Author: David Orenstein

Three bright yellow-green celll cultures on black background

In Down syndrome cells, genome-wide disruptions mimic a senescence-like state

Extra chromosome alters chromosomal conformation and DNA accessibility across the whole genome in neural progenitor cells, disrupting gene transcription and cell functions much like in cellular aging

In Down syndrome, the third copy of chromosome 21 causes a reorganization of the 3D configuration of the entire genome in a key cell type of the developing brain, a new study shows. The resulting disruption of gene transcription and cell function are so similar to those seen in cellular aging, or senescence, that the scientists leading the study found they could use anti-senescence drugs to correct them in cell cultures.

The study published in Cell Stem Cell therefore establishes senescence as a potentially targetable mechanism for future treatment of Down syndrome, said Hiruy Meharena, a new assistant professor at the University of California San Diego who led the work as a Senior Alana Fellow in the Alana Down Syndrome Center at MIT.

“There is a cell-type specific genome-wide disruption that is independent of the gene dosage response,” Meharena said. “It’s a very similar phenomenon to what’s observed in senescence. This suggests that excessive senescence in the developing brain induced by the third copy of chromosome 21 could be a key reason for the neurodevelopmental abnormalities seen in Down syndrome.”

The study’s finding that neural progenitor cells (NPCs), which develop into major cells in the brain including neurons, have a senescent character is remarkable and novel, said senior author Li-Huei Tsai, but it is substantiated by the team’s extensive work to elucidate the underlying mechanism of the effects of abnormal chromosome number, or aneupoloidy, within the nucleus of the cells.

“This study illustrates the importance of asking fundamental questions about the underlying mechanisms of neurological disorders,” said Tsai, Picower Professor of Neuroscience, director of the Alana Center, and of The Picower Institute for Learning and Memory at MIT. “We didn’t begin this work expecting to see senescence as a translationally relevant feature of Down syndrome, but the data emerged from asking how the presence of an extra chromosome affects the architecture of all of a cell’s chromosomes during development.”

Genomewide changes

Meharena and co-authors spent years measuring distinctions between human cell cultures that differed only by whether they had a third copy of chromosome 21. Stem cells derived from volunteers were cultured to turn into NPCs. In both the stem cells and the NPCs, the team examined 3D chromosome architecture, several metrics of DNA structure and interaction, gene accessibility and transcription, and gene expression. They also looked at the consequences of the gene expression differences on important functions of these developmental cells, such as how well they proliferated and migrated in 3D brain tissue cultures. Stem cells were not particularly different, but NPCs were substantially affected by the third copy of chromosome 21.

Li-Huei Tsai stands in a lab and points to an image of a cell on a computer screen. Hiruy Meharena sits at the desk with his hand on the mouse and looks on.
Li-Huei Tsai and Hiruy Meharena consult about images produced during the research in this 2019 photo

Overall, the picture that emerged in NPCs was that the presence of a third copy causes all the other chromosomes to squish inward, not unlike when people in a crowded elevator must narrow their stance when one more person squeezes in. The main effects of this “chromosomal introversion,” meticulously quantified in the study, are more genetic interactions within each chromosome and less interactions among them. These changes and differences in DNA conformation within the cell nucleus lead to changes in how genes are transcribed and therefore expressed, causing important differences in cell function that affect brain development.

Treated as senescence

For the first couple of years as these data emerged, Meharena said, the full significance of the genomic changes were not apparent, but then he read a paper showing very similar genomic rearrangement and transcriptional alterations in senescent cells.

After validating that the Down syndrome cells indeed bore such a similar signature of transcriptional differences, the team decided to test whether anti-senescence drugs could undo the effects. They tested a combination of two: dasatinib and quercetin. The medications improved not only gene accessibility and transcription, but also the migration and proliferation of cells.

That said, the drugs have very significant side effects—dasatinib is only given to cancer patients when other treatments have not done enough—so they are not appropriate for attempting to intervene in brain development amid Down syndrome, Meharena said. Instead an outcome of the study could be to inspire a search for medications that could have anti-senolytic effects with a safer profile.

A schematic shows the process of how a trisomy 21 cell experiences genomiwide chromosomal reconfiguration leading to a senescence-like response
A new study’s findings indicate that amid trisomy 21, neural progenitor cells experience a genome-wide chromosomal reorganization leading to a senescence-like response including altered chromatin states and gene transcription.

Senescence is a stress response of cells. At the same time, years of research by former MIT biology professor Angelika Amon, who co-directed the Alana Center with Tsai, has shown that aneuploidy is a source of considerable stress for cells. A question raised by the new findings, therefore, is whether the senescence-like character of Down syndrome NPCs is indeed the result of an aneuploidy induced stress and if so, exactly what that stress is.

Another implication of the findings is how excessive senescence among brain cells might affect people with Down syndrome later in life. The risk of Alzheimer’s disease is much higher at a substantially earlier age in the Down syndrome population than among people in general. In large part this is believed to be because a key Alzheimer’s risk gene, APP, is on chromosome 21, but the newly identified inclination for senescence may also accelerate Alzheimer’s development.

In addition to Meharena and Tsai, the paper’s other authors are Asaf Marco, Vishnu Dileep, Elana Lockshin, Grace Akatsu, James Mullahoo, Ashley Watson, Tak Ko, Lindsey Guerin, Fatema Abdurrob, Shruti Rengarajan, Malvina Papanastasiou and Jacob Jaffe.

The Alana Foundation, the LuMind Foundation, Burroughs Wellcome Fund, UNCF-Merck  and the National Institutes of Health funded the research.

Boston Globe op-ed: How science, technology, and industry can work together to cure Alzheimer’s

The Alzheimer’s research community must acknowledge the gaps in the current approach to curing the disease and make significant changes.

In The Boston Globe Nov. 29, Li-Huei Tsai penned an op-ed as part of Globe’s “The Longevity Hub” collaboration with MIT Professor Joe Coughlin.

