New Tool for Turning Genes on and Off Could Help Uncover Protein Functions

Sunday, May 08, 2011

ROCHESTER, Minn. — Mayo Clinic researchers have designed a new tool for identifying protein function from genetic code. A team led by Stephen Ekker, Ph.D., succeeded in switching individual genes off and on in zebrafish, then observing embryonic and juvenile development. The study appears in the journal Nature Methods.

The work could help shed light on health-related problems such as how cancerous cells spread, what makes some people more prone to heart attacks, or how genes factor in addiction. More complicated issues, like the genetics of behavior, plasticity and cellular memory, stress, learning and epigenetics, could also be studied with this method.

The research at Mayo Clinic's Zebrafish Core Facility could help further unify biology and genomics by describing the complex interrelations of DNA, gene function and gene-protein expression and migration. The study examines protein expression and function from 350 loci among the zebrafish's approximately 25,000 protein-encoding genes. Researchers plan to identify another 2,000 loci.

"I consider this particular system a toolbox for answering fundamental scientific questions," says Dr. Ekker, a Mayo Clinic molecular biologist and lead author of the article. "This opens up the door to a segment of biology that has been impossible or impractical with existing genomics research methods."

The study includes several technical firsts in genetic research. Those include a highly effective and reversible insertional transposon mutagen. In nearly all loci tested, endogenous expression knockdown topped 99 percent.

The research yielded the first collection of conditional mutant alleles outside the mouse; unlike popular mouse conditional alleles that are switched from "on" to "off," zebrafish mutants conditionally go from "off" to "on," offering new insight into localized gene requirements. The transposon system results in fluorescence-tagged mutant chromosomes, opening the door to an array of new genetic screens that are difficult or impossible to conduct using more traditional mutagenesis methods, such as chemical or retroviral insertion.

The project also marks the first in vivo mutant protein trap in a vertebrate. Leveraging the natural transparency of the zebrafish larvae lets researchers document gene function and protein dynamics and trafficking for each protein-trapped locus. The research also ties gene/protein expression to function in a single system, providing a direct link among sequence, expression and function for each genetic locus. Researchers plan to integrate information from this study into a gene codex that could serve as a reference for information stored on the vertebrate genome.

Researchers exposed translucent zebrafish to transposons, "jumping genes" that move around inside the genome of a cell. The transposons instructed zebrafish cells to mark mutated proteins with a fluorescent protein 'tag.'

"This makes investigation of a whole new set of issues possible," Dr. Ekker says. "It adds an additional level of complexity to the genome project."

Dr. Ekker's team maintains about 50,000 fish in the Zebrafish Core Facility. To observe, photograph and document mutations of that many minnow-sized fish, the team works with an international team of researchers and gets helps from Rochester public elementary school teachers. Under a program with Mayo Clinic and Winona State University called InSciEd Out (Integrated Science Education Outreach), teachers document mutations and learn about the scientific method.

Other members of the research team include Karl Clark, Ph.D.; Yonghe Ding, Ph.D.; Stephanie Westcot; Victoria Bedell; Tammy Greenwood; Mark Urban; Kimberly Skuster; Andrew Petzold, Ph.D.; Jun Ni, Ph.D.; and Xiaolei Xu, Ph.D., all of Mayo Clinic; Darius Balciunas, Ph.D.; Aubrey Nielsen; and Sridhar Sivasubbu, Ph.D., all of the University of Minnesota; Hans-Martin Pogoda, Ph.D., and Matthias Hammerschmidt, Ph.D., of the University of Cologne in Germany; and Ashok Patowary and Vinod Scaria, Ph.D., of the Institute of Genomic and Integrative Biology in New Delhi.

The National Institute on Drug Abuse, National Institute of General Medical Sciences, National Institute of Diabetes and Digestive and Kidney Diseases, and Mayo Clinic funded the study.

###

Mayo Clinic is a nonprofit worldwide leader in medical care, research and education for people from all walks of life. For more information, visit MayoClinic.com or MayoClinic.org/news.

For more information, contact:

Robert Nellis
507-284-5005 (days)
507-284-2511 (evenings)
newsbureau@mayo.edu

View the original article here

The Way Doctors Treat Patients With Cancer And Autoimmune Diseases Could Change Following New Discovery

Researchers in the Faculty of Medicine & Dentistry at the University of Alberta have made an important discovery that provides a new understanding of how our immune system "learns" not to attack our own body, and this could affect the way doctors treat patients with autoimmune diseases and cancer.

