# News this Week

Science  07 Dec 2012:
Vol. 338, Issue 6112, pp. 1268
1. # Around the World

1 - Washington, D.C.
U.S. Supreme Court Reconsiders Gene Patents
2 - Rome
Italy Cancels €1 Billion Accelerator Project
3 - Argonne, Illinois
Science ‘Hub’ to Focus on Batteries
4 - Washington, D.C.
Lamar Smith to Head House Science Panel

## Washington, D.C.

### U.S. Supreme Court Reconsiders Gene Patents

The U.S. Supreme Court intends to address a far-reaching question in biology and law: Are human genes patentable? The biotech world thought that the answer was clear already: Many companies have been built on the assumption that DNA sequences can be patented exclusively. But on 30 November, the court indicated that may not be so. It granted certiorari to a case known as Association for Molecular Pathology v. Myriad Genetics, agreeing to hear a challenge against Myriad, a diagnostics firm in Salt Lake City, which owns patents on the human breast and ovarian cancer genes BRCA1 and BRCA2. Myriad has created a database of DNA variants and uses a patented test to check individuals for cancer risk. The group challenging Myriad argues that the key genes are a product of nature and, therefore, not patentable—a position backed by many researchers—including Nobel winner James Watson—and a number of medical groups, including the American Medical Association. The court will hear the case this term, which ends in June.

## Rome

### Italy Cancels €1 Billion Accelerator Project

The Italian government has scrapped plans to build a particle accelerator known as SuperB in the outskirts of Rome after a new study calculated its total cost to be about €1 billion—some €350 million more than previously estimated. SuperB was to have been built on the campus of the University of Rome Tor Vergata by an international collaboration of scientists. It would have collided beams of electrons and positrons to produce B mesons and other exotic particles.

The Italian government had promised €250 million; other countries, including France and Russia, said they might pay a share of the costs; and the United States had agreed to donate parts from a decommissioned accelerator at the SLAC laboratory in California. But the growing price tag and an unbridgeable funding gap sank the project. The Italian government has invited Italy's National Institute of Nuclear Physics to pitch proposals for new projects that could be funded with the €250 million it had originally promised. http://scim.ag/NoSuperB

O'Shea replaces Jack Dixon, who after 6 years at HHMI will return to his lab at the University of California, San Diego. With an endowment of $16.1 billion in 2011, HHMI is the largest private funder of academic biomedical research in the United States. 4. # Growing Pains in the Desert 1. Jeffrey Mervis A 3-year-old graduate research university in Saudi Arabia is finding that it will take more than money to create a global research powerhouse. Tony Eastham wasn't planning to finish his academic career in Saudi Arabia. And David Ketcheson didn't think his first faculty job would be at a new, graduate-only research university in the Middle East. But in 2009, both Eastham, a British physicist with an international CV, and Ketcheson, a U.S.-born-and-bred applied mathematician, wound up working at King Abdullah University of Science and Technology (KAUST). The country's octogenarian monarch gave his name—and an estimated$20 billion—to what he hoped would be a Bayt al-Hikma, a house of wisdom, in the grand tradition of Islamic scholarship (Science, 16 October 2009, p. 354). The money, in addition to providing KAUST with a huge endowment to be tapped for operating expenses, has bought what Eastham describes as “resources not available to any other university in the world.”

For many faculty members, the job has exceeded their expectations. “The funding opportunities are astounding, and I've had the chance to do things that wouldn't normally be possible for someone at my level,” says Ketcheson, born and educated in the United States, who was hired at age 29 right out of graduate school as an assistant professor. “Coming here also appealed to my sense of adventure,” he adds, noting that his wife and three small children also enjoy living within the gated community that surrounds the campus.

The British-born Eastham, now 67, has had a different, and ultimately much less satisfying, experience. “There was a tremendous sense of camaraderie the first year,” recalls Eastham, who agreed to run KAUST's core labs after having spent the previous 13 years managing research and technology development at Hong Kong University of Science and Technology, an institution whose rapid rise KAUST hopes to emulate (Science, 7 September, p. 1162). “We were all part of this pioneering experiment.”

