Seeking clues in the sequence of proteins

Brown University proteomics center gives RI EPSCoR researchers tools to explore new frontiers in science

In establishing the Proteomics Shared Resource Facility at Brown University in 2007, Rhode Island NSF EPSCoR set the stage for cutting edge research to take place in the Ocean State with implications reaching far beyond its borders.

Located in Brown’s Laboratories for Molecular Medicine, 70 Ship Street, Providence, the RI NSF EPSCoR core facility provides state-of-the-art instrumentation and expertise in the proteomics field.

Facility Manager James Clifton

“Just about every process in cells — all cells — is mediated through proteins,” explains Facility Manager James Clifton. “In proteomics, we attempt to characterize all the proteins in a particular system.”

The founding grant for RI NSF EPSCoR provided funds for the majority of the facility’s equipment; additional support came from the Rhode Island Science and Technology Advisory Council (STAC), the Rhode Island Research Alliance (RIRA), and Brown University.

This research capacity, paired with the Rhode Island Genomics and Sequencing Center, another EPSCoR core facility, located at the University of Rhode Island, gives scientists in the EPSCoR community the tools they need to explore new frontiers and charter the unknown.

Having the capability in the state to explore the ramifications of climate change provides a fundamental tool to researchers. And, the protocol for sharing not only increases capacity, but also makes it more affordable and accessible, which ultimately multiplies the potential for discovery.

Such goals sound lofty and noble, but it is the best way to put into context the potential these capabilities provide. We look to genomics for insight into the instructions of life, the essential structure and the make-up of an organism. Proteomics guides us to understanding life functions, what organisms are doing under any set of circumstances.

Genomics will tell us where an aberration exists in a sequence of DNA. But to determine what exactly is taking place, the mechanisms occurring at the cellular level, we need to investigate the expression of protein — the how and the why of the system at work.

More specifically, says Clifton, if we sequence the genome of a cancer cell, we can see how it is different than a normal cell, which leads to understanding what causes the disease. However, the problem does not usually lie within the gene, but rather in the RNA or protein being expressed.

“So the idea of proteomics — let’s characterize everything if we can — stems from the fact that your DNA in every cell is the same, but individual cells are different, which is almost always caused by the different expression of proteins,” Clifton says. “If we can identify the proteins and ultimately quantify their levels, that, hopefully, leads to understanding what is going on.”

A work in progress

To be sure, though, even with the advanced technological advantages gained through the last two decades, identifying every protein is no simple task.

The early technology could separate and define 500 to 1,000 proteins. Today’s equipment can identify upward of 8,000 to 10,000 proteins from one single analysis. Once defined, however, those proteins may not hold the most interest; rather, they may just be the most abundant.

Proteomics research
The shared facility provides well-maintained, state-of-the-art instrumentation and fundamental proteomics expertise.

Given the fact that any given cell produces 10,000 to 20,000 different proteins, there remains ample territory to discover. Whereas every cell in an organism contains the exact same genome, cells don’t necessarily express the same protein; the eye and stomach cells have the exact same DNA, but express different proteins relevant to the cell function.

“We are early on, but ultimately the idea is to use this to understand basic things or to give leads,” Clifton says. “If you find a new protein or this protein is 10 times higher than others, it becomes a potential drug target.”

Called biomarkers, or an indicator of biological condition, these proteins can be either diagnostic or prognostic in nature. Perhaps they indicate an underlying disease or point to a specific treatment. Either way, obtaining this information and understanding the details is part of the trend toward personalized or individually targeted medicine.

Still, Clifton notes, much of proteomics centers on basic biology and efforts to divine the various developmental processes. Proteomics can be viewed as a tool and applicable to any system, whether seeking clues to the underlying causes of extreme autism or understanding the sequence of events during and after a heart attack.

Proteomics also can be used to figure out how climate change alters a marine organism at the molecular level, the implications of which carry no less importance than curing disease.

How organisms respond

Professor Tom Meedel, Biology Department, Rhode Island College, came to the Proteomics Center through his work with the sea squirt Ciona intestinalis and a project with Associate Professor Steve Irvine, URI College of the Environment and Life Sciences (CELS).

IMG_3134 IMG_3133 IMG_3131The intent wasn’t so much determining the sea squirt proteome, but rather investigating physiological changes wrought by climate change. Meedel anticipates the next question:

“Who cares about sea squirts?” he asks. “First, as a filter feeding organism, they do process a lot of the water that exists in Narragansett Bay. They play a major role in the composition — one Ciona could filter several liters of water in an hour.”

Consequently, if all the sea squirts disappeared, the absence would have a dramatic impact on water quality not to mention the food chain, both scenarios that would wreak havoc with the money we make, the food we eat and the coastal areas that attract Rhode Islanders and tourists alike.

Having the capability in the state to explore the ramifications of climate change provides a fundamental tool to researchers. And, the protocol for sharing not only increases capacity, but also makes it more affordable and accessible, which ultimately multiplies the potential for discovery.

Prior to the center’s establishment in the EPSCoR community, the only option for proteomics was either sending out a sequence to an out-of-state lab and paying a fee for the service or finding a lab with the equipment and a project that aligned with a particular research area.

Clifton says that like genomics, proteomics is a tool that can be applied to any number of systems. Since the knowledge base remains relatively young, he notes that in addition to supplying the instrumentation, the Brown center also works with researchers and gives insight on the possibilities of what can be achieved with this technology.

What the future holds

Clifton took on his role at the center in 2006, at the tail end of the first EPSCoR grant. Since then, he says, the center, under the direction of Associate Dean for Biology Ed Hawrot, also an RI NSF EPSCoR Steering Committee member, steadily has ramped up its capabilities.

The 2010 start of the current five-year RI NSF EPSCoR grant initiated steps toward increasingly powerful technology and advanced instrumentation, allowing the center to build a user base and enhance the state’s research infrastructure.

Clifton says genomics had about a 10-year start on the proteomics field, and ultimately proteomics depends on the sequencing of genes: “But, they’re doing things that maybe in five to 10 years we’ll be doing.”

Although it is difficult at this point to say with any clarity what the outcome may be and where proteomics will lead us, Clifton figures the potential exists to answer just about any question. The only limitation will be people, not technology.

“We might be seeing a plateauing of instrumentation,” he says. “To have more complete descriptions, we need more people. Technology will solve some of our problems, but we need to invest in more infrastructure and more people.”

Far from having the full capability that comes with having various types of instrumentation needed for technically demanding proteomics research, the proteomics center at Brown has the manager — Clifton — and one mass spectrometer.

“If instead we had five mass spectrometers,” he says, “then we could do all sorts of complete proteomics.”

By Amy Dunkle | from the Spring 2015 issue of The Current