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Chromosome breaks translocations gene editing CRISPR TALENs ZFNs zinc fingers Frederick Alt

When chromosomes break, the ends can join together in a number of ways, some of which can cause trouble. A new QA method could help researchers avoid making problematic breaks when using gene editing technologies like CRISPR.

Labs the world over are jumping onto the gene editing bandwagon (and into the inevitable patent arguments). And it’s hard to blame them. As these technologies have evolved over the last two decades starting with the zinc finger nucleases (ZFNs), followed by transcription activator-like effector nucleases (TALENs) and CRISPR—they’ve become ever more powerful and easier to use.

But one question keeps coming up: How precise are these systems? After all, a method that selectively mutates, deletes or swaps specific gene sequences (and now can even turn genes on) is only as good as its accuracy.

Algorithms can predict the likely “off-target” edits based on the target’s DNA sequence, but they’re based on limited data. “The algorithms are getting better,” says Richard Frock, PhD, a fellow in the laboratory of Frederick Alt, PhD, at Boston Children’s Hospital. “But you still worry about the one rare off-target effect that’s not predicted but falls in a coding region and totally debilitates a gene.”

Frock, Alt (who leads Boston Children’s Program in Cellular and Molecular Medicine, or PCMM), fellow Jiazhi Hu, PhD, and their collaborators recently turned a method first developed in Alt’s lab for studying broken chromosomes into a quality assurance tool for genome editing. As a bonus, the method—called high-throughput genome translocation sequencing (HTGTS)—also reveals the “collateral damage” gene editing methods might create in a cell’s genome, information that could help researchers make better choices when designing gene editing experiments. Full story »

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From a series on researchers and innovators at Boston Children’s Hospital

Improbable as it sounds, autism researcher Susan Faja, PhD, likens her job to improv. “I really like Tina Fey’s description of her days as an improv comedian,” says Faja, who joined Boston Children’s Hospital’s Laboratories of Cognitive Neuroscience in July 2014 as a research associate. “In improv, you have to say ‘yes’ to the lead handed to you by your partner and then add an ‘and’ with your own contribution. My research approach is similar. Understanding how a particular neural system is working provides a starting point. Designing a targeted intervention starting at that point is like saying, ‘yes, and…’”

Like an improv routine where new elements keep getting added, Faja loves to investigate how brain and behavior and research and clinical application can be combined. Currently, she is examining whether computer training can change brain responses and behavior in children with autism spectrum disorder.

She first investigates how neural responses correlate to symptoms of autism and then tests a targeted training, using electrophysiology to understand which aspects of brain and behavior it changes. Her work was recently recognized by the National Institutes of Health Career Development Award. Full story »

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UV light-activated aptamers Dan Kohane drug delivery

Short snippets of DNA called aptamers (red) readily get into cancer cells (green and blue) on their own (left panel). They can't penetrate cells when stuck to an oligonucleotide (center), but regain the ability when the oligonucleotide's bonds are broken by UV light (right). (Images courtesy Lele Li, PhD.)

You have a drug. You know what you want it to do and where in the body you need it to go. But when you inject it into a patient, how can you make sure your drug does what you want, where you want, when you want it to?

Daniel Kohane, MD, PhD, who runs the Laboratory of Biomaterials and Drug Delivery at Boston Children’s Hospital, has one potential solution. In the Proceedings of the National Academy of Sciences, Kohane; postdoctoral fellows LeLe Li, PhD, and Rong Tong, PhD; and Robert Langer, PhD, of Massachusetts Institute of Technology, describe a drug- targeting system that’s based on a combination of ultraviolet (UV) light and short, single strands of DNA called aptamers. Full story »

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Dolly sheep cloning somatic cell nuclear transfer epigenetics

Dolly the sheep, the first mammalian example of successful somatic cell nuclear transfer. (Toni Barros/Wikimedia Commons)

We all remember Dolly the sheep, the first mammal to be born through a cloning technique called somatic cell nuclear transfer (SCNT). As with the thousands of other SCNT-cloned animals ranging from mice to mules, researchers created Dolly by using the nucleus from a grown animal’s cell to replace the nucleus of an egg cell from the same species.

The idea behind SCNT is that the egg’s cellular environment kicks the transferred nucleus’s genome into an embryonic state, giving rise to an animal genetically identical to the nucleus donor. SCNT is also a technique for generating embryonic stem cells for research purposes.

While researchers have accomplished SCNT in many animal species, it could work better than it does now. It took the scientists who cloned Dolly 277 tries before they got it right. To this day, SCNT efficiency—that is, the percent of nuclear transfers it takes generate a living animal—still hovers around 1 to 2 percent for mice, 5 to 20 percent in cows and 1 to 5 percent in other species. By comparison, the success rate in mice of in vitro fertilization (IVF) is around 50 percent.

