Francis Collins

‘Robot Mouse’ Marks New Step Forward in Neuroscience

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The mouse walked, the mouse stopped; the mouse ignored a bowl of food, then scampered back and gobbled it up, and it was all controlled by neuroscientists, researchers reported on Thursday.

The study, describing a way to manipulate a lab animal’s brain circuitry accurately enough to turn behaviors both on and off, is the first to be published under President Barack Obama’s 2013 BRAIN Initiative, which aims to advance neuroscience and develop therapies for brain disorders.

The point of the remote-control mouse is not to create an army of robo-rodents. Instead, neuroscientists hope to perfect a technique for identifying brain wiring underlying any behavior, and control that behavior by activating and deactivating neurons.

If scientists are able do that for the circuitry involved in psychiatric or neurological disorders, it may lead to therapies. That approach reflects a shift away from linking such illnesses to “chemical imbalances” in the brain, instead tracing them to miswiring and misfiring in neuronal circuits.

“This tool sharpens the cutting edge of research aimed at improving our understanding of brain circuit disorders, such as schizophrenia and addictive behaviors,” said Dr. Francis Collins, director of the National Institutes of Health, which funded the $1 million study.

The technique used to control neurons is called DREADDs (designer receptors exclusively activated by designer drugs).

Brain neurons are genetically engineered to produce a custom-made — “designer” — receptor. When the receptor gathers in a manmade molecule that fits like a key in a lock, the neuron is activated.

Because the receptor does not respond to other molecules, including natural ones in the brain, the only way to activate the neurons is via the manmade one. DREADDs allow scientists to manipulate neurons without implanting anything in the brain.

DREADDs, invented about a decade ago, had been used to turn neurons on or off, but not both. DREADDs 2.0 are the first to do that, scientists led by Bryan Roth of the University of North Carolina reported April 30 in the journal Neuron.

Targeting hunger-promoting neurons, the scientists made mice ignore food bowls or dive into them. Targeting movement neurons, they made mice scamper or stop.

In a competing remote-control technique called optogenetics, engineered neurons are activated upon receiving a pulse of light. That turns them on and off more quickly than with DREADDs, but the hardware required for delivering light to a spot in the brain is invasive and cumbersome.

NIH Human Microbiome Project defines normal bacterial makeup of the body.

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Genome sequencing creates first reference data for microbes living with healthy adults

Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for human survival. For the first time, a consortium of researchers organized by the National Institutes of Health has mapped the normal microbial makeup of healthy humans, producing numerous insights and even a few surprises.

Researchers found, for example, that nearly everyone routinely carries pathogens, microorganisms known to cause illnesses. In healthy individuals, however, pathogens cause no disease; they simply coexist with their host and the rest of the human microbiome, the collection of all microorganisms living in the human body. Researchers must now figure out why some pathogens turn deadly and under what conditions, likely revising current concepts of how microorganisms cause disease.

In a series of coordinated scientific reports published on June 14, 2012, in Nature and several journals in the Public Library of Science (PLoS), some 200 members of the Human Microbiome Project (HMP) Consortium from nearly 80 universities and scientific institutions report on five years of research. HMP has received $153 million since its launch in fiscal year 2007 from the NIH Common Fund, which invests in high-impact, innovative, trans-NIH research. Individual NIH institutes and centers have provided an additional $20 million in co-funding for HMP consortium research.

“Like 15th century explorers describing the outline of a new continent, HMP researchers employed a new technological strategy to define, for the first time, the normal microbial makeup of the human body,” said NIH Director Francis S. Collins, M.D., Ph.D. “HMP created a remarkable reference database by using genome sequencing techniques to detect microbes in healthy volunteers. This lays the foundation for accelerating infectious disease research previously impossible without this community resource.”

Methods and Results

The human body contains trillions of microorganisms — outnumbering human cells by 10 to 1. Because of their small size, however, microorganisms make up only about 1 to 3 percent of the body’s mass (in a 200-pound adult, that’s 2 to 6 pounds of bacteria), but play a vital role in human health.

To define the normal human microbiome, HMP researchers sampled 242 healthy U.S. volunteers (129 male, 113 female), collecting tissues from 15 body sites in men and 18 body sites in women. Researchers collected up to three samples from each volunteer at sites such as the mouth, nose, skin (two behind each ear and each inner elbow), and lower intestine (stool), and three vaginal sites in women; each body site can be inhabited by organisms as different as those in the Amazon Rainforest and the Sahara Desert.

