Category: Uncategorized

Study finds brain connections key to learning

Anne Trafton |

A new study from MIT reveals that a brain region dedicated to reading has connections for that skill even before children learn to read.

By scanning the brains of children before and after they learned to read, the researchers found that they could predict the precise location where each child’s visual word form area (VWFA) would develop, based on the connections of that region to other parts of the brain.

Neuroscientists have long wondered why the brain has a region exclusively dedicated to reading — a skill that is unique to humans and only developed about 5,400 years ago, which is not enough time for evolution to have reshaped the brain for that specific task. The new study suggests that the VWFA, located in an area that receives visual input, has pre-existing connections to brain regions associated with language processing, making it ideally suited to become devoted to reading.

“Long-range connections that allow this region to talk to other areas of the brain seem to drive function,” says Zeynep Saygin, a postdoc at MIT’s McGovern Institute for Brain Research. “As far as we can tell, within this larger fusiform region of the brain, only the reading area has these particular sets of connections, and that’s how it’s distinguished from adjacent cortex.”

Saygin is the lead author of the study, which appears in the Aug. 8 issue of Nature Neuroscience. Nancy Kanwisher, the Walter A. Rosenblith Professor of Brain and Cognitive Sciences and a member of the McGovern Institute, is the paper’s senior author.

Specialized for reading

The brain’s cortex, where most cognitive functions occur, has areas specialized for reading as well as face recognition, language comprehension, and many other tasks. Neuroscientists have hypothesized that the locations of these functions may be determined by prewired connections to other parts of the brain, but they have had few good opportunities to test this hypothesis.

Reading presents a unique opportunity to study this question because it is not learned right away, giving scientists a chance to examine the brain region that will become the VWFA before children know how to read. This region, located in the fusiform gyrus, at the base of the brain, is responsible for recognizing strings of letters.

Children participating in the study were scanned twice — at 5 years of age, before learning to read, and at 8 years, after they learned to read. In the scans at age 8, the researchers precisely defined the VWFA for each child by using functional magnetic resonance imaging (fMRI) to measure brain activity as the children read. They also used a technique called diffusion-weighted imaging to trace the connections between the VWFA and other parts of the brain.

The researchers saw no indication from fMRI scans that the VWFA was responding to words at age 5. However, the region that would become the VWFA was already different from adjacent cortex in its connectivity patterns. These patterns were so distinctive that they could be used to accurately predict the precise location where each child’s VWFA would later develop.

Although the area that will become the VWFA does not respond preferentially to letters at age 5, Saygin says it is likely that the region is involved in some kind of high-level object recognition before it gets taken over for word recognition as a child learns to read. Still unknown is how and why the brain forms those connections early in life.

Pre-existing connections

Kanwisher and Saygin have found that the VWFA is connected to language regions of the brain in adults, but the new findings in children offer strong evidence that those connections exist before reading is learned, and are not the result of learning to read, according to Stanislas Dehaene, a professor and the chair of experimental cognitive psychology at the College de France, who wrote a commentary on the paper for Nature Neuroscience.

“To genuinely test the hypothesis that the VWFA owes its specialization to a pre-existing connectivity pattern, it was necessary to measure brain connectivity in children before they learned to read,” wrote Dehaene, who was not involved in the study. “Although many children, at the age of 5, did not have a VWFA yet, the connections that were already in place could be used to anticipate where the VWFA would appear once they learned to read.”

The MIT team now plans to study whether this kind of brain imaging could help identify children who are at risk of developing dyslexia and other reading difficulties.

“It’s really powerful to be able to predict functional development three years ahead of time,” Saygin says. “This could be a way to use neuroimaging to try to actually help individuals even before any problems occur.”

Divide and conquer

Anne Trafton |

Cell populations are remarkably diverse—even within the same tissue or cell type. Each cell, no matter how similar it appears to its neighbor, behaves and responds to its environment in its own way depending on which of its genes are expressed and to what degree. How genes are expressed in each cell—how RNA is “read” and turned into proteins—determines what jobs the cell performs in the body.

