From Wyss Institute at Harvard: “Activating genes on demand”

Harvard University

Mar 3, 2015
Wyss Institute for Biologically Inspired Engineering at Harvard University
Kat J. McAlpine, katherine.mcalpine@wyss.harvard.edu, +1 617-432-8266

Harvard Medical School
David Cameron, david_cameron@hms.harvard.edu, +1 617-432-0441

New mechanism for engineering genetic traits governed by multiple genes paves the way for various advances in genomics and regenerative medicine

When it comes to gene expression – the process by which our DNA provides the recipe used to direct the synthesis of proteins and other molecules that we need for development and survival – scientists have so far studied one single gene at a time. A new approach developed by Harvard geneticist George Church, Ph.D., can help uncover how tandem gene circuits dictate life processes, such as the healthy development of tissue or the triggering of a particular disease, and can also be used for directing precision stem cell differentiation for regenerative medicine and growing organ transplants.

In these images, the ability of the new Cas9 approach to differentiate stem cells into brain neuron cells is visible. On the left, a previous attempt to direct stem cells to develop into neuronal cells shows a low level of success, with limited red–colored areas indicating low growth of neuron cells. On the right, the new Cas9 approach shows a 40–fold increase in the number of neuronal cells developed, visible as red-colored areas on the image. Credit: Wyss Institute at Harvard University

The findings, reported by Church and his team of researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University and Harvard Medical School in Nature Methods, show promise that precision gene therapies could be developed to prevent and treat disease on a highly customizable, personalized level, which is crucial given the fact that diseases develop among diverse pathways among genetically–varied individuals.

The approach leverages the Cas9 protein, which has already been employed as a Swiss Army knife for genome engineering, in a novel way. The Cas9 protein can be programmed to bind and cleave any desired section of DNA – but now Church’s new approach activates the genes Cas9 binds to rather than cleaving them, triggering them to activate transcription to express or repress desired genetic traits. And by engineering the Cas9 to be fused to a triple–pronged transcription factor, Church and his team can robustly manipulate single or multiple genes to control gene expression.

“In terms of genetic engineering, the more knobs you can twist to exert control over the expression of genetic traits, the better,” said Church, a Wyss Core Faculty member who is also Professor of Genetics at Harvard Medical School and Professor of Health Sciences and Technology at Harvard and MIT. “This new work represents a major, entirely new class of knobs that we could use to control multiple genes and therefore influence whether or not specific genetics traits are expressed and to what extent – we could essentially dial gene expression up or down with great precision.”

Such a capability could lead to gene therapies that would mitigate age–related degeneration and the onset of disease; in the study, Church and his team demonstrated the ability to manipulate gene expression in yeast, flies, mouse and human cell cultures.

“We envision using this approach to investigate and create comprehensive libraries that document which gene circuits control a wide range of gene expression,” said one of the study’s lead authors Alejandro Chavez, Ph.D., Postdoctoral Fellow at the Wyss Institute. Jonathan Schieman, Ph.D, of the Wyss Institute and Harvard Medical School, and Suhani Vora, of the Wyss Institute, Massachusetts Institute of Technology, and Harvard Medical School, are also lead co–authors on the study.

In this technical animation, Wyss Institute researchers instruct how they engineered a Cas9 protein to create a powerful and robust tool for activating gene expression. The novel method enables Cas9 to switch a gene from off to on and has the potential to precisely induce on-command expression of any of the countless genes in the genomes of yeast, flies, mice, or humans. Credit: Wyss Institute at Harvard University

The new Cas9 approach could also potentially target and activate sections of the genome made up of genes that are not directly responsible for transcription, and which previously were poorly understood. These sections, which comprise up to 90% of the genome in humans, have previously been considered to be useless DNA “dark matter” by geneticists. In contrast to translated DNA, which contains recipes of genetic information used to express traits, this DNA dark matter contains transcribed genes which act in mysterious ways, with several of these genes often having influence in tandem.

But now, that DNA dark matter could be accessed using Cas9, allowing scientists to document which non-translated genes can be activated in tandem to influence gene expression. Furthermore, these non-translated genes could also be turned into a docking station of sorts. By using Cas9 to target and bind gene circuits to these sections, scientists could introduce synthetic loops of genes to a genome, therefore triggering entirely new or altered gene expressions.

The ability to manipulate multiple genes in tandem so precisely also has big implications for advancing stem cell engineering for development of transplant organs and regenerative therapies.

“In order to grow organs from stem cells, our understanding of developmental biology needs to increase rapidly,” said Church. “This multivariate approach allows us to quickly churn through and analyze large numbers of gene combinations to identify developmental pathways much faster than has been previously capable.”

To demonstrate this point, the researchers used it to grow brain neuron cells from stem cells and found that using the approach to program development of neuronal cells was 40–fold more successful than prior established methods. This is the first time that Cas9 has been leveraged to efficiently differentiate stem cells into brain cells.

The new approach is also compatible to be used in combination with other gene editing technologies. Church and his team have previously made breakthroughs by developing a gene editing mechanism for therapeutic applications and gene drives for altering traits in plant and animal species.