“Alzheimer’s disease, the sixth leading cause of death in the United States, has defied our best efforts to find a cure or even a treatment that can substantially slow its devastating degradation of the brain. The now decades-long sequence of high-profile setbacks in Alzheimer’s drug discovery and development underscores the unique challenge this disease presents.

For the sake not only of tens of millions of patients and families worldwide, but also the sustainability of the US health care system and economy, the Alzheimer’s research community must acknowledge the gaps in the current approach to curing the disease and make significant changes in how science, technology, and industry work together to meet this challenge…”

Read the full Op-Ed in the Globe here..


Study links gene to cognitive resilience in the elderly

The findings may help explain why some people who lead enriching lives are less prone to Alzheimer’s and age-related dementia

Many people develop Alzheimer’s or other forms of dementia as they get older. However, others remain sharp well into old age, even if their brains show underlying signs of neurodegeneration.

Among these cognitively resilient people, researchers have identified education level and amount of time spent on intellectually stimulating activities as factors that help prevent dementia. A new study by MIT researchers shows that this kind of enrichment appears to activate a gene family called MEF2, which controls a genetic program in the brain that promotes resistance to cognitive decline.

The researchers observed this link between MEF2 and cognitive resilience in both humans and mice. The findings suggest that enhancing the activity of MEF2 or its targets might protect against age-related dementia

“It’s increasingly understood that there are resilience factors that can protect the function of the brain,” says Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory. “Understanding this resilience mechanism could be helpful when we think about therapeutic interventions or prevention of cognitive decline and neurodegeneration-associated dementia.”

Above: When researchers knocked down a Mef2 gene in the frontal cortex of mice (blank areas), it prevented the mice from attaining a cognitive benefit of being raised in an enriched environment.

Tsai, a founding director of MIT’s Aging Brain Initiative, is the senior author of the study, which appears today in Science Translational Medicine. The lead authors are recent MIT PhD recipient Scarlett Barker and MIT postdoctoral fellow and Boston Children’s Hospital physician Ravikiran (Ravi) Raju.

Scarlett Barker stands at a podium with audience members sitting in the foreground.
Co-lead author Scarlett Barker delivered remarks about the research at Neuroscience 2019 while it was in progress.

Protective effects

A large body of research suggests that environmental stimulation offers some protection against the effects of neurodegeneration. Studies have linked education level, type of job, number of languages spoken, and amount of time spent on activities such as reading and doing crossword puzzles to higher degrees of cognitive resilience.

The MIT team set out to try to figure how these environmental factors affect the brain at the neuronal level. They looked at human datasets and mouse models in parallel, and both tracks converged on MEF2 as a critical player.

MEF2 is a transcription factor that was originally identified as a factor important for cardiac muscle development, but later was discovered to play a role in neuron function and neurodevelopment. In two human datasets comprising slightly more than 1,000 people all together, the MIT team found that cognitive resilience was highly correlated with expression of MEF2 and many of the genes that it regulates.

Many of those genes encode ion channels, which control a neuron’s excitability, or how easily it fires an electrical impulse. The researchers also found, from a single-cell RNA-sequencing study of human brain cells, that MEF2 appears to be most active in a subpopulation of excitatory neurons in the prefrontal cortex of resilient individuals.

To study cognitive resilience in mice, the researchers compared mice who were raised in cages with no toys, and mice placed in a more stimulating environment with a running wheel and toys that were swapped out every few days. As they found in the human study, MEF2 was more active in the brains of the mice exposed to the enriched environment. These mice also performed better in learning and memory tasks.

When the researchers knocked out the gene for MEF2 in the frontal cortex, this blocked the mice’s ability to benefit from being raised in the enriched environment, and their neurons became abnormally excitable.

“This was particularly exciting as it suggested that MEF2 plays a role in determining overall cognitive potential in response to variables in the environment,” Raju says.

Ravi Raju stands at a podium. A blue and white Picower Institute logo is behind him as a backdrop.
Co-lead author Ravikiran (Ravi) Raju presents some of his early research during a 2018 talk. Image by Adrienne Mathiowetz.

The researchers then explored whether MEF2 could reverse some of the symptoms of cognitive impairment in a mouse model that expresses a version of the tau protein that can form tangles in the brain and is linked with dementia. If these mice were engineered to overexpress MEF2 at a young age, they did not show the usual cognitive impairments produced by the tau protein later in life. In these mice, neurons overexpressing MEF2 were less excitable.

“A lot of human studies and mouse model studies of neurodegeneration have shown that the neurons become hyperexcitable in early stages of disease progression,” Raju says. “When we overexpressed MEF2 in a mouse model of neurodegeneration, we saw that it was able to prevent this hyperexcitability, which might explain why they performed cognitively better than control mice.”

Enhancing resilience

The findings suggest that enhancing MEF2 activity could help to protect against dementia; however, because MEF2 also affects other types of cells and cellular processes, more study is needed to make sure that activating it wouldn’t have adverse side effects, the researchers say.

The MIT team now hopes to further investigate how MEF2 becomes activated by exposure to an enriching environment. They also plan to examine some of the effects of the other genes that MEF2 controls, beyond the ion channels they explored in this study. Such studies could help to reveal additional targets for drug treatments.

“You could potentially imagine a more targeted therapy by identifying a subset or a class of effectors that is critically important for inducing resilience and neuroprotection,” Raju says.

The research was funded by the Glenn Center for Biology of Aging Research, the National Institute of Aging, the Cure Alzheimer’s Fund, and the Eunice Kennedy Shriver National Institute of Child Health and Human Development.

-From MIT News

A colorful cartoon of a DNA double helix with a gap through the middle

Memory making involves extensive DNA breaking

To quickly express genes needed for learning and memory, brain cells snap both strands of DNA in many more places and cell types than previously realized, a new study shows

The urgency to remember a dangerous experience requires the brain to make a series of potentially dangerous moves: Neurons and other brain cells snap open their DNA in numerous locations—more than previously realized, according to a new study—to provide quick access to genetic instructions for the mechanisms of memory storage.

