From genes to brains

Many brain disorders are strongly influenced by genetics, and researchers have long hoped that the identification of genetic risk factors will provide clues to the causes and possible treatments of these mysterious conditions. In the early years, progress was slow. Many claims failed to replicate, and it became clear that in order to identify the important risk genes with confidence, researchers would need to examine the genomes of very large numbers of patients.

Until recently that would have been prohibitively expensive, but genome research has been accelerating fast. Just how fast was underlined by an announcement in January from a California-based company, Illumina, that it had achieved a long-awaited milestone: sequencing an entire human genome for under $1000. Seven years ago, this task would have cost $10M and taken weeks of work. The new system does the job in a few hours, and can sequence tens of thousands of genomes per year.

In parallel with these spectacular advances, another technological revolution has been unfolding over the past several years, with the development of a new method for editing the genome of living cells. This method, known as CRISPR, allows researchers to make precise changes to a DNA sequence—an advance that is expected to transform many areas of biomedical research and may ultimately form the basis of new treatments for human genetic disease.

The CRISPR technology, which is based on a natural bacterial defense system against viruses, uses a short strand of RNA as a “search string” to locate a corresponding DNA target sequence. This RNA string can be synthesized in the lab and can be designed to recognize any desired sequence of DNA. The RNA carries with it a protein called Cas9, which cuts the target DNA at the chosen location, allowing a new sequence to be inserted—providing researchers with a fast and flexible “search-and-replace” tool for editing the genome.

One of the pioneers in this field is McGovern Investigator Feng Zhang, who along with George Church of Harvard, was the first to show that CRISPR could be used to edit the human genome in living cells. Zhang is using the technology to study human brain disorders, building on the flood of new genetic discoveries that are emerging from advances in DNA sequencing. The Broad Institute, where Zhang holds a joint appointment, is a world leader in human psychiatric genetics, and will be among the first to acquire the new Illumina sequencing machines when they reach the market later this year.

By sequencing many thousands of individuals, geneticists are identifying the rare genetic variants that contribute to risk of diseases such as autism, schizophrenia and bipolar disorder. CRISPR will allow neuroscientists to study those gene variants in cells and in animal models. The goal, says McGovern Institute director Bob Desimone, is to understand the biological roots of brain disorders. “The biggest obstacle to new treatments has been our ignorance of fundamental mechanisms. But with these new technologies, we have a real opportunity to understand what’s wrong at the level of cells and circuits, and to identify the pressure points at which therapeutic intervention may be possible.”

Culture Club

In other fields, the influence of genetic variations on disease has turned out to be surprisingly difficult to unravel, and for neuropsychiatric disease, the challenge may be even greater. The brain is the most complex organ of the body, and the underlying pathologies that lead to disease are not yet well understood. Moreover, any given disorder may show a wide variation in symptoms from patient to patient, and it may also have many different genetic causes. “There are hundreds of genes that can contribute to autism or schizophrenia,” says McGovern Investigator Guoping Feng, who is also Poitras Professor of Neuroscience.

To study these genes, Feng and collaborators at the Broad Institute’s Stanley Center for Psychiatric Research are planning to screen thousands of cultures of neurons, grown in the tiny wells of cell culture plates. The neurons, which are grown from stem cells, can be engineered using CRISPR to contain the genetic variants that are linked to neuropsychiatric disease. Each culture will contain neurons with a different variant, and these will be examined for abnormalities that might be associated with disease.

Feng and colleagues hope this high-throughput platform will allow them to identify cellular traits, or phenotypes, that may be related to disease and which can then be studied in animal models to see if they cause defects in brain function or in behavior. In the longer term, this high-throughput platform can also be used to screen for new drugs that can reverse these defects.

Animal Kingdom

Cell cultures are necessary for large-scale screens, but ultimately the results must be translated into the context of brain circuits and behavior. “That means we must study animal models too,” says Feng.

Feng has created several mouse models of human brain disease by mutating genes that are linked to these disorders and examining the behavioral and cellular defects in the mutant animals. “We have models of obsessive-compulsive disorder and autism,” he explains. “By studying these mice we want to learn what’s wrong with their brains.”

So far, Feng has focused on single-gene models, but the majority of human psychiatric disorders are triggered by multiple genes acting in combination. One advantage of the new CRISPR method is that it allows researchers to introduce several mutations in parallel, and Zhang’s lab is now working to create autistic mice with more than one gene alteration.

Perhaps the most important advantage of CRISPR is that it can be applied to any species. Currently, almost all genetic modeling of human disease is restricted to mice. But while mouse models are convenient, they are limited, especially for diseases that affect higher brain functions and for which there are no clear parallels in rodents. “We also need to study species that are closer to humans,” says Feng.

Accordingly, he and Zhang are collaborating with colleagues in Oregon and China to use CRISPR to create primate models of neuropsychiatric disorders. Earlier this year, a team in China announced that they had used CRISPR to create transgenic monkeys that will be used to study defects in metabolism and immunity.