But for Eastham, the initial excitement gave way to frustration, disappointment, and, finally, disillusionment. In December 2011, Eastham left what he had begun to call the King Abdullah University of Stress and Tension and retired to his beloved Vancouver. (He had spent more than 2 decades as a Canadian academic before going to Hong Kong.) “The atmosphere had become poisoned, and KAUST was no longer a comfortable place to work. After 3 years, I decided I had had enough.”

Eastham is one of several senior administrators who have left KAUST in the past year. All still embrace the king's vision but believe that it is being undermined by management decisions that have trampled upon the openness, collegiality, and transparency common at Western institutions. Those decisions include sudden changes in admissions standards to increase the share of Saudi students, revisions in the rules governing internal funding, and a failure to uphold agreements with international collaborators. Compounding the problem, current and former staff members say, is a work environment that discourages any airing of these concerns.

Without a change in leadership, they worry, KAUST will fall short of its quest to become a global research university.

## More than a vision

KAUST owes its existence to King Abdullah's belief that the country needed a top-rated research university. In 2007, he assigned the task of building one to his oil minister—an ironic choice given that one of KAUST's goals is to wean the kingdom from its dependence on oil—and the minister chose Saudi Aramco to make it happen.

Deploying a round-the-clock crew of 30,000 and up to 50 cranes poking skyward, the state-owned giant oil company completed the 36-million-square-meter campus in only 2 years. And in September 2009, the king himself presided over a gala opening celebration for foreign dignitaries and scientific luminaries.

In retrospect, however, building the institution was the easy part. Making it work like a research university is proving to be much harder.

In addition to Eastham, the list of senior academics who have left KAUST in the past year includes the director of admissions, the heads of two of the university's nine initial research centers, the founding provost, the first dean of life sciences and engineering, and the head of university communications. Without exception, these former employees are still rooting for KAUST to succeed. They believe that a world-class university in Saudi Arabia would strengthen global science, provide technology-based solutions to pressing problems in the region, and perhaps even ease political tensions in this volatile part of the world. And they agree that the unprecedented investment in equipment and facilities has attracted talented scientists from around the world.

KAUST's tight control over information makes it hard to generalize about how most faculty members and administrators feel about their employer. Even so, Science has learned that some have tried to express their concerns through private channels, with uncertain results.

In one notable case, several senior KAUST officials and scientists responded to a request last fall from the king's inner circle for information on KAUST management practices. Their statements, which Science obtained after agreeing not to identify the authors, provide a frank assessment of what they regard as pressing problems. And the same themes recur. “The current atmosphere in the administration and finance of the university is one of brutality,” notes one writer, adding that “dedicated talents who believed in the dream of the university from the start are leaving because they can no longer tolerate this hostile climate.” The author ends with a plea: “The management of a university must be in the hands of academic professionals.”

Eastham was at first reluctant to speak out and says he decided to do so only because he believes KAUST's fate is important to the scientific community. (Several persons requested anonymity as a condition of talking to Science, saying that they feared reprisals.) Another former senior administrator who has come forward publicly is James Luyten, who resigned last December as founding director of KAUST's Red Sea Research Center.

