UND School of Medicine & Health Sciences epigenetics team awarded $5.3 million from NIH for third phase of its ongoing project
GRAND FORKS, N.D.—The UND School of Medicine & Health Sciences (SMHS) epigenetics team has been awarded a third and final Centers of Biomedical Research Excellence (CoBRE) grant from the National Institutes of Health (NIH). The award, known by the NIH as a P30 award, consists of $5.3 million and will be used to help the School’s epigenetics program not only continue to understand a variety of health conditions affecting North Dakotans, but become more self-sufficient.
A combination of the Greek term epi, meaning “above,” and genetics, epigenetics is the study of the cellular mechanisms that regulate gene expression and the activation and deactivation of specific genes in living organisms. Improved understanding of how the human body can turn genes on and off during growth, aging, and in response to the environment has important implications for the diagnosis and treatment of many diseases, including cancer, diabetes, and neurodegenerative disorders such as Parkinson’s disease.
“The beauty of epigenetics is that it doesn’t matter what your research focus is,” explained Dr. Archana Dhasarathy, associate professor in the UND School of Medicine & Health Sciences Department of Biomedical Sciences and program coordinator of the CoBRE’s Phase 3. “Whether it’s Alzheimer’s disease or cancer, epigenetic mechanisms are fundamental and in many cases, universally applicable to all cell types and diseases.”
This is why UND took the bold step of working to make the Red River Valley into a hub of epigenetics and epigenomics (study of the complete set of epigenetic modifications on the genetic material of a cell) back in 2013, when it was first awarded a grant from NIH’s National Institute of General Medical Sciences.
Understanding the versatility and value of focusing on epigenetics, Dhasarathy’s colleague and Principal Investigator of the CoBRE, Dr. Roxanne Vaughan, led the School as it applied for and received its original $10.5 million grant from the NIH to build an epigenetics program at UND. Having spent the past ten years building a viable program for the study of multiple conditions at the genetic level, Vaughan said that this third and final CoBRE grant allows her epigenetics team to focus on expanding its many efforts.
“We’ve come a long way – when we started this there was almost nothing,” said Vaughan, whose team includes researchers studying cancer, blood cells, drug addiction, neuronal and muscle disorders, embryonic development, vector-borne diseases, and the basic science behind the human genome. “UND has the only functional Genomics Core of its kind in the region for this type of research, and with Phase 3 we hope to help the Core become more self-sustaining – so it’s not relying exclusively on CoBRE funding.”
The Genomics Core provides users with state-of-the-art tools and technologies to investigate changes in epigenetic profiles across diverse cell types and diseases. While these advanced technologies enable groundbreaking research, genomics projects often face a significant challenge: the need for expertise in bioinformatics (the use of complex software and computer programming to organize and analyze the vast amounts of biological data generated). This challenge is particularly acute in genomics because these projects typically generate enormous datasets, often comprising spreadsheets and tables with millions of lines of data that exceed the capabilities of standard software platforms and require specialized computing skills to extract meaningful information.
In other words, even the simplest genomics projects, such as the sequencing of cellular RNA that measures gene expression genome-wide (known as RNA-seq), require focused bioinformatics knowledge to conduct accurately.
This is where Dr. Damien Parrello comes in. As manager of the SMHS Genomics Core, established during the CoBRE Phase 1 in 2013, Parrello is responsible for helping researchers across the region produce and analyze “big data” of all sorts. He has done so by developing a solution not only for UND, but the broader research community: an online platform called GenomEX.
“This entire platform is designed to empower biologists – any researcher – to manipulate big data the way they want to,” Parrello said from his office at UND. “Right now, most researchers rely on cores like ours, or collaborations, to analyze their data. However, it can take weeks or months for them to get answers to their questions based on their data. This is due to the numerous back-and-forth exchanges needed to articulate what the researcher wants and what the bioinformatician needs or can do.”
With GenomEX, though, researchers can do such analysis themselves in only a few days’ time.
Recognizing that many researchers lack robust coding skills, Parrello built a user-friendly platform – which can be used either on local UND servers or on the cloud – that simplifies big data analysis without sacrificing depth of analysis.
“From data upload to analysis, including the ability to input specific keywords for searching through vast datasets, GenomEX makes bioinformatics very flexible and easy to use,” he said. “Researchers just need to put their raw data in the correct folder, and then, with a few clicks, GenomEX will do the work. We can adapt it, too, so that people who need to manipulate their big data in a very specific way can do so without having to learn an entire programming language.”
Think of it this way: UND developed a simplified input-output platform that enables researchers from anywhere to input potentially millions of lines of data – to get it online themselves with a few clicks – and then generate outputs from the data with only a few more clicks. All without needing to learn a new computing language.
“Damien developed a web-based tool that makes the process a lot simpler for researchers,” said Dhasarathy. “If it’s simpler for the researcher, they’ll start using this software, and hopefully to the point where our genomics core is almost self-sustaining through researcher subscriptions for the technology.”
All of this, said Vaughan, will help the research group continue to grow.
“The epigenetics group has grown to 25 faculty members who utilize epigenetics approaches to address mechanisms in human health,” she said, noting how in 2013 the epigenetics team at UND consisted of only four or five core faculty. “The development of the Genomics Core today serves the needs of researchers not only at UND but across the state and region.”
Such partners, Vaughan said, include researchers at United Tribes Technical College in Bismarck, N.D., Minot State University, Altru Health System, North Dakota State University, and Sanford Health – plus teams operating out of Japan and the University of Manitoba in Canada.
“Our goal now is to increase our efforts to move into clinical and translational research to provide direct support to clinics and hospitals, and also to forge relationships with more departments at UND, including researchers in Computer Science and Biomedical Engineering,” she concluded. “This will extend our research capabilities into arenas that include artificial intelligence and machine learning. Our long-term goal is to maintain the momentum we have generated and provide resources to aid investigators across disciplines in their high-quality research into human health.”
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Brian James Schill
Director, Office of Alumni & Community Relations
UND School of Medicine & Health Sciences
701.777.6048 direct | 701.777.4305 office
brian.schill@UND.edu | www.UND.edu