Finding a way in

Our perception of the world arises within the brain, based on sensory information that is sometimes ambiguous, allowing more than one interpretation. Familiar demonstrations of this point include the famous Necker cube and the “duck-rabbit” drawing (right) in which two different interpretations flip back and forth over time.

Another example is binocular rivalry, in which the two eyes are presented with different images that are perceived in alternation. Several years ago, this phenomenon caught the eye of Caroline Robertson, who is now a Harvard Fellow working in the lab of McGovern Investigator Nancy Kanwisher. Back when she was a graduate student at Cambridge University, Robertson realized that binocular rivalry might be used to probe the basis of autism, among the most mysterious of all brain disorders.

Robertson’s idea was based on the hypothesis that autism involves an imbalance between excitation and inhibition within the brain. Although widely supported by indirect evidence, this has been very difficult to test directly in human patients. Robertson realized that binocular rivalry might provide a way to perform such a test. The perceptual switches that occur during rivalry are thought to involve competition between different groups of neurons in the visual cortex, each group reinforcing its own interpretation via excitatory connections while suppressing the alternative interpretation through inhibitory connections. Thus, if the balance is altered in the brains of people with autism, the frequency of switching might also be different, providing a simple and easily measurable marker of the disease state.

To test this idea, Robertson recruited adults with and without autism, and presented them with two distinct and differently colored images in each eye. As expected, their perceptions switched back and forth between the two images, with short periods of mixed perception in between. This was true for both groups, but when she measured the timing of these switches, Robertson found that individuals with autism do indeed see the world in a measurably different way than people without the disorder. Individuals with autism cycle between the left and right images more slowly, with the intervening periods of mixed perception lasting longer than in people without autism. The more severe their autistic symptoms, as determined by a standard clinical behavioral evaluation, the greater the difference.

Robertson had found a marker for autism that is more objective than current methods that involve one person assessing the behavior of another. The measure is immediate and relies on brain activity that happens automatically, without people thinking about it. “Sensation is a very simple place to probe,” she says.

A top-down approach

When she arrived in Kanwisher’s lab, Robertson wanted to use brain imaging to probe the basis for the perceptual phenomenon that she had discovered. With Kanwisher’s encouragement, she began by repeating the behavioral experiment with a new group of subjects, to check that her previous results were not a fluke. Having confirmed that the finding was real, she then scanned the subjects using an imaging method called Magnetic Resonance Spectroscopy (MRS), in which an MRI scanner is reprogrammed to measure concentrations of neurotransmitters and other chemicals in the brain. Kanwisher had never used MRS before, but when Robertson proposed the experiment, she was happy to try it. “Nancy’s the kind of mentor who could support the idea of using a new technique and guide me to approach it rigorously,” says Robertson.

For each of her subjects, Robertson scanned their brains to measure the amounts of two key neurotransmitters, glutamate, which is the main excitatory transmitter in the brain, and GABA, which is the main source of inhibition. When she compared the brain chemistry to the behavioral results in the binocular rivalry task, she saw something intriguing and unexpected. In people without autism, the amount of GABA in the visual cortex was correlated with the strength of the suppression, consistent with the idea that GABA enables signals from one eye to inhibit those from the other eye. But surprisingly, there was no such correlation in the autistic individuals—suggesting that GABA was somehow unable to exert its normal suppressive effect. It isn’t yet clear exactly what is going wrong in the brains of these subjects, but it’s an early flag, says Robertson. “The next step is figuring out which part of the pathway is disrupted.”

A bottom-up approach

Robertson’s approach starts from the top-down, working backward from a measurable behavior to look for brain differences, but it isn’t the only way in. Another approach is to start with genes that are linked to autism in humans, and to understand how they affect neurons and brain circuits. This is the bottom-up approach of McGovern Investigator Guoping Feng, who studies a gene called Shank3 that codes for a protein that helps build synapses, the connections through which neurons send signals to each other. Several years ago Feng knocked out Shank3 in mice, and found that the mice exhibited behaviors reminiscent of human autism, including repetitive grooming, anxiety, and impaired social interaction and motor control.

These earlier studies involved a variety of different mutations that disabled the Shank3 gene. But when postdoc Yang Zhou joined Feng’s lab, he brought a new perspective. Zhou had come from a medical background and wanted to do an experiment more directly connected to human disease. So he suggested making a mouse version of a Shank3 mutation seen in human patients, and testing its effects.

Zhou’s experiment would require precise editing of the mouse Shank3 gene, previously a difficult and time-consuming task. But help was at hand, in the form of a collaboration with McGovern Investigator Feng Zhang, a pioneer in the development of genome-editing methods.

