Archives for category: Genetics

Among the bloodletting boxes, ether inhalers, kangaroo-tendon sutures and other artifacts stored at the Indiana Medical History Museum in Indianapolis are hundreds of scuffed-up canning jars full of dingy yellow liquid and chunks of human brains.

Until the late 1960s the museum was the pathology department of the Central Indiana Hospital for the Insane. The bits of brain in the jars were collected during patient autopsies performed between 1896 and 1938. Most of the jars sat on a shelf until the summer of 2010, when Indiana University School of Medicine pathologist George Sandusky began popping off the lids.

Frustrated by a dearth of postmortem brain donations from people with mental illness, Sandusky—who is on the board of directors at the museum—seized the chance to search this neglected collection for genes that contribute to mental disorders.

Sandusky is not alone. Several research groups are now seeking ways to mine genetic and other information hidden in old, often forgotten tissue archives—a handful of which can be found in the U.S., along with many more in Europe. Several technical hurdles stand in the way, but if these can be overcome, the archives would offer several advantages. Beyond supplying tissues that can be hard to acquire at a time when autopsies are on the decline, the vintage brains are untainted by modern psychiatric drugs and are often paired with detailed clinical notes that help researchers make more accurate post hoc diagnoses.

“There are probably a fair number of these collections around the country that grew out of state hospitals,” says John Allman, professor of biology at the California Institute of Technology. “It is an untapped resource. If it were carefully planned and reasonably funded, it could become quite a valuable thing.”

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Scientific American, January 2012.

On June 26, 2000, three famous men — one president, two scientists — made a big announcement at the White House. Two independent teams — one public, one private — had published a first draft of the human genome, or as one of the scientists called it, the “book of life.” It was a feat. It would change the world. It would “revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases,” the president said. Everybody was proud.

Ten years later, a journalist at a big newspaper pointed out that, well, no, the $3 billion we spent on the human genome — a dollar for each pair of DNA letters — had not bought us the ability to diagnose, prevent or treat common diseases. The genome had revolutionized basic biology, sure, but done little for human health.

The newspaper article made a lot of scientists angry. (Some of them are still sputtering about it at conferences.) It also launched a broader discussion about science communication and hype. A month ago, I went to a public event at the American Museum of Natural History, in Manhattan, called “The Human Genome and Human Health: Will the Promise Be Fulfilled?” Four experts on genetics, medicine, ethics and law discussed whether the promises of that 2000 announcement would ever come true. The general consensus was that the White House hoopla had raised expectations much too high, inevitably leading to disappointment. Pride goeth before the fall.

As a journalist, I hate hype, and I will never argue that journalists should be anything but skeptical of scientific advancements. But I recently learned that, like all of the Seven Deadly Sins, pride is necessary for survival. So I wonder, does science need hubris?

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The Last Word on Nothing, December 2011.

After a challenging two-decade hunt, scientists have pinpointed the gene responsible for a rare disease that causes seizures in infancy and sudden, uncontrollable movements in adolescence and early adulthood.

The findings, published December 15, 2011, in Cell Reports, could pave the way to new therapies for more common forms of seizures and dyskinesias, or abnormal movements, the researchers say.

“There are a lot of dyskinesias for which we don’t have good treatments and they are a big problem, such as in Huntington’s disease and Parkinson’s disease,” says Howard Hughes Medical Institute investigator Louis Ptáček, professor of neurology at the University of California San Francisco, who led the new study. “If we can understand the pathways in the brain that regulate dyskinesia, then it’s my hope that we’ll be able to target better drugs.”

Ptáček’s interest in dyskinesia dates to 1985 when, as a third-year medical student at the University of Wisconsin, Madison, he met a 16-year-old boy who was having bizarre spasms. Every time the boy switched from one movement to another, like from sitting to standing or walking to running, his limbs would inexplicably flail or twist, as if performing an odd dance.”Nobody knew what the heck was going on,” Ptáček recalls.

One night around 2 a.m., after scouring the library’s medical databases, Ptáček figured out the diagnosis: paroxysmal kinesigenic dyskinesia, or PKD, which had been reported in just a handful of other cases. He knew from those papers that PKD could be treated with a low dose of a common anticonvulsant medication. When doctors gave the boy the drug, carbamazepine, he quickly improved.

“He had been having attacks hundreds of times per day. A few weeks after treatment, he was essentially having zero attacks,” Ptáček says. “It felt so satisfying to have gotten it right.”

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HHMI News, December 2011.

A couple of weeks ago, I attended a public discussion about the future of genomics at the American Museum of Natural History in Manhattan. My favorite part of the evening was when Paul Billings, chief medical officer at Life Technologies, pulled out of his pocket his company’s latest genome sequencer: a square chip, about the size of a quarter. Next year, he said, researchers will be decoding whole genomes with this device for about $1,000 each.

For most researchers, the rise of whole-genome sequencing is old news, and so are its potential pitfalls. The sheer volume of data will be difficult to store and, at least for a while, impossible to interpret. Then there are those frightening scenarios of how your genetic information might be used against you that routinely make it into headlines and Hollywood blockbusters.

But one aspect that is rarely discussed is that the rise of whole-genome sequencing may well result in a deluge of lawsuits against doctors. That’s the sobering prediction by two lawyers in an essay published 25 November in the online magazine Slate.

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SFARI, December 2011.