Luyten is a former head of the Woods Hole Oceanographic Institution (WHOI) in Massachusetts, which in 2007 became KAUST's first international research partner. Saudi officials made a splash when they inked a 3-year, $25 million agreement with WHOI to carry out a range of marine activities that included five 16-day cruises on the Red Sea. But even with a 2-year extension, fewer than half the cruises were conducted, and on 31 October the partnership ended with a whimper. Luyten believes that KAUST hasn't provided the mutual respect and transparency needed to carry out world-class, collaborative research. His repeated efforts to address those problems while he directed the Red Sea center were thwarted by his superiors, he adds. “I have to say that every promise that has been made to us has been broken, except for the payment of our actual salaries,” he says. ## Calling the shots One fundamental problem, Luyten, Eastham, and others say, is that Aramco has retained a prominent role in running the institution it built. Its top-down management style may be fine for operating an oil-production facility, they say, but that style is ill-suited to a graduate research university. “There's a lack of trust at the top. They just don't trust anybody,” says Alyn Rockwood, a professor of applied mathematics and associate director of the Geometric Modeling and Scientific Visualization Center, who this fall announced that he would be leaving KAUST in January. Critics are particularly unhappy with the management style of one senior KAUST administrator, Nadhmi Al-Nasr. He's a former Aramco vice president for engineering services whose title at KAUST is executive vice president for administration and finance. Although he reports to KAUST's president, Choon Fong Shih, Al-Nasr is widely viewed as the de facto head of the university. (Al-Nasr was interim president before Shih arrived in 2008 as the much-admired president of the National University of Singapore, and Shih's pending retirement, announced in May, appears to have further strengthened Al-Nasr's hand.) “Personally, I like Nadhmi. But he does some strange things,” says Rockwood, who notes that his pending departure gives him greater freedom than other faculty members to express his opinions. “And he's from a culture where fear and intimidation are part of the way you do business. He's not an academic. He's an oil manager, and I guess that you have to be pretty hard-nosed to be successful in that field.” Al-Nasr, who has never before been a university administrator and who holds a bachelor's degree in chemical engineering, acknowledges that he was jumping into the deep end when he joined KAUST. “Learning how to work in an academic culture was a totally new game for me,” he explained during an interview in which he was by turns combative, cagey, and cajoling. “In industry, business decisions are all top-down. The corporation decides, and the staff executes the plan. Academia is different. The ideas of people at all levels count, and you need to learn how to listen.” A successful academic administrator needs to be patient, Al-Nasr adds. “Faculty debate things for a long time,” he notes. “In industry, time is money, so you don't have that luxury.” There was no template for Aramco to follow for building such a well-endowed graduate research university from scratch. And even if there had been one, it probably wouldn't have applied to a country without such institutions. Although the administrative and classroom buildings opened on time, equipping the labs to do science took much, much longer. The delays were especially hard on researchers with wet labs. “It was horrible for those people,” says David Keyes, an applied mathematician who left a tenured professorship at Columbia University to join KAUST in 2009 as a founding dean. “They were very much impacted by the unexpected difficulties in starting supply chains and getting clearances.” Keyes has spent the past 3 years dealing with those problems as head of two of KAUST's three academic divisions—one spanning the physical sciences and engineering and the second encompassing applied mathematics and computer science and engineering. But he doesn't fault the university or Aramco. “Any start-up has challenges. I'd like to see General Electric run a university,” he says. “Maybe Google could do it and get it right the first time. But for a company that is used to ordering valves to suddenly be asked to order spectrometers and textbooks, everything is likely to go wrong.” Al-Nasr acknowledges the slow start but doesn't think there was much that KAUST could have done differently. “It was a big shock to the system,” he admits. “Our demands were way more than the kingdom has ever seen before, in terms of both our focus on research and the absolute amount of research that faculty wanted to do. People had come from all over the world, and we wanted to meet their expectations. It was pretty frustrating for faculty. But I think most of those problems have been worked out.” Keyes certainly hopes so. Once his successors are in place—in August, Yves Gnanou of the École Polytechnique in Paris became dean of physical sciences, and the appointment of a dean for math and computer sciences is imminent—Keyes can return to his first love: research. He's