State-of-the-Art Proteomics Lab Opens at CUMC

If you think genomics is revolutionary and complex, wait until you hear about proteomics, says Dr. Emily Chen, PhD, director of the new Proteomics Shared Resource in the Herbert Irving Comprehensive Cancer Center.

“Think of it this way: The genome is the commander of the body, but the proteins are the soldiers who carry out the orders,” Dr. Chen explains. “While a gene stays relatively static throughout one’s life, proteins are always changing in ways we don’t expect.”

It’s a challenging task, but by monitoring thousands of proteins as they come and go inside cells—proteomics—researchers can learn more about how disease develops and takes root than they can by studying only genes.

The study of proteins on such a massive scale has been made possible only with the recent development of machines that can detect large biological molecules and by sophisticated computer analysis. The new Proteomics Shared Resource at HICCC has some of the latest technology available for researchers studying cancer and other diseases and biological processes.

Dr. Chen recently described the emerging field in an interview—adapted below—with the Herbert Irving Comprehensive Cancer Center. [Read the full interview here].

Why study multiple proteins at once?

Proteins work together. We have to study a whole bunch of these soldiers, to understand the tactics of the disease and the layout of the battlefield. What are the significant changes in a network of proteins, and what are the scenarios they instigate?

Chronic diseases like cancer are very complex processes. Today we can study groups of proteins, see how they interact with each other and how they support the pathology of each disease.

How does proteomics give us a broader view of the way disease develops?

Investigators now recognize the power of taking a global approach to genes and proteins—the power that comes with looking at them all, at the same time. This field will help us figure out more complicated systems and understand the pathology of diseases, creating a picture of how a disease unfolds.

Genes give the command, but proteins carry out the tasks that help us resolve challenges to our overall health and stability.

Every single second, proteins are being degraded and re-synthesized in the body. We need to know how fast or how slowly these proteins are changing. When you’re young they get turned over more quickly, and new proteins replace both normal and damaged proteins. When we age, however, that process slows down and we start accumulating lots of “bad proteins.”

With mass spectrometry, we have ways to monitor these changes and understand the difference between the old and new proteins. At the same time, we gain insight into abnormal processes or pathologies—in short, how illness forms and then takes hold.

What kinds of studies have you conducted using proteomics?

We study how breast cancer spreads to the brain. One thing we want to know is how the cells survive in the brain. If you move to a different country and live there for a period of time, you learn to speak the language, to blend in. Cancer cells have to do that, too. They use the resources they find in this new site, to survive and grow.

We first looked at 3,000 proteins and asked which ones changed significantly. That narrowed the field down to 300 proteins. Then we asked which ones fit into the same pathways. This narrowed it down to 60 that were active in a metabolic pathway.

Eventually we found a common theme. There is a specialized process cells have to go through to survive in the brain—this can take from five to 30 years from the discovery of the initial breast tumor.

Our ultimate goal is to develop a targeted therapy that will prevent these cells from adapting to their new environment.

The lab is focused on cancer research, but we can help researchers from all areas of medicine and biology. When I was at Stony Brook, we worked with researchers who wanted to know if 500-year-old Incan mummies from the Andes were ill. We are starting a project with biologists who are investigating symbiotic relationships. And I’m talking with a researcher about using proteomics to better understand anxiety.

For more information about the lab, see the Proteomics Shared Resource website or attend the lab's open house on July 10, 2–5 p.m., on the first floor of the Irving Cancer Research Center (ICRC).