Researchers have uncovered cellular abnormalities in Timothy syndrome by regenerating neurons from individuals with the rare autism-related disorder, according to a study published 27 November in Nature Medicine.

Using a mix of chemicals in a dish, the researchers reprogrammed skin cells from individuals with Timothy syndrome into so-called induced pluripotent stem (iPS) cells and then coaxed these cells to differentiate into neural precursor cells and neurons.

The cells derived from individuals with Timothy syndrome show a host of defects, including abnormal calcium signaling and low numbers of cells that can form long-range connections. Notably, Timothy neurons produce more catecholamines, a class of chemical messengers, compared with neurons reprogrammed from healthy individuals. These chemicals have been linked to autism and, more often, to bipolar disorder and depression.

This chemical excess is largely reversed when researchers expose the cells to a drug called roscovitine, which blocks the flow of calcium across the cell membrane.

The Timothy syndrome gene, CACNA1C, makes a protein needed for a certain type of calcium channel. Mutations in the gene, reported in only a few dozen people, cause heart defects, physical malformations and, usually, autism.

Using the iPS cell approach with rare forms of autism, “you can find things that are interesting potential clinical leads,” says lead investigator Ricardo Dolmetsch, assistant professor of neurobiology at Stanford University in Palo Alto, California. “In a way, it gives you a better preclinical model than we’ve had before.”

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SFARI, December 2011.

In the brains of individuals with autism, chemical changes to histones, proteins entwined with DNA, tend to show up near genes linked to the disorder, according to a study of postmortem brains published 7 November in the Archives of General Psychiatry.

In the nucleus of every cell, threads of DNA wrap tightly around spools of histones. Methyl and other chemical groups that attach to either the DNA or histones can turn genes on or off. These so-called epigenetic changes add an extra layer of genetic control by tweaking the amount of RNA and protein produced without changing the underlying DNA sequence.

Looking at postmortem brain tissue from 16 individuals with autism and 10 age-matched controls, the researchers found hundreds of places in the genome where histone methylation is different in individuals with autism.

Many of these abnormal epigenetic marks land on or near known autism risk genes, suggesting that the biological pathways involving these genes may be important even in children with autism who do not carry mutations in the genes, the researchers say.

“You could say that the epigenetic risk architecture that’s described is tracking the genetic risk architecture,” says lead investigator Schahram Akbarian, professor of psychiatry at the University of Massachusetts Medical School.

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SFARI, December 2011.

Some forms of autism are caused by too many proteins at the synapse, the junction between neurons, whereas other forms result from too few, according to a study published 23 November inNature.

The findings suggest that drugs that effectively treat people with one form of autism may not help, and may even harm, individuals with another form, the researchers say.

“One implication is, boy, it’s going to be important to know where you are on this spectrum to devise the right therapy,” says lead investigator Mark Bear, professor of neuroscience at the Massachusetts Institute of Technology.

The work, first presented at the 2010 Society for Neuroscience annual meeting in San Diego, focuses on mouse models of two genetic diseases: fragile X syndrome, the most common inherited cause of autism, and tuberous sclerosis complex (TSC), characterized by benign tumors, seizures and, often, autism.

Autism is notoriously diverse. But the new study suggests that many forms of the disorder stem from a spectrum of disruptions to the same biological pathway, Bear says. “The hope is we’re gaining insights that will be broadly applicable.”

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SFARI, December 2011.

Since the unveiling of the first draft of the human genome in June 2000, you’ve probably heard a lot about the potential power of genomic data for diagnosing, preventing and even curing disease.

Progress was slow at first, partly because of money: The first sequencing efforts cost hundreds of millions of dollars. But with the price tag now at less than $5,000 per person, researchers can begin building large collections of DNA data.

In October, for example, the autism science and advocacy organization Autism Speaks announced its plans to sequence whole genomes of 10,000 individuals —children with the disorder and their family members — over the next two years.

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SFARI, November 2011.

Sigma Life Science, a St. Louis-based research company, debuted seven new rat models of autism Tuesday evening at the 2011 Society for Neuroscience annual meeting in Washington, D.C.

Six of the rats each lack one autism candidate gene — FMR1, NLGN3, MeCP2, NRXN1, CACNA1C and PTEN — and a seventh lacks mGluR5, which encodes a neuronal signaling receptor that is important in fragile X syndrome.

The impetus for making the rat models is to make autism research more attractive to the pharmaceutical industry. The standard approach in the industry is to test dosage and toxicology in rats, not in mice.

“Unless there’s investment, it doesn’t matter how many great ideas — which tend to be risky — you generate, they will not proceed forward,” says Robert Ring, vice president of translational research at the advocacy organization Autism Speaks. The idea is not to replace mice, Ring adds, but “to begin creating complementary animal models that help facilitate translational research.”

Over the past few months, Richard Paylor at Baylor College of Medicine in Houston, Texas, has done behavioral testing on young rats missing FMR1 — mutations in which lead to fragile X syndrome — and NLGN3, one of the first genes implicated in non-syndromic autism.

Unexpectedly, some of the rat behaviors are the opposite of what’s seen in their mouse counterparts: The FMR1-deficient rats engage in social play less than controls do, for example, whereas some strains of mice lacking FMR1 have more social interactions than controls.

Rats missing either FMR1 or NLGN3 also show some unexpected new characteristics, such as severe female aggression and compulsive chewing on water bottles.

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SFARI, November 2011.