Feng and Zhang are planning to use a similar approach to study brain disorders, but in addition to macacques, they will also work with a smaller primate species, the marmoset. These animals, with their fast breeding cycles and complex behavioral repertoires, are ideal for genetic studies of behavior and brain function. And because they are very social with highly structured communication patterns, they represent a promising new model for understanding the neural basis of social cognition and its disruption in conditions such as autism.

Given their close evolutionary relationship to humans, marmoset models could also help accelerate the development of new therapies. Many experimental drugs for brain disorders have been tested successfully in mice, only to prove ineffective in subsequent human trials. These failures, which can be enormously expensive, have led many drug companies to cut back on their neuroscience R&D programs. Better animal models could reverse this trend by allowing companies to predict more accurately which drug candidates are most promising, before investing heavily in human clinical trials.

Feng’s mouse research provides an example of how this approach can work. He previously developed a mouse model of obsessive-compulsive disorder, in which the animals engage in obsessive self-grooming, and he has now shown that this effect can be reversed when the missing gene is reintroduced, even in adulthood. Other researchers have seemed similar results with other brain disorders such as Rett Syndrome, a condition that is often accompanied by autism. “The brain is amazingly plastic,” says Feng. “At least in a mouse, we have shown that the damage can often be repaired. If we can also show this in marmosets or other primate models, that would really give us hope that something similar is possible in humans.”

Human Race

Ultimately, to understand the genetic roots of human behavior, researchers must sequence the genomes of individual subjects in parallel with measurements of those same individuals’ behavior and brain function.

Such studies typically require very large sample sizes, but the plummeting cost of sequencing is now making this feasible. In China, for instance, a project is already underway to sequence the genomes of many thousands of individuals to uncover genetic influences on cognition and intelligence.

The next step will be to link the genetics to brain activity, says McGovern Investigator John Gabrieli, who also directs the Martinos Imaging Center at MIT. “It’s a big step to go from DNA to behavioral variation or clinical diagnosis. But we know those genes must affect brain function, so neuroimaging may help us to bridge that gap.”

But brain scans can be time-consuming, given that volunteers must perform behavioral tasks in the scanner. Studies are typically limited to a few dozen subjects, not enough to detect the often subtle effects of genomic variation.

One way to enlarge these studies, says Gabrieli, is to image the brain during rest rather than in a state of prompted activity. This procedure is fast and easy to replicate from lab to lab, and patterns of resting state activity have turned out to be surprisingly reproducible; moreover, Gabrieli is finding that differences in resting activity are associated with brain disorders such as autism, and he hopes that in the future it will be possible to relate these differences to the genetic factors that are emerging from genome studies at the Broad Institute and elsewhere.

“I’m optimistic that we’re going to see dramatic advances in our understanding of neuropsychiatric disease over the next few years.” — Bob Desimone

Confirming these associations will require a “big data” approach, in which results from multiple labs are consolidated into large repositories and analyzed for significant associations. Resting state imaging lends itself to this approach, says Gabrieli. “To find the links between brain function and genetics, big data is the direction we need to go to be successful.”

How soon might this happen? “It won’t happen overnight,” cautions Desimone. “There are a lot of dots that need to be connected. But we’ve seen in the case of genome research how fast things can move once the right technologies are in place. I’m optimistic that we’re going to see equally dramatic advances in our understanding of neuropsychiatric disease over the next few years.”

MIT researchers to win awards from the Society for Neuroscience

Three neuroscientists at MIT have been selected to receive awards from the Society for Neuroscience (SfN).

Tomaso Poggio, a founding member of the McGovern Institute for Brain Research at MIT, will receive the Swartz Prize for Theoretical and Computational Neuroscience; Feng Zhang, a member of the McGovern Institute and an assistant professor in the Department of Brain and Cognitive Sciences, will receive the Young Investigator Award; and Sung-Yon Kim, a Simons postdoctoral fellow of the Life Sciences Research Foundation at MIT, will receive the Donald B. Lindsley Prize in Behavioral Neuroscience.
 
The awards will be presented during Neuroscience 2014, the SfN’s annual meeting in Washington, D.C.

Swartz Prize for Theoretical and Computational Neuroscience
 

The $25,000 Swartz Prize for Theoretical and Computational Neuroscience, supported by the Swartz Foundation, recognizes an individual who has produced a significant cumulative contribution to theoretical models or computational methods in neuroscience.

“Dr. Poggio’s contributions to the development of computational and theoretical models of the human visual system have served to advance our understanding of how human systems learn from experience,” said Carol Mason, president of SfN. “It is an honor to recognize him as a founder and driving force in the field of computational neuroscience.”

Poggio, the Eugene McDermott Professor in the Department of Brain and Cognitive Sciences and the director of the Center for Brains, Minds and Machines, develops computational models of the brain to understand human intelligence. Specifically, he has developed models that mimic the ways that humans learn to recognize objects, such as faces, and actions, such as motion — applications now present in digital cameras and some cars. Poggio is currently working to develop more complex models that mimic the forward as well as feedback signals that the human brain uses during visual recognition. The ultimate goal of this research is to better understand how the brain works and to apply this technology to build intelligent machines.