The extent of these DNA double-strand breaks (DSBs) in multiple key brain regions is surprising and concerning, said study senior author Li-Huei Tsai, Picower Professor of Neuroscience at MIT and director of The Picower Institute for Learning and Memory, because while the breaks are routinely repaired, that process may become more flawed and fragile with age. Tsai’s lab has shown that lingering DSBs are associated with neurodegeneration and cognitive decline and that repair mechanisms can falter.

“We wanted to understand exactly how widespread and extensive this natural activity is in the brain upon memory formation because that can give us insight into how genomic instability could undermine brain health down the road,” said Tsai, who is also a professor in the Department of Brain and Cognitive Sciences and a leader of MIT’s Aging Brain Initiative. “Clearly memory formation is an urgent priority for healthy brain function but these new results showing that several types of brain cells break their DNA in so many places to quickly express genes is still striking.”

Tracking breaks

In 2015, Tsai’s lab provided the first demonstration that neuronal activity caused DSBs and that they induced rapid gene expression. But those findings, mostly made in lab preparations of neurons, did not capture the full extent of the activity in the context of memory formation in a behaving animal and did not investigate what happened in cells other than neurons.

IIn the new study published July 1 in PLOS ONE, lead author and former graduate student Ryan Stott and co-author and former research technician Oleg Kritsky sought to investigate the full landscape of DSB activity in learning and memory. To do so, they gave mice little electrical zaps to the feet when they entered a box, to condition a fear memory of that context. They then used several methods to assess DSBs and gene expression in the brains of the mice over the next half hour, particularly among a variety of cell types in the prefrontal cortex and hippocampus, two regions essential for the formation and storage of conditioned fear memories. They also made measurements in the brains of mice who did not experience the foot shock to establish a baseline of activity for comparison.

The creation of a fear memory doubled the number of DSBs among neurons in the hippocampus and the prefrontal cortex, affecting more than 300 genes in each region. Among 206 affected genes common to both regions, the researchers then looked at what those genes do. Many were associated with the function of the connections neurons make with each other, called synapses. This makes sense because learning arises when neurons change their connections (a phenomenon called “synaptic plasticity”) and memories are formed when groups of neurons connect together into ensembles called engrams.

“Many genes essential for neuronal function and memory formation, and significantly more of them than expected based on previous observations in cultured neurons…are potentially hotspots of DSB formation,” the authors wrote in the study.

In another analysis, the researchers confirmed through measurements of RNA that the increase in DSBs indeed correlated closely with increased transcription and expression of affected genes, including ones affecting synapse function, as quickly as 10-30 minutes after the foot shock exposure.

“Overall, we find transcriptional changes are more strongly associated with [DSBs] in the brain than anticipated,” they wrote. “Previously we observed 20 gene-associated [DSB] loci following stimulation of cultured neurons, while in the hippocampus and prefrontal cortex we see more than 100-150 gene associated [DSB] loci that are transcriptionally induced.”

Snapping with stress

In the analysis of gene expression, the neuroscientists looked at not only neurons but also non-neuronal brain cells, or glia, and found that they also showed changes in expression of hundreds of genes after fear conditioning. Glia called astrocytes are known to be involved in fear learning, for instance, and they showed significant DSB and gene expression changes after fear conditioning.

Among the most important functions of genes associated with fear conditioning-related DSBs in glia was the response to hormones. The researchers therefore looked to see which hormones might be particularly involved and discovered that it was glutocortocoids, which are secreted in response to stress. Sure enough, the study data showed that in glia, many of the DSBs that occurred following fear conditioning occurred at genomic sites related to glutocortocoid receptors. Further tests revealed that directly stimulating those hormone receptors could trigger the same DSBs that fear conditioning did and that blocking the receptors could prevent transcription of key genes after fear conditioning.

Tsai said the finding that glia are so deeply involved in establishing memories from fear conditioning is an important surprise of the new study.

“The ability of glia to mount a robust transcriptional response to glutocorticoids suggest that glia may have a much larger role to play in the response to stress and its impact on the brain during learning than previously appreciated,” she and her co-authors wrote.

Damage and danger?

More research will have to be done to prove that the DSBs required for forming and storing fear memories are a threat to later brain health, but the new study only adds to evidence that it may be the case, the authors said.

“Overall we have identified sites of DSBs at genes important for neuronal and glial functions, suggesting that impaired DNA repair of these recurrent DNA breaks which are generated as part of brain activity could result in genomic instability that contribute to aging and disease in the brain,” they wrote.

The National Institutes of Health, The Glenn Foundation for Medical Research and the JPB Foundation provided funding for the research.

Li-Huei Tsai is shown in profile as she stands smiling at a podium

Li-Huei Tsai elected to American Academy of Arts & Sciences

The American Academy of Arts & Sciences announced today that Li-Huei Tsai, Picower Professor of Neuroscience and Director of The Picower Institute for Learning & Memory, is among 252 luminaries elected to join its esteemed membership.

“We are honoring the excellence of these individuals, celebrating what they have achieved so far, and imagining what they will continue to accomplish,” said David Oxtoby, President of the American Academy, in the announcement. “The past year has been replete with evidence of how things can get worse; this is an opportunity to illuminate the importance of art, ideas, knowledge, and leadership that can make a better world.”

Tsai’s laboratory focuses on advancing understanding the molecular-, circuit- and systems-level mechanisms underlying neurodegenerative diseases such as Alzheimer’s. She has translated many of her lab’s fundamental insights into potential therapeutic approaches.

“I’m very honored to be elected to the academy and to be in the company of so many leading scholars and luminaries,” Tsai said. “The Academy’s mission of advancing the public good is also a philosophy that guides our work to understand and address neurodegenerative diseases such as Alzheimer’s disease. This recognition encourages us to continue our efforts with urgency and rigor.”

With her election, Tsai joins other Picower Institute faculty in the academy including Mark Bear, Emery N. Brown, Earl Miller, Mriganka Sur, Susumu Tonegawa and Matt Wilson. Also this year, four other MIT faculty members were elected to membership.

