DNA, RNA and RNA Interference {RNAI}

Retrieved From: 

http://web.mit.edu/newsoffice/2009/explained-rna.html


November 12, 2009


Exploiting the recently discovered mechanism could allow biologists to develop disease treatments by shutting down specific genes.

Anne Trafton, MIT News Office

Science and technology journalists pride themselves on the ability to explain complicated ideas in accessible ways, but there are some technical principles that we encounter so often in our reporting that paraphrasing them or writing around them begins to feel like missing a big part of the story. So in a new series of articles called "Explained," MIT News Office staff will explain some of the core ideas in the areas they cover, as reference points for future reporting on MIT research.


Every high school biology student learns the basics of how genes are expressed: DNA, the cell’s master information keeper, is copied into messenger RNA, which carries protein-building instructions to the ribo-some, the part of the cell where proteins are assembled.

But it turns out the picture is far more complicated than that. In recent years, biologists have discovered a myriad of other molecules that fine-tune this process, including several types of RNA (ribonucleic acid). Through a naturally occurring phenomenon known as RNA interference, short strands of RNA can selectively intercept and destroy messenger RNA before it delivers its instructions. Scientists are now pursuing disease treatments based on RNA interference (RNAi), which offers the tantalizing ability to shut down any gene in the body.

“With RNAi, we have the possibility to design small RNA that matches any gene, or any part of that gene, and silence it. Then we can ask what is the potential benefit of silencing that gene in the disease process,” says MIT Institute Professor Phillip Sharp, whose lab is pursuing such studies.

In 2006, the Nobel Prize in Physiology or Medicine was awarded to two scientists, including Andrew Fire, who earned his MIT PhD in 1983 under Sharp’s supervision, for the discovery of RNA interference. Fire and Craig Mello showed in 1998 that when short, double-stranded RNA molecules with sequences complementary to a specific messenger RNA were injected into the worm C. elegans, production of the protein encoded by that messenger RNA was halted.

Here’s how it works: Double-stranded RNA molecules called siRNA (short interfering RNA) bind to complementary messenger RNA, then enlist the help of proteins, the RNA-induced silencing complex. Those proteins cleave the chemical bonds holding messenger RNA together,and prevent it from delivering its protein-building instructions.











This mechanism occurs naturally and may have evolved to give cells additional control over gene expression, particularly during embryonic development. It may also serve as a defense mechanism against viruses that try to insert their genetic material into cells.

RNA interference can also be mediated by microRNA, which is a short, single-stranded RNA molecule. RNA interference has been observed in a wide range of species, including plants, bacteria and fruit flies as well as humans.

Scientists have shown that synthetic siRNA injected into human cells in the lab can successfully shut off genes, raising hopes that diseases such as cancer, cystic fibrosis, Huntington’s disease and others caused by malfunctioning genes could be treated with RNA interference.

Before such therapies can become useful, scientists must figure out how to efficiently deliver small RNA molecules into target cells. Sharp and others at MIT, including Institute Professor Robert Langer and research scientist Daniel Anderson, are working on a delivery method that packages RNA inside a layer of fat-like molecules called lipidoids, which can cross cells’ fatty outer membrane. They have used the lipidoids to successfully deliver RNA to liver and lung cells in mice and monkeys, and hope to begin clinical trials within the next two years.

Sharp is also working with Sangeeta Bhatia, professor in the Harvard-MIT Division of Health Sciences and Technology, on better ways to target the RNA-carrying nanoparticles to specific cells, such as tumor cells.

There is a long way to go, says Sharp, but the potential of RNA interference is very large. “The discovery of RNA interference opened our eyes to a whole new aspect of biomedical science and biology that we just had never been aware of.”