“This newest tool in the Cas9 genome engineering arsenal offers a powerful new way to control cell and tissue function that could revolutionize virtually all areas of science and medicine, ranging from gene therapy to regenerative medicine and anti–aging,” said Wyss Institute Founding Director Donald Ingber, M.D., Ph.D, who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children’s Hospital and Professor of Bioengineering at Harvard SEAS.

See the full article here.

Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

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From NYT: “I’ve Just Seen a (DNA-Generated) Face”

The New York Times

Predictions of what people look like using a DNA analysis tool compared with photos of the actual people. Credit The New York Times; Images and renderings by Mark D. Shriver/Penn State University

The faces here, which look a bit like video game avatars, are actually portraits drawn from DNA.

Each rendering was created by plugging an individual genetic profile into a predictive tool created by Mark D. Shriver, a professor of anthropology and genetics at Penn State University. Dr. Shriver and his colleagues have studied the ways that genes influence facial development.

Their software yields an image in a matter of minutes, rapidly drawing connections beween genetic markers and points on the face. In less time than it takes to make a cup of coffee, a sketch emerges inferred solely from DNA.

How accurate or useful are these predictions? That is something that Dr. Shriver is still researching – and that experts are still debating. Andrew Pollack writes about the issues in an article on genetic sleuthing in Science Times.

On The New York Times’s science desk, we wondered whether it would be possible to identify our colleagues based on the formula that Dr. Shriver has developed. So we tried a somewhat unscientific experiment.

We asked New York Times employees if they could identify their colleagues based on these DNA renderings, explaining that these were not adjusted for age. Credit Mark D. Shriver/Penn State University

John Markoff, a reporter, and Catherine Spangler, a video journalist, each volunteered to share their genetic profile, downloaded from 23andMe, a consumer DNA-testing company. The files we sent to Dr. Shriver did not include their names or any information about their height, weight or age.

Dr. Shriver processed the genotype data and sent us renderings of the donors’ faces.

We distributed the images to colleagues via email and a private Facebook group, and asked them if they could identify these individuals. We told them that because age and weight could not be determined from DNA, the person might be older or younger, heavier or lighter than the image suggested. At least a dozen people immediately responded that they could not guess because the images felt too generic. Among the 50 or so people who did venture guesses, none identified the man as Mr. Markoff, who is 65.

The man who received the most votes was Andrew Ross Sorkin, a business columnist and editor of Dealbook. A number of other possibilities were suggested, too — mostly white men who work on the science desk.

The correct answer — that no one guessed — was John Markoff. New York Times employees were shown the face, top right. Dr. Shriver’s team later adjusted for age and height and the bottom right image emerged.

When it came to the computer’s DNA portrait of Ms. Spangler, 31, staffers had more luck. About 10 people correctly identified her.

Although there was no close second, participants put forth the names of nearly 10 other women. About half of them were of European ancestry, half of Asian ancestry.

To build his model, Dr. Shriver measured 7,000 three-dimensional coordinates on the face and analyzed their links to thousands of genetic variants. Though sex and ancestral mix are not the only predictor of face shape in this model, they are the primary influencers — something that has raised concerns about the potential for racial profiling.

About ten employees correctly guessed Catherine Spangler. Employees were shown the top right image. The face, bottom right, was adjusted for age, weight and height

Ms. Spangler’s ancestry is half Korean and half northern European. Mr. Markoff’s is almost entirely Ashkenazi Jewish, with a tenth of a percent Asian, according to his 23andMe analysis.

Using DNA portraiture, would every male or female with these genetic percentages wind up looking exactly the same? Dr. Shriver says no.

“People with same ancestry levels can come out looking different,” he said. But just how different — and how much like the actual flesh-and blood-person — is something he and his team are still testing.

See the full article here.

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From NOVA: “In Once-Mysterious Epigenome, Scientists Find What Turns Genes On”

NOVA

19 Feb 2015
R.A. Becker

A handful of new studies provide epigenetic roadmaps to understanding the human genome in action.(No image credit)

Over a decade ago, the Human Genome Project deciphered the “human instruction book” of our DNA, but how cells develop vastly different functions using the same genetic instructional text has remained largely a mystery.

As of yesterday, it became a bit less mysterious. A massive NIH consortium called the Roadmap Epigenomics Program published eight papers in the journal Nature which report on their efforts to map epigenetic modifications, or the changes to DNA that don’t alter its code. These subtle modifications make genes more or less likely to be expressed, and the collection of epigenetic modifications is called the epigenome.

One of the eight studies mapped over 100 epigenomes characterizing every epigenetic modification occurring in human tissue cells. “These 111 reference epigenome maps are essentially a vocabulary book that helps us decipher each DNA segment in distinct cell and tissue types,” Roadmap researcher Bing Ren, a professor of cellular and molecular medicine at the University of California, San Diego, said in a news release. “These maps are like snapshots of the human genome in action.”

This kind of mapping has challenged the field because of the huge amount of data needed to make sense of the chaotic arrangements of genes and their regulators. “The genome hasn’t nicely arranged the regulatory elements to be cheek by jowl with the elements they regulate,” Broad Institute director Eric Lander told Gina Kolata at The New York Times. “It can be very hard to figure out which regulator lines up with which genes.”

