Category Archives: Transhuman News

From left, Dr. Teresa Sim, Dr. Magdalena Walkiewicz and Dr. Jason Heaney discuss their recent paper in the American Journal of Human Genetics.

An international team of researchers from institutions around the world, including Baylor College of Medicine, has discovered that mutations of the OTUD6B gene result in a spectrum of physical and intellectual deficits. This is the first time that this gene, whose functions are beginning to be explored, has been linked to a human disease. The study appears in the American Journal of Human Genetics.

Our interest in this gene began when we carried out whole exome sequencing the analysis of all the protein-coding genes of one of our patients who had not received a genetic diagnosis for his condition that includes a number of intellectual and physical disabilities, said co-first author Dr. Teresa Sim, a postdoctoral associate of molecular and human genetics and a fellow in Clinical Molecular Genetics and Genomics. We identified OTUD6B, a gene that until now had not been linked to a health condition.

We identified a presumed loss-of-function mutation in the OTUD6B gene in our first patient, said co-senior author Dr. Magdalena Walkiewicz, assistant professor of molecular and human genetics at Baylor and assistant laboratory director at Baylor Genetics. We discovered that this gene seemed to be highly involved in human development; when the gene cannot fulfill its function, the individual presents with severe intellectual disability, a brain that does not develop as expected and poor muscular tone that limits the ability to walk, as well as cardiovascular problems.

Making a convincing case for OTUD6B

However, one case does not represent sufficient evidence to support the involvement of OTUD6B in the medical condition.

To make a convincing case that this gene is essential for human development we needed to find more individuals carrying mutations in OTUD6B, Walkiewicz said.

Mutations in OTUD6B are rare so the researchers had to look into the exomes all the protein-coding genes of a large number of individuals to find others carrying mutations in this gene. Walkiewicz and her colleagues first looked into their clinical exome database at Baylor Genetics labs, specifically into the data of nearly 9,000 unrelated, mostly pediatric-age individuals, many of which carrying neurologic conditions, and found an additional individual carrying genetic changes in the same gene. The clinical characteristics of this individual were strikingly similar to those of the first patient, which led the team to expand their search for more patients.

When we study very rare disorders we rely on collaborations with scientists around the world to find other families affected by mutations in one gene, said Walkiewicz.

One of the strategies that helps researchers find more cases is running the gene of interest through GeneMatcher, a web-tool developed as part of the Baylor-Hopkins Center for Mendelian Genomics for rare disease researchers. Similar to online dating websites that match couples, GeneMatcher allows researchers to find others that are interested in the same genes they are working on.

Without this type of collaborations it would be very difficult to make a convincing case. Between GeneMatcher and our database we found a total of 12 individuals carrying mutations in OTUD6B and presenting with similar clinical characteristics, Walkiewicz said.

An animal model corroborates the human findings

Animal models are one way to determine whether a change in this gene is actually causing the condition, said co-senior author Dr. Jason Heaney, assistant professor of molecular and human genetics and director of the Mouse Embryonic Stem Cell Core at Baylor. Having a similar change in an animal model gene that results in similar characteristics in a mouse can show us whether the gene is causing the condition.

Baylor is part of the International Mouse Phenotyping Consortium. Its goal is to generate a knockout model for every gene in the mouse genome, about 20,000 protein-coding genes, and determine what each gene is involved with.

In this case we learned in the animal model lacking the OTUD6B gene that the gene is highly expressed in the brain and we knew that the patients had reduced intellectual capacities. The animals had cardiovascular defects very similar to those in the patient population. The animal models allowed us to see that having this mutation of this gene causes the clinical characteristics observed in the patients. It highlights how useful animal models can be for understanding human disease, Heaney said.

Through multiple lines of evidence the researchers have established that mutations in OTUD6B can cause a range of neurological and physical conditions and highlight the role of this gene in human development.

In addition, our collaborators in Germany performed functional analysis for this gene on blood cells from patients, Walkiewicz said. Their findings suggest that the OTUD6B protein contributes to the function of proteasomes, large molecular complexes that are at the center of the cellular process that degrades proteins that are damaged or are not needed by the cell. This discovery strengthens the notion that disturbances of the proteasome can cause human disease.

