Genetic device performs DNA diagnosis

Weizmann Institute researchers have succeeded in creating genetic device that operates independently in bacterial cells.

By JUDY SIEGEL-ITZKOVICH
DNA laboratory 311 (photo credit: iStockphoto)
DNA laboratory 311
(photo credit: iStockphoto)
The 1966 science fiction movie called Fantastic Voyage presented a miniaturized submarine that traveled through the bloodstream to prevent a clot from causing a stroke. Scientists hope that someday day in the distant future, intelligent miniature computers will roam our bodies, detecting early stage diseases and treating them on the spot by releasing a suitable drug, without any outside help. To make this vision a reality, computers must be sufficiently small to fit into body cells and be able to “talk” to various cellular systems. These challenges can be best addressed by creating computers based on biological molecules such as DNA or proteins.
The idea is far from ridiculous.
After all, biological organisms are capable of receiving and processing information, and of responding accordingly, in a way that resembles a computer. Now Weizmann Institute of Science researchers have made an important step in this direction: They have succeeded in creating a genetic device that operates independently in bacterial cells. The device has been programmed to identify certain parameters and mount an appropriate response.
The device searches for transcription factors – proteins that control the expression of genes in the cell. A malfunction of these molecules can disrupt gene expression. In cancer cells, for example, the transcription factors regulating cell growth and division do not function properly, leading to increased cell division and the formation of a tumor. The device, composed of a DNA sequence inserted into a bacterium, performs a “roll call” of transcription factors. If the results match pre-programmed parameters, it responds by creating a protein that emits green light – supplying a visible “positive” diagnosis.
In follow-up research, the scientists, Prof. Ehud Shapiro and Dr. Tom Ran of the departments of biological chemistry and computer science and of applied mathematics, plan to replace the light-emitting protein with one that will affect the cell’s fate, for example, a protein that can cause the cell to commit suicide. In this manner, the device will cause only “positively” diagnosed cells to self-destruct.
In the present study, published in Nature’s Scientific Reports, the researchers first created a device that functioned like what is known in computing as a NOR logic gate: It was programmed to check for the presence of two transcription factors and respond by emitting a green light only if both were missing.
When the scientists inserted the device into four types of genetically engineered bacteria – those making both transcription factors, those making none of the transcription factors, and two types making one of the transcription factors each – only the appropriate bacteria shone green. Next, the research team – which also included graduate students Yehonatan Douek and Lilach Milo – created more complex genetic devices, corresponding to additional logical gates.
Following the success of the study in bacterial cells, the researchers are planning to test ways of recruiting such bacteria as an efficient system to be conveniently inserted into the human body for medical purposes (which shouldn’t be a problem; recent research reveals there are already 10 times more bacterial cells in the human body than human cells). Yet another research goal is to operate a similar system inside human cells, which are much more complex than bacteria.
DEAFNESS MUTATION
As half of all cases of hearing loss are not due to environmental causes but rather to genetic mutations, it isn’t surprising that advanced gene research is increasingly being used to learn more about the gene-deafness connection. Now Prof. Karen Avraham of Tel Aviv University’s Sackler Faculty of Medicine at Tel Aviv University has discovered a significant mutation in a LINC family protein — part of the cells of the inner ear— that she believes could lead to new treatments for hearing disorders.
The discovery was recently reported in the Journal of Clinical Investigation.
Her team of researchers, including Dr. Henning Horn and Profs. Colin Stewart and Brian Burke of Singapore Institute of Medical Biology, discovered that the mutation causes chaos in a cell’s anatomy. The cell nucleus, which contains our entire DNA, moves to the top of the cell rather than being anchored to its normal place at the bottom. Though this has little impact on the functioning of most of the body’s cells, it is devastating for the cells responsible for hearing, explains Avraham.
“The position of the nucleus is important for receiving the electrical signals that determine proper hearing.
Without the ability to receive these signals correctly, the entire cascade of hearing fails.”
This discovery, she says, may be a starting point for the development of new therapies. In the meantime, the research could lead toward work on a drug that is able to mimic the mutated protein’s anchoring function, which could potentially restore hearing in some cases.
The TAU geneticist originally uncovered the mutation while attempting to explain the cause of deafness in two families of Iraqi- Jewish descent. For generations, members of these families had been suffering from hearing loss, but the cause remained a mystery.
Using genetic sequencing, she discovered that the hearing impaired members of both families had a mutated version of the protein Nesprin4, a part of the LINC group of proteins that links the cell’s nucleus to the inner wall of the cell.
Avraham recreated this phenomenon in her lab by engineering the mutation in single cells. With the mutation in place, Nesprin4 was not found in the area around the cell nucleus, as in healthy cells, but was spread throughout the entire cell.
Investigating further, she studied lab mice that were engineered to be completely devoid of the protein.
Created in Singapore, the mice were originally engineered to study the biology of LINC proteins. The fact that they were deaf came as a complete surprise to researchers.
Without this protein serving as an anchor, the cell nucleus is not located in the correct position within inner ear cells, but seems to float throughout. This causes the cells’ other components to reorient as well, ultimately harming the polarity of the cells and hindering electrical signals.
It’s a mutation that took a heavy toll on the cells’ ability to transfer sound signals, causing the mice to be born deaf. Given the similarity between mouse and human inner ear cells, researchers predict that the same phenomenon is occurring in human patients with a mutation in the Nesprin4 gene.
Avraham says that she and her collaborators are the first to reveal this mutation as a cause of deafness.
“Now that we have reported it, scientists around the world can test for mutations in this gene,” she suggests.
The mutation could indeed be a more common genetic cause of deafness in a number of populations.
And because Nesprin4 belongs to a family of proteins that have been linked to other diseases, such as muscular coordination and degeneration disorders, this could prove a ripe area for further research.
MIGRAINE TRIGGERS NOT SO STRONG
A new study suggests that triggers for migraine with auras may not be as strong as some people think. The research was just published in the online issue of the journal Neurology.
Auras that occur with migraine include visual disturbances, with symptoms such as flashing lights or wavy lines.
According to Dr. Mark Green, director of the Center for Headache and Pain Medicine at Mount Sinai Hospital in New York, these results are not a surprise. Although occasionally dietary management can be helpful, he has for years not recommended routine use of strict anti-migraine diets, which were very burdensome to patients and produce minimum benefits. Some “triggers” like chocolate are probably not triggers at all but rather a neurobiological craving that is associated with the migraine attack, rather than causing the attack.
Furthermore, triggers are likely to be additive and are a “perfect storm” when they trigger an attack.
For example, in women before their menstrual periods, triggers may become relevant, whereas at other times of the month, they are harmless.
It is important to remember that triggers are just triggers; not the cause; those with migraine may just have a somewhat increased susceptibility, which might be genetically driven.