Tuesday, December 17, 2013

Pseudogenes can play a key role in the discovery of new biomarkers

Tags

Pseudogenes can play a key role in the discovery of new biomarkers -

Unfortunately, the ungrateful pseudogene.

Dysfunctional, unloved and seemingly of little use, these genes -cousin poor parents have lost their protein coding capacity. They contain non-essential equipment for the survival of the body and are the "last stop" for the disposal of waste genomics.

No more. The day of pseudogene may have arrived with scientists from the University of Texas MD Anderson Cancer Center in Houston.

Han Liang, PhD, assistant professor in the department of bioinformatics and computational biology at Cancer Center is the advancement of knowledge of these genetic quirks largely overlooked, but increasingly attractive. He and his team conducted a study that generated the pseudogene expression profiles in 2,808 patient samples from seven types of cancer. This meant analysis 378 billion RNA sequences to measure levels of expression near 10,000 pseudogenes.

The results indicated that the science of analyzing the pseudogene expression may very well play a key role in explaining how cancer occurs in assisting medical experts to discover new biomarkers. The results of the study appear in today's issue of Nature Communications.

The understanding of biomarkers is important for the development of therapies targeting specific tumor sites and to obtain new information on how patients will in various cancers and treatments. Biomarkers are molecules that can indicate the presence of a condition or disease, and are increasingly used to measure how the body reacts to therapies. The emerging field of personalized medicine is built on customizing the treatment for patients based on biomarkers.

The Liang study is new in the understanding of pseudogenes based on the analysis of large numbers of patient samples. Previous studies have been limited by the size of the sample groups of patients. Liang The team analyzed the data provided by the research program Cancer Genome Atlas. The program is supported by the National Cancer Institute and the National Human Genome Research Institute at the National Institutes of Health and is looking at genomic changes in more than 20 different types of cancer.

"The study included seven subtypes of cancer, including breast, kidney, ovarian, colon, lung and uterus," said Liang. "through cancer types, subtypes of tumors revealed by expression of pseudogene showed significant and strong similarities with subtypes defined by other molecular data."

Liang believes the study highlights the potential of analyzing the expression of pseudogene as a new "gold standard" to investigate the mechanisms of cancer and the discovery of prognostic biomarkers. These biomarkers will allow medical experts to predict more accurately rates of cancer survival.

"pseudogene expression alone can accurately classify major subtypes of endometrial cancer," said Liang. "It is striking, in renal cancer subtypes pseudogene expression not only significantly correlated with patient survival, but also help to stratify patients in combination with clinical variables."


EmoticonEmoticon