Study offers an explanation for why the APOE4 gene enhances Alzheimer’s risk

Gene variant disrupts lipid metabolism, but in experiments the effects were reversed by choline supplements

One of the most significant genetic risk factors for developing Alzheimer’s disease is a gene called APOE4, which is carried by almost half of all Alzheimer’s patients. A new study from MIT shows that this gene has widespread effects on brain cells’ ability to metabolize lipids and respond to stress.

In studies of human brain cells and yeast cells, the researchers found that the APOE4 gene significantly disrupts brain cells’ ability to carry out their normal functions. They also showed that treating these cells with extra choline, a widely available supplement that is considered safe for human use, could reverse many of these effects.

The researchers hope that their findings will lead to clinical studies of choline in people who carry the APOE4 gene, who make up about 14 percent of the overall population. Previous trials looking at choline’s effects on cognition showed mixed results, but those trials were not targeted specifically to people with the APOE4 gene.

“What we would really like to see is whether in the human population, in those APOE4 carriers, if they take choline supplements to a sufficient amount, whether that would delay or give them some protection against developing dementia or Alzheimer’s disease,” says Li-Huei Tsai, the director of MIT’s Picower Institute for Learning and Memory.

Tsai and the late Susan Lindquist, former director of MIT’s Whitehead Institute for Biomedical Research, are the senior authors of the study, which appears today in Science Translational Medicine. The paper’s three lead authors are former Whitehead and MIT postdocs Grzegorz Sienski and Priyanka Narayan, and current MIT postdoc Julia Maeve Bonner.

Lipid dysregulation

The human gene for APOE, or apolipoprotein E, comes in three versions. While APOE4 is linked to higher risk for Alzheimer’s, APOE2 is considered protective, and APOE3, the most common variant, is neutral.

APOE is known to be involved in lipid metabolism, but its role in the development of Alzheimer’s has been unclear, Tsai says. To try to learn more about this connection, the researchers created human induced pluripotent stem cells that carry either the APOE3 or APOE4 gene in an otherwise identical genetic background. They then stimulated these cells to differentiate into astrocytes, the brain cells that produce the most APOE.

APOE4 astrocytes showed dramatic changes in how they process lipids compared to APOE3. In APOE4 astrocytes, there was a significant buildup of neutral lipids and cholesterol. These astrocytes also accumulated droplets containing a type of lipids called triglycerides, and these triglycerides had many more unsaturated fatty acid chains than normal. These changes all disrupt the normal lipid balance inside the cells. The authors also noted APOE4-dependent lipid disruptions in another important brain cell, microglia.

“When lipid homeostasis is compromised, then a lot of very essential processes are affected, such as intracellular trafficking, vesicular trafficking, and endocytosis. A lot of the cells’ essential functions are compromised,” Tsai says.

“This balance is really important for cells to be able to perform normal functions like generate membranes and so on, but also to be able to absorb stress,” Bonner says. “We think that one of the things that’s happening is that these cells are less able to absorb stress because they’re already in this heightened lipid dysregulation state.”

The researchers also found that yeast cells engineered to express the human version of APOE4 showed many of the same defects. Using these cells, they performed a systematic genetic screen to determine the molecular basis of the defects seen in APOE4 cells. This screen showed that turning on a pathway that normally produces phospholipids, an essential component of cell membranes, can reverse some of the damage seen in APOE4 cells. This suggests that APOE4 somehow increases the requirement for phospholipid synthesis.

The researchers also found that growing APOE4 yeast cells on a very nutrient-rich growth medium helped them to survive better than APOE4 yeast cells grown on the typical growth medium. Further experiments revealed that the nutrient that helped APOE4 cells survive is choline, a building block that cells use to make phospholipids. The researchers then treated their human APOE4 astrocyte cells with choline to promote phospholipid synthesis, and found that it also reversed much of the damage they had seen in those cells, including the accumulation of cholesterol and lipid droplets.

Choline deficiency

The researchers have now begun studying a mouse model of Alzheimer’s that is also engineered to express the human APOE4 gene. They hope to investigate whether choline can help to reverse some of the symptoms of Alzheimer’s in these mice.

Choline is naturally found in foods such as eggs, meat, fish, and some beans and nuts. The minimum recommended intake of choline is 550 milligrams per day for men and 425 milligrams per day for women, but most people don’t consume that much, Tsai says. The new study offers preliminary evidence that people who carry the APOE4 gene may benefit from taking choline supplements, she says, although clinical trials are necessary to confirm that.

“What our results suggest is that if you are an APOE2 or APOE3 carrier, even you are somewhat choline deficient you can cope with it,” Tsai says. “But if you are an APOE4 carrier, then if you don’t take enough choline, then that will have a more dire consequences. The APOE4 carriers are more susceptible to choline deficiency.”

The research was funded by the EMBO Fellowship, the Helen Hay Whitney Foundation, the National Institutes of Health, the Damon Runyon Foundation, the Neurodegeneration Consortium, the Robert A. and Renee E. Belfer Foundation, the Howard Hughes Medical Institute, the Ludwig Family Foundation, and Kara and Stephen Ross.

–From MIT News

A cross section of a mouse brain stained in a rainbow of colors

Neuroscientists discover a molecular mechanism that allows memories to form

When the brain forms a memory of a new experience, neurons called engram cells encode the details of the memory and are later reactivated whenever we recall it. A new MIT study reveals that this process is controlled by large-scale remodeling of cells’ chromatin.

This remodeling, which allows specific genes involved in storing memories to become more active, takes place in multiple stages spread out over several days. Changes to the density and arrangement of chromatin, a highly compressed structure consisting of DNA and proteins called histones, can control how active specific genes are within a given cell.

“This paper is the first to really reveal this very mysterious process of how different waves of genes become activated, and what is the epigenetic mechanism underlying these different waves of gene expression,” says Li-Huei Tsai, the director of MIT’s Picower Institute for Learning and Memory and the senior author of the study.