Here’s how Lander described the detective process used to Kolata:

If you knew when service on the Red Line was disrupted and when various employees were late for work, you might be able to infer which employees lived on the Red Line, he said. Likewise, when a genetic circuit was shut down, certain genes would be turned off. That would indicate that those genes were connected, like the employees who were late to work when the Red Line shut down.

Diseases can be linked to epigenetic variations as well. For example, another of the eight papers published yesterday proposed that the roots of Alzheimer’s disease lie in immune cell genetic dysfunction and epigenetic alterations in brain cells.

Creating an epigenetic road map is a huge step, but it’s just a first step. As Collins wrote in 2001 when the human genome had been mostly mapped, “This is not even the beginning of the end. But it may be the end of the beginning.”

See the full article here.

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NOVA is the highest rated science series on television and the most watched documentary series on public television. It is also one of television’s most acclaimed series, having won every major television award, most of them many times over.

From NYT: “A New Theory on How Neanderthal DNA Spread in Asia”

The New York Times

FEB. 19, 2015
Carl Zimmer

Chinese passengers wait on a train platform at the Beijing Railway Station. Researchers have discovered that Neanderthals interbred with the ancestors of Asians at two points in history, giving this population an extra infusion of Neanderthal DNA. Credit European Pressphoto Agency

In 2010, scientists made a startling discovery about our past: About 50,000 years ago, Neanderthals interbred with the ancestors of living Europeans and Asians.

Now two teams of researchers have come to another intriguing conclusion: Neanderthals interbred with the ancestors of Asians at a second point in history, giving them an extra infusion of Neanderthal DNA.

The findings are further evidence that our genomes contain secrets about our evolution that we might have missed by looking at fossils alone. “We’re learning new, big-picture things from the genetic data, rather than just filling in details,” said Kirk E. Lohmueller, a geneticist at the University of California, Los Angeles, and co-author of one of the new studies.

The oldest fossils of Neanderthals date back about 200,000 years, while the most recent are an estimated 40,000 years old. Researchers have found Neanderthal bones at sites across Europe and western Asia, from Spain to Siberia.

Some of those bones still retain fragments of Neanderthal DNA. Scientists have pieced those DNA fragments together, reconstructing the entire Neanderthal genome. It turns out that Neanderthals had a number of distinct genetic mutations that living humans lack. Based on these differences, scientists estimate that the Neanderthals’ ancestors diverged from ours 600,000 years ago.

Our own ancestors remained in Africa until about 60,000 years ago, then expanded across the rest of the Old World. Along the way, they encountered Neanderthals. And our DNA reveals that those encounters led to children.

Today, people who are not of African descent have stretches of genetic material almost identical to Neanderthal DNA, comprising about 2 percent of their entire genomes. These DNA fragments are the evidence that Neanderthals interbred with the early migrants out of Africa, likely in western Asia.

Researchers also have found a peculiar pattern in non-Africans: People in China, Japan and other East Asian countries have about 20 percent more Neanderthal DNA than do Europeans.

Last year, Sriram Sankararaman, a postdoctoral researcher at Harvard Medical School, and his colleagues proposed that natural selection was responsible for the difference. Most Neanderthal genes probably had modestly bad effects on the health of our ancestors, Dr. Sankararaman and other researchers have found. People who inherited a Neanderthal version of any given gene would have had fewer children on average than people with the human version.

As a result, Neanderthal DNA became progressively rarer in living humans. Dr. Sankararaman and his colleagues proposed that it disappeared faster in Europeans than in Asians. The early Asian population was small, the researchers suggested, and natural selection eliminates harmful genes more slowly in small groups than in large populations. Today, smaller ethnic groups, like Ashkenazi Jews and the Amish, can have unusually high rates of certain genetic disorders.

Joshua M. Akey, a geneticist at the University of Washington, and the graduate student Benjamin Vernot recently set out to test this hypothesis. They took advantage of the fact that only some parts of our genome have a strong influence on health. Other parts — so-called neutral regions — are less important.

A mutation in a neutral region won’t affect our odds of having children and therefore won’t be eliminated by natural selection. If Dr. Sankararaman’s hypothesis were correct, you would expect Europeans to have lost more harmful Neanderthal DNA than neutral DNA. In fact, the scientists did not find this difference in the DNA of living Europeans.

Dr. Akey and Mr. Vernot then tested out other possible explanations for the comparative abundance of Neanderthal DNA in Asians. The theory that made the most sense was that Asians inherited additional Neanderthal DNA at a later time.

In this scenario, the ancestors of Asians and Europeans split, the early Asians migrated east, and there they had a second encounter with Neanderthals. Dr. Akey and Mr. Vernot reported their findings in the American Journal of Human Genetics.

Dr. Lohmueller and the graduate student Bernard Y. Kim approached the same genetic question, but from a different direction. They constructed a computer model of Europeans and Asians, simulating their reproduction and evolution over time. They added some Neanderthal DNA to the ancestral population and then watched as Europeans and Asian populations diverged genetically.

The scientists ran the model many times over, trying out a range of likely conditions. But no matter which variation they tried, they couldn’t find one explaining why Asians today have extra Neanderthal DNA.

But when they ran a model that included a second interbreeding, another “pulse” of Neanderthal genes into the Asian population, the researchers had better luck. “We find that the two-pulse model can fit the data really well,” Dr. Lohmueller said. He and Mr. Kim published their results in a separate paper in the American Journal of Human Genetics.