Traditionally, researchers have taken an en masse approach to studying gene expression, extracting an averaged measurement derived from an entire cell population. But over the past few years, single cell sequencing has emerged as a transformative tool, enabling scientists to look at gene expression within cells at an unprecedented resolution. With single-cell technologies, researchers have been able to examine the heterogeneity within cell populations; identify rare cells; observe interactions between diverse cell types; and better understand how these interactions influence health and disease.

This week in Science, researchers from the labs of Broad core institute members Aviv Regev and Feng Zhang, of MIT and MIT’s McGovern Institute respectively, report on their newest contribution to this field: Div-Seq, a method that enables the study of previously intractable and rare cell types in the brain. The study’s first authors, Naomi Habib, a postdoctoral fellow in the Regev and Zhang labs, and Yinqing Li, also a postdoc in the Zhang lab, sat down to answer questions about this groundbreaking approach.

Why is it so important to study neurons at the single cell level?

Li: Neuropsychiatric diseases are often too complex to find an effective treatment, partly because the neurons, that underly the disease are heterogeneous. Only when we have a full atlas of every neuron type at single-cell resolution—and figure out which ones are the cause of the pathology—can we develop a targeted and effective therapy. With this goal in mind, we developed sNuc-Seq and Div-Seq to make it technologically possible to profile neurons from the adult brain at significantly improved resolution, fidelity, and sensitivity.

Scientifically, what was the need that you were trying to address when you started this study?

Habib: Going into this study we were specifically interested in studying so-called “newborn” neurons, which are rare and hard to find. We think of our brain as being non-regenerative, but in fact there are rare, neuronal stem cells in specific areas of the brain that divide and create new neurons throughout our lives. We wanted to understand how gene expression changed as these cells developed. Typically when people studied gene expression in the brain they just mashed up tissue and took average measurements from that mixture. Such “bulk” measurements are hard to interpret and we lose the gene expression signals that come from individual cell types.

When I joined the Zhang and Regev labs, some of the first single cell papers were coming out, and it seemed like the perfect approach for advancing the way we do neuroscience research; we could measure RNA at the single cell level and really understand what different cell types were there, including rare cells, and what they contribute to different brain functions. But there was a problem. Neurons do not look like regular cells: they are intricately connected. In the process of separating them, the cells do not stay intact and their RNA gets damaged, and this problem increases with age.

So what was your solution?

Habib: Isolating single neurons is problematic, but the nucleus is nice and round and relatively easy to isolate. That led us to ask, “Why not try single nucleus RNA sequencing instead of single cell sequencing?” We called it “sNuc-Seq.”

It worked well. We get a lot of information from the RNA in the nucleus; we can learn what cell type we’re looking at, what state of development it’s in, and what kind of processes are going on in the cell—all of the key information we would want to get from RNA sequencing.

Then, to make it possible to find the rare newborn neurons, we developed Div-Seq. It’s based on sNuc-Seq, but we introduce a compound that incorporates into DNA and labels the DNA while it’s replicating, so it’s specific for newly divided cells. Because we already isolated the nuclei, it’s fairly simple from there to fluorescently tag the labeled cells, sort them, and get RNA for sequencing.

You tested this method while preparing your paper. What did you find?

Habib: We studied “newborn” neurons from the brain across multiple time-points. We could see the changes in gene expression that occur throughout adult neurogenesis; the cells transition from state-to-state—from stem cells to mature neurons—and during these transitions, we found a coordinated change in the expression of hundreds of genes. It was beautiful to see these signatures, and they enabled us to pinpoint regulatory genes expressed during specific points of the cell differentiation process.

We were also able to look at where regeneration occurs. We decided to look in the spinal cord because there is a lot of interest in understanding the potential of regeneration to help with spinal cord injury. Div-Seq enabled us to scan millions of neurons and isolate the small percentage that were dividing and characterize each by its RNA signature. We found that within the spinal cord there is ongoing regeneration of a specific type of neuron—GABAergic neurons. That was an exciting finding that also showed the utility of our method.

Are the data you get from this method compatible with data from previous single-cell techniques?

Li: Because this method is specifically designed to address the particular challenges of profiling neurons, the data from this method is distinct from that obtained from previous single-cell techniques. Since the data was new to this approach, a novel computational tool was developed in this project in order to fully reveal the rich information, which is now available to the scientific community.

Are there other benefits of using this method?