currently working on algorithms for extreme computing applications. Arguably the university's most prominent active scientist, Keyes believes that KAUST has survived the worst and is starting to make real progress. “People here still have faith in the unique opportunity represented by an interdisciplinary, graduate science and engineering institution with 5-year funding for research,” he says. “So the things that made it distinctive in the first place are still there.” One area where KAUST has been able to hit the ground running is in the mathematical and computer sciences and engineering, which are less dependent on good supply chains. Keyes says that the division “has carved out a niche of developing enabling technologies while continuing to do good research.” In turn, Ketcheson says that Keyes is the reason he decided to start his academic career in the Arabian desert after earning a Ph.D. in applied mathematics from the University of Washington. “David's famous in the field,” Ketcheson says. “He mentioned KAUST when I called him about possible positions at Columbia while I was still in graduate school. At first I shrugged it off. You don't go to the Middle East if you want a tenure-track position at a top university, because that caliber of institution doesn't generally exist there. But once I looked into it, I was really impressed.” ## Admissions reversal Academics like to say that a university is only as good as the graduate students it attracts. That truism also explains why the researchers who spoke with Science are so troubled by how the 2011 entering class was chosen. KAUST has no shortage of applicants thanks to its full scholarships, generous stipends, subsidized housing, and outstanding facilities. And while one of KAUST's missions is to train the next generation of Saudi scientists, KAUST hasn't been able to find enough high-quality candidates from the kingdom to fill all the available slots. “I realize that this is a sensitive topic,” says the provost, Stefan Catsicas, a neurobiologist who came to KAUST in January 2011 from the Swiss Federal Institute of Technology in Lausanne. “But we are a university in Saudi Arabia.” At the same time, Catsicas says, KAUST does not want an entirely domestic class and believes that a good mix of international students is essential. So the university has tried to strike a balance without imposing a quota. The 15% share of Saudi students in each of the first two classes, out of a total of roughly 360, was lower than desired, however, Catsicas says. Even more troubling for a university hoping to become a predominantly doctoral-granting institution was the fact that only 10% of the arriving students seeking doctoral degrees were from the kingdom. (A majority of the students in the first two classes were aiming for master's degrees.) So in late winter of 2011, KAUST decided to boost the Saudi representation in the next class to 30%. That decision was made so late in the admissions cycle, however, that it forced officials to take the unusual step of sending an update to 125 foreign students who had already received acceptance letters. The students were told that they faced one more hurdle—an interview—before they could enroll. “The questions were very casual, about my family and my future plans. They could have gotten most of the information from my CV,” says one African student who requested anonymity. Two months later, most of the students were told that the offer had been withdrawn. Others discovered that they could not obtain a visa to study at KAUST. Although faculty members had recruited some of these students, they were shut out of the final selection process. When they learned what had happened, many pleaded with Catsicas to reverse the decisions, and KAUST agreed to welcome back some 30 “highvalue” students. The reshuffling created more slots for Saudi students. In the end, 24% of the entering class of 2011 was from Saudi Arabia, including one-third of those seeking master's degrees. This year, KAUST upped the percentage of Saudi students to 35% of the whole, including 51% of those seeking master's degrees. But officials did it by reducing the overall size of the entering class. The number of new students plummeted from 383 to 245, and the size of the Asian contingent dropped by more than half, from roughly 120 in each of the first three classes to only 54 in the newest class. Asked if he thought last year's admissions process had damaged KAUST's reputation among future applicant pools, Catsicas says that quality is more important than quantity. And he doesn't think that KAUST had been hurt: “This is a young institution, and I'm sure we will make mistakes. But it is not an arbitrary process, and the objective is quality.” ## Building global ties When it comes to luring prized senior faculty members like Rockwood, KAUST is willing to pull out all the stops. At least, that's how it looked at first to Rockwood, whose career in computer graphics and geometric modeling has straddled industry and academia. Full professors were promised an annual research budget “equivalent to a NSF [National Science Foundation] center,” he says—in his case,$1 million—“and we were told that, if we needed more, we could write a two-page grant to the provost and it would be approved.”

