When scientists sequenced the human genome in 2003, the achievement was heralded as one of the great feats in the history of humanity. For the first time, we had Nature’s blueprint for building a human being. But piecing together the blueprint was only the beginning of the journey. “Now that we have the full sequence, the next step is to figure out what it all means,” says Praveen Sethupathy, Biomedical Sciences. “Only one to two percent of the genome actually codes for proteins—the so-called building blocks of life. What is the rest of the genome doing?”
Over the past few decades, scientists have begun to understand the functions of the multitude of other DNA sequences—known as regulatory elements, or rheostats—which turn up or turn down gene expression. Many of the mutations that predispose a person to complex diseases, like heart disease or diabetes, for instance, do not occur within genes themselves, Sethupathy explains. Instead, they alter the workings of the rheostats.
“Once we knew this, it caused a paradigm shift in how we viewed complex diseases,” he says. “A lot of times, the gene sequences themselves are unaffected. However, it may be that the body is making too much or too little of a gene. So if gene X has to be made in ten copies for proper health, perhaps someone predisposed to diabetes, for instance, is making 100 copies or only one copy. It becomes a quantitative issue, as opposed to a qualitative one.”
The GI System—a Constantly Changing Environment
The Sethupathy lab is interested in where the rheostats are located in the genome, which ones are active in which organs of the body, and which ones become defective in the context of the development of a disease. In particular, the researchers focus on diseases of the gastrointestinal (GI) tract and liver, including diabetes, Crohn’s disease, and cancer.
“The GI system, including the gut microbiome, is a fascinating organ complex,” Sethupathy says. “The gut microbiome is made up of all the bacteria, viruses, and fungi living in the GI tract. It’s a dynamic, constantly changing environment. So we are asking, ‘What rheostats are relevant to the gut? Which ones are critical for the gut to be able to respond properly to a constantly changing environment, and which ones are going awry in individuals who appear to have a predisposition to the development of diseases such as Crohn’s disease?’”
Identifying Crohn’s Disease Subtypes
In one project, Sethupathy and his collaborators are molecularly subtyping Crohn’s disease, a condition of the gut characterized by severe inflammation and often debilitating pain. Using high-resolution genome-scale technologies, the researchers peer into gut cells, seeking to describe, at the molecular level, the landscape of a healthy gut versus that of a gut with Crohn’s.
“Clinicians have long thought that Crohn’s is probably not one disease but, rather, a collection of similar diseases,” Sethupathy explains. “You can take two people diagnosed with Crohn’s, who have no tangible difference between them in terms of age, gender, and so on, and treat them with the same medication, and one will get better and one won’t. Why is there this striking variation in response to the medication? Well, likely because it’s not the same disease. Clinically things may appear similar, but at the molecular level, there are different things going on.”
“Now that we have the full [human genome] sequence, the next step is to figure out what it all means.”
Collaborating with Shehzad Sheikh and Terry Furey at the University of North Carolina, Chapel Hill, the researchers in the Sethupathy lab were among the first to define two molecular subtypes of Crohn’s disease: Type A and Type B. “We conjecture that there are likely more,” Sethupathy says. “Crohn’s is the result of complex interactions among genetics, environment, microbiome, and the immune system. There is a lot we still don’t understand about how different Crohn’s disease subtypes develop.”
In further research, Sethupathy and his collaborators demonstrated that by measuring the levels of a particular microRNA—a small, single-stranded, non-coding RNA molecule—at the onset of Crohn’s disease, they can predict whether a patient will likely develop Type A or Type B. “This is exciting because one of those subtypes responds better to the current medications,” Sethupathy explains. “By knowing which subtype a patient is likely to develop, a clinician might be able to make more effective decisions about treatment.”
A Liver Cancer Like No Other
In another series of projects, the Sethupathy lab is investigating a rare liver cancer called fibrolamellar carcinoma, which afflicts primarily adolescents and young adults. “It’s really devastating,” Sethupathy says. “It’s completely unlike any other liver cancer ever studied. We barely understand anything about it, and there’s no standard of care or therapy for it. All that can be done is to try to surgically remove it, which is often very challenging because many patients present with metastatic disease.”
Funded by the Fibrolamellar Cancer Foundation, the researchers have been studying the cancer from a number of angles, trying to pinpoint how it forms and spreads. They know that the cancer is the result of a mutation that causes the deletion of a chunk of chromosome 19, Sethupathy explains. The two chromosomes at each end of the remaining DNA then fuse together, forming a chimera—a gene that doesn’t normally exist. “This chimera ends up creating a lot of havoc in the liver cells,” he says. “We think it’s the only—or main—driver of this cancer.”
Working in concert with Alnylam Pharmaceuticals, Inc., Sethupathy and his colleagues are trying to develop a method to treat the cancer. “One of our strategies is to use a technique called RNA interference to develop a short, interfering molecule that can hit and incapacitate the chimera without affecting anything else in the patient’s body,” he says.
Sophisticated Pattern Finding
Sethupathy began his academic training at Cornell, majoring in computer science. While he enjoyed the computational and quantitative skill sets he was developing, he realized his real passion was biology and went on to study genomics in graduate school. “It was the turn of the millennium, and everyone could see that biology was changing,” he says. “We were going to be able to collect petabytes of data, but needed creative and powerful means of analysis in order to gain biological insight. It was apparent that computational sciences were going to be important.
“To this day I still think about genomics and computational biology as sophisticated pattern finding. In a lot of ways, it’s like those games you play as a kid where you connect the dots and find patterns. I feel like that’s what I’m doing today, but with genomics data that has implications for human health. It’s both enjoyable and extraordinarily rewarding.”