DNA-RNA-Protein Introduction

 

http://nobelprize.org/educational_games/medicine/dna/index.html





Edited From Nobelprize.org

DNA carries the genetic information of a cell and consists of thousands of genes. Each gene serves as a recipe on how to build a protein molecule. Proteins perform important tasks for the cell functions or serve as building blocks. The flow of information from the genes determines the protein composition and thereby the functions of the cell. The DNA is situated in the nucleus, organized into chromosomes. Every cell must contain the genetic information and the DNA is therefore duplicated before a cell divides (replication). When proteins are needed, the corresponding genes are transcribed into RNA (transcription). The RNA is first processed so that non-coding parts are removed (processing) and is then transported out of the nucleus (transport). Outside the nucleus, the proteins are built based upon the code in the RNA (translation). The document has two levels, basic and advanced. This page is an introduction to both levels. You start at the basic level, then you can advance if you want more and deeper information. Learn how to navigate in the document

Possible New Alzheimer's Gene Identified

Edited from Science Daily

Science News

ScienceDaily (Nov. 22, 2007) — A variant of the gene CDC2 could possibly be used as a risk marker for Alzheimer’s disease. The gene variant is considerably more common among Alzheimer’s patients. This is shown in a dissertation from the Sahlgrenska Academy at Göteborg University in Sweden.

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See Also:

Health; Medicine

• Alzheimer's Research
• Diseases and Conditions
• Gene Therapy

Mind: Brain

• Alzheimer's
• Huntington's Disease
• Dementia

Reference

• Huntington's disease
• Introduction to genetics
• Vector (biology)
• Dementia

Alzheimer’s disease has several different causes. Since many patients have a close relative who also developed the disease, heredity is believed to be one of the most important factors. “There is a previously identified Alzheimer’s gene that indicates an elevated risk of developing the disease, but we want to find more genes with a strong connection to Alzheimer’s. The earlier we can predict that a patient risks developing the disease, the better health-care providers can prevent and treat it,” says the research Annica Sjölander.

In her dissertation, Annica Sjölander studied different variants of a gene called CDC2. DNA analyses of blood samples from both patients and healthy individuals showed that one gene variant was considerably more common among patients with Alzheimer’s disease. “This is the first discovery of a connection between this specific gene and Alzheimer’s. The findings must be confirmed in several other studies before we can be absolutely certain that it is a new Alzheimer’s gene that we have found,” explains Annica Sjölander. In the study this gene variant was found in roughly half of all patients with Alzheimer’s, compared with 35 percent of the healthy control group.

The dissertation shows that patients with Alzheimer’s disease who were carriers of the gene variant also had higher levels of the protein tau, which is associated with the disease. In patients with the disease the mean level of tau in the spinal marrow fluid is about three times higher than the level in healthy individuals of the same age.
The gene CDC2 is responsible for one of the phases when a cell divides and is only active when cell division is in progress. Other research has shown that CDC2 in Alzheimer’s patients is turned on inside nerve cells where cell division does not normally take place. “No one knows why the gene is activated, but it may be the result of a defect in the gene. It is also possible to speculate that the body is perhaps trying to compensate for lost nerve cells by having nerve cells divide,” says Annica Sjölander.

Alzheimer's disease

Alzheimer’s disease is one of our major public health disorders, with more than 100,000 people afflicted in Sweden. Pathological changes in the nerve cells of the brain cause the disease, which primarily affects the memory. The disorder often leads to premature death. Alzheimer’s entails not only immense suffering among patients and their loved ones, but also tremendous costs to society.

Title of dissertation: Alzheimer’s Disease: effect of tau-related genes on the pathology, neurochemistry and risk
of disease.

Scientists Discover New Genes Linked To Rheumatoid Arthritis

Edited From ScienceDaily

Identical Twins Identical Problems

July 1, 2007 — A University of Michigan Medical School rheumatologist and his colleagues are beginning to comprehend how identical twins can be so different when it comes to the development of diseases such as rheumatoid arthritis. This newfound understanding and appreciation stems from the recent findings of three over-expressed genes in RA that were not previously linked with the ailment. This discovery could provide the necessary avenues for understanding the widely variable nature of RA and open the door for new and improved treatment.