There is interest in better understanding the mechanisms of the disorder at the cellular and molecular level. By understanding the processes that lead to the disease, we can then hope to develop therapies for those patients, said Walkiewicz. One of the highlights of this project is the tremendous collaboration with a number of different centers and labs and putting this tremendous effort together resulted in a publication that is very strong.

Another important contribution of this project is that we provided some answers for the families, and brought them together which offers the opportunity of mutual support, said Sim.

For a complete list of the authors and their affiliations and financial support for this project click here.

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OTUD6B gene mutations cause intellectual, physical disability - Baylor College of Medicine News (press release)

Thuy Truong thought her aching back was just a pulled muscle from working out. But then came a high fever that wouldn't go away during a visit to Vietnam. When a friend insisted Truong, 30, go to an emergency room, doctors told her the last thing she expected to hear: She had lung cancer. Back in Los Angeles, Truong learned the cancer was at stage 4 and she had about eight months to live.

"My whole world was flipped upside down," says Truong, who had been splitting her time between the San Francisco Bay Area and Asia for a new project after selling her startup. "I've been a successful entrepreneur, but I'm not married. I don't have kids yet. [The diagnosis] was devastating."

Doctors at the University of Southern California took a blood sample for genetic testing. The "liquid biopsy" was able to detect tumor cells in her blood, sparing her the risky procedure of collecting cells in her lungs.

Genetic sequencing allowed the lab to isolate the mutation that caused her cancer to produce too much of the EGFR (epidermal growth factor receptor) protein, triggering cancer cells to grow and proliferate. Fortunately, her type of mutation responds to EGFR-targeting drugs, such as Tarceva or Iressa, slowing tumor growth.

Personalized medicine uses genetic information to design treatments targeted to individual patients.

Unlike chemotherapy, which blasts all fast-growing cells in its wake, targeted treatments go after specific molecules. That makes them more effective at fighting particular types of cancers, including breast, colorectal and lung cancers. Now the approach is being expanded to fight an even broader range of cancers. It's all part of a new wave in health care called personalized, or precision, medicine.

"This is the future of medicine," says Dr. Massimo Cristofanilli, associate director for translational research and precision medicine at Northwestern University. "There is no turning back. The technology is available and there are already so many targeted therapies."

Most medical treatments have been designed for the average patient, leading to a one-size-fits-all approach. But with vast amounts of data at their disposal, researchers now can analyze information about our genes, our family histories and other health conditions to better understand which types of treatments work best for which segments of the population.

This is a big deal. But it requires the know-how of geneticists, biologists, experts in artificial intelligence and computer scientists who understand big-data analytics. Several startups have already begun this work.

Deep Genomics, founded by researchers at the University of Toronto, uses AI to predict how genetic mutations will change our cells and the impact those changes will have on the human body. Epinomics, co-founded by scientists and physicians from Stanford University, is building a map of what turns our genes on and off, giving physicians a guide they could use to craft personalized therapies. And Vitagene, a small San Francisco startup, provides personalized advice on nutrition and wellness based on your DNA.

Dr. Massimo Cristofanilli

Just like Facebook learns to automatically recognize Aunt Martha in your family photos, Deep Genomics finds and categorizes patterns in genetic data. Once it's found those patterns, the company's deep learning system can infer if and how changes to your DNA affect your body.

That's a big step forward compared with current genetic tests. Most can only give a probability of, say, getting breast cancer based on data from an entire population. Other tests can't even tell you if the genetic changes they've detected mean anything.

The work is personal for Brendan Frey, CEO and co-founder of Deep Genomics and a professor at the University of Toronto. Fourteen years ago, he and his wife discovered their unborn baby had a genetic condition.

"We knew there was a genetic problem, but our counselor couldn't tell us if it was serious or if it was going to turn out to be nothing," Frey says. "We were plunged into this very difficult, emotional situation."

The experience made Frey want to bridge the divide between identifying genetic anomalies and understanding what they mean.

Deep learning or machine learning -- when computers teach themselves as they see more data -- can also help doctors know which drugs will most effectively treat a patient's illness and whether that person is more likely to experience side effects.

