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!
Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München
Second research flight into zero gravity
21.10.2016 | Universität Zürich
Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.
"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...
In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.
A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...
By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.
"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...
COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.
In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...
'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.
Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...
14.10.2016 | Event News
14.10.2016 | Event News
12.10.2016 | Event News
21.10.2016 | Health and Medicine
21.10.2016 | Information Technology
21.10.2016 | Materials Sciences