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Rheumatoid arthritis is a painful, chronic disease that affects about two-million Americans. It's also genetic -- but most of the time, only one twin in a pair will inherit it.
They look the same ... sound the same ... and share the same genetic code. But what has stumped scientists -- why some of them develop genetic diseases while their twin stays healthy. "That brings the question whether there is beyond the genes, whether there is another factor that is playing a role," says Joseph Holoshitz, M.D. and rheumatologist at the University of Michigan.
Getting to the root of the disease's cause could pave the way for targeted treatments for patients like Barbara D'Amico who has struggled with it for more than 30 years. "Physically, I feel like it's a broken bone that never heals. It's just a constant ache," explains D'Amico. She has taken up to 20 pain pills in a day -- and tried dozens of mediations that haven't worked.
"We might be able to, in the future, to design specific therapies for individuals based on what we know about their gene makeup," Holoshitz says. The research team thinks these genes are susceptible to something called oxidative stress, which affects how cells repair themselves. But there's only a small chance it will trigger the disease, which is why most of the time, only one twin inherits the disease.

BACKGROUND: Based on a recent study, scientists at the University of Michigan are now beginning to understand how genetically identical twins can still be different when it comes to the development of diseases such as rheumatoid arthritis. The researchers found three new genes that were overactive in the twin with rheumatoid arthritis compared to the one without the disease. The discovery could open the door to understanding the widely variable nature of the disease and provide avenues for new treatments.
ABOUT THE STUDY: The advantage of studying twins is that they start out with the same genetic information, so differences in the way the genes act can be attributed to differences in the person's surroundings. Those differences could cause a random genetic mutation, or affect how DNA is packaged. Only 15% of identical twins will both develop as rheumatoid arthritis. To find out why, the UM scientists compared gene expression patterns of 11 pairs of monozygotic twins who shared the same egg and were genetically identical, but only one of them had rheumatoid arthritis. In addition to the three new overexpressed genes, the researchers also found that non-genetic factors influenced the action of these genes, and that if only one twin in the family had rheumatoid arthritis, the actions of the genes were different than if neither twin had rheumatoid arthritis.
ABOUT RHEUMATOID ARTHRITIS: Rheumatoid arthritis is a chronic inflammatory disease that damages joints, causing pain, loss of movement, and bone deformities. It affects 2.1 million Americans. In the early stages, the tissue in the joint begins to grow and divide, much like a benign tumor. The growing mass gives off proteins that disintegrate tissue. Although there are currently some rheumatoid arthritis treatments available, they are for non-specific processes that do not address the root cause of rheumatoid arthritis, and they don’t work for all patients. The new study results help identify new treatment targets that could lead to better drugs that are more effective against the disease, with fewer side effects.
WHAT IS EPIGENETICS? : Epigenetics literally means “on genes,” and refers to modifications to genes other than changes in the DNA sequence itself (mutation). Genes carry the blueprints to make proteins in the cell, and the DNA sequence of a gene is transcribed into RNA, which is then translated into the sequence of a protein. Every cell or tissue has the same genetic information; what differentiates them is that in each, different sets of genes that are turned on, or “expressed.” Epigenetic marks are chemical additions to the DNA sequence that turn genes on or off.
HOW DNA MICROARRAYS WORK: Microfluidics studies how fluids behave at microscopic levels: volumes of water, for example, that are thousands of times smaller than a single droplet. At these size scales, tiny effects that wouldn't be noticeable on a large scale play a much larger role. By understanding these effects, scientists can use them manipulate fluids on the microscopic scale. This has led to such beneficial technologies as ink jet printers and labs-on-a-chip (called microarrays) for fast and cheap DNA sequencing. These devices have been on the market for several years. A blood sample is inserted into the chip, which rapidly searches the sample for telltale genetic variations

Stem Cell Treatment of Cerebral Palsy

Cerebral palsy

 

Cerebral palsy refers to a group of non-progressive, non-contagious conditions that cause physical disability and applies to the cerebrum in the brain and the disorder of movement. The brain damage normally doesn't worsen, but secondary diseases are very common. Most notable are various orthopedic difficulties and motor disorders, arthritis and osteoporosis. It cannot be cured. Standard treatments include drugs, mechanical aids, physical therapy, behavioral therapy, occupational therapy and speech therapy. All these approaches are focused at helping the patient overcome developmental disabilities or learn new ways to accomplish difficult tasks.