Using Zhang’s techniques, Zhou was able to generate mice with two different mutations: one that had been linked to human autism, and another that had been discovered in a few patients with schizophrenia.

The researchers found that mice with the autism-related mutation exhibited behavioral changes at a young age that paralleled behaviors seen in children with autism. They also found early changes in synapses within a brain region called the striatum. In contrast, mice with the schizophrenia-related gene appeared normal until adolescence, and then began to exhibit changes in behavior and also changes in the prefrontal cortex, a brain region that is implicated in human schizophrenia. “The consequences of the two different Shank3 mutations were quite different in certain aspects, which was very surprising to us,” says Zhou.

The fact that different mutations in just one gene can produce such different results illustrates exactly how complex these neuropsychiatric disorders can be. “Not only do we need to study different genes, but we also have to understand different mutations and which brain regions have what defects,” says Feng, who received funding from the Poitras Center for Affective Disorders research and the Simons Center for the Social Brain. Robertson and Kanwisher were also supported by the Simons Center.

Surprising plasticity

The brain alterations that lead to autism are thought to arise early in development, long before the condition is diagnosed, raising concerns that it may be difficult to reverse the effects once the damage is done. With the Shank3 knockout mice, Feng and his team were able to approach this question in a new way, asking what would happen if the missing gene were to be restored in adulthood.

To find the answer, lab members Yuan Mei and Patricia Monteiro, along with Zhou, studied another strain of mice, in which the Shank3 gene was switched off but could be reactivated at any time by adding a drug to their diet. When adult mice were tested six weeks after the gene was switched back on, they no longer showed repetitive grooming behaviors, and they also showed normal levels of social interaction with other mice, despite having grown up without a functioning Shank3 gene. Examination of their brains confirmed that many of the synaptic alterations were also rescued when the gene was restored.

Not every symptom was reversed by this treatment; even after six weeks or more of restored Shank3 expression, the mice continued to show heightened anxiety and impaired motor control. But even these deficits could be prevented if the Shank3 gene was restored earlier in life, soon after birth.

The results are encouraging because they indicate a surprising degree of brain plasticity, persisting into adulthood. If the results can be extrapolated to human patients, they suggest that even in adulthood, autism may be at least partially reversible if the right treatment can be found. “This shows us the possibility,” says Zhou. “If we could somehow put back the gene in patients who are missing it, it could help improve their life quality.”

Converging paths

Robertson and Feng are approaching the challenge of autism from different starting points, but already there are signs of convergence. Feng is finding early signs that his Shank3 mutant mice may have an altered balance of inhibitory and excitatory circuits, consistent with what Robertson and Kanwisher have found in humans.

Feng is continuing to study these mice, and he also hopes to study the effects of a similar mutation in non-human primates, whose brains and behaviors are more similar to those of humans than rodents. Robertson, meanwhile, is planning to establish a version of the binocular rivalry test in animal models, where it is possible to alter the balance between inhibition and excitation experimentally (for example, via a genetic mutation or a drug treatment). If this leads to changes in binocular rivalry, it would strongly support the link to the perceptual changes seen in humans.

One challenge, says Robertson, will be to develop new methods to measure the perceptions of mice and other animals. “The mice can’t tell us what they are seeing,” she says. “But it would also be useful in humans, because it would allow us to study young children and patients who are non-verbal.”

A multi-pronged approach

The imbalance hypothesis is a promising lead, but no single explanation is likely to encompass all of autism, according to McGovern director Bob Desimone. “Autism is a notoriously heterogeneous condition,” he explains. “We need to try multiple approaches in order to maximize the chance of success.”

McGovern researchers are doing exactly that, with projects underway that range from scanning children to developing new molecular and microscopic methods for examining brain changes in animal disease models. Although genetic studies provide some of the strongest clues, Desimone notes that there is also evidence for environmental contributions to autism and other brain disorders. “One that’s especially interesting to us is a maternal infection and inflammation, which in mice at least can affect brain development in ways we’re only beginning to understand.”

The ultimate goal, says Desimone, is to connect the dots and to understand how these diverse human risk factors affect brain function. “Ultimately, we want to know what these different pathways have in common,” he says. “Then we can come up with rational strategies for the development of new treatments.”

Newly discovered neural connections may be linked to emotional decision-making

MIT neuroscientists have discovered connections deep within the brain that appear to form a communication pathway between areas that control emotion, decision-making, and movement. The researchers suspect that these connections, which they call striosome-dendron bouquets, may be involved in controlling how the brain makes decisions that are influenced by emotion or anxiety.