Asaf Marco, an MIT postdoc, is the lead author of the paper, which appears today in Nature Neuroscience.

Above: The hippocampus is the large yellow structure near the top. Green indicates neurons that were activated in memory formation; red shows the neurons that were activated in memory recall; blue shows the DNA of the cells; and yellow shows neurons that were activated in both memory formation and recall, and are thus considered to be the engram neurons.

Epigenomic control

Engram cells are found in the hippocampus as well as other parts of the brain. Many recent studies have shown that these cells form networks that are associated with particular memories, and these networks are activated when that memory is recalled. However, the molecular mechanisms underlying the encoding and retrieval of these memories are not well-understood.

Neuroscientists know that in the very first stage of memory formation, genes known as immediate early genes are turned on in engram cells, but these genes soon return to normal activity levels. The MIT team wanted to explore what happens later in the process to coordinate the long-term storage of memories.

“The formation and preservation of memory is a very delicate and coordinated event that spreads over hours and days, and might be even months — we don’t know for sure,” Marco says. “During this process, there are a few waves of gene expression and protein synthesis that make the connections between the neurons stronger and faster.”

Tsai and Marco hypothesized that these waves could be controlled by epigenomic modifications, which are chemical alterations of chromatin that control whether a particular gene is accessible or not. Previous studies from Tsai’s lab have shown that when enzymes that make chromatin inaccessible are too active, they can interfere with the ability to form new memories.

To study epigenomic changes that occur in individual engram cells over time, the researchers used genetically engineered mice in which they can permanently tag engram cells in the hippocampus with a fluorescent protein when a memory is formed. These mice received a mild foot shock that they learned to associate with the cage in which they received the shock. When this memory forms, the hippocampal cells encoding the memory begin to produce a yellow fluorescent protein marker.

“Then we can track those neurons forever, and we can sort them out and ask what happens to them one hour after the foot shock, what happens five days after, and what happens when those neurons get reactivated during memory recall,” Marco says.

At the very first stage, right after a memory is formed, the researchers found that many regions of DNA undergo chromatin modifications. In these regions, the chromatin becomes looser, allowing the DNA to become more accessible. To the researchers’ surprise, nearly all of these regions were in stretches of DNA where no genes are found. These regions contain noncoding sequences called enhancers, which interact with genes to help turn them on. The researchers also found that in this early stage, the chromatin modifications did not have any effect on gene expression.

The researchers then analyzed engram cells five days after memory formation. They found that as memories were consolidated, or strengthened, over those five days, the 3D structure of the chromatin surrounding the enhancers changed, bringing the enhancers closer to their target genes. This still doesn’t turn on those genes, but it primes them to be expressed when the memory is recalled.

Next, the researchers placed some of the mice back into the chamber where they received the foot shock, reactivating the fearful memory. In engram cells from those mice, the researchers found that the primed enhancers interacted frequently with their target genes, leading to a surge in the expression of those genes.

Many of the genes turned on during memory recall are involved in promoting protein synthesis at the synapses, helping neurons strengthen their connections with other neurons. The researchers also found that the neurons’ dendrites — branched extensions that receive input from other neurons — developed more spines, offering further evidence that their connections were further strengthened.

Primed for expression

The study is the first to show that memory formation is driven by epigenomically priming enhancers to stimulate gene expression when a memory is recalled, Marco says.

“This is the first work that shows on the molecular level how the epigenome can be primed to gain accessibility. First, you make the enhancers more accessible, but the accessibility on its own is not sufficient. You need those regions to physically interact with the genes, which is the second phase,” he says. “We are now realizing that the 3D genome architecture plays a very significant role in orchestrating gene expression.”

The researchers did not explore how long these epigenomic modifications last, but Marco says he believes they may remain for weeks or even months. He now hopes to study how the chromatin of engram cells is affected by Alzheimer’s disease. Previous work from Tsai’s lab has shown that treating a mouse model of Alzheimer’s with an HDAC inhibitor, a drug that helps to reopen inaccessible chromatin, can help to restore lost memories.

The research was funded by the JBP Foundation and the Alzheimer’s Association.

–From MIT News

Long, thin,spiny cells stained yellow and blue appear above a black background

Alzheimer’s risk gene disrupts endocytosis, but another disease-linked gene could help

In a new study, a team of scientists based at The Picower Institute for Learning and Memory at MIT and the Whitehead Institute for Biomedical Research reveals evidence showing that the most prominent Alzheimer’s disease risk gene may disrupt a fundamental process in a key type of brain cell. Moreover, in a sign of how important it is to delve into the complex ways that genes intersect in disease, they found that increasing the expression of another Alzheimer’s-associated gene in those cells could help alleviate the problem.

About 25 percent of people have the APOE4 variant of the APOE gene, which puts them at substantially greater risk for Alzheimer’s disease than those with the more common APOE3 version. Scientists have been working for decades to understand why this is so. The new study in Cell Reports finds that in astrocytes, which are the most common non-neuron cell in the brain, the variant hampers the process of endocytosis, which is a major way that cells bring materials in from outside. That functional deficit could undermine several of the vital roles that astrocytes play in the brain, the researchers noted, including how they facilitate communication among neurons or maintain the blood-brain barrier, which stringently filters what circulates into or out of the brain.

“We have identified that APOE4 imposes an endocytosis deficiency in astrocytes,” said Priyanka Narayan, a researcher at the National Institutes of Health who co-led the work while a postdoc in the labs of the late Susan Lindquist, member of the Whitehead Institute, and of Li-Huei Tsai, Picower Professor of Neuroscience and the study’s corresponding author. “This effect could have a number of downstream consequences such as impaired communication with other cell types, poor clearance of extracellular material, or poor maintenance of metabolic homeostasis.”

Above: Astrocytes, such as these cells derived from induced pluripotent stem cells, are critical for brain function.

The research began in the lab of Lindquist, who was also a Professor of Biology at MIT. Lindquist and Tsai, were close collaborators. After Lindquist died, the research team completed the work in the Tsai lab at MIT. The study’s co-lead author is Grzegorz Sienski of the Whitehead Institute.