Historically, doctors studied microorganisms in their patients by isolating pathogens and growing them in culture. This painstaking process typically identifies only a few microbial species, as they are hard to grow in the laboratory. In HMP, researchers purified all human and microbial DNA in each of more than 5,000 samples and analyzed them with DNA sequencing machines. Using computers, researchers sorted through the 3.5 terabases of genome sequence data to identify specific genetic signals found only in bacteria — the variable genes of bacterial ribosomal RNA called 16S rRNA. Bacterial ribosomal RNA helps form the cellular structures that manufacture protein and can identify the presence of different microbial species.

Focusing on this microbial signature allowed HMP researchers to ignore the human genome sequences and analyze only the bacterial DNA. In addition, metagenomic sequencing, or sequencing all of the DNA in a microbial community, allowed the researchers to study the metabolic capabilities encoded in the genes of these microbial communities.

“Recently developed genome sequencing methods now provide a powerful lens for looking at the human microbiome,” said Eric D. Green, M.D., Ph.D., director of the National Human Genome Research Institute, which managed HMP for NIH. “The astonishing drop in the cost of sequencing DNA has made possible the kind of large survey performed by the Human Microbiome Project.”

Where doctors had previously isolated only a few hundred bacterial species from the body, HMP researchers now calculate that more than 10,000 microbial species occupy the human ecosystem. Moreover, researchers calculate that they have identified between 81 and 99 percent of all microorganismal genera in healthy adults.

“We have defined the boundaries of normal microbial variation in humans,” said James M. Anderson, M.D., Ph.D., director of the NIH Division of Program Coordination, Planning and Strategic Initiatives, which includes the NIH Common Fund. “We now have a very good idea of what is normal for a healthy Western population and are beginning to learn how changes in the microbiome correlate with physiology and disease.”

HMP researchers also reported that this plethora of microbes contribute more genes responsible for human survival than humans contribute. Where the human genome carries some 22,000 protein-coding genes, researchers estimate that the human microbiome contributes some 8 million unique protein-coding genes or 360 times more bacterial genes than human genes.

This bacterial genomic contribution is critical for human survival. Genes carried by bacteria in the gastro-intestinal tract, for example, allow humans to digest foods and absorb nutrients that otherwise would be unavailable.

“Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, Ph.D., NHGRI’s HMP program manager. “Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.” Anti-inflammatories are compounds that regulate some of the immune system’s response to disease, such as swelling.

Researchers were surprised to discover that the distribution of microbial metabolic activities matters more than the species of microbes providing them. In the healthy gut, for example, there will always be a population of bacteria needed to help digest fats, but it may not always be the same bacterial species carrying out this job.

“It appears that bacteria can pinch hit for each other,” said Curtis Huttenhower, Ph.D., of Harvard School of Public Health and lead co-author for one of the HMP papers in Nature. “It matters whether the metabolic function is present, not which microbial species provides it.”

Moreover, the components of the human microbiome clearly change over time. When a patient is sick or takes antibiotics, the species that makeup of the microbiome may shift substantially as one bacterial species or another is affected. Eventually, however, the microbiome returns to a state of equilibrium, even if the previous composition of bacterial types does not.

Clinical Applications

As a part of HMP, NIH funded a number of studies to look for associations of the microbiome with diseases and several PLoS papers include medical results. For example, researchers at the Baylor College of Medicine in Houston compared changes in the vaginal microbiome of 24 pregnant women with 60 women who were not pregnant and found that the vaginal microbiome undergoes a dramatic shift in bacterial species in preparation for birth, principally characterized by decreased species diversity. A newborn is a bacterial sponge as it populates its own microbiome after leaving the sterile womb; passage through the birth canal gives the baby its first dose of microbes, so it may not be surprising that the vaginal microbiome evolved to make it a healthy passage.

Researchers at the Washington University School of Medicine in St. Louis examined the nasal microbiome of children with unexplained fevers, a common problem in children under 3 years of age. Nasal samples from the feverish children contained up to five-fold more viral DNA than children without fever, and the viral DNA was from a wider range of species. Previous studies show that viruses have ideal temperature ranges in which to reproduce. Fevers are part of the body’s defense against pathogenic viruses, so rapid tests for viral load may help children avoid inappropriate treatment with antibiotics that do not kill the viruses but may harm the child’s healthy microbiome.

These are among the earliest clinical studies using microbiome data to study its role in specific illnesses. NIH has funded many more medical studies using HMP data and techniques, including the role of the gut microbiome in Crohn’s disease, ulcerative colitis and esophageal cancer; skin microbiome in psoriasis, atopic dermatitis and immunodeficiency; urogenital microbiome in reproductive and sexual history and circumcision; and a number of childhood disorders, including pediatric abdominal pain, intestinal inflammation, and a severe condition in premature infants in which the intestine actually dies.