This circuit may also be one of the targets of the neural degeneration seen in Parkinson’s disease, says Ann Graybiel, an Institute Professor at MIT, member of the McGovern Institute for Brain Research, and the senior author of the study.

Graybiel and her colleagues were able to find these connections using a technique developed at MIT known as expansion microscopy, which enables scientists to expand brain tissue before imaging it. This produces much higher-resolution images than would otherwise be possible with conventional microscopes.

That technique was developed in the lab of Edward Boyden, an associate professor of biological engineering and brain and cognitive sciences at the MIT Media Lab, who is also an author of this study. Jill Crittenden, a research scientist at the McGovern Institute, is the lead author of the paper, which appears in the Proceedings of the National Academy of Sciences the week of Sept. 19.

Tracing a circuit

In this study, the researchers focused on a small region of the brain known as the striatum, which is part of the basal ganglia — a cluster of brain centers associated with habit formation, control of voluntary movement, emotion, and addiction. Malfunctions of the basal ganglia have been associated with Parkinson’s and Huntington’s diseases, as well as autism, obsessive-compulsive disorder, and Tourette’s syndrome.

Much of the striatum is uncharted territory, but Graybiel’s lab has previously identified clusters of cells there known as striosomes. She also found that these clusters receive very specific input from parts of the brain’s prefrontal cortex involved in processing emotions, and showed that this communication pathway is necessary for making decisions that require an anxiety-provoking cost-benefit analysis, such as choosing whether to take a job that pays more but forces a move away from family and friends.

Her studies also suggested that striosomes relay information to cells within a region called the substantia nigra, one of the brain’s main dopamine-producing centers. Dopamine has many functions in the brain, including roles in initiating movement and regulating mood.

To figure out how these regions might be communicating, Graybiel, Crittenden, and their colleagues used expansion microscopy to image the striosomes and discovered extensive connections between those clusters of cells and dopamine-producing cells of the substantia nigra. The dopamine-producing cells send down many tiny extensions known as dendrites that become entwined with axons that come up to meet them from the striosomes, forming a bouquet-like structure.

“With expansion microscopy, we could finally see direct connections between these cells by unraveling their unusual rope-like bundles of axons and dendrites,” Crittenden says. “What’s really exciting to us is we can see that it’s small discrete clusters of dopamine cells with bundles that are being targeted.”

Hard decisions

This finding expands the known decision-making circuit so that it encompasses the prefrontal cortex, striosomes, and a subset of dopamine-producing cells. Together, the striosomes may be acting as a gatekeeper that absorbs sensory and emotional information coming from the cortex and integrates it to produce a decision on how to react, which is initiated by the dopamine-producing cells, the researchers say.

To explore that possibility, the researchers plan to study mice in which they can selectively activate or shut down the striosome-dendron bouquet as the mice are prompted to make decisions requiring a cost-benefit analysis.

The researchers also plan to investigate whether these connections are disrupted in mouse models of Parkinson’s disease. MRI studies and postmortem analysis of brains of Parkinson’s patients have shown that death of dopamine cells in the substantia nigra is strongly correlated with the disease, but more work is needed to determine if this subset overlaps with the dopamine cells that form the striosome-dendron bouquets.

From Cells to Cognition: Understanding Brain Function in Health and Disease

TITLE: “From Cells to Cognition: Understanding Brain Function in Health and Disease”
DATE: Tuesday November 8, 2016
TIME: 8:30am – 5:00pm
LOCATION: MIT Bldg 46-3002 (Singleton Auditorium)
QUESTIONS? Naomi Berkowitz | naomiber@mit.edu | 617.715.5396
Registration is now closed.

 

 

PROGRAM

8:30 am
Continental Breakfast Served in Atrium

9:00 am – 9:10 am
ROBERT DESIMONE | McGovern Institute
, MIT
Welcoming Remarks

Session I (Chair: TBA)

9:10 am – 9:50 am
BAILONG XIAO | IDG/McGovern Institute, Tsinghua University
In touch with the mechanosensitive Piezo channels: structure, ion permeation and mechano-gating

9:50 am – 10:30 am
JING YANG | IDG/McGovern Institute, Peking University
The mechanism underlying neuronal response to axonal injury

10:30 am – 10:45 am
Break

10:45 am – 11:25 am
JUN YAO | IDG/McGovern Institute, Tsinghua University
Ca2+ dependent synaptic vesicle cycling

11:25 am – 12:05 pm
YONG ZHANG | IDG/McGovern Institute, Peking University
Visualizing AMPA receptor synaptic plasticity in vivo