Dr. Akey is pleased that the two studies reached the same conclusion. “Together, they tell the same story, just from different perspectives,” he said.

Dr. Sankararaman agreed that the new research cast doubt on his proposal that natural selection stripped Neanderthal DNA from Europeans more quickly than from Asians. “The analysis from both papers gives strong support to the two-pulse model in Asians,” he said.

But the two-pulse hypothesis also poses a puzzle of its own.

If Neanderthals became extinct 40,000 years ago, they may have disappeared before Europeans and Asian populations genetically diverged. How could there have been Neanderthals left to interbreed with Asians a second time?

It’s conceivable that the extinction of the Neanderthals happened later in Asia. If that is true, there might yet more recent Neanderthal fossils waiting to be discovered there.

Or perhaps Asians interbred with some other group of humans that had interbred with Neanderthals and carried much of their DNA. Later, that group disappeared.

“That’s a paradox the field needs to address,” Dr. Lohmueller said.

See the full article here.

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From Princeton: “A gene that shaped the evolution of Darwin’s finches”

Princeton University

February 11, 2015
Catherine Zandonella, Office of the Dean for Research

Researchers from Princeton University and Uppsala University in Sweden have identified a gene in the Galápagos finches studied by English naturalist Charles Darwin that influences beak shape and that played a role in the birds’ evolution from a common ancestor more than 1 million years ago.

The study illustrates the genetic foundation of evolution, including how genes can flow from one species to another, and how different versions of a gene within a species can contribute to the formation of entirely new species, the researchers report in the journal Nature. The study was published online Feb. 11, one day before the birthday of Darwin, who studied the finches during the 1835 voyage that would lead him to publish the seminal work on evolution, On the Origin of Species, in 1859.

New research from Princeton University and Uppsala University in Sweden reveals a gene associated with beak shape in Darwin’s finches in the Galápagos islands. Evolutionary biologists Peter and Rosemary Grant (above) provided DNA samples collected during 40 years of field work on the islands. The team in Uppsala led by Leif Andersson provided the whole-genome sequencing that resulted in detection of the gene. The findings illustrate several aspects of the genetic foundation of evolution. (Photo by Denise Applewhite, Office of Communications)

“We now know more about the genetic basis for our evolutionary studies, and this is a highly satisfactory, very exciting discovery after all these years,” said Peter Grant, Princeton’s Class of 1877 Professor of Zoology, Emeritus, and a professor of ecology and evolutionary biology, emeritus. Along with co-author and wife B. Rosemary Grant, a senior biologist in ecology and evolutionary biology, Grant has studied the finches for 40 years on the arid, rocky islands of Daphne Major and Genovesa in the Galápagos archipelago.

The latest study reveals how evolution occurs in halting and disordered steps, with many opportunities for genes to spread in different species and create new lineages. Given the right conditions, such as isolation from the original population and an accumulation of genetic differences, these lineages can eventually evolve into entirely new species.

Working with DNA samples collected by the Grants, researchers at Uppsala identified the gene that influences beak shape by comparing the genomes of 120 birds, all members of the 15 species known as “Darwin’s finches.” They spotted a stretch of DNA that looked different in species with blunt beaks, such as the large ground finch (Geospiza magnirostris), versus species with pointed beaks, such as the large cactus finch (G. conirostris).

Within that stretch of DNA, the researchers found a gene known as ALX1, which has previously been identified in humans and mice as being associated with the formation of facial features. Mutations that inactivate this gene cause severe birth defects in humans.

The large ground finch (Geospiza magnirostris) on Daphne Major Island, Galápagos archipelago. (Photo B.R. Grant, Department of Ecology and Evolutionary Biology. Reproduced with the permission of Princeton University Press)

“This is an interesting example where mild mutations in a gene that is critical for normal development leads to phenotypic [observable] evolution,” said lead researcher Leif Andersson, a professor of functional genomics at Uppsala University, the Swedish University of Agricultural Sciences, and Texas A&M University.

But the most exciting and interesting finding of the study, Andersson said, was that the gene also varied among individuals from the same species. For example, the medium ground finch (G. fortis) species includes some birds with blunt beaks and others with pointed ones.

This finding is significant because it shows how evolution can happen, Peter Grant said. Within a species, when some individuals have a trait that aids their survival — such as a blunt beak that allows them to crack open tough seed coverings — they will pass on the genes for that trait to their offspring, whereas individuals with pointed beaks will have died. “This is the genetic variation upon which natural selection can work,” he said.

The shape and size of the beak are crucial for finch survival on the islands, which periodically experience extreme droughts, El Niño-driven rains and volcanic activity. The birds use their beaks as tools to crack open the hard and woody outer coverings of seeds, pry insects from twigs, and sip nectar from cactus flowers. In times of drought, a bird that can extract food from multiple sources will survive whereas other birds will not.

During the past four decades, the Grants and their research team have found that beak shape and size played a significant role in the evolution of finch species via natural selection when droughts hit Daphne Major in 1977, 1985 and 2004. “Now we have a genetic underpinning of something we have seen three times during the last 40 years,” Rosemary Grant said.