Habib: Single nucleus RNA-seq enables the study of the adult and aging brain at the single cell level, which is now being applied to study cellular diversity across the brain during health and disease. Our approach also makes it easier to explore any complex tissue where single cells are hard to obtain for technical reasons. One important aspect is that it works on frozen and fixed tissue, which opens up opportunities to study human samples, such as biopsies, that may be collected overseas or frozen for days or even years.

Additionally, Div-Seq opens new ways to look at the rare process of adult neurogenesis and other regenerative processes that might have been challenging before. Because Div- Seq specifically labels dividing cells, it is a great tool to use to see what cells are dividing in a given tissue and to track gene expression changes over time.

What is the endgame of studying these processes? Can you put this work in context of human health and disease?

Li: We hope that the methods in this study will provide a starting point and method for future work on neuropsychiatric diseases. As we expand our understanding of cell types and their signatures, we can start to ask questions like: Which cells express disease associated genes? Where are these cells located in the brain? What other genes are expressed in these cells, and which might serve as potential drug targets? This approach could help bridge human genetic association studies and molecular neurobiology and open new windows into disease pathology and potential treatments.

Habib: These two methods together enable many applications, which were either very hard or impossible to do before. For example, we characterized the cellular diversity of a region of the brain important for learning and memory—the first region affected in Alzheimer’s disease. Having that understanding—knowing what the normal state of cells is at the molecular level and what went wrong in each individual cell type—can advance our understanding of the disease and perhaps aid in the search for a treatment. We are also excited by the prospect of finding naturally-occurring regeneration in the brain and spine, which could have implications for the field of regenerative medicine in treating, for example, neuronal degeneration or spinal injury.

Paper cited:

Habib N, Li Y, et al. Div-Seq: Single nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science. Online July 28, 2016.

Baby diapers inspired this new way to study the brain

Anne Trafton |

TEDSummit June 2016

Neuroengineer Ed Boyden wants to know how the tiny biomolecules in our brains generate emotions, thoughts and feelings — and he wants to find the molecular changes that lead to disorders like epilepsy and Alzheimer’s. Rather than magnify these invisible structures with a microscope, he wondered: What if we physically enlarge them and make them easier to see? Learn how the same polymers used to make baby diapers swell could be a key to better understanding our brains.

Building 46 Retreat 2016

Anne Trafton |

On June 6, McGovern researchers and staff joined with colleagues from the Picower Institute for Learning and Memory and the Department of Brain and Cognitive Sciences for a joint retreat in Newport, Rhode Island.The overnight retreat featured talks, a poster session, a dance party and a clam bake. Photo: McGovern Institute

Seeing RNA at the nanoscale

Anne Trafton |

Cells contain thousands of messenger RNA molecules, which carry copies of DNA’s genetic instructions to the rest of the cell. MIT engineers have now developed a way to visualize these molecules in higher resolution than previously possible in intact tissues, allowing researchers to precisely map the location of RNA throughout cells.

Key to the new technique is expanding the tissue before imaging it. By making the sample physically larger, it can be imaged with very high resolution using ordinary microscopes commonly found in research labs.

“Now we can image RNA with great spatial precision, thanks to the expansion process, and we also can do it more easily in large intact tissues,” says Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT, a member of MIT’s Media Lab and McGovern Institute for Brain Research, and the senior author of a paper describing the technique in the July 4 issue of Nature Methods.

Studying the distribution of RNA inside cells could help scientists learn more about how cells control their gene expression and could also allow them to investigate diseases thought to be caused by failure of RNA to move to the correct location.

Boyden and colleagues first described the underlying technique, known as expansion microscopy (ExM), last year, when they used it to image proteins inside large samples of brain tissue. In a paper appearing in Nature Biotechnology on July 4, the MIT team has now presented a new version of the technology that employs off-the-shelf chemicals, making it easier for researchers to use.

MIT graduate students Fei Chen and Asmamaw Wassie are the lead authors of the Nature Methods paper, and Chen and graduate student Paul Tillberg are the lead authors of the Nature Biotechnology paper.

A simpler process

The original expansion microscopy technique is based on embedding tissue samples in a polymer that swells when water is added. This tissue enlargement allows researchers to obtain images with a resolution of around 70 nanometers, which was previously possible only with very specialized and expensive microscopes.