“The efficiency is very low,” says Yi Zhang, PhD, a stem cell biologist in Boston Children’s Hospital’s Program in Cellular and Molecular Medicine. “This indicates that there are some barriers preventing successful cloning. Thus our first goal was to identify such barriers.” Full story »

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BCH_InnoSummit14_FriedNaomi-2

Some innovators, Naomi Fried, PhD, chief innovation officer at Boston Children’s Hospital, says, can end up alone on an island and make something out of just sand and water. But a lot of other innovators could benefit from getting help. In her role as lead of Boston Children’s Innovation Acceleration Program, Fried and her team help established and potential innovators alike connect with that help: navigating vendor/manufacturer contracts, accessing specialists like designers and coders, and raising funding. “You can’t have an innovative organization unless you have a plan and a structure for that.” Full story »

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Breast cancer cholesterol ezetimibe Zetia angiogenesisYou are what you eat, the saying goes. For some conditions (think cardiovascular disease or type 2 diabetes), there are clear connections between diet, health and illness.

For breast cancer, the picture is less clear. Many epidemiologic and laboratory studies have examined the Western diet (in particular, cholesterol) and its relation to breast cancer, with conflicting results.

“There’s been a raging debate in the field,” says Christine Coticchia, PhD, who works in the laboratory of Boston Children’s Hospital’s Vascular Biology Program director, Marsha Moses, PhD. “The biology of cancer and of cholesterol are so complex, and there are many subsets of breast cancer. In order to find any connections, you have to ask very specific questions.”

Banding together with Keith Solomon, PhD, in Boston Children’s Urology Department,  Coticchia and Moses asked whether dietary cholesterol might encourage progression of the most aggressive, so-called “triple-negative” breast tumors. As they report in the American Journal of Pathology, they found a big impact, at least in mice. But it’s too early to say just yet that cutting back on cholesterol will help women avoid breast cancer. Full story »

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This interactive map of the Ebola outbreak, produced by HealthMap, paints a picture of the epidemic's course from its first public signs in March. Mouse around, scroll down, zoom and explore. And click play to see how events have unfolded thus far.

Sobering news keeps coming out of the West African Ebola outbreak. According to numbers released on August 6, the virus has sickened 1,711 and claimed 932 lives across four nations. The outbreak continues to grow, with a high risk of continued regional spread, according to a threat analysis released by HealthMap (an outbreak tracking system operated out of Boston Children’s Hospital) and Bio.Diaspora (a Canadian project that monitors communicable disease spread via international travel).

“What we’ve seen here—because of inadequate public health measures, because of general fear—is [an outbreak that] truly hasn’t been kept under control,” John Brownstein, PhD, co-founder of HealthMap and a computational epidemiologist at Boston Children’s Hospital, told ABC News. “The event started, calmed down and jumped up again. Now, we’re seeing movement into densely populated areas, which is highly concerning.”

If you’re interested in keeping tabs on the outbreak yourself, there are several tools that can help. Full story »

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Daniel Kohane of Boston Children's Hospital is developing drug delivery technologies that rely on nanoparticles and the spectrum of light.Getting drugs where they need to be, and at the right time, can be more challenging than you think. Tumors, for example, tend to have blood vessels that are tighter and twistier than normal ones, making it hard for drugs to penetrate them. Despite decades of research on antibodies, peptides and other guidance methods, drug makers struggle to target drugs to specific tissues or cell types.

And even once a drug arrives at the right place, the ability to fine-tune the dose so that the drug is released at the right time and in the right amount remains an elusive goal.

What’s needed is some kind of trigger, a stimulus that a clinician can turn on and off to guide when a drug is available and where it goes to make sure it does its job with the fewest side effects.

Daniel Kohane, MD, PhD, a critical care specialist and director of the Laboratory for Biomaterials and Drug Delivery at Boston Children’s Hospital, thinks he’s hit upon a promising trigger, one that’s all around us: light. Full story »

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Cameron with Galina Lipton, MD

By the time Cameron Shearing arrived at the South Shore Hospital Emergency Department (ED) during a December snowstorm, he wasn’t breathing. He didn’t have much time. The two-year-old had aspirated a chocolate-covered pretzel, which sent tiny bits of material into his lungs.

The odds of a good outcome were not high. Pretzel is one of the worst foods to aspirate for two reasons: The small pieces can block multiple small airways, and the salt, which is very irritating, causes a lot of inflammation.

“Cameron was one of the sickest patients I ever cared for as an emergency physician. I did everything I could within my scope of practice, but he needed the tools and expertise of pediatric subspecialists,” recalls Galina Lipton, MD, from Boston Children’s Department of Emergency Medicine, who was staffing the South Shore Hospital emergency room that evening. Full story »

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A clinician's-eye view of a patient with spinal muscular atrophy during a telemedicine visit.

A clinician's-eye view of a patient with spinal muscular atrophy during a telemedicine visit.

The jury is still out on telemedicine. Proponents and many patients appreciate its ability to deliver virtual patient care and to extend the reach of experts beyond the brick-and-mortar setting of a hospital. But the real question about telemedicine is: Does it make it difference? Does is it improve care and if so, in what circumstances?

TeleCAPE, a small pilot project at Boston Children’s Hospital, inches the dial toward “yes” for some patients—in particular, home-ventilated patients.

Home-ventilated patients require an inordinate amount of health care resources for even minor conditions. Costs for a simple urinary tract or viral respiratory infection that might be managed without hospitalization can reach up to $83,000 because the child’s complex medical needs require ICU admission. Full story »

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