Young Investigator Award
 

The SfN has also named two winners of this year’s Young Investigator Award: Feng Zhang of MIT and Diana Bautista of the University of California at Berkeley.

The $15,000 award recognizes the outstanding achievements and contributions by a young neuroscientist who has recently received his or her advanced professional degree.

“Drs. Zhang and Bautista are two young neuroscientists who have demonstrated remarkable dedication to their work,” Mason said. “Their creative research is advancing their respective fields, and their commitment to helping other scientists succeed is an inspiration to us all.”

Zhang, who is also a core member of the Broad Institute of MIT and Harvard and the W. M. Keck Career Development Professor in Biomedical Engineering, uses synthetic biology methods to study brain disease.
 
As a graduate student at Stanford University, Zhang was instrumental in advancing the development of optogenetic technology, which allows researchers to manipulate genetically modified neurons with light. More recently, Zhang was a leader in the development of the CRISPR-Cas9 method for genome editing – a powerful new technology with many applications in biomedical research, including the potential to treat human genetic disease.

Donald B. Lindsley Prize in Behavioral Neuroscience
 


The SfN will award the Donald B. Lindsley Prize to Sung-Yon Kim, a postdoc in Kwanghun Chung’s lab at the Picower Institute for Learning and Memory.

Supported by The Grass Foundation, the prize recognizes an outstanding PhD thesis in the area of general behavioral neuroscience.
 
Kim, who earned his PhD at Stanford University, used optogenetics to study the brain circuits underlying anxiety.

“The Society is pleased to honor Dr. Kim’s groundbreaking research in the neuroanatomical basis of anxiety behavior,” said Mason. “His approach to behavioral neuroscience will likely have a broad and lasting impact on biology and medicine.”

Genome Editing with CRISPR – Cas9

This animation depicts the CRISPR-Cas9 method for genome editing – a powerful new technology with many applications in biomedical research, including the potential to treat human genetic disease. Feng Zhang, a leader in the development of this technology, is a faculty member at MIT, an investigator at the McGovern Institute for Brain Research, and a core member of the Broad Institute.

 

Feng Zhang shares Gabbay Award for CRISPR research

Feng Zhang of MIT and the Broad Institute, Jennifer Doudna of the University of California, Berkeley and the Howard Hughes Medical Institute, and Emmanuelle Charpentier of Umeå University have been awarded Brandeis University’s 17th Annual Jacob Heskel Gabbay Award in Biotechnology and Medicine.

The researchers are being honored for their work on the CRISPR/cas system, a genome editing technology that allows scientists to make precise changes to a DNA sequence — an advance that is expected to transform many areas of biomedical research and may ultimately form the basis of new treatments for human genetic disease.

Feng Zhang wins NSF’s Alan T. Waterman Award

The National Science Foundation (NSF) named Feng Zhang the 2014 recipient of its Alan T. Waterman Award. This award is NSF’s highest honor that annually recognizes an outstanding researcher under the age of 35 and funds his or her research in any field of science or engineering. Zhang’s research focuses on understanding how the brain works.

“It is a great pleasure to honor Feng Zhang with this award for his young, impressive career,” said NSF Director France Córdova. “It is exciting to support his continued fundamental research, which is certain to impact the field of brain research. Imagine a future free of schizophrenia, autism and other brain disorders that wreak havoc on individuals, families and society. Feng’s research moves us in that direction.”

Zhang seeks to understand the molecular machinery of brain cells through the development and application of innovative technologies. He created and is continuing to perfect tools that afford researchers precise control over biological activities occurring inside the cell. With these tools, researchers can deepen their understanding of how the genome works, and how it influences the development and function of the brain. Zhang also examines failures within the systems that cause disease.

Two different lines of fundamental research and technology development are helping him do that: optogenetics and genome engineering. With Edward Boyden and Karl Deisseroth at Stanford University, he developed optogenetics to study brain circuits, a technique in which light is used to affect signaling and gene expression of neurons involved in complex behaviors. Zhang also developed the CRISPR system to enable new, cheaper, more effective ways to “edit” animal genomes–that is, to identify and cut a short DNA sequence underlying a disorder so that it may be deleted or substituted out for other genetic material. Although Zhang’s main area of focus is the brain, the potential applications of CRISPR technology extend well beyond neuroscience.

“This is an immensely exciting time for the field because of the tremendous potential of tools like CRISPR, which allows us to modify the genomes of mammalian cells,” Zhang said. “One of my long-term goals is to better understand the molecular mechanisms of brain function and identify new ways to treat devastating neurological disorders.”

Since high school, Zhang has devoted his time, energy and intellectual prowess to developing ways to study and repair the nervous system. Today, he is one of 11 core faculty members at the Broad Institute of MIT and Harvard; an investigator at MIT’s McGovern Institute for Brain Research; and the W. M. Keck Career Development Professor with a joint appointment in MIT’s Departments of Brain and Cognitive Sciences and Biological Engineering.