The medium ground finch (Geospiza fortis) on Daphne Major Island, Galápagos archipelago. (Photo B.R. Grant, Department of Ecology and Evolutionary Biology. Reproduced with the permission of Princeton University Press)

The Nature study also adds to what is known about how genes are transferred from one species to another when individuals from two closely related species mate. Although in many species of birds the resulting chicks would be sterile, the hybrid offspring of Galápagos finches can mate with an individual from either of the two parental species. The resulting chicks will identify with one or the other of the parent species through song and appearance, but they will carry genes from both parents.

Through this process, known as gene flow, or introgression, genetic material can move between species and contribute to the development of new species. The Grants had shown that gene flow has occurred in the finches of Daphne Major during the past 40 years, but the new study found extensive evidence for gene flow throughout the roughly 1 million years that the birds have occupied the archipelago, which has helped the researchers update their understanding of how the lineages diverged over time.

“We’ve been able to get a much more confident estimate,” Peter Grant said, “of which species are old and which are young, and the time course over which evolution happened.”

The article, Evolution of Darwin’s finches and their beaks revealed by genome sequencing, was published online Feb. 11 by Nature. The study was supported by the Knut and Alice Wallenberg Foundation, Uppsala University and Hospital, SciLifeLab and Swedish Research Council. The collection of samples was funded by the National Science Foundation under permits from the Galápagos and Costa Rica National Parks Services.

See the full article here.

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About Princeton: Overview

Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

From U Maryland: “New Mechanism of Epigenetic Inheritance Could Advance Study of Evolution and Disease Treatment”

University of Maryland

February 2, 2015
Matthew Wright, 301-405-9267, mewright@umd.edu

Results show that gene silencing can last for 25+ generations

For more than a century, scientists have understood the basics of inheritance: if good genes help parents survive and reproduce, the parents pass those genes along to their offspring. And yet, recent research has shown that reality is much more complex: genes can be switched off, or silenced, in response to the environment or other factors, and sometimes these changes can be passed from one generation to the next.

UMD scientists have discovered a mechanism for transgenerational gene silencing in the roundworm Caenorhabditis elegans. Special fluorescent dyes help to visualize neurons (magenta) and germ cells (green) in the roundworm’s body. Photo: Sindhuja Devanapally

The phenomenon has been called epigenetic inheritance, but it is not well understood. Now, UMD geneticist Antony Jose and two of his graduate students are the first to figure out a specific mechanism by which a parent can pass silenced genes to its offspring. Importantly, the team found that this silencing could persist for multiple generations—more than 25, in the case of this study.

The research, which was published in the Feb. 2, 2015 online early edition of the Proceedings of the National Academy of Sciences, could transform our understanding of animal evolution. Further, it might one day help in the design of treatments for a broad range of genetic diseases.

“For a long time, biologists have wanted to know how information from the environment sometimes gets transmitted to the next generation,” said Jose, an assistant professor in the UMD Department of Cell Biology and Molecular Genetics. “This is the first mechanistic demonstration of how this could happen. It’s a level of organization that we didn’t know existed in animals before.”

Jose and graduate students Sindhuja Devanapally and Snusha Ravikumar worked with the roundworm Caenorhabditis elegans, a species commonly used in lab experiments. They made the worms’ nerve cells produce molecules of double-stranded RNA (dsRNA) that match a specific gene. (RNA is a close relative of DNA, and has many different varieties, including dsRNA.) Molecules of dsRNA are known to travel between body cells (any cell in the body except germ cells, which make egg or sperm cells) and can silence genes when their sequence matches up with the corresponding section of a cell’s DNA.

This schematic illustrates how the gene silencing mechanism works in C. elegans. Neurons (magenta) can export double-stranded RNA (orange arrow) that match a gene (green) in germ cells. Import of RNA into germ cells results in silencing of the gene (black) within germ cells. This silencing can persist for more than 25 generations. Photo: Antony Jose

The team’s biggest finding was that dsRNA can travel from body cells into germ cells and silence genes within the germ cells. Even more surprising, the silencing can stick around for more than 25 generations. If this same mechanism exists in other animals—possibly including humans—it could mean that there is a completely different way for a species to evolve in response to its environment.

“This mechanism gives an animal a tool to evolve much faster,” Jose said. “We still need to figure out whether this tool is actually used in this way, but it is at least possible. If animals use this RNA transport to adapt, it would mean a new understanding of how evolution happens.”

The long-term stability of the silencing effect could prove critical in developing treatments for genetic diseases. The key is a process known as RNA interference, more commonly referred to as RNAi. This process is how dsRNA silences genes in a cell. The same process has been studied as a potential genetic therapy for more than a decade, because you can target any disease gene with matching dsRNA. But a main obstacle has been achieving stable silencing, so that the patient does not need to take repeated high doses of dsRNA.

“RNAi is very promising as a therapy, but the efficacy of the treatment declines over time with each new cell division,” Jose said. “This particular dsRNA, from C. elegans nerve cells, might have some chemical modifications that allow stable silencing to persist for many generations. Further study of this molecule could help solve the efficacy problem in RNAi therapy.”

Jose acknowledges the large gap between roundworms and humans. Unlike simpler animals, mammals have known mechanisms that reprogram silenced genes every generation. On the surface, it would seem as though this would prevent epigenetic inheritance from happening. And yet, previous evidence suggests that the environment may be able to cause some sort of transgenerational effect in mammals as well. Jose believes that his team’s work provides a promising lead in the search for how this happens.

