In the summer of 2015, a team at Boston Children’s Hospital and Harvard Medical School reported restoring rudimentary hearing in genetically deaf mice using gene therapy. Now the Boston Children’s research team reports restoring a much higher level of hearing — down to 25 decibels, the equivalent of a whisper — using an improved gene therapy vector developed at Massachusetts Eye and Ear.
While previous vectors have only been able to penetrate the cochlea’s inner hair cells, the first Nature Biotechnology study showed that a new synthetic vector, Anc80, safely transferred genes to the hard-to-reach outer hair cells when introduced into the cochlea (see images). This study’s three Harvard Medical School senior investigators were Jeffrey R. Holt PhD, of Boston Children’s Hospital; Konstantina Stankovic, MD, PhD, of Mass. Eye and Ear and Luk H. Vandenberghe, PhD, who led Anc80’s development in 2015 at Mass. Eye and Ear’s Grousbeck Gene Therapy Center.
“We have shown that Anc80 works remarkably well in terms of infecting cells of interest in the inner ear,” says Stankovic, an otologic surgeon at Mass. Eye and Ear and associate professor of otolaryngology at Harvard Medical School. “With more than 100 genes already known to cause deafness in humans, there are many patients who may eventually benefit from this technology.”
The second study, led by Gwenaëlle Géléoc, PhD, of the Department of Otolaryngology and F.M. Kirby Neurobiology Center at Boston Children’s, used Anc80 to deliver a specific corrected gene in a mouse model of Usher syndrome, the most common genetic form of deaf-blindness that also impairs balance function.
“This strategy is the most effective one we’ve tested,” Géléoc says. “Outer hair cells amplify sound, allowing inner hair cells to send a stronger signal to the brain. We now have a system that works well and rescues auditory and vestibular function to a level that’s never been achieved before.”
Ushering in gene therapy for deafness
Géléoc and colleagues at Boston Children’s Hospital studied mice with a mutation in Ush1c, the same mutation that causes Usher type 1c in humans. The mutation causes a protein called harmonin to be nonfunctional. As a result, the sensory hair cell bundles that receive sound and signal the brain deteriorate and become disorganized, leading to profound hearing loss.
When a corrected Ush1c gene was introduced into the inner ears of the mice, the inner and outer hair cells in the cochlea began to produce normal full-length harmonin. The hair cells formed normal bundles (see images) that responded to sound waves and signaled the brain, as measured by electrical recordings.
Most importantly, deaf mice treated soon after birth began to hear. Géléoc and colleagues showed this first in a “startle box,” which detects whether a mouse jumps in response to sudden loud sounds. When they next measured responses in the auditory regions of the brain, a more sensitive test, the mice responded to much quieter sounds: 19 of 25 mice heard sounds quieter than 80 decibels, and a few could heard sounds as soft as 25-30 decibels, like normal mice.
“Now, you can whisper, and they can hear you,” says Géléoc, also an assistant professor of otolaryngology at Harvard Medical School.
Margaret Kenna, MD, MPH, a specialist in genetic hearing loss at Boston Children’s who does research on Usher syndrome, is excited about the work. “Anything that could stabilize or improve native hearing at an early age would give a huge boost to a child’s ability to learn and use spoken language,” she says. “Cochlear implants are great, but your own hearing is better in terms of range of frequencies, nuance for hearing voices, music and background noise, and figuring out which direction a sound is coming from. In addition, the improvement in balance could translate to better and safer mobility for Usher Syndrome patients.”
Restoring balance and potentially vision
Since patients (and mice) with Usher 1c also have balance problems caused by hair-cell damage in the vestibular organs, the researchers also tested whether gene therapy restored balance. It did, eliminating the erratic movements of mice with vestibular dysfunction (see images) and, in another test, enabled the mice to stay on a rotating rod for longer periods without falling off.
Further work is needed before the technology can be brought to patients. One caveat is that the mice were treated right after birth; hearing and balance were not restored when gene therapy was delayed 10-12 days. The researchers will do further studies to determine the reasons for this. However, when treated early, the effects persisted for at least six months, with only a slight decline between 6 weeks and 3 months. The researchers also hope to test gene therapy in larger animals, and plan to develop novel therapies for other forms of genetic hearing loss.
Usher syndrome also causes blindness by causing the light-sensing cells in the retina to gradually deteriorate. Although these studies did not test for vision restoration, gene therapy in the eye is already starting to be done for other disorders.