However, that method posed some challenges because it requires generating a complicated chemical tag consisting of an antibody that targets a specific protein, linked to both a fluorescent dye and a chemical anchor that attaches the whole complex to a highly absorbent polymer known as polyacrylate. Once the targets are labeled, the researchers break down the proteins that hold the tissue sample together, allowing it to expand uniformly as the polyacrylate gel swells.

In their new studies, to eliminate the need for custom-designed labels, the researchers used a different molecule to anchor the targets to the gel before digestion. This molecule, which the researchers dubbed AcX, is commercially available and therefore makes the process much simpler.

AcX can be modified to anchor either proteins or RNA to the gel. In the Nature Biotechnology study, the researchers used it to anchor proteins, and they also showed that the technique works on tissue that has been previously labeled with either fluorescent antibodies or proteins such as green fluorescent protein (GFP).

“This lets you use completely off-the-shelf parts, which means that it can integrate very easily into existing workflows,” Tillberg says. “We think that it’s going to lower the barrier significantly for people to use the technique compared to the original ExM.”

Using this approach, it takes about an hour to scan a piece of tissue 500 by 500 by 200 microns, using a light sheet fluorescence microscope. The researchers showed that this technique works for many types of tissues, including brain, pancreas, lung, and spleen.

Imaging RNA

In the Nature Methods paper, the researchers used the same kind of anchoring molecule but modified it to target RNA instead. All of the RNAs in the sample are anchored to the gel, so they stay in their original locations throughout the digestion and expansion process.

After the tissue is expanded, the researchers label specific RNA molecules using a process known as fluorescence in situ hybridization (FISH), which was originally developed in the early 1980s and is widely used. This allows researchers to visualize the location of specific RNA molecules at high resolution, in three dimensions, in large tissue samples.

This enhanced spatial precision could allow scientists to explore many questions about how RNA contributes to cellular function. For example, a longstanding question in neuroscience is how neurons rapidly change the strength of their connections to store new memories or skills. One hypothesis is that RNA molecules encoding proteins necessary for plasticity are stored in cell compartments close to the synapses, poised to be translated into proteins when needed.

With the new system, it should be possible to determine exactly which RNA molecules are located near the synapses, waiting to be translated.
“People have found hundreds of these locally translated RNAs, but it’s hard to know where exactly they are and what they’re doing,” Chen says. “This technique would be useful to study that.”

Boyden’s lab is also interested in using this technology to trace the connections between neurons and to classify different subtypes of neurons based on which genes they are expressing.

The research was funded by the Open Philanthropy Project, the New York Stem Cell Foundation Robertson Award, the National Institutes of Health, the National Science Foundation, and Jeremy and Joyce Wertheimer.

Schwerpunkt

Anne Trafton |

There’s a new focal point at the McGovern Institute and it’s called Schwerpunkt. From the German word meaning “main focus” or “focal point,” Schwerpunkt is a suspended anamorphic neuron sculpture by Ralph Helmick.

Anamorphosisis a distorted image that becomes recognizable only when viewed from a particular point. The word anamorphosis originates from the Greek words anamorphoun (to transform) and morphe (form, shape). Examples of anamorphic art date back to the early Renaissance, with Leonardo’s Eye (Leonardo da Vinci, c. 1485) being the first example of perspective anamorphosis in modern times.

In Schwerpunkt, one hundred gold neurons seemingly float at random above the McGovern Institute lobby and make a beautiful transformation at the focal point on the third floor atrium level. This sculpture is made possible by a gift from Hugo Shong in memory of Patrick J. McGovern.

Photos from the June 28 opening of Schwerpunkt may be viewed below.

Feng Zhang named 2016 Tang Prize Laureate

Anne Trafton |

Feng Zhang, a core institute member of the Broad Institute, an investigator at the McGovern Institute for Brain Research at MIT, and W. M. Keck Career Development Associate Professor in MIT’s Department of Brain and Cognitive Sciences with a joint appointment in Biological Engineering, has been named a 2016 Tang Prize Laureate in Biopharmaceutical Science for his role in developing the CRISPR-Cas9 gene-editing system and demonstrating pioneering uses in eukaryotic cells.