The roundworm C. elegans, seen here, is commonly used in laboratory studies because it reproduces quickly and has a simple body. Photo: Hai Le

“This is a fertile research field that will keep us busy for 10 years or more into the future,” Jose said. “The goal is to achieve a very clear understanding—in simple terms—of all the tools an animal can use to evolve.”

This research was supported by the National Institute of General Medical Sciences of the National Institutes of Health. The content of this article does not necessarily reflect the views of this organization.

The research paper, Double-stranded RNA made in C. elegans neurons can enter the germline and cause transgenerational gene silencing, Sindhuja Devanapally, Snusha Ravikumar and Antony M. Jose, was published online in the Feb. 2, 2015 early edition of the journal Proceedings of the National Academy of Sciences.

See the full article here.

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From MIT Tech Review: “U.S. To Develop DNA Study of One Million People”

M.I.T Technology Review

January 30, 2015
Antonio Regalado

U.S. President Barack Obama is proposing to spend $215 million on a “precision medicine” initiative the centerpiece of which will be a national study involving the health records and DNA of one million volunteers, administration officials said yesterday.

Precision medicine refers to treatments tailored to a person’s genetic profile, an idea already transforming how doctors fight cancer as well as some rare diseases.

The Obama plan, including support for studies of cancer and rare disease, is part of a shift away from “one-size-fits-all” medicine, Jo Handelsman, associate director for the White House Office of Science and Technology Policy, said in a briefing yesterday. She called precision medicine “a game changer that holds the potential to revolutionize how we approach health in this country and around the world.”

The White House said the largest part of the money, $130 million, would go to the National Institutes of Health in order to create a population-scale study of how peoples’ genes, environment, and lifestyle affect their health.

According to Francis Collins, director of the National Institutes of Health, the study would reach a million people by merging data from several large studies already underway, as well as by recruiting new volunteers. Details of the study still need to be sorted out, said Collins, but it could eventually involve completely decoding the genomes of hundreds of thousands of people.

Officials indicated that patients might have more access to data generated about them than is usually the case in research studies. That is partly because scientists will need the ability to re-contact them, should their genes prove interesting.

“We aren’t just talking about research but also about patients’ access to their own data, so they can participate fully in decisions about their health that affect them,” said John Holdren, director of the White House Office of Science and Technology Policy.

Collins said the U.S. is not seeking to create a single bio-bank. Instead, it would be look to combine data from among what he called more than 200 large American health studies involving at least two million people. “Fortunately we don’t have to start from scratch,” said Collins. “The challenge of this initiative is to link those together. It’s more a distributed approach than centralized.”

Collins warned that “interoperability” of medical record systems and gene databases could be the most significant obstacle to the NIH’s plans.

A lack of standards is one reason why the U.S. lags some European countries, which already have large, well-organized studies linking genomics to national health records. There is competition from the private sector as well, where precision medicine is a hot subject drawing large investments.

For instance, one of the world’s largest private bio-banks, of 800,000 spit samples, is owned by a startup, 23andMe, in Silicon Valley with its eyes on being a kind of Facebook of gene research.

The entrepreneur J. Craig Venter, a one-time rival of the NIH in sequencing the first human genome, announced plans a year ago to sequence one million genomes by 2020 using private funding.

In recent weeks, NIH officials met with administrators from the Veteran’s Health Administration, whose ongoing “Million Veterans Project” has already collected DNA samples from 343,000 former soldiers, and partially analyzed the DNA of 200,000 participants.

“There is a lot of effort to avoid duplication since no one has enough money, and I would expect these programs to work together,” said Timothy O’Leary, chief research and development officer for the V.A., which is already spending $30 million a year on its study. However, he added that before sharing data the VA would need guarantees that veterans’ private information was not at risk.

If Obama’s budget is approved, the NIH will hand out the money to academic centers. However, much of the cash will trickle down to tech companies hired to store and organize the data, as well as to makers of gene sequencing instruments. Illumina of San Diego, which sells the most popular models of DNA sequencing machines, is likely to be the single largest financial beneficiary of Obama’s plan in the short term.

David Goldstein, director of a new institute for genome medicine at Columbia University, called the Obama plan part of an irreversible drive towards obtaining more and more complete genetic information on people as part of routine medicine. “The writing is one the wall. We are all going to be sequenced, the question is just who does it and what is done with it,” said Goldstein. “The challenge will be to do good things with the data.”

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From Stanford: “Stanford bioengineers develop tool for reprogramming genetic code”

Stanford University

January 26, 2015
Bjorn Carey

Biology relies upon the precise activation of specific genes to work properly. If that sequence gets out of whack, or one gene turns on only partially, the outcome can often lead to a disease.

Now, bioengineers at Stanford and other universities have developed a sort of programmable genetic code that allows them to preferentially activate or deactivate genes in living cells. The work is published in the current issue of Cell, and could help usher in a new generation of gene therapies.

Stanford bioengineers have developed a new tool that allows them to preferentially activate or deactivate genes in living cells.

The technique is an adaptation of CRISPR, itself a relatively new genetic tool that makes use of a natural defense mechanism that bacteria evolved over millions of years to slice up infectious virus DNA.