“We already know the vector works in the retina,” says Géléoc, “and because deterioration is slower in the retina, there is a longer window for treatment.”
“Progress in gene therapy for blindness is much further along than for hearing, and I believe our studies take an important step toward unlocking a future of hearing gene therapy,” says Vandenberghe, also an assistant professor of ophthalmology at Harvard Medical School. “In the case of Usher syndrome, combining both approaches to ultimately treat both the blinding and hearing aspects of disease is very compelling, and something we hope to work toward.”
“This is a landmark study,” says Holt, director of otolaryngology research at Boston Children’s Hospital, who was also a co-author on the second paper. “Here we show, for the first time, that by delivering the correct gene sequence to a large number of sensory cells in the ear, we can restore both hearing and balance to near-normal levels.”
Mechanisms underlying direct programming of stem cells could eventually lead to cell-replacement therapies
A team of scientists has uncovered details of the cellular mechanisms that control the direct programming of stem cells into motor neurons. The scientists analyzed changes that occur in the cells over the course of the reprogramming process. They discovered a dynamic, multi-step process in which multiple independent changes eventually converge to change the stem cells into motor neurons.
“There is a lot of interest in generating motor neurons to study basic developmental processes as well as human diseases like ALS and spinal muscular atrophy,” said Shaun Mahony, assistant professor of biochemistry and molecular biology at Penn State and one of the lead authors of the paper. “By detailing the mechanisms underlying the direct programing of motor neurons from stem cells, our study not only informs the study of motor neuron development and its associated diseases, but also informs our understanding of the direct programming process and may help with the development of techniques to generate other cell types.”
The direct programming technique could eventually be used to regenerate missing or damaged cells by converting other cell types into the missing one. The research findings, which appear online in the journal Cell Stem Cell on December 8, 2016, show the challenges facing current cell-replacement technology, but they also outline a potential pathway to the creation of more viable methods.
“Despite having a great therapeutic potential, direct programming is generally inefficient and doesn’t fully take into account molecular complexity,” said Esteban Mazzoni, an assistant professor in New York University’s Department of Biology and one of the lead authors of the study. “However, our findings point to possible new avenues for enhanced gene-therapy methods.”
The researchers had shown previously that they can transform mouse embryonic stem cells into motor neurons by expressing three transcription factors — genes that control the expression of other genes — in the stem cells. The transformation takes about two days. In order to better understand the cellular and genetic mechanisms responsible for the transformation, the researchers analyzed how the transcription factors bound to the genome, changes in gene expression, and modifications to chromatin at 6-hour intervals during the transformation.
“We have a very efficient system in which we can transform stem cells into motor neurons with something like a 90 to 95 percent success rate by adding the cocktail of transcription factors,” said Mahony. “Because of that efficiency, we were able to use our system to tease out the details of what actually happens in the cell during this transformation.”
“A cell in an embryo develops by passing through several intermediate stages,” noted Uwe Ohler, senior researcher at the Max Delbrück Center for Molecular Medicine (MDC) in Berlin and one of the lead authors of the work. “But in direct programming we don’t have that: we replace the gene transcription network of the cell with a completely new one at once, without the progression through intermediate stages. We asked, what are the timing and kinetics of chromatin changes and transcription events that directly lead to the final cell fate?”
The research team found surprising complexity — programming of these stem cells into neurons is the result of two independent transcriptional processes that eventually converge. Early on in the process, two of the transcription factors — Isl1 and Lhx3 — work in tandem, binding to the genome and beginning a cascade of events including changes to chromatin structure and gene expression in the cells. The third transcription factor, Ngn2, acts independently making additional changes to gene expression. Later in the transformation process, Isl1 and Lhx3 rely on changes in the cell initiated by Ngn2 to help complete the transformation. In order for direct programming to successfully achieve cellular conversion, it must coordinate the activity of the two processes.
“Many have found direct programming to be a potentially attractive method as it can be performed either in vitro — outside of a living organism — or in vivo — inside the body and, importantly, at the site of cellular damage,” said Mazzoni. “However, questions remain about its viability to repair cells — especially given the complex nature of the biological process. Looking ahead, we think it’s reasonable to use this newly gained knowledge to, for instance, manipulate cells in the spinal cord to replace the neurons required for voluntary movement that are destroyed by afflictions such as ALS.”
