Thursday, March 28, 2013

DNA scissors promise permanent fixes (cures?)

Many people face a routine of pills, shots, ointments or eye drops that will go on and on for the rest of their lives. If they can remember and stand to keep taking them, such treatments make temporary, biochemical changes in cells to counter chronic diseases, but then wear off and must be taken again.

What if doctors could make one-time, permanent changes in patients' genes that had the same benefits as their pills?  Along with eliminating the "pill burden," one-time fixes would eliminate billions of dollars in healthcare costs by rendering unnecessary the most expensive and profitable kind of drug: one that must be taken daily for life.

The promise of permanent cures through gene therapy was first envisioned in the 1950s when Nobel laureate Arthur Kornberg and his team at Stanford discovered the enzymes that enabled researchers to manipulate DNA chains for the first time. That lead to a better understanding of how genes work, and of how to clone them.

Among these early discoveries was that DNA-editing enzymes called nucleases cut DNA chains at certain spots. Nucleases are in the spotlight again as part of "audacious" plans to permanently cure diseases. In combination with newer, more precise DNA editing systems like CRISPR, discovered in an effort to make a better yogurt, researchers are closing in on the ability to cut DNA exactly where they want to, say at either end of a disease-causing snippet of genetic code in need of removal.

Steven Pittler, Ph.D., director of the UAB Vision Science Research Center, sat down with The Mix to talk about his efforts to do just that in eye diseases with genetic components. He is among the winners of the National Eye Institute's recent "Audacious Goals Challenge," which challenged Americans (not just vision scientists) to come up with one-page research ideas that are not possible yet, but that could be realized with some planning. His winning idea: let's use molecular scissors, a funky term for nucleases, to edit genes inside eye cells and cure ocular diseases.

Show notes for the podcast:

0:58 The NEI challenge asked all comers to finish sentences like "if this idea were to come true, it would mean XX for the field of vision research."

1:52 As opposed the typical call for in-depth grant proposals from researchers, the challenge was blinded.  Those reviewing the proposals had no idea whether a given idea came from a scientist or a lay person. It turned out that all of the winning proposals came vision scientists, proof that they are a creative group.

3:00 Dr. Pittler's winning idea was to use "molecular scissors" to cut out disease-causing snippets within genes particular to the eyes combined with other steps that replace them with healthy DNA sequences. Such scissors represent a set of enzymes familiar to scientists called a DNA nucleases or restriction enzymes. Such enzymes cut DNA at certain sport in the DNA chain only where a certain sequence of bases, the units that make up DNA code, are present.

3:54 Doctor Pittler and others seek to build on the historic early use of nucleases to achieve highly precise cuts in DNA on the way to making precise adjustments in the code. Recently, the field has been exploring the use two kinds of nucleases, zinc fingers and TALENs, that enable much more precise editing and  replacement of disease-causing genes. Researcher are now coupling nucleases such that the combination targets only a specific sequence they want to cut, rather than making 100,000 cuts too many like older systems.

5:20  All nuclease systems are useful because they recognize a specific sequence of DNA code and cut the chain there. They all use an enzyme called FOK1, which can be split into two parts, and that only cuts the DNA chain when, under circumstances carefully controlled by researchers, the two parts come back together. That quality has allowed for the design of artificial nucleases that do specific jobs as part of gene therapy. Zinc fingers, TALEN nucleases and CRISPR all work on similar principles, and newer DNA editing technologies may make possible efforts to address diseases caused by multiple genes.

7:04 Viruses are designed perfectly by evolution to invade our cells and use our genetic machinery to make copies of themselves. Thus, an early approach to gene therapy involved taking a virus, stripping it of its disease-causing elements and changing it such that it delivered a useful gene sequence into cells to counter disease. The problem is that these changes are "extra-chromosomal," so disease-countering changes occur in one generation of cells, but not in their descendants. Thus, virus-delivered gene therapies may correct a genetic disease temporarily, the but the effect fades as the treated cells die and are replaced in the constant turnover underway in many tissues. Dr, Pittler seeks to develop a technique that would alter DNA at the chromosomal level to bring about permanent cures.

8:41 Eye diseases that Dr. Pittler would like to help cure include retinitis pigmentosa (RP), an inherited eye disease that causes severe vision loss in 100,000 people in the United States. Also of interest is macular degeneration, often seen with aging and causing vision loss in 1.75 million affected Americans. One of three people will have macular degeneration by the time they are 75.

9:15 Curing such diseases will involve changing genes and related proteins at work in the specialized cells that make vision possible. RP, for instance, involves problems with the retinal pigment epithelium, a layer of cells required for the function of the retina. One its most important functions is that it engulfs and destroys old photoreceptor cells as they are replaced by new ones in the turnover that maintains the integrity of vision.

10:20 Photoreceptor cells absorb light and process color via chemicals groups called chromophores within the protein rhodopsin. When light is absorbed by the chromophore, it changes shape, which changes the shape of rhodopsin, which triggers chemical signals that are processed into images by the brain.

11:16 Dr. Pittler attended a recent NEI meeting where eye researchers from lead institutions nationwide gave input into the plan that will shape federally funded eye research for the next ten years. The next step for the institute will be to formalize a plan and presumably, direct resources toward its goals. While he waits for that plan and the chance to compete for grants, Dr. Pittler is looking to create funding sources to keep the research moving toward clinically useful, genome-based medicine. One solution may be to found a company that uses nuclease technology to genetically engineer mice to the specifications of client labs nationally.

13:54 One step toward the founding of new field is developing mice with genetic changes that accurately represent human diseases. For instance, researchers have identified hundreds of small changes, called mutations, in the gene for rhodopsin. Only a few of them have been introduced into mice and studied to identify their contribution to healthy vision or disease. Pittler;s envisioned company may even be able to manufacture cassettes, entire replacement genes with only the mutations desired by each client present.


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