Alas, the thankless pseudogene.
Dysfunctional, unloved and seemingly of little use, these poor-cousin relatives of genes have lost their protein-coding abilities. They contain material not essential for an organism's survival and are the "last stop" for removal of genomic waste.
This is Han Liang, Ph.D.
Credit: MD Anderson Cancer Center
Not any more. The pseudogene's day may have arrived thanks to scientists at The University of Texas MD Anderson Cancer Center in Houston.
Han Liang, Ph.D., an assistant professor in the Department of Bioinformatics and Computational Biology at the Cancer Center is advancing knowledge of these largely overlooked but increasingly attractive genetic oddities. He and his team completed a study that generated pseudogene expression profiles in 2,808 patient samples representing seven cancer types. That meant analyzing 378 billion RNA sequences to measure the expression levels of close to 10,000 pseudogenes.
The results indicated that the science of pseudogene expression analysis may very well play a key role in explaining how cancer occurs by helping medical experts in the discovery of new biomarkers. The study's findings appear in today's issue of Nature Communications.
Understanding of biomarkers is important for developing therapies that targeted specific tumor sites and for gaining new insight into how patients will fare with various cancers and treatments. Biomarkers are molecules that can indicate the presence of a condition or disease, and are increasingly being used to measure how the body responds to therapies. The emerging field of personalized medicine is built on customizing treatment for patients based on biomarkers.
Liang's study is novel in that understanding of pseudogenes relies on analyzing large numbers of patient samples. Previous studies have been limited by the size of the patient sample groups. Liang's team analyzed data made available from The Cancer Genome Atlas research program. The program is supported by the National Cancer Institute and National Human Genome Research Institute within the National Institutes of Health and is looking at genomic changes in more than 20 different types of cancer.
"The study surveyed seven cancer subtypes including those for breast, kidney, ovarian, colorectal, lung and uterine," said Liang. "Across the cancer types, the tumor subtypes revealed by pseudogene expression showed extensive and strong similarities with subtypes defined by other molecular data."
Liang believes that the study highlights the potential of pseudogene expression analysis as a new "gold standard" for investigating cancer mechanisms and discovering prognostic biomarkers. These biomarkers will allow medical experts to more accurately predict cancer survival rates.
"Pseudogene expression alone can accurately classify the major subtypes of endometrial cancer," said Liang. "Strikingly, in kidney cancer, the pseudogene expression subtypes not only significantly correlate with patient survival, but also help stratify patients in combination with clinical variables."
Other collaborating institutions included Baylor College of Medicine and, The University of Texas Health Science Center School of Public Health, both in Houston.
The study was funded by the National Institutes of Health (NIH) (CA143883, CA016672), the NIH/MD Anderson Uterine SPORE Career Development Award, and the Lorraine Dell Program in Bioinformatics for Personalization of Cancer Medicine funded by the Michael & Susan Dell Foundation.
Ron Gilmore | Eurek Alert!
Quasi-sexual gene transfer drives genetic diversity of hot spring bacteria
29.05.2015 | Carnegie Institution
Scientists use unmanned aerial vehicle to study gray whales from above
29.05.2015 | NOAA National Marine Fisheries Service
Many joining and cutting processes are possible only with lasers. New technologies make it possible to manufacture metal components with hollow structures that are significantly lighter and yet just as stable as solid components. In addition, lasers can be used to combine various lightweight construction materials and steels with each other. The Fraunhofer Institute for Laser Technology ILT in Aachen is presenting a range of such solutions at the LASER World of Photonics trade fair from June 22 to 25, 2015 in Munich, Germany, (Hall A3, Stand 121).
Lightweight construction materials are popular: aluminum is used in the bodywork of cars, for example, and aircraft fuselages already consist in large part of...
Using ultrashort laser pulses, scientists in Max Planck Institute of Quantum Optics have demonstrated the emission of extreme ultraviolet radiation from thin dielectric films and have investigated the underlying mechanisms.
In 1961, only shortly after the invention of the first laser, scientists exposed silicon dioxide crystals (also known as quartz) to an intense ruby laser to...
The only professorship in Germany to date, one master's programme, one laboratory with worldwide unique equipment and the corresponding research results: The University of Würzburg is leading in the field of biofabrication.
Paul Dalton is presently the only professor of biofabrication in Germany. About a year ago, the Australian researcher relocated to the Würzburg department for...
Physicists have developed an innovative method that could enable the efficient use of nanocomponents in electronic circuits. To achieve this, they have developed a layout in which a nanocomponent is connected to two electrical conductors, which uncouple the electrical signal in a highly efficient manner. The scientists at the Department of Physics and the Swiss Nanoscience Institute at the University of Basel have published their results in the scientific journal “Nature Communications” together with their colleagues from ETH Zurich.
Electronic components are becoming smaller and smaller. Components measuring just a few nanometers – the size of around ten atoms – are already being produced...
Development and implementation of an advanced automobile parking navigation platform for parking services
To fulfill the requirements of the industry, PolyU researchers developed the Advanced Automobile Parking Navigation Platform, which includes smart devices,...
20.05.2015 | Event News
18.05.2015 | Event News
12.05.2015 | Event News
29.05.2015 | Life Sciences
29.05.2015 | Earth Sciences
29.05.2015 | Physics and Astronomy