Diagram of the possible mechanism for CRISPR.

CRISPRs (clustered regularly interspaced short palindromic repeats) are DNA loci containing short repetitions of base sequences. Each repetition is followed by short segments of “spacer DNA” from previous exposures to a virus.[2]

Standard CRISPR consists of two components: a short RNA that matches a particular spot in the genome, and a protein called Cas9 that snips the DNA in that location. For the purposes of gene editing, scientists can control where the protein snips the genome, insert a new gene into the cut and patch it back together.

Inserting new genetic code, however, is just one way to influence how the genome is expressed. Another involves telling the cell how much or how little to activate a particular gene, thus controlling how much protein a cell produces from that gene and altering its behavior.

It’s this action that Lei Stanley Qi, an assistant professor of bioengineering and of chemical and systems biology at Stanford, and his colleagues aim to manipulate.

Influencing the genome

In the new work, the researchers describe how they have designed the CRISPR molecule to include a second piece of information on the RNA, instructing the molecule to either increase (upregulate) or decrease (downregulate) a target gene’s activity, or turn it on/off entirely.

Additionally, they designed it so that it could affect two different genes at once. In a cell, the order or degree in which multiple genes are activated can produce different metabolic products.

“It’s like driving a car. You control the wheel to control direction, and the engine to control the speed, and how you balance the two determines how the car moves,” Qi said. “We can do the same thing in the cell by up- or downregulating genes, and produce different outcomes.”

As a proof of principle, the scientists used the technique to take control of a yeast metabolic pathway, turning genes on and off in various orders to produce four different end products. They then tested it on two mammalian genes that are important in cell mobility, and were able to control the cell’s direction and how fast it moved.

Future therapies

The ability to control genes is an attractive approach in designing genetic therapies for complex diseases that involve multiple genes, Qi said, and the new system may overcome several of the challenges of existing experimental therapies.

“Our technique allows us to directly control multiple specific genes and pathways in the genome without expressing new transgenes or uncontrolled behaviors, such as producing too much of a protein, or doing so in the wrong cells,” Qi said. “We could eventually synthesize tens of thousands of RNA molecules to control the genome over a whole organism.”

Next, Qi plans to test the technique in mice and refine the delivery method. Currently the scientists use a virus to insert the molecule into a cell, but he would eventually like to simply inject the molecules into an organism’s blood.

“That is what is so exciting about working at Stanford, because the School of Medicine’s immunology group is just around the corner, and working with them will help us address how to do this without triggering an immune response,” said Qi, who is a member of the interdisciplinary Stanford ChEM-H institute. “I’m optimistic because everything about this system comes naturally from cells, and should be compatible with any organism.”

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Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

From Wash U.: “Scientists find gene vital to central nervous system development”

Washington University in St.Louis

January 21, 2015
Julia Evangelou Strait

Using Washington University’s zebrafish facility, graduate student Sarah Ackerman (left) and senior author Kelly Monk, PhD, identified a gene that regulates how well the wiring of the central nervous system is insulated.

Scientists have identified a gene that helps regulate how well nerves of the central nervous system are insulated, researchers at Washington University School of Medicine in St. Louis report.

Healthy insulation is vital for the speedy propagation of nerve cell signals. The finding, in zebrafish and mice, may have implications for human diseases like multiple sclerosis, in which this insulation is lost.

The study appears Jan. 21 in Nature Communications.

Nerve cells send electrical signals along lengthy projections called axons. These signals travel much faster when the axon is wrapped in myelin, an insulating layer of fats and proteins. In the central nervous system, the cells responsible for insulating axons are called oligodendrocytes.

The research focused on a gene called Gpr56, which manufactures a protein of the same name. Previous work indicated that this gene likely was involved in central nervous system development, but its specific roles were unclear.

In the new study, the researchers found that when the protein Gpr56 is disabled, there are too few oligodendrocytes to provide insulation for all of the axons. Still, the axons looked normal. And in the relatively few axons that were insulated, the myelin also looked normal. But the researchers observed many axons that were simply bare, not wrapped in any myelin at all.

Without Gpr56, the cells responsible for applying the insulation failed to reproduce themselves sufficiently, according to the study’s senior author, Kelly R. Monk, PhD, assistant professor of developmental biology. These cells actually matured too early instead of continuing to replicate as they should have. Consequently, in adulthood, there were not enough mature cells, leaving many axons without insulation.

Monk and her team study zebrafish because they are excellent models of the vertebrate nervous system. Their embryos are transparent and mature outside the body, making them useful for observing developmental processes.

“We first saw this defect in the developing zebrafish embryo,” said first author Sarah D. Ackerman, a graduate student in Monk’s lab. “But it’s not simply a temporary defect that only results in delayed myelination. When I looked at fish that were six months old, I still saw this problem of undermyelinated axons.”

In a companion paper in the same issue of Nature Communications, senior author Xianhua Piao, MD, PhD, of Harvard University, and her co-authors, including Monk, showed similar defects in mice without Gpr56. In past work, Piao also has shown evidence that human defects in Gpr56 lead to brain malformations related to a lack of myelin.