It can also help predict how cancer cells will mutate. And that can help drug companies come up with new treatments as tumor cells change and patients no longer respond to the drugs that worked.

That could help turn a disease like cancer into a manageable chronic ailment, says Cristofanilli.

Where Deep Genomics analyzes patterns in genetic data to predict when mutations will make you sick, Epinomics looks at epigenomics, or the study of what turns our genes on and off.

The company describes it like this: If your genome, which shows what genes we have, is the hardware of our bodies, then the epigenome is its software programming. Epinomics aims to decode that programming.

Every cell in the body carries the same genetic code. But cells in the heart, brain, bone and skin function differently based on this programming. It happens because chemical markers attach to DNA to activate or silence genes. These markers, known as the epigenome, vary from one cell type to another and are affected by both nature (inheritance) and nurture, which can include the air we breathe and the food we eat.

Researchers think a disruption to the epigenome can cause illnesses such as Alzheimer's disease, diabetes or cancer. Understanding it could give physicians a guide to the best options for each patient, like having a GPS for treatments at the molecular level.

"We are focusing on what is happening at the programming level of each cell," says Epinomics co-founder Fergus Chan. "Once we understand how genes are being turned on and off, we'll be able to better predict which treatments will work or whether changes to lifestyle will have an impact on health."

When Vitagene co-founder and CEO Mehdi Maghsoodnia asked a doctor what vitamins he should be taking, he was handed a bottle of pills and told to hope for the best.

Fergus Chan

That was the beginning of Vitagene, which uses genetic data and other health information culled from a detailed questionnaire to deliver a personalized nutritional supplement plan that lists which vitamins you need and in what doses, as well as what to avoid.

Maghsoodnia offers an alternative to the one-size-fits-all $27 billion US dietary supplement industry. Customers pay $99 to have their DNA tested and blood analyzed. And for $69 a month, Vitagene will package and ship supplements in dosages tailored to your individual needs.

The Food and Drug Administration estimates there are more than 85,000 dietary supplements on the US market, most of which are unregulated. Nearly all are "promising everything from anti-aging to weight loss, and no science behind it to tell you what works for you," says Maghsoodnia. "We help filter through the noise."

Vitagene's algorithm has been tested on patients who've had bariatric surgery for weight loss, which often leaves them deprived of key nutrients. Vitagene helped develop a supplement regimen to get these patients the nutrition they need after surgery.

Precision medicine is in its early days.

This is especially true for psychiatry and its exploration of how the brain responds to the environment, stress and genetic disorders. Now several companies are selling tests to help psychiatrists select drug treatments by looking at patients' DNA mutations and their metabolizing rate.

See more from CNET Magazine.

But critics caution that these genetic tests may be overselling their capabilities.

"Precision medicine has been very promising in oncology," says Jose de Leon, a professor of psychiatry at the University of Kentucky who specializes in psychopharmacology. "But we know a lot more about cancer and how it works. In psychiatry, it's much harder because we don't know enough about how the brain works."

Yes, precision medicine holds enormous promise.

Even so, Northwestern's Cristofanilli cautions clinicians to stay grounded in reality. "It can be difficult to understand where reality becomes imagination," he says. "We want to make sure we are protecting patients from claims that we may not deliver."

For her part, Truong is grateful to benefit from the work that's already been done. "I'm an engineer," she says.

"I don't believe in miracles. I believe in science."

This story appears in the spring 2017 edition of CNET Magazine. For other magazine stories, click here.

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Gene therapy: What personalized medicine means for you - CNET - CNET

Leon Csernohlavek

In September 2015, Elizabeth Parrish flew from Seattle to Colombia to receive an experimental treatment.

She had spent more than two years studying literature, talking to experts, and had decided to undergo gene therapy a treatment for genetic disorders that adds genes into cells to replace those that are faulty or absent. She ordered the therapeutic cells months in advance and arranged for a technician to administer the therapy in a clean room within a short distance of a hospital, in case she suffered a bad immune response. The gene therapy was shipped in a closed container and administered via an IV over approximately five hours. Parrish remained under observation for a few days and then flew home.