Rockwood says he wasn't surprised when the second promise never materialized: “It just seemed too easy.” But he was disappointed when his package was suddenly trimmed back to $800,000. And he was annoyed to discover the hidden costs within his budget, such as being charged up to$70,000 a year to support a doctoral student. “And then there were just silly things, like having to pay our own phone bills.”

Al-Nasr declined to discuss KAUST's operating budget (it's believed to be roughly $750 million a year), explaining that KAUST “doesn't share its financial information with anyone except our board of trustees.” But he says that “there haven't been any budget cuts affecting research that I'm aware of.” He says the endowment provides “the biggest portion” of the funds needed to operate the university, although officials are hoping a growing share will come from industry, philanthropic organizations, and private donors. At the same time, he says, KAUST has reduced its “nonacademic expenditures” by 20%. Those cost-saving measures may annoy faculty members, Keyes says, but they are hardly unique to KAUST. “Now that the global economy is much less secure, we are striving to live within a budget that will not require breaking promises,” he says. “That means every new faculty member's requests for start-up funds and equipment is getting more scrutiny.” In addition to growing its own talent, KAUST decided early on that institutional collaborations with global heavyweights would be a good way to jump-start its research activities. So KAUST inked dozens of deals using an array of mechanisms. The first one, with WHOI, covered research in three areas: coral reef ecology, marine resources and fisheries management, and physical oceanography. Each was designed to take advantage of KAUST's location along the Red Sea, a body of water with special characteristics. It promised to be a boon to scientists around the world who had been prohibited from working there because of its strategic and military importance to the countries—Egypt, Sudan, Somalia, and Ethiopia, as well as Saudi Arabia—along its shores. The cruises, across all seasons, were designed to generate the first large-scale, top-to-bottom hydrographic survey of this poorly explored sea. But only one came off as originally planned, says Amy Bower, a senior scientist at WHOI and project leader. (Fortunately, it yielded what Bower calls “an unprecedented data set” on nutrient flows into the sea from the Gulf of Aden.) The first cruise was “pretty much a debacle,” Bower says, after WHOI's ship was blocked from working in Saudi coastal waters and rerouted to study brine pools in the middle of the sea, fed by an unknown hydrothermal vent. A second cruise was moved to the Caribbean. WHOI scientists also complain about being left in the dark as to why certain decisions were made. “The one thing I've learned is that there are always 10 more reasons than you've been told,” Bower says. Summing up her experience, Bower says “I wouldn't say it was a failure. But it was a big disappointment. KAUST was poised to become a major player in oceanography; they had water access and lots of money. They could have done a lot for Red Sea science and for research throughout the region. Instead, this [shift in priorities] makes them a limited, parochial coastal lab, of which there are many around the world.” Xabier Irigoien, who a year ago succeeded Luyten as director of the Red Sea center, sees things quite differently. He says the collaboration was flawed from the beginning because it was not a good match with the research interests of KAUST faculty members. “We do not consider physical oceanography to be a priority,” Irigoien says. “We are moving toward a focus on marine biology and the unique systems on hand, here in the Red Sea. Pure basic mapping is less of a priority.” ## Looking for answers Such shifts in research focus are easier to make at a small university—KAUST now has about 120 faculty members and 700 students—that is still wet behind the ears. And the more collaborative the research, the better: Instead of departments, faculty members are clustered in three large divisions and carry out most of their research at centers that cover broad interdisciplinary topics such as desalination, catalysis, clean combustion, and solar engineering. KAUST also has no tenure system, instead offering faculty members 5-year contracts that can be extended indefinitely after annual reviews. Those features appealed to plant geneticist Nina Fedoroff, a renowned academic scientist. After completing a 3-year stint as science adviser to the U.S. Secretary of State, Fedoroff postponed retirement and accepted an invitation last year to create a desert agriculture research center. “I realized from my experiences at State that, despite all the verbiage about the need to adapt to climate change, there wasn't much going on substantively with respect to food and water needs,” she explains. “There are many inefficiencies in how we do agriculture in terms of water, nutrients, and land use. And the reason I came here, in a nutshell, was to see if we could make progress in those areas.” “This is exactly the kind of thing they should be doing,” says biochemist Barry Halliwell, deputy president for research and technology at the National University of Singapore and a member of a blue-ribbon International Advisory Council that advises KAUST's president. “It's highly relevant to the kingdom, and it's quite an exciting area. People have messed around with it for awhile. And the place that could really tackle it, and one with unlimited solar energy, is Saudi Arabia.” Another type of collaboration at KAUST begins with competitive research grants of up to$10 million to scientists from around the world (Science, 28 March 2008, p. 1748). The hope is that these scientists would find a way to involve KAUST faculty members and students in their work. Ted Sargent, a professor of nanotechnology at the University of Toronto in Canada, says he has been “blown away” by what he has seen at KAUST since receiving one of these global research awards in 2008.

