The finding offers clues about the development of colorectal cancer and could—potentially—provide targets for new therapies. Jason Moore, Third Century Professor of genetics and the director of the Institute for Quantitative Biomedical Sciences, and Richard Cowper-Sal.lari, a graduate student in Moore's lab, were part of a team that included researchers from Case Western Reserve University and the Cleveland Clinic. The team published its findings in Science Express, the online prepublication site for the journal Science, on April 12.
Many studies of cancer and other diseases have looked for genetic variations that lead to disease. But for this study, Moore, Cowper-Sal.lari, and their colleagues examined sections of DNA that do not code for proteins—sections that have sometimes been referred to as "junk" DNA. Long overlooked, junk DNA has gained more attention of late as it has become clear that it can regulate the expression of genes.
"We're now starting to assign function to what historically has been known as the junk DNA—stuff in between genes that we weren't really sure what it did, if it did anything at all," Moore says. Proteins that bind to noncoding sections far away from a gene, Moore explains, can help turn that gene on or off.
The researchers looked at specific sections of noncoding DNA in nine colorectal cancer samples and three samples of healthy colon tissue. They found patterns in the sections of noncoding DNA that differed depending on whether the tissue was cancerous or healthy. They refer to these sections as variant enhancer loci (VELs). Cowper-Sal.lari says that the patterns they found are more reliable indicators of the presence of colorectal cancer than any currently known patterns of gene expression. "You get a very crisp signal," he says. The tumor samples were taken from patients at various stages of disease, adding to the strength of the finding.
Moore, who is also the associate director for bioinformatics at the Norris Cotton Cancer Center, adds that what he and Cowper-Sal.lari added to the study was their ability to make sense of mountains of data by developing computer programs and algorithms.
"It's an exciting time in cancer research because we can now sequence entire human genomes and measure the genome on a massive scale, but what's lagging behind are the computational methods—the software, the algorithms, the statistical approaches—to allow us to make sense of this vast amount of information," Moore says. "The DNA sequencing technology to generate the data is moving a lot faster than the computational methods for making sense of it."
Cowper-Sal.lari adds that the intense computation required to do the analysis was only possible because of access to Discovery—Dartmouth's supercomputing cluster.
There are a number of directions the research could go in the future. Cowper-Sal.lari says that if they are able to look at additional samples and find the same patterns, then "the genes that are the targets of these VELs are going to be really good potential therapeutic targets for colorectal cancer."
"That's the ultimate goal—to develop drugs," Moore says. "If we can understand the biology of how these genes are turned on and off in cancer, then we can develop drugs to target them and turn them on or off."
Derik Hertel | EurekAlert!
New study finds distinct microbes living next to corals
22.05.2019 | Woods Hole Oceanographic Institution
Summit charts a course to uncover the origins of genetic diseases
22.05.2019 | DOE/Oak Ridge National Laboratory
Engineers at the University of Tokyo continually pioneer new ways to improve battery technology. Professor Atsuo Yamada and his team recently developed a...
With a quantum coprocessor in the cloud, physicists from Innsbruck, Austria, open the door to the simulation of previously unsolvable problems in chemistry, materials research or high-energy physics. The research groups led by Rainer Blatt and Peter Zoller report in the journal Nature how they simulated particle physics phenomena on 20 quantum bits and how the quantum simulator self-verified the result for the first time.
Many scientists are currently working on investigating how quantum advantage can be exploited on hardware already available today. Three years ago, physicists...
'Quantum technologies' utilise the unique phenomena of quantum superposition and entanglement to encode and process information, with potentially profound benefits to a wide range of information technologies from communications to sensing and computing.
However a major challenge in developing these technologies is that the quantum phenomena are very fragile, and only a handful of physical systems have been...
Working group led by physicist Professor Ulrich Nowak at the University of Konstanz, in collaboration with a team of physicists from Johannes Gutenberg University Mainz, demonstrates how skyrmions can be used for the computer concepts of the future
When it comes to performing a calculation destined to arrive at an exact result, humans are hopelessly inferior to the computer. In other areas, humans are...
Scientists develop a molecular recording tool that enables in vivo lineage tracing of embryonic cells
The beginning of new life starts with a fascinating process: A single cell gives rise to progenitor cells that eventually differentiate into the three germ...
29.04.2019 | Event News
17.04.2019 | Event News
15.04.2019 | Event News
22.05.2019 | Life Sciences
22.05.2019 | Life Sciences
22.05.2019 | Physics and Astronomy