The Xcell-Center Cerebral Palsy treatment

The XCell-Center's cerebral palsy treatment differs from standard methods because it attacks the root cause of CP inside the brain. Stem cell therapy is a drug-free alternative focused on affecting physical changes in the brain that can improve a child's quality of life.

Almost 70% of the cerebral palsy patients treated with stem cells at the XCell-Center show improvement.
Most cerebral palsy patients are treated by lumbar puncture; injecting the stem cells into the cerebrospinal fluid which transports them up the spinal canal and into the brain. A new procedure, by which the stem cells are surgically implanted directly into the brain, is also available. Lumbar puncture is an outpatient procedure that requires patients to stay in Germany 4 or 5 nights. Direct surgical implantation is an inpatient procedure that requires patients to stay in Germany for about 10 nights.

Bone Marrow Collection

On the first day, bone marrow is collected from the patient's iliac crest (hip bone) using thin-needle mini-puncture under local anesthesia. Although some pain is felt when the needle is inserted, most patients do not find the bone marrow collection procedure particularly painful. The entire procedure normally takes about 30 minutes. The bone marrow collection procedure requires patients to sit still, it is performed under general anesthesia for children. Once the bone marrow collection is complete, patients may return to their hotel and go about normal activities. Patients who receive general anesthesia must lie down for a short recovery period before returning to their hotel. More detailed information on the bone marrow collection procedure is available in the Bone Marrow Informed Consent document

Laboratory Processing

The next day, the stem cells are processed from the bone marrow in a state-of-the-art, government approved (cGMP) laboratory. In the lab, both the quantity and quality of the stem cells are measured. These cells have the potential to transform into multiple types of cells and are capable of regenerating or repairing damaged tissue.

Stem Cell Implantation

On the third day, the stem cells are implanted back into the patient by lumbar puncture or surgical implantation. Surgical implantation is performed under general anesthesia for all patients.

Lumbar Puncture

A spinal needle is inserted between L4 and L5 vertebrae and a small amount of spinal fluid is removed. A portion of that spinal fluid is mixed with the stem cell solution which is then injected into back into the patient's spinal fluid, not the spinal cord. After the stem cells have been implanted, the patient will lie down in the recovery room for a few hours before returning to his or her hotel room. The lumbar puncture procedure is performed under local anesthesia for adults and general anesthesia for children. Under normal circumstances, procedures performed under local anesthesia are not painful.

Surgical Implantation

Prior to surgery, physical and functional damage will be assessed by computer tomography (CT), magnetic resonance imaging (MRI) and positron emission tomography (PET). Once the affected brain regions have been identified and mapped, the neurosurgeon will implant the stem cells using a high tech navigation system that allows the cells to be placed with high accuracy.
All surgical implantation procedures are performed under general anesthesia.

Following Treatment

Patients who are treated by lumbar puncture are required to stay in town on the day after their procedure for general safety purposes. They may return home on the fifth day.
Surgical implantation patients may leave upon discharge from the hospital, usually on the ninth or tenth day, depending upon how their recovery progresses.