Was I anxious afterwards? Yes, Parrish says. I was definitely looking for indications that anything was wrong with my body. I was acutely aware of every ache and pain. She had become the first person to subject herself to gene therapy for the disease that affected her. Her condition? Ageing.

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In January 2013, Liz Parrish son was diagnosed with Type 1 diabetes. Every few days, he would have some devastatingly low blood sugar levels, Parrish says. I was continually reminded that we as humans spend a lot of time trying to pretend as if our death is not eminent. She remembers being told that her son was lucky because diabetes was treatable. I was really hit hard by the time I spent in children's' hospitals, Parrish says. She had read about the promises of modern medicine, in particular, gene therapy. I began trying to figure out why nothing was translating to hospitals where kids were dying.

Parrish began attending medical conferences on her own. I found this conference in Cambridge that looked to be about genetics, Parrish says. It turned out to be about longevity. There she learned how gene modifications had already extended the normal lifespan of worms up to 11 times and of mice by five times. It made me realise that if ageing was a disease and everyone was suffering from an illness, the fastest way to fund this research would be to essentially educate the world that was the case and get them to put money behind finding a cure, Parrish says.

At that point, Parrish, who up until then had been working part-time for software companies, started her own company, BioViva, to expedite therapeutics and give access to patients. Why did so many patients have to wait, suffer and die? Parrish asks. We became so risk adverse that patients die waiting for treatment. We have to change that drastically. We have millions of terminally ill patients on the planet right now. These patients should have access to the most promising therapeutics that don't have a myriad of off-target effects. There is no artificial intelligence or meta analysis of these therapies that is going to replace what happens in the human body. And we let people die because we're so concerned that a therapy might kill them. This is lawyering at its absolute worst.

Parrish then made another decision: she was going to try the first therapy on herself. I believed it was the most responsible and ethical thing to do. I believed the company should take its own medicine first before moving onto patients.

Parrish tried two therapies. One was a myostatin inhibitor, a drug designed to increase muscle mass, and the second was telomerase therapy, which lengthens the telomeres, a part of the chromosomes that protect genetic material from damage and allows the replication of DNA. Lengthening the telomeres can, at least in theory, extend cellular lifespan and make cells more resilient to damage.

The telomerase therapy had reversed ageing and extended lifespan in mice, Parrish says. I assumed this was the most promising therapy ever, and it was just sitting in research and wasn't moving forward as a viable option due to what appeared to be patenting issues and a lot of academics sitting on the fence bickering. We will never know unless we get it in humans. It's almost a moot point to try to continue to argue whether it works or not if we never use it. Its just like lemmings walking off the cliff, waiting for someone else to solve the problems.

A few weeks after the treatment, Parrish undertook follow-up exams, conducted by independent third parties. Her telomeres in her white blood cells had lengthened by more than 600 base pairs which, according to Parrish, implies they had extended by the equivalent of 20 years. A full-body MRI imaging revealed an increase in muscle mass and reduction in intramuscular fat. Other tests indicate Parrish now has improved insulin sensitivity and reduced inflammation levels.

The company was built essentially to prove these therapies work or not, Parrish says. Remember BioViva is not a research organisation. We are taking things like gene therapies and using them like technology. We would like to create an open market where people have access to acquiring these technologies, much like you would acquire a cellphone or a computer.

Further tests are being conducted at George Churchs lab in Harvard. Parrish and her team are currently working with other hospital clinics around the world to conduct more safety and feasibility studies in human subjects. I had already put things into perspective that without medicine, my son would be dead and he really was the meaning of my life, Parrish says. I was a person who quite honestly felt I had not really contributed that much to society and this was my opportunity to do so.

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Ageing is a disease. Gene therapy could be the 'cure' - Wired.co.uk

BOSTON (January 27, 2010) Researchers at Tufts University School of Medicine and the Sackler School of Graduate Biomedical Sciences at Tufts have developed a new tool for gene therapy that significantly increases gene delivery to cells in the retina compared to other carriers and DNA alone, according to a study published in the January issue of The Journal of Gene Medicine. The tool, a peptide called PEG-POD, provides a vehicle for therapeutic genes and may help researchers develop therapies for degenerative eye disorders such as retinitis pigmentosa and age-related macular degeneration.