As part of their work, the team also found that in APOE4-carrying astrocytes increasing expression of an Alzheimer’s associated gene called PICALM reversed the endocytosis defects.

“Both APOE and PICALM are Alzheimer’s risk genes,” said Tsai, a founding director of MIT’s Aging Brain Initiative. “It is really interesting that the two genes converge on endocytosis. This indicates that faulty endocytosis plays a key role in the etiology of Alzheimer’s.”

Reduction and rescue

For at least a decade, studies have suggested connections among Alzheimer’s, APOE4 and errant endocytosis, but have not pinpointed specific mechanisms. The team sought them out—and also looked for ways to remediate the deficits—through a series of lab experiments in cultures of stem cell-derived human astrocytes and genetically engineered yeast. Tsai’s team focused on astrocytes because they produce the most ApoE protein in the brain.

By comparing astrocytes that were identical except in whether they had the APOE4 or APOE3 variants, the researchers found several signs of disrupted endocytosis, specifically in the early stage of the process when key proteins were notably reduced in the APOE4 carrying cells. They were able to directly observe that the afflicted astrocytes were less capable of bringing in materials from the outside. When they knocked out the APOE gene they no longer saw a defect in early endocytosis, affirming that the problem related to having the APOE4 variant.

By engineering human APOE3 and APOE4 into yeast cells, Tsai’s team was able to replicate clear signs of APOE4’s early endocytic disruption. This is possible because the function is so fundamental to how cells work, it is similar, or “conserved,” in yeast and people.  Once they knew they could use yeast as a model, they could then set out to look for endocytosis proteins that, if manipulated, could rescue the observed defect. They found one: a yeast protein called Yap1802p. When they made the yeast cells express extra Yap1802p, early endocytosis proteins were produced at normal levels, endocytosis function operated better and APOE4 cells, which had failed to grow as healthfully as APOE3 cells did, exhibited better growth.

Importantly, the gene that encodes Yap1802p has a human counterpart: PICALM. Studies have shown PICALM to have a complex but significant role in affecting Alzheimer’s disease risk.

A 3 by 2 grid shows cells with blue and white staining
In the bottom row, APOE4 astrocytes (blue) in which PICALM was overexpressed show greater uptake of transferrin protein (white) than APOE4 astrocytes without PICALM overexpression (top row).

With their promising results in yeast, the researcher team returned to their human astrocyte cultures. Overexpressing PICALM in APOE4 astrocytes repaired early endocytosis function, as measured by the increased intake of test proteins. But they also saw that overexpressing PICALM in APOE3 astrocytes caused an endocytosis defect, illustrating that the effects of PICALM varies markedly in astrocytes based on APOE variant.

Although, it is difficult to find drugs that specifically increase endocytosis,  this study could help scientists and clinicians better understand patients’ risk, Narayan said.

“In our study, we see that in the context of an APOE4 genotype, increasing PICALM can alleviate deficiencies in early endocytosis,” she said. “Given that APOE4 carriers represent a significant proportion of AD patients, this functional interaction between APOE4 and PICALM could be relevant to assessing their level of disease risk. It also gives an example of how the genetic background of an individual can interact and potentially modulate the detrimental effects of the APOE4 genotype.”

Moreover, the team’s method of going back and forth between human cell cultures and yeast, provides a way of identifying how AD risk genes impact cellular biology, and how other genes can modulate these effects.

In addition to Narayan, Sienski and Tsai, the study’s other authors are Julia Maeve Bonner, Yuan-Ta Lin, Jinsoo Seo, Valeriya Baru, Aftabul Haque, Blerta Milo, Leyla Akay, Agnese Graziosi, Yelena Freyzon, Dirk Landgraf, William Hesse, Julie Valastyan, M. Inmaculada Barrasa and the late Susan Lindquist, a former Professor of Biology at MIT and The Whitehead Institute.

The National Institutes of Health, the Whitehead Institute, the Robert A. and Renee E. Belfer Family Foundation, the JPB Foundation, the Edward N. and Della L. Thome Foundation and the Howard Hughes Medical Institute funded the research.

Li-Huei Tsai smiles in a picture with a video play button superposed in the foreground

On The Same Wavelength

In a new video, MIT’s School of Science provides an inside look behind the Tsai lab’s discovery that stimulating 40Hz “gamma” frequency brain activity in mice can address Alzheimer’s pathology and symptoms, including memory loss and neuronal death.  Part of the “Moments of Discovery” series, the video recreates former graduate student Hannah Iaccarino’s key early experiments.

Rainbow hued blood vessels spread out in a weblike formation

Study finds path for addressing Alzheimer’s blood-brain barrier impairment

By developing a lab-engineered model of the human blood-brain barrier (BBB), neuroscientists at MIT’s Picower Institute for Learning and Memory have discovered how the most common Alzheimer’s disease risk gene causes amyloid protein plaques to disrupt the brain’s vasculature and showed they could prevent the damage with medications already approved for human use.

About 25 percent of people have the APOE4 variant of the APOE gene, which puts them at substantially greater risk for Alzheimer’s disease. Almost everyone with Alzheimer’s, and even some elderly people without, suffer from cerebral amyloid angiopathy (CAA), a condition in which amyloid protein deposits on blood vessel walls impairs the ability of the BBB to properly transport nutrients, clear out waste and prevent the invasion of pathogens and unwanted substances.

In the new study, published June 8 in Nature Medicine, the researchers pinpointed the specific vascular cell type (pericytes) and molecular pathway (calcineurin/NFAT) through which the APOE4 variant promotes CAA pathology.

A grayish loop of blood vessel on a black background is covered with green blotches
A 3D rendering of an APOE4 carrying engineered blood vessel shows heavy accumulation of amyloid protein (green).