“Enabling disease-specific studies is the whole point of the Human Microbiome Project,” said Barbara Methé, Ph.D., of the J. Craig Venter Institute, Rockville, MD, and lead co-author of the Nature paper on the framework for current and future human microbiome research. “Now that we understand what the normal human microbiome looks like, we should be able to understand how changes in the microbiome are associated with, or even cause, illnesses.”

The NIH Common Fund also invested in a series of studies to evaluate the ethical, legal and social implications of microbiome research. While the results of these studies are yet to be published, a number of important issues already have been identified, ranging from how products designed to manipulate the microbiome — such as probiotic concoctions that include live microorganism believed to benefit the body — might be regulated, to whether individuals should begin to consider storing their microbiome while healthy.

After NIH launched HMP in December 2007, the International Human Microbiome Consortium formed in 2008 to represent funding organizations, including NIH, and scientists from around the world interested in studying the human microbiome. The consortium has coordinated research to avoid duplication of effort and insured rapid release of molecular and clinical data sets. It also has developed common data quality standards and tools to share research results.

Deal done over HeLa cell line.

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Deborah Lacks wanted answers. In 1974, she asked a leading medical geneticist to tell her about HeLa cells, a tissue-culture cell line derived from the cancer that had killed her mother Henrietta in 1951. The researcher, who was collecting blood from the Lacks family to map HeLa genes, autographed a medical textbook he had written and said that everything she needed to know lay within its dense pages.

It would be more than 30 years before the family got a better explanation.

Now the director of the US National Institutes of Health (NIH), Francis Collins, is trying to make up for decades of slights. Over the past four months, he has met Lacks family members to answer questions and to discuss what should be done with genome data from their matriarch’s cell line.

“We wanted to get a better understanding of what information was going to be out there about Henrietta, and what information was going to be out there about us,” says Henrietta’s grandson David Lacks Jr. (Deborah Lacks died in 2009.) On 7 August, Collins announced that the family has endorsed case-by-case release of the information, subject to approval by a committee that will include family members .

The consensual approach is a sea change from the dismissive treatment of the past, says Rebecca Skloot, the journalist who recounted the scene between Deborah Lacks and the researcher in her 2010 book The Immortal Life of Henrietta Lacks. “It was the first time in the very long history of HeLa cells that any scientists have sat down and devoted complete attention to explaining to the family what was going on,” she says (see ‘The Lacks legacy‘).

The agreement allows the publication of a US government-funded HeLa genome sequence as well as the re-release of data that were pulled from public view soon after publication in March because of the family’s concerns. Nature’s News team learned of the negotiations last month but agreed to delay coverage so as not to impede the talks. Brokered during meetings at Johns Hopkins School of Medicine in Baltimore, Maryland, the deal rekindles debates over consent and ownership of tissues, and data that arise from their study, at a time when the NIH is updating such rules.

The HeLa cell line was established in 1951 from a biopsy of a cervical tumour taken from Henrietta Lacks, a working-class African-American woman living near Baltimore. The cells were taken without the knowledge or permission of her or her family, and they became the first human cells to grow well in a lab. They contributed to the development of a polio vaccine, the discovery of human telo­merase and countless other advances. A PubMed search for ‘HeLa’ turns up more than 75,000 papers. “My lab is growing HeLa cells today,” Collins told Nature in an interview on the NIH campus in Bethesda, Maryland. “We’re using them for all kinds of gene-expression experiments, as is almost every molecular-biology lab.”

On 11 March, weeks before Collins drove to Baltimore to meet the Lacks family for the first time, a team led by Lars Steinmetz at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, published a paper called ‘The genomic and transcriptomic landscape of a HeLa cell line’ (J. J. M. Landry et al. Genes Genomes Genet. http://dx.doi.org/10.1534/g3.113.005777; 2013). News coverage (see go.nature.com/inxzuw) noted the link to Henrietta Lacks, but not privacy concerns.

Skloot, in a later article for The New York Times, made clear that family members were unhappy that — yet again — they had not been consulted. “I think it’s private information,” Henrietta’s granddaughter Jeri Lacks-Whye told Nature. “I look at it as though these are my grandmother’s medical records that are just out there for the world to see.” The EMBL team removed the data from public access, and hoped that a solution could be reached.