Zhang is widely recognized for his pioneering work in optogenetics and genome editing. He shared the Perl/UNC Neuroscience Prize with Karl Deisseroth and Edward Boyden in 2012. In 2013, MIT Technology Review recognized him as a “pioneer” and one of its 35 Innovators Under 35; Popular Science magazine placed Zhang on its Brilliant 10, an annual list of the most promising scientific innovators. Nature also named him as one of the “ten people who mattered” in 2013 for his work on developing the CRISPR system for genome editing in mammalian cells.

The Waterman award will be presented to Zhang at an evening ceremony at the U.S. Department of State in Washington, D.C., on May 6. At that event, the National Science Board will also present its 2014 Vannevar Bush award to mathematician Richard Tapia and Public Service awards to bioethicist Arthur Caplan and to the AAAS Science & Technology Policy Fellowships Program.

Plans are underway for Zhang to deliver a lecture at a meeting of the National Science Board at NSF and to meet with students at Thomas Jefferson High School for Science and Technology during his visit this spring.

Broad, MIT researchers reveal structure of key CRISPR complex

Researchers from the Broad Institute and MIT have teamed up with colleagues from the University of Tokyo to form the first high definition picture of the Cas9 complex – a key part of the CRISPR-Cas system used by scientists as a genome-editing tool to silence genes and probe the biology of cells. Their findings, which are reported this week in Cell, are expected to help researchers refine and further engineer the tool to accelerate genomic research and bring the technology closer to use in the treatment of human genetic disease.

First discovered in bacteria in 1987, CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) have recently been harnessed as so-called genome editing tools. These tools allow researchers to home in on “typos” within the three-billion-letter sequence of the human genome, and cut out and even alter the problematic sequence. The Cas9 complex, which includes the CRISPR “cleaving” enzyme Cas9 and an RNA “guide” that leads the enzyme to its DNA target, is key to this process.

“We’ve come to view the Cas9 complex as the ultimate guided missile that we can use to target precise sites in the genome,” said co-senior author Feng Zhang, a core member of the Broad Institute, an investigator at the McGovern Institute for Brain Research, and an assistant professor at MIT. “This study provides a schematic of the entire system – it shows the missile (the Cas9 protein), the programming instructions (the guide RNA) that send it to the right location, and the target DNA. It also reveals the secret of how these pieces function together to make the whole system work.”

To deconstruct this system, Zhang approached the paper’s co-senior author Osamu Nureki at the University of Tokyo. Together, they assembled a team to work out the complicated structure.

“Cas9-based genome editing technologies are proving to be revolutionary in a wide range of life sciences, enabling many new experimental techniques, so my colleagues and I were excited to work with Feng’s lab on this important research,” said first author Hiroshi Nishimasu, an assistant professor of biophysics and biochemistry who works in Nureki’s lab at the University of Tokyo.

The two teams worked closely to reveal the structural details of the Cas9 complex and to test their functional significance. Their efforts revealed a division of labor within the Cas9 complex. The researchers determined that the Cas9 protein consists of two lobes: one lobe is involved in the recognition of the RNA and DNA elements, while the other lobe is responsible for cleaving the target DNA, causing what is known as a “double strand break” that disables the targeted gene. The team also found that key structures on Cas9 interface with the guide RNA, allowing Cas9 to organize itself around the RNA and the target DNA as it prepares to cut the strands.

Identifying the key features of the Cas9 complex should enable researchers to improve the genome-editing tool to better suit their needs.

“Up until now, it has been very difficult to rationally engineer Cas9. Now that we have this structural information, we can take a principled approach to engineering the protein to make it more effective,” said Zhang, who is also a co-founder of Editas Medicine, a company that was started last year to develop Cas9 and other genome editing technologies into a novel class of human therapeutics.

Currently, Cas9 is used in experiments to silence genes in mammalian cells – sometimes at multiple sites across the genome – and large libraries of RNA sequences have been created to guide Cas9 to genes of interest. However, the system can only target specific types of sites. Some studies have also shown that the RNA could lead Cas9 “off-target,” potentially causing unexpected problems within the cellular machinery.

The researchers plan to use this new, detailed picture of the Cas9 complex to address these concerns.

“Understanding this structure may help us engineer around the current limitations of the Cas9 complex,” said study author F. Ann Ran, a graduate student in Zhang’s lab. “In the future, it could allow us to design versions of these editing tools that are more specific to our research needs. We may even be able to alter the type of nucleic acid sequences that Cas9 can target.”

Such technological improvements will be needed if the CRISPR-Cas system is to evolve into a therapeutic tool for the treatment of genetic disease.

The study was supported by the National Institute of Mental Health (NIMH); an NIH Director’s Pioneer Award; the Japan Science and Technology Agency; the Japan Society for the Promotion of Science; the Keck, McKnight, Poitras, Merkin, Vallee, Damon Runyon, Searle Scholars, Klingenstein, and Simons Foundations; as well as Bob Metcalfe and Jane Pauley.

Other researchers who worked on the study include Patrick D. Hsu, Silvana Konermann, Soraya Shehata, Naoshi Dohmae, and Ryuichiro Ishitani.

Written by Veronica Meade-Kelly, Broad Institute

Paper cited:

Nishimasu H et al. “Crystal structure of Cas9 in complex with guide RNA and target DNA.” Cell DOI: 10.1016/j.cell.2014.02.001

About the Broad Institute of Harvard and MIT
The Eli and Edythe L. Broad Institute of Harvard and MIT was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.

Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to http://www.broadinstitute.org.

About the McGovern Institute for Brain Research at MIT
The McGovern Institute for Brain Research at MIT is led by a team of world-renowned neuroscientists committed to meeting two great challenges of modern science: understanding how the brain works and discovering new ways to prevent or treat brain disorders. The McGovern Institute was established in 2000 by Patrick J. McGovern and Lore Harp McGovern, who are committed to improving human welfare, communication and understanding through their support for neuroscience research. The director is Robert Desimone, formerly the head of intramural research at the National Institute of Mental Health.

Speeding up gene discovery

Since the completion of the Human Genome Project, which identified nearly 20,000 protein-coding genes, scientists have been trying to decipher the roles of those genes. A new approach developed at MIT, the Broad Institute, and the Whitehead Institute should speed up the process by allowing researchers to study the entire genome at once.

The new system, known as CRISPR, allows researchers to permanently and selectively delete genes from a cell’s DNA. In two new papers, the researchers showed that they could study all the genes in the genome by deleting a different gene in each of a huge population of cells, then observing which cells proliferated under different conditions.

“With this work, it is now possible to conduct systematic genetic screens in mammalian cells. This will greatly aid efforts to understand the function of both protein-coding genes as well as noncoding genetic elements,” says David Sabatini, a member of the Whitehead Institute, MIT professor of biology, and a senior author of one of the papers, both of which appear in this week’s online edition of Science.

Using this approach, the researchers were able to identify genes that allow melanoma cells to proliferate, as well as genes that confer resistance to certain chemotherapy drugs. Such studies could help scientists develop targeted cancer treatments by revealing the genes that cancer cells depend on to survive.

Feng Zhang, the W.M. Keck Assistant Professor in Biomedical Engineering and senior author of the other Science paper, developed the CRISPR system by exploiting a naturally occurring bacterial protein that recognizes and snips viral DNA. This protein, known as Cas9, is recruited by short RNA molecules called guides, which bind to the DNA to be cut. This DNA-editing complex offers very precise control over which genes are disrupted, by simply changing the sequence of the RNA guide.

“One of the things we’ve realized is that you can easily reprogram these enzymes with a short nucleic-acid chain. This paper takes advantage of that and shows that you can scale that to large numbers and really sample across the whole genome,” says Zhang, who is also a member of MIT’s McGovern Institute for Brain Research and the Broad Institute.

Genome-wide screens

For their new paper, Zhang and colleagues created a library of about 65,000 guide RNA strands that target nearly every known gene. They delivered genes for these guides, along with genes for the CRISPR machinery, to human cells. Each cell took up one of the guides, and the gene targeted by that guide was deleted. If the gene lost was necessary for survival, the cell died.

“This is the first work that really introduces so many mutations in a controlled fashion, which really opens a lot of possibilities in functional genomics,” says Ophir Shalem, a Broad Institute postdoc and one of the lead authors of the Zhang paper, along with Broad Institute postdoc Neville Sanjana.

This approach enabled the researchers to identify genes essential to the survival of two populations of cells: cancer cells and pluripotent stem cells. The researchers also identified genes necessary for melanoma cells to survive treatment with the chemotherapy drug vemurafenib.

In the other paper, led by Sabatini and Eric Lander, the director of the Broad Institute and an MIT professor of biology, the research team targeted a smaller set of about 7,000 genes, but they designed more RNA guide sequences for each gene. The researchers expected that each sequence would block its target gene equally well, but they found that cells with different guides for the same gene had varying survival rates.

“That suggested that there were intrinsic differences between guide RNA sequences that led to differences in their efficiency at cleaving the genomic DNA,” says Tim Wang, an MIT graduate student in biology and lead author of the paper.

From that data, the researchers deduced some rules that appear to govern the efficiency of the CRISPR-Cas9 system. They then used those rules to create an algorithm that can predict the most successful sequences to target a given gene.

“These papers together demonstrate the extraordinary power and versatility of the CRISPR-Cas9 system as a tool for genomewide discovery of the mechanisms underlying mammalian biology,” Lander says. “And we are just at the beginning: We’re still uncovering the capabilities of this system and its many applications.”

Efficient alternative

The researchers say that the CRISPR approach could offer a more efficient and reliable alternative to RNA interference (RNAi), which is currently the most widely used method for studying gene functions. RNAi works by delivering short RNA strands known as shRNA that destroy messenger RNA (mRNA), which carries DNA’s instructions to the rest of the cell.

The drawback to RNAi is that it targets mRNA and not DNA, so it is impossible to get 100 percent elimination of the gene. “CRISPR can completely deplete a given protein in a cell, whereas shRNA will reduce the levels but it will never reach complete depletion,” Zhang says.

Michael Elowitz, a professor of biology, bioengineering, and applied physics at the California Institute of Technology, says the demonstration of the new technique is “an astonishing achievement.”