The research indicates that in people with the APOE4 variant, pericytes in their vessels churn out too much APOE protein, explained senior author Li-Huei Tsai, Picower Professor of Neuroscience and director of the Picower Institute. APOE causes amyloid proteins, which are more abundant in Alzheimer’s disease, to clump together. Meanwhile, the diseased pericytes’ increased activation of the calcineurin/NFAT molecular pathway appears to encourage the elevated APOE expression.There are already drugs that suppress the pathway. Currently they are used to subdue the immune system after a transplant. When the researchers administered some of those drugs, including cyclosporine A and FK506, to the lab-grown BBBs with the APOE4 variant, they accumulated much less amyloid than untreated ones did.

“We identify that there is a specific genetic pathway that is expressed differently in a population that is susceptible to Alzheimer’s disease,” said study lead author Joel Blanchard, a postdoc in Tsai’s lab. “By identifying this we could identify drugs that change this pathway back to a non-diseased state and correct this outcome that’s associated with Alzheimer’s.”

Building barriers

To investigate the connection between Alzheimer’s, the APOE4 variant and CAA, Blanchard, Tsai and co-authors coaxed human induced pluripotent stem cells to become the three types of cells that make up the BBB: brain endothelial cells, astrocytes and pericytes. Pericytes were modeled by mural cells that they tested extensively to ensure they exhibited pericyte-like properties and gene expression.

Grown for two weeks within a three-dimensional hydrogel scaffold, the BBB model cells assembled into vessels that exhibited natural BBB properties, including low permeability to molecules and expression of the same key genes, proteins and molecular pumps as natural BBBs. When immersed in culture media high in amyloid proteins, mimicking conditions in Alzheimer’s disease brains, the lab-grown BBB models exhibited the same kind of amyloid accumulation seen in human disease.

With a model BBB established, they then sought to test the difference APOE4 makes. They showed by several measures that APOE4-carrying BBB models accumulated more amyloid from culture media than those carrying APOE3, the more typical and healthy variant.

To pinpoint how APOE4 makes that difference, they engineered eight different versions covering all the possible combinations of the three cell types having either APOE3 or APOE4. When exposed these month-old models to amyloid-rich media, only versions with APOE4 pericyte-like mural cells showed excessive accumulation of amyloid proteins. Replacing APOE4 mural cells with APOE3-carrying ones reduced amyloid deposition. These results put blame for CAA-like pathology squarely on pericytes.

To further validate the clinical relevance of these findings, the team also looked at APOE expression in samples of human brain vasculature in the prefrontal cortex and the hippocampus, two regions crucially affected in Alzheimer’s disease. Consistent with the team’s lab BBB model, people with APOE4 showed higher expression of the gene in the vasculature, and specifically in pericytes, than people with APOE3.

“That is a salient point of this paper,” said Tsai, a founding member of MIT’s Aging Brain Initiative. “It’s really cool because it stresses the cell-type specific function of APOE.”

A pathway toward treatment?

The next step was to determine how APOE4 becomes so overexpressed by pericytes. The team therefore identified hundreds of transcription factors – proteins that determine how genes are expressed – that were regulated differently between APOE3 and APOE4 pericyte-like mural cells. Then they scoured that list to see which factors specifically impact APOE expression. A set of factors that were upregulated in APOE4 cells stood out: ones that were part of the calcineurin/NFAT pathway. They observed similar upregulation of the pathway in pericytes from human hippocampus samples.

As part of their investigation of whether elevated signaling activity of this pathway caused increased amyloid deposition and CAA, they tested cyclosporine A and FK506 because they tamp pathway activity down. They found that the drugs reduced APOE expression in their pericyte-like mural cells and therefore APOE4-mediated amyloid deposits in the BBB models. They also tested the drugs in APOE4-carrying mice and saw that the medicines reduced APOE expression and amyloid buildup.

Blanchard and Tsai noted that the drugs can have significant side effects, so their findings might not suggest using exactly those drugs to address CAA in patients.

“Instead it points toward the value of understanding the mechanism,” Blanchard said. “It allows one to design a small molecule screen to find more potent drugs that have less off-target effects.”

In addition to Blanchard and Tsai, the paper’s other authors are Michael Bula, Jose Davila-Velderrain, Leyla Akay, Lena Zhu, Alexander Frank, Matheus Victor, Julia Maeve Bonner, Hansruedi Mathys, Yuan-Ta Lin, Tak Ko, David Bennett, Hugh Cam, and Manolis Kellis.

The Robert A. and Renee E. Belfer Family Foundation, the Cure Alzheimer’s Fund, The National Institutes of Health, the Glenn Foundation for Medical Research and the American Federation for Aging Research funded the research.

A six panel grid showing neurons stained in red or green

Study finds that aging neurons accumulate DNA damage

MIT neuroscientists have discovered that an enzyme called HDAC1 is critical for repairing age-related DNA damage to genes involved in memory and other cognitive functions. This enzyme is often diminished in both Alzheimer’s patients and normally aging adults. In a study of mice, the researchers showed that when HDAC1 is lost, a specific type of DNA damage builds up as the mice age. They also showed that they could reverse this damage and improve cognitive function with a drug that activates HDAC1.

The study suggests that restoring HDAC1 could have positive benefits for both Alzheimer’s patients and people who suffer from age-related cognitive decline, the researchers say.

“It seems that HDAC1 is really an anti-aging molecule,” says Li-Huei Tsai, the director of MIT’s Picower Institute for Learning and Memory and the senior author of the study. “I think this is a very broadly applicable basic biology finding, because nearly all of the human neurodegenerative diseases only happen during aging. I would speculate that activating HDAC1 is beneficial in many conditions.”

Picower Institute research scientist Ping-Chieh Pao is the lead author of the study, which appears today in Nature Communications.

DNA repair and aging

There are several members of the HDAC family of enzymes, and their primary function is to modify histones — proteins around which DNA is spooled. These modifications control gene expression by blocking genes in certain stretches of DNA from being copied into RNA.

In 2013, Tsai’s lab published two papers that linked HDAC1 to DNA repair in neurons. In the current paper, the researchers explored what happens when HDAC1-mediated repair fails to occur. To do that, they engineered mice in which they could knock out HDAC1 specifically in neurons and another type of brain cells called astrocytes.