When patients undergo chemotherapy for cancer or as part of experimental therapies to treat autoimmune diseases such as diabetes and lupus, the treatment kills the patients' white blood cells. What can be done afterwards, is to give these patients blood stem cells through transplantation. Stem cells are taken from patients then injected back into them - with the theory being that the patients' immune system won't attack their own cells, and the stem cells can get to work healing their bodies.

But U of A medical researchers Govindarajan Thangavelu, Colin Anderson and their collaborators discovered that if a particular molecule is not working properly in T-cells, the body will attack itself. This is significant for stem-cell transplantation treatment because it means the immune systems of the patients could consider their own cells "foreign" and initiate an attack.

"So your own cells would be killing you," says Thangavelu, a PhD student specializing in immunology, who was the first author in the research study, which was recently published in the peer-reviewed Journal of Autoimmunity. "What we found is if this molecule is absent in T-cells, if the pathway isn't intact, it will cause severe autoimmunity to the subject's own body. In essence, subjects become allergic to their own cells."

Anderson, an associate professor with the Alberta Diabetes Institute and Principal Investigator added: "The ability of our immune system to attack dangerous microbes while not attacking our own cells or tissues is a delicate balance. Restarting the immune system after wiping it out in patients with autoimmune diseases or cancer requires re-establishing this appropriate balance. We discovered that a particular immune system molecule is critical to prevent the immune system from attacking our own cells or tissues when the immune system is restarted. If that molecule is missing, the immune system will wreak havoc on the body."

T-cells are supposed to protect people and animals from things invading their bodies. But this research demonstrates if these cells become unregulated because they are missing a molecule, it can lead to autoimmunity - particularly dangerous in scenarios where patients have lost white blood cells when they are being treated for autoimmune diseases or cancer.

Thangavelu has won awards for this research. He was invited to present his work at an international conference of immunology in Japan last year. He has also travelled to the United Kingdom to talk about his findings with the medical community.

This research was funded by: the Juvenile Diabetes Research Foundation, the Canadian Institutes of Health Research, Alberta Innovates-Health Solutions and the Alberta Diabetes Institute.

Source:
Raquel Maurier
University of Alberta Faculty of Medicine & Dentistry

Stem Cell Voice Box Transplant Trials Could Begin In 2013, UK

Speaking at the UK National Stem Cell Network annual science meeting in York, Professor Martin Birchall will announce that the first clinical trials for stem cell voice transplants will begin in 2013, thanks to a million pounds provided by the Medical Research Council (MRC). This revolutionary new kind of transplant treatment could change the lives of to 1300 patients a year in the UK who suffer serious problems with breathing, speaking and swallowing.

Loss of a working larynx (voice box) not only affects speech, swallowing, breathing, but also smell, taste, coughing, lifting and kissing, affecting thousands of people in the UK. Having carried out the world's first stem cell transplant of a windpipe in 2008, Professor Birchall will be heading up a team to formally assess whether a similar approach can be used to repair problems in a voice box.

This research opens up new possibilities for patients receiving other kinds of transplants as well. One of the main problems currently facing those in need of donor organs is that they will need to take drugs for the rest of their lives as a result of the transplant. This new project, known as RegenVOX proposes that by using stem cells, this method could potentially help restore the patient's own immune system and reduce the need for immuno-suppresant drugs.

Professor Martin Birchall at UCL says:

"We have assembled a large multi-disciplinary team of scientists, surgeons, nanotechnologists and bioengineers, all leading experts in their fields to create the RegenVOX project. We're very grateful to the MRC for the support for this team to perform the necessary experimental and preparatory, including regulatory, work required to make laryngeal replacements available for patients. Without this funding, trials could quite easily have been delayed by another three to five years."

Dr Rob Buckle, Head of Regenerative Medicine at the Medical Research Council says:

"This investment by the MRC is part of our long-standing commitment to turning the potential offered by stem cells into real treatments that can change the lives of patients. Regenerative medicine is a key priority for the MRC and Professor Birchall's project could have a huge impact on how transplants are carried out in the future."

Source:
Medical Research Council
UK National Stem Cell Network (UKNSCN)