12:05 pm – 01:30 pm
Poster Session and Lunch in Atrium

Session II (Chair: TBA)

1:30 pm – 2:10 pm
GUOPING FENG |
McGovern Institute, MIT
Thalamic reticular nucleus dysfunction in neurodevelopmental disorders

2:10 pm – 2:50 pm
HUAN LUO | IDG/McGovern Institute, Peking University
Serial-like sampling of visual objects during sustained attention

2:50 pm – 3:30 pm
XIAOHONG WAN | IDG/McGovern Institute Beijing Normal University
Investigating neural mechanisms of metacognition

3:30 pm – 3:45 pm
Break

3:45 pm – 4:25 pm
YINA MA | IDG/McGovern Institute, Beijing Normal University
Oxytocin and social adaptation

4:25 pm – 5:05 pm
BO HONG | IDG/McGovern Institute, Tsinghua University
Spatio-temporal organization and assembly of human cortical networks

5:05 pm – 6:05 pm
Reception 5th floor overlooking Atrium

Supported by Hugo Shong and the McGovern Institutes

 

Genome Editing with CRISPR-Cas9 (Chinese Translation)

A Chinese translation of an animation depicting 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. Further information can be found on Prof. Zhang’s website at http://zlab.mit.edu.

Images and footage courtesy of Sputnik Animation, the Broad Institute of MIT and Harvard, Justin Knight and pond5.

How the brain builds panoramic memory

When asked to visualize your childhood home, you can probably picture not only the house you lived in, but also the buildings next door and across the street. MIT neuroscientists have now identified two brain regions that are involved in creating these panoramic memories.

These brain regions help us to merge fleeting views of our surroundings into a seamless, 360-degree panorama, the researchers say.

“Our understanding of our environment is largely shaped by our memory for what’s currently out of sight,” says Caroline Robertson, a postdoc at MIT’s McGovern Institute for Brain Research and a junior fellow of the Harvard Society of Fellows. “What we were looking for are hubs in the brain where your memories for the panoramic environment are integrated with your current field of view.”

Robertson is the lead author of the study, which appears in the Sept. 8 issue of the journal Current Biology. Nancy Kanwisher, the Walter A. Rosenblith Professor of Brain and Cognitive Sciences and a member of the McGovern Institute, is the paper’s lead author.

Building memories

As we look at a scene, visual information flows from our retinas into the brain, which has regions that are responsible for processing different elements of what we see, such as faces or objects. The MIT team suspected that areas involved in processing scenes — the occipital place area (OPA), the retrosplenial complex (RSC), and parahippocampal place area (PPA) — might also be involved in generating panoramic memories of a place such as a street corner.

If this were true, when you saw two images of houses that you knew were across the street from each other, they would evoke similar patterns of activity in these specialized brain regions. Two houses from different streets would not induce similar patterns.

“Our hypothesis was that as we begin to build memory of the environment around us, there would be certain regions of the brain where the representation of a single image would start to overlap with representations of other views from the same scene,” Robertson says.

The researchers explored this hypothesis using immersive virtual reality headsets, which allowed them to show people many different panoramic scenes. In this study, the researchers showed participants images from 40 street corners in Boston’s Beacon Hill neighborhood. The images were presented in two ways: Half the time, participants saw a 100-degree stretch of a 360-degree scene, but the other half of the time, they saw two noncontinuous stretches of a 360-degree scene.

After showing participants these panoramic environments, the researchers then showed them 40 pairs of images and asked if they came from the same street corner. Participants were much better able to determine if pairs came from the same corner if they had seen the two scenes linked in the 100-degree image than if they had seen them unlinked.

Brain scans revealed that when participants saw two images that they knew were linked, the response patterns in the RSC and OPA regions were similar. However, this was not the case for image pairs that the participants had not seen as linked. This suggests that the RSC and OPA, but not the PPA, are involved in building panoramic memories of our surroundings, the researchers say.

Priming the brain

In another experiment, the researchers tested whether one image could “prime” the brain to recall an image from the same panoramic scene. To do this, they showed participants a scene and asked them whether it had been on their left or right when they first saw it. Before that, they showed them either another image from the same street corner or an unrelated image. Participants performed much better when primed with the related image.

“After you have seen a series of views of a panoramic environment, you have explicitly linked them in memory to a known place,” Robertson says. “They also evoke overlapping visual representations in certain regions of the brain, which is implicitly guiding your upcoming perceptual experience.”

The research was funded by the National Science Foundation Science and Technology Center for Brains, Minds, and Machines; and the Harvard Milton Fund.