“Being able to do things on this enormous scale, at high accuracy, is going to revolutionize biology, because for the first time we can start to contemplate the kinds of comprehensive and complex genetic manipulations of cells that are necessary to really understand how complex genetic circuits work,” says Elowitz, who was not involved in the research.

In future studies, the researchers plan to conduct genomewide screens of cells that have become cancerous through the loss of tumor suppressor genes such as BRCA1. If scientists can discover which genes are necessary for those cells to thrive, they may be able to develop drugs that are highly cancer-specific, Wang says.

This strategy could also be used to help find drugs that counterattack tumor cells that have developed resistance to existing chemotherapy drugs, by identifying genes that those cells rely on for survival.

The researchers also hope to use the CRISPR system to study the function of the vast majority of the genome that does not code for proteins. “Only 2 percent of the genome is coding. That’s what these two studies have focused on, that 2 percent, but really there’s that other 98 percent which for a long time has been like dark matter,” Sanjana says.

The research from the Lander/Sabatini group was funded by the National Institutes of Health; the National Human Genome Research Institute; the Broad Institute, and the National Science Foundation. The research from the Zhang group was supported by the NIH Director’s Pioneer Award; the NIH; the Keck, McKnight, Merkin, Vallee, Damon Runyon, Searle Scholars, Klingenstein, and Simon Foundations; Bob Metcalfe; the Klarman Family Foundation; the Simons Center for the Social Brain at MIT; and Jane Pauley.

Editas Medicine to develop new class of genome editing therapeutics

Editas Medicine, a transformative genome editing company, today announced it has secured a $43 million Series A financing led by Flagship Ventures, Polaris Partners and Third Rock Ventures with participation from Partners Innovation Fund. Following an explosion of high profile publications on CRISPR/Cas9 and TALENs, genome editing has emerged as one of the most exciting new areas of scientific research. These recent advances have made it possible to modify, in a targeted way, almost any gene in the human body with the ability to directly turn on, turn off or edit disease-causing genes. Editas’ mission is to translate its genome editing technology into a novel class of human therapeutics that enable precise and corrective molecular modification to treat the underlying cause of a broad range of diseases at the genetic level.

“Editas is exclusively positioned to leverage the very latest in genome editing to develop life-changing medicines for patients,” said Kevin Bitterman, Ph.D., interim president, Editas Medicine and principal, Polaris Partners. “Our suite of foundational intellectual property, combined with the proprietary know-how of our founding team and our financial resources, will enable us to rapidly translate these groundbreaking discoveries into important medicines.”

Leading Foundational Science & Team

The company’s five founders have published much of the foundational work that has elevated genome editing technology to a level where it can now be optimized and developed for therapeutic use. Feng Zhang, Ph.D., core member of the Broad Institute, Investigator at the McGovern Institute for Brain Research and joint assistant professor in the Departments of Brain and Cognitive Sciences and Biological Engineering at Massachusetts Institute of Technology; George Church, Ph.D., founding core faculty member at the Wyss Institute for Biologically Inspired Engineering at Harvard University and Robert Winthrop professor of genetics at Harvard Medical School; and Jennifer Doudna, Ph.D., Howard Hughes Medical Institute investigator and professor of biochemistry, biophysics and structural biology at the University of California, Berkeley, are eminent academic leaders who described and invented key elements of the CRISPR/Cas technology. Keith Joung, M.D., Ph.D., associate chief of pathology for research and associate pathologist at Massachusetts General Hospital and associate professor of pathology at Harvard Medical School, is a pioneer in the development and translation of genome editing technologies. David Liu, Ph.D., Howard Hughes Medical Institute investigator and professor of chemistry and chemical biology at Harvard University, is a renowned protein evolution and engineering biologist.

The company has generated substantial patent filings and has access to intellectual property covering foundational genome editing technologies, as well as essential advancements and enablements that will uniquely allow the company to translate early findings into viable human therapeutic products.

Dr. Zhang commented, “Advances in genome editing have opened the door for an entirely new and promising approach to treating disease by correcting causative errors directly in a patient’s genome. Editas is optimizing and refining existing genome editing technology to create a versatile platform for the development of potential human therapeutics.”

Genome Editing

CRISPR (clustered, regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) and TALENs (transcription activator-like effector nucleases) comprise novel gene editing methods that overcome the challenges associated with previous technologies. Early published research on CRISPR/Cas9, coupled with a growing body of work on TALENs, suggests the potential to pursue therapeutic indications that have previously been intractable to traditional gene therapy, gene knock-down or other genome modification techniques. The CRISPR/Cas9 system, the most recent and exciting approach to emerge, acts by a mechanism in which the Cas9 protein binds to specific RNA molecules. The RNA molecules then guide the Cas9 complex to the exact location in the genome that requires repair. CRISPR/Cas9 uniquely enables highly efficient knock-out, knock-down or selective editing of defective genes in the context of their natural promoters, unlocking the ability to treat the root cause of a broad range of diseases.

“Editas is poised to bring genome editing to fruition as a new therapeutic modality, essentially debugging errors in the human software that cause disease,” said Alexis Borisy, director, Editas Medicine and partner, Third Rock Ventures. “Our CRISPR/Cas9 technology is favorably differentiated due to its ability to pursue almost the entire genome, allowing broad therapeutic application and the targeting of defective genes in a highly specific, selective and efficient manner.”