For the first time, we have demonstrated an efficient way to transfer DNA into cells without using a virus, currently the most common means of DNA delivery. Many non-viral vectors for gene therapy have been developed but few, if any, work in post-mitotic tissues such as the retina and brain. Identifying effective carriers like PEG-POD brings us closer to gene therapy to protect the retinal cells from degeneration, said senior author Rajendra Kumar-Singh, PhD, associate professor of ophthalmology and adjunct associate professor of neuroscience at Tufts University School of Medicine (TUSM) and member of the genetics; neuroscience; and cell, molecular, and developmental biology program faculties at the Sackler School of Graduate Biomedical Sciences at Tufts.

Safe and effective delivery of therapeutic genes has been a major obstacle in gene therapy research. Deactivated viruses have frequently been used, but concerns about the safety of this method have left scientists seeking new ways to get therapeutic genes into cells.

We think the level of gene expression seen with PEG-POD may be enough to protect the retina from degeneration, slowing the progression of eye disorders and we have preliminary evidence that this is indeed the case, said co-author Siobhan Cashman, PhD, research assistant professor in the department of ophthalmology at TUSM and member of Kumar-Singhs lab.

What makes PEG-POD especially promising is that it will likely have applications beyond the retina. Because PEG-POD protects DNA from damage in the bloodstream, it may pave the way for gene therapy treatments that can be administered through an IV and directed to many other parts of the body, said Kumar-Singh.

Kumar-Singh and colleagues used an in vivo model to compare the effectiveness of PEG-POD with two other carriers (PEG-TAT and PEG-CK30) and a control (injections of DNA alone).

Gene expression in specimens injected with PEG-POD was 215 times greater than the control. While all three carriers delivered DNA to the retinal cells, PEG-POD was by far the most effective, said first author Sarah Parker Read, an MD/PhD candidate at TUSM and Sackler and member of Kumar-Singhs lab.

Age-related macular degeneration, which results in a loss of sharp, central vision, is the number one cause of vision loss in Americans age 60 and older. Retinitis pigmentosa, an inherited condition resulting in retinal damage, affects approximately 1 in 4,000 individuals in the United States.

This study was supported by grants from the National Eye Institute of the National Institutes of Health, the Foundation for Fighting Blindness, The Ellison Foundation, The Virginia B. Smith Trust, the Lions Eye Foundation, and Research to Prevent Blindness. Sarah Parker Read is part of the Sackler/TUSM Medical Scientist Training Program, which is funded by the National Institute of General Medical Sciences, part of the National Institutes of Health.

Read SP, Cashman SM, Kumar-Singh R. The Journal of Gene Medicine. 2010 (January). 12(1): 86-96. A poly(ethylene) glycolylated peptide for ocular delivery compacts DNA into nanoparticles for gene delivery to post-mitotic tissues in vivo. Doi: 10.1002/jgm.1415

About Tufts University School of Medicine and the Sackler School of Graduate Biomedical Sciences

Tufts University School of Medicine and the Sackler School of Graduate Biomedical Sciences at Tufts University are international leaders in innovative medical education and advanced research. The School of Medicine and the Sackler School are renowned for excellence in education in general medicine, biomedical sciences, special combined degree programs in business, health management, public health, bioengineering and international relations, as well as basic and clinical research at the cellular and molecular level. Ranked among the top in the nation, the School of Medicine is affiliated with six major teaching hospitals and more than 30 health care facilities. Tufts University School of Medicine and the Sackler School undertake research that is consistently rated among the highest in the nation for its impact on the advancement of medical science.

If you are a member of the media interested in learning more about this topic, or speaking with a faculty member at the Tufts University School of Medicine, the Sackler School of Graduate Biomedical Sciences, or another Tufts health sciences researcher, please contact Siobhan Gallagher at 617-636-6586 or, for this study, Lindsay Peterson at 617-636-2789.

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Researchers develop new tool for gene delivery - ScienceBlog.com (blog)