Faculty at MIT and beyond respond forcefully to an article critical of Suzanne Corkin

On August 7, 2016, the New York Times Magazine published “The Brain That Couldn’t Remember,” an article adapted from the forthcoming book “Patient H.M.: A Story of Memory, Madness, and Family Secrets,” by Luke Dittrich. The article is highly critical of the late Suzanne Corkin, who was a professor emerita of neuroscience until her death on May 24.

In response to the article, more than 200 members of the international scientific community — most from outside MIT — have signed a letter in support of Corkin and her research with the amnesic patient Henry Molaison.

What follows is a statement by James DiCarlo, the Peter de Florez Professor of Neuroscience and head of the Department of Brain and Cognitive Sciences at MIT.

***

In “The Brain That Couldn’t Remember,” three allegations are made against Professor Suzanne Corkin, who died on May 24. Professors John Gabrieli and Nancy Kanwisher at MIT have examined evidence in relation to each allegation, and, as detailed below, have found significant evidence that contradicts each allegation. In our judgment, the evidence below rebuts each claim.

1. Allegation that research records were or would be destroyed or shredded.

We believe that no records were destroyed and, to the contrary, that Professor Corkin worked in her final days to organize and preserve all records. Even as her health failed (she had advanced cancer and was receiving chemotherapy), she instructed her assistant to continue to organize, label, and maintain all records related to Henry Molaison. The records currently remain within our department.

Assuming that the interview is accurately and fully reported by Mr. Dittrich, we cannot explain why Professor Corkin made the comments reported in the article. This may have been related to tensions between the author and Professor Corkin because she had turned down his request to examine Mr. Molaison’s confidential medical and research records.

Regardless, the critical point is not what was said in an interview, but rather what actions were actually taken by Professor Corkin. The actions were to preserve the records.

2. Allegation that the finding of an additional lesion in left orbitofrontal cortex was suppressed.

The public record is clear that Professor Corkin communicated this discovery of an additional lesion in Mr. Molaison to both scientific and public audiences. This factual evidence is contradictory to any allegation of the suppression of a finding.

The original scientific report (Nature Communications, 2014) of the post-mortem examination of Mr. Molaison’s brain included this information in the most prominent and widely read portion of the report, the abstract.

In addition, Professor Corkin herself disseminated this information in public forums, including a 2014 interview, posted on MIT News and subsequently elsewhere online, in which she said: “We discovered a new lesion in the lateral orbital gyrus of the left frontal lobe. This damage was also visible in the postmortem MRI scans. The etiology of this lesion is presently unknown; future histological studies will clarify the cause and timeframe of this damage. Currently, it is unclear whether this lesion had any consequence for H.M.’s behavior.”

3. Allegation that there was something inappropriate in the selection of Tom Mooney as Mr. Molaison’s guardian.

In her book “Permanent Present Tense” (2013), Professor Corkin describes precisely the provenance of Mr. Molaison’s guardianship (page 201).

Briefly, in 1974 Mr. Molaison and his mother (who was in failing health; his father was deceased) moved in with Lillian Herrick, whose first husband was related to Mr. Molaison’s mother. Mrs. Herrick is described as caring for Mr. Molaison until 1980, when she was diagnosed with advanced cancer, and Mr. Molaison was admitted to a nursing home founded by her brother.

In 1991, the Probate Court in Windsor Locks, Connecticut, appointed Mrs. Herrick’s son, Tom Mooney, as Mr. Molaison’s conservator. (Mr. Mooney is referred to as “Mr. M” in the book because of his desire for privacy.) This family took an active interest in helping Mr. Molaison and his mother, and was able to help place him in the nursing home that took care of him.

Mr. Dittrich provides no evidence that anything untoward occurred, and we are not aware of anything untoward in this process. Mr. Dittrich identifies some individuals who were genetically closer to Mr. Molaison than Mrs. Herrick or her son, but it is our understanding that this family took in Mr. Molaison and his mother, and took care of Mr. Molaison for many years. Mr. Mooney was appointed conservator by the local court after a valid legal process, which included providing notice of a hearing and appointment of counsel to Mr. Molaison.

Journalists are absolutely correct to hold scientists to very high standards. I — and over 200 scientists who have signed a letter to the editor in support of Professor Corkin — believe she more than achieved those high standards. However, the author (and, implicitly, the Times) has failed to do so.

James J. DiCarlo MD, PhD
Peter de Florez Professor of Neuroscience
Head, Department of Brain and Cognitive Sciences
Investigator, McGovern Institute for Brain Research
Massachusetts Institute of Technology

Study finds brain connections key to learning

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

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

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

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