Treatment Results

Follow up statistics from 45 cerebral palsy patients completed in July 2009 show that close to 67% experienced improvements after stem cell therapy.
The mean age of the patients was 8.9 years, while the median age was 6 years. The oldest treated patient was 44 years of age. There was no apparent correlation between positive outcome and the number of stem cells administered.
The type of improvements reported include: decreased spasticity; better coordination; improved motor function, improved posture stability; better cognition resulting in communication improvements; gaining the ability to sit, stand or even walk unassisted.
Improved speech was observed in 40% of patients. 16.7% reported a decrease or even absence of epileptic seizures following treatment. About 20% showed improved cognition.



For complete results including more graphs, please view the complete July 2009 Cerebral Palsy Treatment Results.
For safety information on 350 patients treated by lumbar puncture, please view our Lumbar Puncture Safety Statistics (PDF file).

Patient Stories

Read what our patients have to say about their treatment:
Nicholas Schilling, 5 years old, Periventricular Leucomalacia
"…he is now training to stand with support…"
Christopher Giacobbe, 13 years old, Cerebral Palsy
"…he has begun talking in complete sentences…"
Myrthe Wallet, 6 years old, Myocarditis and Brain Hypoxia
"…Myrthe keeps getting better and better…"
Anneke van Iwaarden, 42 years old, Severe Oxygen Deficiency
"…for the first time in her life, Anneke was able to stand on her own…"

Costs

Stem cell implantation via lumbar puncture: 7,545 Euros (adults) - 9,000 Euros (children).
Minimally invasive surgical implantation of stem cells directly into the brain: 25,500 Euros.

'Junk DNA' Could Spotlight Breast and Bowel Cancer

The researchers, led by Dr Cristina Tufarelli, in the School of Graduate Entry Medicine and Health Sciences, discovered that seven of these faulty genetic elements -- known as chimeric transcripts -- are more common in breast cancer cells. Five were only present in breast cancer cells while two were found in both normal and breast cancer cells.
These rogue elements are produced by DNA sequences called LINE-1 (L1). Despite being labelled as 'junk DNA' it is clear that some of these sequences have important roles in the genome, such as influencing when genes are switched on.
L1s carry a switch that is able to randomly turn on nearby genes. When genes are inappropriately switched on in this way they make the genetic rogue elements that can sabotage the normal functioning of cells. To prevent the potentially damaging effects of these rogue elements, normal cells silence L1s with a chemical 'off switch'. In cancerous cells this 'off switch' is often missing, leading to the production of these genetic rogue elements.
Dr Tufarelli, a lecturer at the University who has also received funding from a Royal Society Dorothy Hodgkin Research Fellowship, said: "This study has generated new research tools to investigate the role of 'junk DNA' in cancer development. The next step is to find out if the switching on of these genes is driving cancer or if they are a result of the cancer. Even if they are innocent bystanders of cancer they could be useful biomarkers helping us to diagnose or monitor the disease."
The researchers extended their studies to look at two bowel cancer cell lines. Two of the genetic rogue elements were found in invasive bowel cancer cell lines, but not in the pre-invasive cells, suggesting that these sequences could play a role in cancer progression.
Dr Tufarelli said: "If this 'junk DNA' does turn out to play a role in cancer then we could be at the tip of the iceberg in understanding a completely new mechanism behind the disease. If we do find out that they are playing a role then they could be useful targets for new treatments."
Dr Lesley Walker, Cancer Research UK's director of cancer information, said: "These really interesting findings are the most comprehensive study of these transcripts that have ever been carried out. We are learning more about the genes involved in cancer but these so-called 'junk' regions receive relatively little attention. We are beginning to see that they could play a really important role."

Scanning for Leg Clots CT Scans of Legs May Help Prevent Recurring Pulmonary Embolisms

June 1, 2005 — Pulmonary embolisms kill 60,000 people every year. Often, the clots form in the legs, break free and travel to the lungs, where they can cause sudden death. CAT scans can identify these clots in the lungs. Now, a study has shown that indirect CT venography, or CTV, can give doctors a better view of the smaller arteries that may provide evidence of the clots.