“It's been an incredible partnership because KAUST has hired faculty at the top of their game,” Sargent says. “People have chosen KAUST over MIT [the Massachusetts Institute of Technology] or Cornell, and I think it's fast becoming one of the world's top universities.” KAUST's microscopy facilities, which he calls “outstanding,” have been essential for his work on quantum dots, and Sargent shares students and postdocs with Ghassan Jabbour, who directs the Solar & Photovoltaics Engineering Research Center at KAUST.

Another grant recipient, computational biologist Anna Tramontano of the Sapienza University of Rome, says her 5-year, \$5 million award has ushered in “the most productive period of her career” because it has allowed her to pursue a broad, long-range research program. “The scientific atmosphere is very good there, and I think it's going well,” says Tramontano, who has also helped KAUST evaluate faculty members and programs in her field.

At age 88, King Abdullah probably won't be around to see whether his vision is realized. But senior KAUST administrators believe KAUST can become an example of how to create a global research university attuned to, and serving the needs of, the Middle East.

“Am I worried what will happen after the king dies? A big ‘no’ to that,” Al-Nasr says. “Why should we worry? Things are going well, and KAUST is moving ahead as planned.”

5. Neuroscience

# All Eyes on RNA

1. Ken Garber*

The list of RNA-binding proteins linked to amyotrophic lateral sclerosis is growing; RNA may also explain why a common mutation causes this fatal motor neuron disease—and a dementia.

In the summer of 2011, a 3-year investigation into the genetics of amyotrophic lateral sclerosis (ALS) by research teams on two continents was coming to a head. This international consortium had narrowed the search for a mutation they knew caused ALS in families to just three genes on chromosome 9. Yet detailed and thorough gene analysis, using a variety of new sequencing technologies and massive computational power, failed to turn up any mutations that could be responsible.

Knowing that something unusual must lurk in this segment of DNA, Bryan Traynor, a geneticist at the U.S. National Institute on Aging in Bethesda, Maryland, took a closer look at one particularly suspicious stretch. When a computer algorithm clearly failed to correctly assemble the relevant DNA sequences of affected family members, Traynor arranged them manually. “I had to revert back to papyrus and pencil in order to actually work it out,” he jokes.

At that moment, Traynor became the first person to look upon the most common known cause of both ALS (sometimes called Lou Gehrig's disease in the United States) and another, slightly rarer neurodegenerative disease called frontotemporal dementia (FTD). What he saw in the DNA of the ALS patients was the nucleotide sequence GGGGCC repeating itself over and over, far more than in unaffected family members. Because this type of mutation has been implicated in some other neurodegenerative diseases—repeated DNA sequences cause Huntington's disease and fragile X syndrome, for example—Traynor was confident that the consortium's long quest was over.

Indeed, a team led by Rosa Rademakers of the Mayo Clinic in Jacksonville, Florida, independently discovered the same repeat in the gene, provisionally dubbed C9ORF72, and the two groups published simultaneously in Neuron in September 2011. It quickly became apparent this was the most important ALS gene discovered to date, by far. The C9ORF72 mutation accounts for 40% of familial ALS and 21% of familial FTD. It has also been found in 7% of sporadic ALS, in which there's no family history of the condition—the vast majority of cases—and in 5% of sporadic FTD. “For the first time, really, we are showing that genetics can underlie apparently sporadic disease,” Traynor says.

The whole field is waiting to find out how the mutation causes ALS—or how, in some people, indistinguishable mutations instead paradoxically trigger FTD. ALS robs a person of muscle control but spares the mind, whereas FTD does the opposite. (Many patients show symptoms of both diseases to varying degrees.)