Management and Board

In collaboration with its founders, Editas has assembled a leadership team and board of directors comprised of experienced investors and industry veterans with proven track records for building exceptional life sciences companies. In addition to Dr. Bitterman, the Editas leadership team includes Alexandra Glucksmann, Ph.D., interim chief operating officer and former founding employee and SVP of research and development at Cerulean Pharma; and Lou Tartaglia, Ph.D., interim chief scientific officer and partner, Third Rock Ventures.

The board of directors is composed of leaders from the Editas syndicate including Mr. Borisy; Douglas Cole, M.D., general partner, Flagship Ventures; and Terry McGuire, co-founder and general partner, Polaris Partners.

“The gene editing approaches on which Editas is based represent some of the most exciting and promising scientific breakthroughs in recent years, making it possible, for the first time, to correct the genomic defects responsible for a broad range of diseases,” said Dr. Cole. “The Editas syndicate has come together as a collaborative team dedicated to supporting and advancing the company’s revolutionary approach to improve patients’ lives. Our funds’ collective strength provides Editas the resources to translate this groundbreaking work into important therapeutics.”

About Flagship Ventures

Realizing entrepreneurial innovation is the mission of Flagship Ventures. The firm operates through two synergistic units: VentureLabs™ which invents and launches transformative companies, and Venture Capital, which finances and develops innovative, early-stage companies. Founded in 2000, and based in Cambridge, Massachusetts, Flagship Ventures manages over $900 million in capital. The Flagship team is active in three principal business sectors: therapeutics, health technologies and sustainability/clean technology. For more information, please visit www.flagshipventures.com.

About Polaris Partners

Founded in 1996, Polaris Partners has more than $3.5 billion in capital under management which we invest into a diverse portfolio of technology and healthcare companies throughout their lifecycles. From the earliest startup phases through the growth equity stages, Polaris Partners takes minority and majority positions alongside outstanding management teams to help grow industry leading companies like Ascend, Avila, Ironwood, Receptos, LogMeIn and Akamai. With offices in Boston, San Francisco and Dublin, Polaris partners with an unparalleled network of repeat CEOs, entrepreneurs, top scientists and emerging innovators who are positioned to make a significant impact in their fields and vastly improve the way in which we all live and work. The result: Hundreds of growing companies, thousands of jobs generated, and billions of dollars of value created. For more information, visit: www.polarispartners.com.

About Third Rock Ventures

Third Rock Ventures is a leading healthcare venture firm focused on investing and launching companies that make a difference in people’s lives. The Third Rock team has a unique vision for ideating and building transformative healthcare companies. Working closely with our strategic partners and entrepreneurs, Third Rock has an extensive track record for managing the value creation path to deliver exceptional performance. For more information, please visit the firm’s website at www.thirdrockventures.com.

About Partners Innovation Fund

The Partners Innovation Fund is the strategic venture fund for Partners HealthCare, founded by the Massachusetts General Hospital and Brigham and Women’s Hospital. The mission of the fund is to provide the necessary support to commercialize innovations in medical informatics, diagnostics, drugs and devices that emerge from the Partners HealthCare investigator community.

Feng Zhang named to Popular Science Brilliant 10

Popular Science magazine has named two MIT junior faculty members — Pedro Reis and Feng Zhang — to its 2013 Brilliant 10 list of young stars in science and technology. The list will appear in the magazine’s October issue.

Popular Science prides itself on revealing the innovations and ideas that are laying today’s groundwork for tomorrow’s breakthroughs, and the Brilliant 10 is one of the most exciting ways we do that,” says Jake Ward, editor-in-chief. “This collection of 10 brilliant young researchers is our chance to honor the most promising work — and the most hardworking people — in science and technology today. This year’s winners are particularly distinguished and I’m proud to welcome them all as members of the 2013 Brilliant 10.”

Pedro Reis, the Esther and Harold E. Edgerton Assistant Professor of Civil and Environmental Engineering and Mechanical Engineering, studies the mechanics of slender structures, with a particular focus on devising new ways of turning mechanical failure into functionality.

Over the past few years, Reis, 35, has published a number of eclectic and impactful papers in prominent journals. In 2009 he reported on the delamination of thin films adhered to soft foundations, which is relevant for stretchable electronics. He explained why adhesive films tear into triangular shapes, a problem that applies to both the everyday peeling of adhesive tape from a roll and the manufacturing of tapered graphene nanoribbons. Motivated by the closing of aquatic flowers, he recently discovered a new mechanism for passively pipetting liquids using a petal-shaped object. And last year inspired by a toy, Reis introduced the Buckliball, a new class of structures that uses buckling to provide origami-like folding capabilities to curved structures with potential uses for encapsulation and soft robotics.

In other work undertaken just for fun, Reis and colleagues reported in 2010 that when cats lap fluids (milk or water, for example), they take advantage of a perfect balance between gravity and inertia.