The Tang Prize is a biennial international award granted by judges convened by Academia Sinica, Taiwan’s top academic research institution.

In January 2013 Zhang and his team were first to report CRISPR-based genome editing in mammalian cells, in what has become the most-cited paper in the CRISPR field. Zhang shares the award with Emmanuelle Charpentier of the Max Planck Institute and Jennifer A. Doudna of the University of California at Berkeley.

“To be recognized with the Tang Prize is an incredible honor for our team and it demonstrates the impact of the entire CRISPR field, which began with microbiologists and will continue for years to come as we advance techniques for genome editing,” Zhang said. “Thanks to the scientific community’s commitment to collaboration and an emphasis on sharing across institutions and borders, the last few years have seen a revolution in our ability to understand cancer, autoimmune disease, mental health and infectious disease. We are entering a remarkable period in our understanding of human health.”

Although Zhang is well-known for his work with CRISPR, the 34-year-old scientist has a long track record of innovation. As a graduate student at Stanford University, Zhang worked with Karl Deisseroth and Edward Boyden, who is now also a professor at MIT, to develop optogenetics, in which neuronal activity can be controlled with light. The three shared the Perl-UNC Prize in Neuroscience in 2012 as recognition of these efforts. Zhang has also received the National Science Foundation’s Alan T. Waterman Award (2014), the Jacob Heskel Gabbay Award in Biotechnology and Medicine (2014, shared with Charpentier and Doudna), the Tsuneko & Reiji Okazaki Award (2015), the Human Genome Organization (HUGO) Chen New Investigator Award (2016), and the Canada Gairdner International Award (2016, shared with Charpentier and Doudna, as well as Rodolphe Barrangou from North Carolina State University and Philippe Horvath from DuPont Nutrition & Health).

One of Zhang’s long-term goals is to use genome-editing technologies to better understand the nervous system and develop new approaches to the treatment of neurological and psychiatric diseases. The Zhang lab has shared CRISPR-Cas9 components in response to more than 30,000 requests from academic laboratories around the world and has trained thousands of researchers in the use of CRISPR-Cas9 genome-editing technology through in-person events and online opportunities. In his current research, he and his students and postdoctoral fellows continue to improve and expand the gene-editing toolbox.

“Professor Zhang’s lab has become a global hub for CRISPR research,” said MIT Provost Martin Schmidt. “His group has shared CRISPR-Cas9 components with tens of thousands of scientists, and has trained many more in the use of CRISPR-Cas9 technology. The Tang Prize is a fitting recognition of all that Professor Zhang has done, and continues to do, to advance this field.”

“CRISPR is a powerful new tool that is transforming biological science while promising revolutionary advances in health care,” said Michael Sipser, dean of the School of Science and Donner Professor of Mathematics at MIT. “We are delighted that Feng Zhang, together with Jennifer Doudna and Emmanuelle Charpentier, have been recognized with the Tang Prize.”

“It is wonderful that the Academia Sinica has chosen to recognize the CRISPR field with this year’s Tang Prize,” said Eric Lander, founding director of the Broad Institute. “On behalf of my colleagues at the Broad and MIT, I wish to congratulate Feng, as well as Emmanuelle Charpentier and Jennifer Doudna, along with the many teams of scientists and all others who have contributed to these transformational discoveries.”

Founded in 2012 by Samuel Yin, the Tang Prize is a non-governmental, non-profit educational foundation that awards outstanding contributions in four fields: sustainable development, biopharmaceutical science, sinology, and rule of law. Nomination and selection of laureates is conducted by the Academia Sinica. Each award cycle, the academy convenes four autonomous selection committees, each consisting of an assembly of international experts, until a consensus on the recipients is reached. Recipients are chosen on the basis of the originality of their work along with their contributions to society, irrespective of nationality, ethnicity, gender, and political affiliation.

This year marks the second awarding of the prize. This year’s awardees will receive the medal, diploma, and cash prize at an award ceremony on September 25 in Taipei. Recipients in each Tang Prize category receive a total of approximately $1.24 million (USD) and a grant of approximately $311,000 (USD). The cash prize and grants are divided equally among joint recipients in each category.

