proteomics?
GRAHAM: It’s a really new area of study that takes a look at all the proteins present in a virus. In the case of HIV, the outer coat or layer that surrounds the virus is made of bits of cell membrane and proteins from the host cell. The virus accumulates these bits of the host cell as new viruses release themselves from infected cells. It turns out that the viral coat isn’t uniform and it has clumps of different fats and lipids floating together, lipid rafts, that have specific types of proteins associated with them. We take these lipid rafts out of the virus and see what proteins are inside.
It’s much easier to study lipid rafts and their associated proteins in cells, because you can grow up millions of cells in the lab, remove the lipid rafts and end up with huge protein quantities detected with modern biochemical methods. But viruses are much smaller and are on a whole different scale. We’ve spent time miniaturizing a lot of the same cellular methods used for work in viruses.
How did you get interested in viral proteomics?
GRAHAM: After I graduated with my bachelors and master’s degree from the University of Guelph and McMaster University in Ontario, I got a job as a technician at the National Cancer Institute in a laboratory that manufactures large quantities of HIV for vaccine initiatives. I was also able to participate in research there. The researchers were focused on making vaccines from a whole inactivated HIV virus. With this non-infectious virus, they showed they could protect macaques from HIV, but they found that the protection was due to the body’s immune response to the host-derived proteins in the viral coat. This particular vaccine attempt didn’t come to fruition, but it did inspire me to find out what were the proteins in the viral coat that the immune system responded to with the idea that these proteins could be specifically added to the virus to create a better vaccine.
After a couple years in a great research environment, I decided to go back to school and to pursue my Ph.D. in James Hildreth’s lab, who at the time was in the Department of Pharmacology. My real passion was looking into the host protein composition of the HIV coat. I continued this work as a postdoc in Jennifer van Eyk’s lab at Johns Hopkins Bayview.
We looked at the viral coat to see if the proteins differed depending on which white blood cell type the virus emerged from, and it turns out they did. Not only were the proteins different, but how the immune system responded to those proteins was different too. We are still working on this today.
How will your research contribute to any HIV treatments or cures?
GRAHAM: Actually what we’ve discovered has major implications for vaccine development. In addition to the proteins in the lipid rafts of the virus, we’ve found that cholesterol plays an important role too. If you treat either viruses or white blood cells in a dish with a chemical that removes cholesterol from the cell membrane or the viral coat, then the virus is no longer able to fuse with the cell and infect it. Our most recent work demonstrated that depleting cholesterol in the HIV viral coat prevents HIV from suppressing immune responses. In normal HIV, the virus blocks surveying white blood cells from sending a signal to the body about an intruder, which you don’t want with a viral vaccine—you want the body to recognize the intruder and attack it. However, we may be able to use a cholesterol-depleted HIV virus as a vaccine. Whether it will work still remains to be seen, but we are planning on testing it.
What other research projects are you involved in?
GRAHAM: In addition to my HIV research, I am one of several principle investigators on a National Heart, Lung and Blood Institute proteomics initiative and the Programs of Excellence in Glycobiology. We are studying cardiomyocytes, heart muscle cells, and looking at how lipid rafts in their cell membranes help the cells function properly. We look at how the proteins in the lipid rafts are structurally organized within the lipid raft and how different chemical modifications are added or removed from these proteins. On this project, we do a lot of proteomics technology development and we apply these applications to our other biological projects.
How do you manage to juggle these various projects?
GRAHAM: I believe strongly in maintaining work-life balance. In a laboratory job, you have to burn the midnight oil and sometimes we have to burn it a bit more than we would like, but I think you also have to maintain creativity and imagination. I think the only way you can do that is to disengage—allow your mind to work on the problems without thinking about them—and come back to work fresh.
—Interviewed by Vanessa McMains