Feng Zhang, 31, is the W.M. Keck Career Development Professor in Biomedical Engineering, an assistant professor in the department of Brain and Cognitive Sciences, a member of the McGovern Institute for Brain Research and a core member of the Broad Institute. He received the award for his work on genome editing. Earlier this year he reported a powerful new way to make targeted mutations in genomic DNA, based on a bacterial system known as CRISPR. The new method will greatly accelerate the development of animal models of human genetic diseases, and may eventually make it possible to correct genetic mutations in patients. Zhang, a pioneer in optogenetics, has also recently invented a new method for controlling gene expression with light, in which light-sensitive plant proteins are engineered to create an “optical switch” that can turn other genes on or off at will.

This is the 12th annual Brilliant 10 list. Ten MIT researchers were included on previous lists.

Genome editing becomes more accurate

Earlier this year, MIT researchers developed a way to easily and efficiently edit the genomes of living cells. Now, the researchers have discovered key factors that influence the accuracy of the system, an important step toward making it safer for potential use in humans, says Feng Zhang, leader of the research team.

With this technology, scientists can deliver or disrupt multiple genes at once, raising the possibility of treating human disease by targeting malfunctioning genes. To help with that process, Zhang’s team, led by graduate students Patrick Hsu and David Scott, has now created a computer model that can identify the best genetic sequences to target a given gene.

“Using this, you will be able to identify ways to target almost every gene. Within every gene, there are hundreds of locations that can be edited, and this will help researchers narrow down which ones are better than others,” says Zhang, an assistant professor of brain and cognitive sciences at MIT and senior author of a paper describing the new model, appearing in the July 21 online edition of Nature Biotechnology.

The genome-editing system, known as CRISPR, exploits a protein-RNA complex that bacteria use to defend themselves from infection. The complex includes short RNA sequences bound to an enzyme called Cas9, which slices DNA. These RNA sequences are designed to target specific locations in the genome; when they encounter a match, Cas9 cuts the DNA.

This approach can be used either to disrupt the function of a gene or to replace it with a new one. To replace the gene, the researchers must also add a DNA template for the new gene, which would be copied into the genome after the DNA is cut.

This technique offers a much faster and more efficient way to create transgenic mice, which are often used to study human disease. Current methods for creating such mice require adding small pieces of DNA to mouse embryonic cells. However, the process is inefficient and time-consuming.

With CRISPR, many genes are edited at once, and the entire process can be done in three weeks, says Zhang, who is the W. M. Keck Career Development Professor in Biomedical Engineering at MIT and a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research. The system can also be used to create genetically modified cell lines for lab experiments much more efficiently.

Fine-tuning

Since Zhang and his colleagues first described the original system in January, more than 2,000 labs around the world have started using the system to generate their own genetically modified cell lines or animals. In the new paper, the researchers describe improvements in both the efficiency and accuracy of gene editing.

To modify genes using this system, an RNA “guide strand” complementary to a 20-base-pair sequence of targeted DNA is delivered to cells. After the RNA strand binds to the target DNA, it recruits the Cas9 enzyme, which snips the DNA in the correct location.

The researchers discovered they could minimize the chances of the Cas9-RNA complex accidentally cleaving the wrong site by making sure the target sequence is not too similar to other sequences found in the genome. They found that if an off-target sequence differs from the target sequence by three or fewer base pairs, the editing complex will likely also cleave that sequence, which could have deleterious effects for the cell.

The team’s new computer model can search any sequence within the mouse or human genome and identify 20-base-pair sequences within that region that have the least overlap with sequences elsewhere in the genome.

Another way to improve targeting specificity is by adjusting the dosage of the guide RNA, the researchers found. In general, decreasing the amount of RNA delivered minimizes damage to off-target sites but has a much smaller effect on cleavage of the target sequence. For each sequence, the “sweet spot” with the best balance of high on-target effects and low off-target effects can be calculated, Zhang says.

“The real value of this paper is that it does a very comprehensive and systematic analysis to understand the causes of off-target effects. That analysis suggests a lot of possible ways to eliminate or reduce off-target effects,” says Michael Terns, a professor of biochemistry and molecular biology at the University of Georgia who was not part of the research team.

Zhang and his colleagues also optimized the structure of the RNA guide needed for efficient activation of Cas9. In the January paper describing the original system, the researchers found that two separate RNA strands working together — one that binds to the target DNA and another that recruits Cas9 — produced better results than when those two strands were fused together before delivery. However, in experiments reported in the new paper, the researchers found that they could boost the efficiency of the fused RNA strand by making the strand longer. These longer RNA guide strands include a hairpin structure that may stabilize the molecules and help them interact with Cas9, Zhang says.

Zhang’s team is now working on further improving the specificity of the system, and plans to start generating cell lines and animals that could be used to study how the brain develops and builds neural circuits. By disrupting genes known to be involved in those processes, they can learn more about how they work and how they are impaired in neurological disease.

The research was funded by a National Institutes of Health Director’s Pioneer Award; an NIH Transformative R01 grant; the Keck, McKnight, Damon Runyan, Searle Scholars, Klingenstein and Simons foundations; Bob Metcalfe; and Jane Pauley.