 

Baby Brains: Unlocking Our Humanity

Anne Trafton |

At MIT, Rebecca Saxe studies human brain development, in order to understand how the human mind is built. The challenges and rewards of this research connect her experiences, as a scientist and as a mother.

Project: BIG BRAIN

Anne Trafton |

To celebrate a century in Cambridge, MIT invited members of its community to participate in a unique competition on May 7, 2016 called “Moving Day.” Points would be awarded to teams who crossed the Charles River with the most creativity, spirit and ingenuity. This 3-minute video tells the story of our winning entry: an 8-foot, 200-pound brain based on actual MRI data, constructed and rolled across the Mass Ave bridge by a team of people from MIT’s brain and cognitive sciences community.

New CRISPR system for targeting RNA

Anne Trafton |

Researchers from MIT and the Broad Institute of MIT and Harvard, as well as the National Institutes of Health, Rutgers University at New Brunswick, and the Skolkovo Institute of Science and Technology, have characterized a new CRISPR system that targets RNA, rather than DNA.

The new approach has the potential to open a powerful avenue in cellular manipulation. Whereas DNA editing makes permanent changes to the genome of a cell, the CRISPR-based RNA-targeting approach may allow researchers to make temporary changes that can be adjusted up or down, and with greater specificity and functionality than existing methods for RNA interference.

In a study published today in Science, Feng Zhang and colleagues at the Broad Institute and the McGovern Institute for Brain Research at MIT, along with co-authors Eugene Koonin and his colleagues at the NIH, and Konstantin Severinov of Rutgers University at New Brunswick and Skoltech, report the identification and functional characterization of C2c2, an RNA-guided enzyme capable of targeting and degrading RNA.

The findings reveal that C2c2 — which is the first naturally occurring CRISPR system known to target only RNA, and was discovered by this collaborative group in October 2015 — helps protect bacteria against viral infection. The researchers demonstrate that C2c2 can be programmed to cleave particular RNA sequences in bacterial cells, which would make it an important addition to the molecular biology toolbox.

The RNA-focused action of C2c2 complements the CRISPR-Cas9 system, which targets DNA, the genomic blueprint for cellular identity and function. The ability to target only RNA, which helps carry out the genomic instructions, offers the ability to specifically manipulate RNA in a high-throughput manner — and to manipulate gene function more broadly. This has the potential to accelerate progress to understand, treat, and prevent disease.

“C2c2 opens the door to an entirely new frontier of powerful CRISPR tools,” said senior author Feng Zhang, who is a core institute member of the Broad Institute, an investigator at the McGovern Institute for Brain Research at MIT, and the W. M. Keck Career Development Associate Professor in MIT’s Department of Brain and Cognitive Sciences.
“There are an immense number of possibilities for C2c2, and we are excited to develop it into a platform for life science research and medicine.”

“The study of C2c2 uncovers a fundamentally novel biological mechanism that bacteria seem to use in their defense against viruses,” said Eugene Koonin, senior author and leader of the Evolutionary Genomics Group at the NIH. “Applications of this strategy could be quite striking.”

Currently, the most common technique for performing gene knockdown is small interfering RNA (siRNA). According to the researchers, C2c2 RNA-editing methods suggest greater specificity and hold the potential for a wider range of applications, such as:

  • Adding modules to specific RNA sequences to alter their function — how they are translated into proteins — which would make them valuable tools for large-scale screens and constructing synthetic regulatory networks; and
  • Harnessing C2c2 to fluorescently tag RNAs as a means to study their trafficking and subcellular localization.

In this work, the team was able to precisely target and remove specific RNA sequences using C2c2, lowering the expression level of the corresponding protein. This suggests C2c2 could represent an alternate approach to siRNA, complementing the specificity and simplicity of CRISPR-based DNA editing and offering researchers adjustable gene “knockdown” capability using RNA.

C2c2 has advantages that make it suitable for tool development:

  • C2c2 is a two-component system, requiring only a single guide RNA to function; and
  • C2c2 is genetically encodable — meaning the necessary components can be synthesized as DNA for delivery into tissue and cells.

“C2c2’s greatest impact may be made on our understanding of the role of RNA in disease and cellular function,” said co-first author Omar Abudayyeh, a graduate student in the Zhang Lab.