The leading hypothesis is that the long DNA repeat spawns a bloated gob of RNA that creates a trap inside cells for one or more RNA-binding proteins necessary for a neuron's function or survival. RNA-binding proteins have been under scrutiny in ALS since 2006, when one of them, TDP-43, was reported to make up the abnormal protein deposits, known as inclusions, found in motor neurons in almost all ALS cases (Science, 6 October 2006, p. 42). Mutations in the genes for TDP-43 and in FUS, a related RNAbinding protein, can cause ALS, and mutations in a third RNA-binding protein, ataxin-2, are a powerful risk factor for the disease.

Although ALS neurons suffer many types of dysfunction, the multiple recent discoveries have led to “a convergence of ideas” that errors in RNA processing are central to ALS and they could be linked to all the cellular problems, says biochemist Don Cleveland of the University of California (UC), San Diego. Others in the field caution that ALS might actually be several distinct diseases with different causes, RNA misprocessing being only one. Nevertheless, Cleveland says, “since last September, it's been the most exciting time of discovery in ALS in the history of the planet.”

## Inward bound

What RNA-binding proteins are doing—or not doing as the case may be—in ALS and FTD remains largely a mystery. That's partly because each protein may bind so many RNAs, thousands in some cases, that it is hard to know which RNAs are important in disease. Among other duties, RNA-binding proteins trim, cap, escort, degrade, and otherwise process messenger RNA, which carries the transcribed DNA sequence from the cell nucleus to the cytoplasm for translation into protein. “There isn't a step in the process [without] a halo of RNA-binding proteins surrounding the RNA,” says Robert Bowser, a neurobiologist at the Barrow Neurological Institute in Phoenix.

For ALS and FTD researchers, a key unknown is what triggers RNA-binding proteins to aggregate into the inclusions seen in the neurons and other nervous system cells of patients. One hypothesis is that the inclusions derive from stress granules, dense balls of RNA-binding proteins that arise normally in cells in response to cellular stress. Stress granules trap RNAs and prevent their translation into proteins, presumably to husband the cell's resources until the stress is gone. “But as a consequence of having this great function, they're more susceptible to aggregating in disease in an uncontrollable fashion,” says geneticist Aaron Gitler of Stanford University in Palo Alto, California. Normally, stress granules eventually dissolve and release the trapped RNAs, but under persistent stress—or owing to genetic risk factors—they may persist and transform into the massive cytoplasmic inclusions seen in ALS and FTD.

Genetic evidence supports this idea. In 2010, Gitler, then at the University of Pennsylvania (Penn), and colleague Nancy Bonini reported that about 5% of all ALS patients have a mutation in the gene encoding ataxin-2, an RNA-binding protein involved in stress granule assembly. More recent work suggests that mutated ataxin-2 indeed contributes to inclusion formation.

The six-nucleotide repeat sequence in the C9ORF72 gene may seed a different kind of aggregate—in the cell nucleus, not the cytoplasm. Researchers strongly suspect that this DNA sequence repeat, which is in a noncoding region of the gene, gives rise to an unnatural RNA structure that captures one or more RNA-binding proteins there. And the sheer number of repeat sequences—at least 30, and often hundreds or even thousands—could sequester enough protein to disrupt a neuron and provoke its demise. Indeed, Rademakers's group has documented aggregates dubbed RNA foci in postmortem brain and spinal cord tissue from C9ORF72 mutation carriers. “The race is really on to figure out what RNA-binding protein is being sequestered in there,” Gitler says.

There are precedents for such sequestration causing disease. The best-known case is myotonic dystrophy, an adult form of muscular dystrophy, in which an expanded three-nucleotide repeat sequesters an RNA-binding protein called muscleblind that's involved in RNA splicing, forming RNA foci.