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See also:

Health & Medicine

• Blood Clots
• Today's Healthcare
• Hypertension

Matter & Energy

• Medical Technology
• Detectors
• Weapons Technology

Reference

• Pulmonary embolism
• Emphysema
• CAT scan
• Radiography

CHAROLOTTE, N.C.--Pulmonary embolisms kill 60,000 people every year. Often, the clots form in the legs, break free and travel to the lungs, where they can cause sudden death. CAT scans can identify these clots in the lungs. Now, doctors are using that same technology to get a leg up on their diagnosis.
Walking the long aisles of this warehouse isn't just part of Michael Leyva's job. It's good therapy for his legs and lungs. That's because mike has blood clots in the deep veins of his legs that nearly cost him his life.
"I was in cardiac ICU, and that's when they explained to me that I had blood clots that had broke away from being in my legs from a previous surgery a week before," Leyva says.
CT scans of the chest identify clots in the lungs. Now radiologists are taking the scans a step further -- scanning a patient's legs to spot clots before they travel.
"That's the major advantage of doing CT venography, because it allows us the chance to see the clot in the legs before it breaks off and goes to the lungs," Jeffrey Kline, Director of Emergency Medicine Research at Carolinas Medical Center in Charlotte, N.C., tells DBIS.
CT venography takes only three minutes more than a standard lung scan. But those three minutes can mean life or death.
Dr. Kline says, "It gives us an idea of the duration of treatment, what we have to do, and what we're gonna tell the patient to expect."
For Leyva, the additional scan showed more clots lurking in his legs. Doctors have him on a blood thinner to help dissolve the clots. "It's getting better, and hopefully in July they're gonna tell me, 'OK, you're off the Coumadin. You're off blood thinners,'" he says, a triumph over clots that, without CT venography, would have been a hidden -- and potentially deadly -- threat.
Dr. Kline says only about 20 percent of hospitals with the technology to perform CT venography are actually using the test. Other than a very small amount of extra radiation, there are no associated risks.

ABOUT PULMONARY EMBOLISM: Pulmonary embolism arises from thromboembolic disease, which causes blood clots to form in the blood vessels of the legs. Most pulmonary embolisms occur when a blood clot breaks free from an artery in the leg and travels to the lungs. More than 600,000 people in the U.S. suffer from pulmonary embolism every year, and 10 percent of those cases are fatal.
HOW CT SCANS WORK: CT scans use X-rays to image the body. X-rays can pass through most materials. It all depends on the size of the atoms that make up the material; larger atoms absorb X-ray photons, while smaller atoms do not, and the X-rays pass right through. For instance, the soft tissue in the body is composed of smaller atoms, so it doesn't absorb X-rays very well. But calcium atoms in the bones are much larger and do absorb X-rays. A camera on the other side of the patient records the patterns of X-ray light passing through the patient's body. In a CT scan, a series of X-ray beams is directed through the body from different angles. This creates cross-sections so scientists can get a better view of the body. The images are put together by computer into a stack of pictures that can be viewed rapidly, like flipping through a deck of cards.
THE STUDY: Researchers at New York Presbyterian Hospital in New York City studied more than 1,500 patients undergoing two different types of CT scanning techniques for suspected pulmonary embolism. CT pulmonary angiography (CTPA) scans the lungs to detect the presence of blood clots. But many of the clots in smaller arteries are not visible on this type of scan, so thromboembolic disease can do undiagnosed in some patients. Indirect CT venography (CTV) scans the leg and pelvic veins, giving doctors a more complete picture of what is happening in the body.
RESULTS: Combining CTPA and CTV scans increased the detection rate of thromboembolic disease by 20 percent. Adding indirect CTV following a CTPA exam requires no additional contrast material and takes only three minutes to perform. It also eliminates the need for a separate examination of the patient's lower extremities, which can delay diagnosis.

Note: This story and accompanying video were originally produced for the American Institute of Physics series Discoveries and Breakthroughs in Science by Ivanhoe Broadcast News and are protected by copyright law. All rights reserved.