Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Cancer epigenetics: breakthrough in ID’ing target genes

14.03.2012
CPRIT grant helps Rice, BCM crack problem of predicting gene targets for PcG proteins

Cancer is usually attributed to faulty genes, but growing evidence from the field of cancer epigenetics indicates a key role for the gene “silencing” proteins that stably turn genes off inside the cell nucleus.

A new study from Rice University and Baylor College of Medicine (BCM) promises to speed research in the field by rapidly identifying the genes that epigenetic proteins can target for silencing.

The study, which appears this week in Nucleic Acids Research, shows how a new computer program called EpiPredictor can search any genome to identify specific genes affected by epigenetic proteins. The research includes detailed experimental findings that verify EpiPredictor’s results. The research was funded in part by the Cancer Prevention Research Institute of Texas (CPRIT).
In work that could shed light on the molecular workings of cancer cells, researchers from Rice University and Baylor College of Medicine have developed a method to rapidly identify genes that can be targeted for silencing. The team includes (clockwise from left) Qinghua Wang, Jianpeng Ma, Brian Kirk, Jia Zeng and Yufeng Gou.

“Cancer epigenetics is a new field, and we are still struggling with the basics,” said lead investigator Jianpeng Ma, professor of bioengineering at Rice and the Lodwick T. Bolin Professor of Biochemistry at BCM. “It’s something like a board game. Until now, we’ve understood some of the rules and seen a few of the pieces, but the game board itself has been mostly blank. EpiPredictor lets everyone see the board. It really changes things.”

While many cancers have been linked to mutations in the DNA sequence of particular genes, epigenetic changes do not involve genetic mutations. Instead, epigenetics allows two cells with identical DNA sequences to behave in wholly different ways. Epigenetic proteins effectively edit the genome by turning off genes that are not needed. This editing process is what allows human beings to have specialized cells — like nerve cells, bone cells and blood cells — that look and behave differently, even though they share the same DNA.

The key epigenetic players in cancer are a family of proteins called polycomb-group (PcG) proteins. PcGs are found deep inside the nucleus of cells, in the chamber where DNA is stored. Studies have found abnormally high levels of PcGs in some of the most aggressive forms of breast and prostate cancer.

PcGs are generalists that can be called upon to silence any one of several hundred to several thousand genes. They are recruited to this task by polycomb response elements (PREs), segments of DNA that are located next to the genes the proteins subsequently silence. This is where the playing board goes blank; though scientists know there are literally hundreds to thousands of potential PREs in any given genome — including everything from simple insects to human beings — only a few PREs have ever been found.

“So far, only two PREs have been experimentally verified in mammals — one in mice and one in humans,” said EpiPredictor creator Jia Zeng, a BCM postdoctoral research associate. “We suspect there are so many of them, but finding them has been difficult.”

Zeng, a computer scientist, had no formal biology training when she joined Ma’s laboratory under a CPRIT-funded training program for computational cancer research.

“One of the biggest challenges since the completion of the Human Genome Project has been how to dig useful information out of the enormous amount of genomic data,” Ma said.

Ma said Zeng’s new method for zeroing in on PRE sequences is broadly applicable for genomic data mining in areas beyond cancer research.

“Determining the function of a gene based solely on sequence data is virtually impossible,” Ma said. “Recognizing this, Jia applied some advanced tools from computer science to create a learning program that could be trained to look for PRE sequences based upon the scant experimental data that were available.”

In tests on the genome of the fruit fly Drosphilia melanogaster, the EpiPredictor program found almost 300 epigenetic target genes. Experimental research by Ma’s longtime collaborator, BCM biochemist Qinghua Wang, verified that the EpiPredictor predictions were biologically significant.

“We are now working on using the method to scan the human genome to search for potential genes that play a role in cancer epigenetics,” said Wang, assistant professor of biochemistry and molecular biology. “We also hope that others will explore how this new method may help to identify the location and function of genes beyond the realm of epigenetics.”

Co-authors include Rice graduate students Yufeng Gou and Brian Kirk, a predoctoral training fellow in the National Library of Medicine Training Program of the Keck Center of the Gulf Coast Consortia. The research was supported by the National Institutes of Health, the National Science Foundation, the Welch Foundation and the John and Ann Doerr Fund for Computational Biomedicine at Rice University. Zeng’s CPRIT fellowship is administered by the Keck Center Computational Cancer Biology Training Program of the Gulf Coast Consortia.

A high-resolution image is available for download at:
http://news.rice.edu/wp-content/uploads/2012/03/0301_MA.jpg

CAPTION: In work that could shed light on the molecular workings of cancer cells, researchers from Rice University and Baylor College of Medicine have developed a method to rapidly identify genes that can be targeted for silencing. The team includes (clockwise from left) Qinghua Wang, Jianpeng Ma, Brian Kirk, Jia Zeng and Yufeng Gou.
CREDIT: Jeff Fitlow/Rice University

A copy of the Nucleic Acids Research paper is available at:
http://nar.oxfordjournals.org/content/early/2012/03/12/nar.gks209.full

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation’s top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is known for its “unconventional wisdom.” With 3,708 undergraduates and 2,374 graduate students, Rice’s undergraduate student-to-faculty ratio is 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice has been ranked No. 1 for best quality of life multiple times by the Princeton Review and No. 4 for “best value” among private universities by Kiplinger’s Personal Finance. To read “What they’re saying about Rice,” go to www.rice.edu/nationalmedia/Rice.pdf.

Jade Boyd | EurekAlert!
Further information:
http://www.rice.edu

More articles from Life Sciences:

nachricht Scientists uncover the role of a protein in production & survival of myelin-forming cells
19.07.2018 | Advanced Science Research Center, GC/CUNY

nachricht NYSCF researchers develop novel bioengineering technique for personalized bone grafts
18.07.2018 | New York Stem Cell Foundation

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Future electronic components to be printed like newspapers

A new manufacturing technique uses a process similar to newspaper printing to form smoother and more flexible metals for making ultrafast electronic devices.

The low-cost process, developed by Purdue University researchers, combines tools already used in industry for manufacturing metals on a large scale, but uses...

Im Focus: First evidence on the source of extragalactic particles

For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.

To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...

Im Focus: Magnetic vortices: Two independent magnetic skyrmion phases discovered in a single material

For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.

Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...

Im Focus: Breaking the bond: To take part or not?

Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.

A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...

Im Focus: New 2D Spectroscopy Methods

Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.

"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Leading experts in Diabetes, Metabolism and Biomedical Engineering discuss Precision Medicine

13.07.2018 | Event News

Conference on Laser Polishing – LaP: Fine Tuning for Surfaces

12.07.2018 | Event News

11th European Wood-based Panel Symposium 2018: Meeting point for the wood-based materials industry

03.07.2018 | Event News

 
Latest News

A smart safe rechargeable zinc ion battery based on sol-gel transition electrolytes

20.07.2018 | Power and Electrical Engineering

Reversing cause and effect is no trouble for quantum computers

20.07.2018 | Information Technology

Princeton-UPenn research team finds physics treasure hidden in a wallpaper pattern

20.07.2018 | Materials Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>