Whether or how RNA foci harm neurons is unknown. And researchers still can't agree on whether the cytoplasmic inclusions in ALS and FTD neurons kill the cells because the captured RNA-binding proteins can't carry out their normal function or because the aggregates gained a new, toxic function. The answer may be both. “I personally think that the best data out there indicate that it's both loss and gain of function that's important,” Gitler says.

## Unidentified captives

Any definitive conclusion, says Zissimos Mourelatos, a pathologist at Penn, must wait until identification of the RNAs, if any, that are captured in the inclusions seen in people with ALS and FTD. Such work is now under way in several labs using a new technique called CLIP-seq. The technique uses ultraviolet radiation to create a chemical bond between RNA-binding proteins and their RNAs, enabling purification of the latter and then their sequencing and identification. In September, a group from UC San Diego reported in Nature Neuroscience that they had used CLIP-seq to reveal RNAs common to both TDP-43 and FUS. Several of these RNAs code for proteins important in synapse formation and function, suggesting that aggregation depleted these synaptic proteins, causing neurodegeneration.

TDP-43, FUS, and ataxin-2 won't be the only RNA-binding proteins involved in ALS, Gitler and Mourelatos predict. “We think that this is going to be the tip of the iceberg,” Gitler says. Indeed, in September in Acta Neuropathologica, Bowser's group reported finding inclusions containing the RNA-binding protein RBM45 in the cytoplasm of spinal cord cells from 21 of 23 ALS patients, versus none in seven control cases. (RBM45-containing inclusions were also present in all six FTD patients tested.) No mutations in the gene for RBM45 have yet been found in ALS, but that was also true of TDP-43 when first found in ALS and FTD inclusions back in 2006.

At Penn, Gitler's group cloned the genes for almost 200 RNA-binding proteins and introduced them individually into yeast cells, checking for aggregation and toxicity. Gitler so far has found mutations in two of them, TAF15 and EWSR1, in several people with ALS or FTD, suggesting possible roles in the disease. “I'm pretty confident that there will be additional RNA-binding proteins that you'll be seeing in the literature soon,” he says.

All this begs the question of why neurons are so sensitive to changes in RNA-binding proteins, while most other cell types appear unaffected. “It's a big unknown,” says Mourelatos, who suggests that the large amount of gene splicing required for the generation of specialized protein isoforms at synapses, the connection points between neurons, could be a factor. “There's a lot of RNA processing going on in neurons,” he says. Gitler speculates that the sheer length of motor neurons—in humans, a single motor neuron axon can extend several feet—may make them more dependent on RNA trafficking and processing.

Other researchers stress that, for ALS at least, defects in RNA processing may not be the whole story. “I think it's a much more complicated disease than that,” cautions Lucie Bruijn, chief scientist at the ALS Association, which is headquartered in Washington, D.C. Bruijn cites mitochondrial dysfunction and defects in transport along motor neuron axons as two important features of ALS disease pathology. For example, a recent paper in Nature described ALS-causing mutations in the profilin-1 gene. Profilin-1 affects axon growth and regulates actin, an abundant and critical protein not involved in RNA processing. “It's not clear to me how we would fit that discovery into an RNA-binding protein world,” Cleveland admits. “So it's just a little perplexing.”

And one camp of ALS researchers maintains that it's not RNA misprocessing but a failure of the cell's protein-disposal system that causes the disease; mutations in several genes involved in protein clearance cause a small proportion of familial ALS. Most researchers believe that a combination of RNA misprocessing and failed protein clearance is responsible for most cases. “How the two meet up in the middle, we do not know,” Traynor says.

The current intense focus on disease mechanism should be accompanied by efforts to develop therapies now, even before these controversies are resolved, Bruijn says. The ALS Association, besides funding mouse models of the C9ORF72 expansion, is also collaborating with Isis Pharmaceuticals on developing “antisense” DNA drugs to bind and neutralize the repeat sequences. Although uncovering the mutation's function is important, Bruijn says, “we might never find out exactly, or all agree. And maybe if we get rid of that large expansion there will be therapeutic benefit.”

• * Ken Garber is a freelance writer based in Ann Arbor, Michigan.