“These are nice studies that arrived at the same conclusion independently,” said Monk, who is also with the Hope Center for Neurological Disorders at Washington University. “Our Harvard colleagues used mouse models while we used fish models. And Dr. Piao’s research in human patients suggests that similar mechanisms are at work in people.”

Monk also said that Gpr56 belongs to a large class of cell receptors that are common targets for many commercially available drugs, making the protein attractive for further research. The investigators pointed out its possible relevance in treating diseases associated with a lack of myelin, with particular interest in multiple sclerosis.

“In the case of MS, there are areas where the central nervous system has lost its myelin,” Monk said. “At least part of the problem is that the precursor myelin-producing cells are recruited to that area, but they fail to become adult cells capable of producing nerve cell insulation. Now, we have evidence that Gpr56 modulates the switch from precursor to adult cell.”

In theory, if the precursor cells can be pushed to mature into adulthood, they may become capable of producing myelin. According to Monk and Ackerman, possible future work includes using the zebrafish model system as a drug-screening tool to search for small molecules that may flip that switch.

The work led by Washington University was supported by predoctoral fellowships from the National Institutes of Health (NIH), and from the Edward J. Mallinckrodt Foundation.

Ackerman SD, Garcia C, Piao X, Gutmann DH, Monk KR. The adhesion-GPCR Gpr56 regulates oligodendrocyte development via interactions with G-alpha12/13 and RhoA. Nature Communications. January 21, 2015.

The work led by Harvard University was supported by grants from the NIH, and by the William Randolph Hearst Fund, the Leonard and Isabelle Goldenson Research Fellowship and the Cerebral Palsy International Research Foundation.

Giera S, Deng Y, Luo R, Ackerman SD, Mogha A, Monk KR, Ying Y, Jeong SJ, Makinodan M, Bialis A, Chang B, Stevens B, Corfas G, Piao X. The adhesion G protein-coupled receptor GPR56 is a cell autonomous regulator of oligodendrocyte development. Nature Communications. January 21, 2015.

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From ICL: “‘Titin’ gene mutations will help identify patients at risk of heart failure”

Imperial College London

14 January 2015
Sam Wong

A new study has identified genetic mutations that cause the heart condition dilated cardiomyopathy (DCM), paving the way for more accurate diagnosis.

By sequencing the gene encoding the muscle protein titin in more than 5,000 people, scientists have worked out which variations are linked to disease, providing information that will help screen high-risk patients.

Titin gene mutations were previously associated with DCM, a leading cause of inherited heart failure, but many people have variations in the genetic code that are completely benign.

The new study, published in Science Translational Medicine, sorts the harmful from the harmless mutations, giving doctors a directory to interpret patients’ DNA sequences.

The information could also help researchers develop therapies to prevent or treat heart disease caused by titin mutations.

The study was led by researchers at Imperial College London and Royal Brompton & Harefield NHS Foundation Trust.

Cardiac magnetic resonance imaging of the heart of a patient with dilated cardiomyopathy.

Around one in 250 people are estimated to have DCM. It causes the heart muscle to become thin and weak, often leading to heart failure.

Mutations in the titin gene that make the protein shorter, or truncated, are the most common cause of DCM, accounting for about a quarter of cases. But truncations in the gene are common – around one in 50 people have one – and most are not harmful, making it difficult to develop a useful genetic test.

The researchers sequenced the titin gene from 5,267 people, including healthy volunteers and patients with DCM, and analysed the levels of titin in samples of heart tissue. The results showed that mutations that cause DCM occur at the far end of the gene sequence. Mutations in healthy individuals tend to occur in parts of the gene that aren’t included in the final protein, allowing titin to remain functional.

Professor Stuart Cook, from the Medical Research Council (MRC) Clinical Sciences Centre at Imperial College London, who led the study, said: “These results give us a detailed understanding of the molecular basis for dilated cardiomyopathy. We can use this information to screen patients’ relatives to identify those at risk of developing the disease, and help them to manage their condition early.”

The research was funded by the MRC, the British Heart Foundation, the Fondation Leducq, the Wellcome Trust, the National Institute for Health Research (NIHR) Royal Brompton Cardiovascular Biomedical Research Unit and the NIHR Imperial Biomedical Research Centre.

Professor Dudley Pennell, director of the NIHR Royal Brompton Cardiovascular Biomedical Research Unit, said: “This research reveals which genetic mutations are bad and which are there purely as bystanders. It will benefit patients with cardiomyopathy and enable us to reassure relatives who do not have the disease, allowing them to be discharged from clinic and preventing needless anxiety and unnecessary expensive tests.”

Professor Jeremy Pearson, Associate Medical Director at the British Heart Foundation, said: “Determining which mutations in titin are harmful and which are not has been difficult, in part because titin is one of the largest human proteins.

“This study defines, for the first time, a comprehensive list of mutations in the titin gene, which of these are associated with dilated cardiomyopathy, and which are harmless. This information will be extremely valuable for correct future diagnosis and treatment as we enter an era when many people’s genes will be sequenced.”

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Imperial College London is a science-based university with an international reputation for excellence in teaching and research. Consistently rated amongst the world’s best universities, Imperial is committed to developing the next generation of researchers, scientists and academics through collaboration across disciplines. Located in the heart of London, Imperial is a multidisciplinary space for education, research, translation and commercialisation, harnessing science and innovation to tackle global challenges.