As the controversy erupted, Nature was preparing to publish an even more detailed sequence of the HeLa genome, according to senior author Jay Shendure, a genome scientist at the University of Washington in Seattle. His team, funded by the NIH, started decoding HeLa DNA in 2011, as part of an effort to develop new sequencing techniques. They also hoped that the genome would be useful for other researchers, a motivation shared by the EMBL team. They submitted their paper to Nature in November 2012.

The paper’s reviewers did not raise privacy concerns before recommending it for publication; nor did Nature, Shendure says. He considered contacting the Lacks family before publication, and restricting access. “Figuring out how to reach out to the family was very much on the table when events overtook us.”

After Skloot’s article on the EMBL paper came out in March, Collins learned about Shendure’s NIH-funded project. He saw an opportunity. He was already at work reforming the rules that govern research on human subjects. “It looked as if this was a moment to get everybody in the same room,” he says.

And so, on the evening of 8 April, Collins met a group of Henrietta Lacks’ children and grandchildren for dinner and discussion at the Johns Hopkins campus. Along with Collins was his chief adviser and two mediators from the university. Skloot phoned in to the meeting, which was to be the first of three.

Collins says that family members told him how unsettling it had been to learn about HeLa cells decades after Lacks died. They peppered Collins with questions about genetic sequencing and how Lacks’ cells had been used. “I felt like I was taking ‘Biology 101’,” says Lacks-Whye. Collins told them that Shendure’s team might have identified the genetic change that made their grandmother’s tumour so aggressive and HeLa cells so prolific. The NIH later put the family in touch with experts in clinical genetics who told them what health information could be gleaned from the genome, and the NIH offered to help family members have their own genomes sequenced and interpreted.

Collins says that he did not pressure the family to agree to the release of the HeLa genome data; he was open to leaving the NIH-funded work unpublished. But he told the family that it would be impossible to keep the data locked away. NIH researchers had calculated that 400 genomes’ worth of HeLa data are already publicly available in piecemeal form — parts of projects such as the Encyclopedia of DNA Elements — and that scientists in thousands of labs around the world could easily and cheaply sequence the cell line themselves.

Some Lacks family members raised the possibility of financial compensation, Collins says. Directly paying the family was not on the table, but he and his advisers tried to think of other ways the family could benefit, such as patenting a genetic test for cancer based on HeLa-cell mutations. They could not think of any. But they could at least reassure the family that others would not make a quick buck from their grandmother’s genome, because the US Supreme Court had this year ruled that unmodified genes could not be patented. Lacks-Whye says that the family does not want to dwell on money — and that her father has often said he “feels compensated by knowing what his mother has been doing for the world”.

In the end, the family decided that it wanted the data to be available under a restricted-access system similar to the NIH dbGaP database, which links individuals’ genetic make-up to traits and diseases. Researchers would apply for permission to acquire the data and agree to use them for biomedical research only, and would not contact Lacks family members. A committee that includes family members will handle requests, and papers that use the data will recognize Henrietta Lacks and her kin. The first of these papers, the NIH-funded paper, is published in this issue..

In discussing HeLa cells and the agreement forged with the family, Collins and others often use the word “unique”. No other human sample matches the cell line for ubiquity, notoriety or celebrity (Oprah Winfrey is producing a film based on the story). The NIH does not see the deal with the family as a guide to handling other human samples. “It’s not going to be a precedent,” says Collins’ chief adviser Kathy Hudson.

But it will probably inform other cases, she adds. The US government is redrafting rules that govern the relationship between federally funded researchers and participants. New rules aim to give subjects greater say in how their tissues and personal data are used. “Going forward, I’m very much of the mind that the most appropriate way to show respect for persons is to ask,” Collins says. “Ask people, ‘Are you comfortable having this specimen used for future genomic research for a broad range of biomedical applications?’ — if they say no, no means no.”

As for the myriad other tissues out there that were obtained without consent, Collins says that it would slow science too much to ban their use. Laura Rodriguez, a policy official at the NIH who works on guidelines for genome sequencing, says that there is a low risk of donors of such samples being identified. But in January, researchers working on a genomics project showed that it is possible to identify anonymous participants — and their families — by cross-referencing their genomes with genealogy DNA databases.

Hank Greely, a biotechnology lawyer at Stanford University in California who has advised the EMBL group, says the HeLa agreement is a “good solution”, but applying it to other unconsented cell lines and data would be unwieldy and impractical. “The one thing we really should be doing is making sure every­thing we collect from here into the future is acceptable.”

Lacks-Whye has similar advice. Researchers can make major breakthroughs, she says, while still respecting the wishes of patients and their families. “Have them involved,” she says. “That’s not only for HeLa sequences, but anybody who participates in research.”

Source:Nature