Learn more: How to Make a Motor Neuron
Designer virus acts as a molecular-level switch
The ability to switch disease-causing genes on and off remains a dream for many physicians, research scientists and patients. Research teams from across the world are busy turning this dream into a reality, including a team of researchers from Charité – Universitätsmedizin Berlin and the Max Planck Institute for Medical Research in Heidelberg. Led by Dr. Mazahir T. Hasan, and working under the auspices of the NeuroCure Cluster of Excellence, the team has successfully programmed a virus to transport the necessary genetic material to affected tissue and nerve cells inside the body. A report on their new virus-based method, which delivers instructions to the host genome without becoming part of it, has been published in the journal Molecular Therapy Nucleic Acids*.
From cancer to Alzheimer’s disease, many life-threatening diseases can only be treated using drug-based treatment options, if at all. Many of these treatments are non-specific in nature, or even ineffective. In some cases, the undesirable side-effects may even outweigh the desirable ones. This is because indiscriminate treatments damage healthy cells, impairing their ability to communicate with other cells; as a result, it is hoped that genetically produced and modified mediators will be able to selectively target diseased cells, and improve the way treatment is delivered. “In the laboratory, we use attenuated, i.e. non-replicating,viruses that are known as recombinant adeno-associated viruses (rAAV). We use them to transport genetically encoded material into live organisms affected by disease,” explains Dr. Hasan. “This approach opens up a whole range of options which, in the future, may allow us to treat and heal various diseases.”
By successfully completing the initial step of testing this new method using an animal model, the researchers have laid the groundwork for future genetic treatments for use in humans. Before these can be used, however, they will need to be tested to ensure their safety. It is already known that rAAVs can transport genetically encoded material into any type of cell and tissue, including the brain, and that, once inside the cells, they are capable of repeatedly switching gene therapy applications on and off again. This on/off switch is controlled chemically, via either food intake or drinking water: “The fact that gene function can be switched on and off in this manner is of particular value, and renders the method a perfect candidate for use in controlled gene therapy,” emphasizes Dr. Hasan
A discovery by Washington State University scientist Dan Rodgers and collaborator Paul Gregorevic could save millions of people suffering from muscle wasting disease.
The result of the team’s four-year project is a novel gene therapeutic approach. The work was published (http://stm.sciencemag.org/content/8/348/348ra98) July 20 in Science Translational Medicine, a journal of the American Association for the Advancement of Science.
“Chronic disease affects more than half of the world’s population,” said Rodgers, professor of animal sciences (https://ansci.wsu.edu/people/faculty/dan-rodgers/) and director of the Washington Center for Muscle Biology (http://wcmb.wsu.edu/). “Most of those diseases are accompanied by muscle wasting.
“It occurs with chronic infection, muscular dystrophy, malnutrition and old age,” he said. “About half the people who die from cancer are actually dying from muscle wasting and there’s not one single therapy out there that addresses it.
Family history inspires search for treatment
“I have a strong motivation to do something about this, to do more than simply publish results,” said Rodgers, who teamed with Gregorevic of Baker IDI Heart and Diabetes Institute in Australia (https://www.bakeridi.edu.au/). “My father died from cachexia,” the wasting disease caused by cancer, “and my nephew has Duchenne muscular dystrophy, an incurable, fatal disease that could claim his life in his teens.
Deep learning has already had a huge impact on computer vision and speech recognition, and it’s making inroads in areas as computer-unfriendly as cooking. Now a new startup led by University of Toronto professor Brendan Frey wants to cause similar reverberations in genomic medicine.
Deep Genomics plans to identify gene variants and mutations never before observed or studied and find how these link to various diseases. And through this work the company believes it can help usher in a new era of personalized medicine.
Genomic research is hard. Scientists still know relatively little about our genes and how they interrelate. But Frey and others in the field now know enough that they can equip machines to do the heavy lifting. And there’s an awful lot of this heavy lifting to do. “Genomics is no longer about small datasets,” Frey tells Gizmag. “It’s now about very, very large datasets.”
For context, the first effort to sequence a full human genome took 13 years – running from 1990 to 2003. There are now many companies working to sequence many genomes at a time. The largest of these is called Illumina. “Illumina,” Frey says, “expects to sequence one million genomes in the next year. Each genome contains three billion letters. That’s a lot of data.”