For the first several months of the mice’s lives, there were no discernable differences in their DNA damage levels or behavior, compared to normal mice. However, as the mice aged, differences became more apparent. DNA damage began to accumulate in the HDAC1-deficient mice, and they also lost some of their ability to modulate synaptic plasticity — changes in the strength of the connections between neurons. The older mice lacking HCAC1 also showed impairments in tests of memory and spatial navigation.

The researchers found that HDAC1 loss led to a specific type of DNA damage called 8-oxo-guanine lesions, which are a signature of oxidative DNA damage. Studies of Alzheimer’s patients have also shown high levels of this type of DNA damage, which is often caused by accumulation of harmful metabolic byproducts. The brain’s ability to clear these byproducts often diminishes with age.

An enzyme called OGG1 is responsible for repairing this type of oxidative DNA damage, and the researchers found that HDAC1 is needed to activate OGG1. When HDAC1 is missing, OGG1 fails to turn on and DNA damage goes unrepaired. Many of the genes that the researchers found to be most susceptible to this type of damage encode ion channels, which are critical for the function of synapses.

Targeting neurodegeneration

Several years ago, Tsai and Stephen Haggarty of Harvard Medical School, who is also an author of the new study, screened libraries of small molecules in search of potential drug compounds that activate or inhibit members of the HDAC family. In the new paper, Tsai and Pao used one of these drugs, called exifone, to see if they could reverse the age-related DNA damage they saw in mice lacking HDAC1.

The researchers used exifone to treat two different mouse models of Alzheimer’s, as well as healthy older mice. In all cases, they found that the drug reduced the levels of oxidative DNA damage in the brain and improved the mice’s cognitive functions, including memory.

Exifone was approved in the 1980s in Europe to treat dementia but was later taken off the market because it caused liver damage in some patients. Tsai says she is optimistic that other, safer HDAC1-activating drugs could be worth pursuing as potential treatments for both age-related cognitive decline and Alzheimer’s disease.

“This study really positions HDAC1 as a potential new drug target for age-related phenotypes, as well as neurodegeneration-associated pathology and phenotypes,” she says.

Tsai’s lab is now exploring whether DNA damage and HDAC1 also play a role in the formation of Tau tangles — misfolded proteins in the brain that are a signature of Alzheimer’s and other neurodegenerative diseases.

The research was funded by the National Institute on Aging, the National Institute of Neurological Disorders and Stroke, and a Glenn Award for Research in Biological Mechanisms of Aging.

–From MIT News

Chinna Adaikkan stands before a research poster and talks to two onlookers.

Scientists eager to explain brain rhythm boost’s broad impact in Alzheimer’s models

The sweeping extent to which increasing 40Hz “gamma” rhythm power in the brain can affect the pathology and symptoms of Alzheimer’s disease in mouse models has been surprising, even to the MIT neuroscientists who’ve pioneered the idea. So surprising, in fact, they can’t yet explain why it happens.

In three papers, including two this year in Cell and Neuron, they’ve demonstrated that exposing mice to light flickering or sound buzzing at 40Hz, a method dubbed “GENUS” for Gamma ENtrainment Using Sensory stimuli, strengthens the rhythm across the brain and changes the gene expression and activity of multiple brain cell types. Pathological amyloid and tau protein buildups decline, neurons and their circuit connections are protected from degeneration and learning and memory endure significantly better than in disease model mice who do not receive GENUS.

In a new review article in Trends in Neurosciences two researchers leading those efforts lay out the few knowns and many unknowns that must be understood to determine how the widespread effects take place. It’s a challenge they relish because the answers could both break new scientific ground and help them improve how GENUS could become a therapeutic or preventative approach for people.

“While we know it affects pathology in mice, we want to understand how because that will help us understand and refine potential treatment,” said lead author Chinnakkaruppan Adaikkan, a postdoc in the lab of senior author Li-Huei Tsai, Picower Professor of Neuroscience and director of The Picower Institute for Learning and Memory.

Adaikkan has been interested in understanding how neural activity produces brain rhythms since his doctoral research. At MIT, he is channeling that passion into understanding how sensory stimulation can entrain oscillations.

“That’s what drives me to come to the lab every day to study these mechanisms,” Adaikkan said. “When we got the data from the first mouse where we recorded from the visual cortex, the hippocampus and the prefrontal cortex we were surprised to see that visual stimulation entrains in these brain regions. That was very exciting but we have a very long way to go to understand how this happens.”

The new paper raises that question and many others for the field. What cells underlie the brain’s response to GENUS? How do gamma rhythms engage non-neuronal cells such as astrocytes and microglia? How does it propagate beyond the brain regions responsible for perception? How extensively can enhancing gamma affect cognition? Does long-term stimulation affect brain circuit connections and how they change?

Cell roles

Studies of how groups of neurons engage in coherent oscillations of electrical activity have yielded two models to explain gamma rhythms. Both involve an interplay between excitatory and inhibitory neurons but differ on which type leads the interaction, Adaikkan and Tsai wrote. In his work, Adaikkan is attempting to dissect the roles of specific neuron types in GENUS and how closely those patterns mirror other sources of gamma, such as that invoked by cognitive tasks.

GENUS affects more than neurons. Tsai’s lab has found that microglia change their gene expression, their physical form, their protein-consuming behavior and their inflammatory response depending on the Alzheimer’s model involved. Work from another group showed that blocking vesicle release in astrocytes can hinder gamma power in mice and Tsai’s group found that auditory GENUS recruits an increase reactive astrocytes, which are more inclined to consume pathological proteins.

The new paper offers three hypotheses about how such “glial” cells are involved: They might contribute directly to gamma entrainment by regulating the flow of ions that carry electrical charge; even if they don’t contribute to rhythms, their ionic sensitivity may still make them responsive to gamma changes; they might instead be affected by changes in levels of neurotransmitters as a result of gamma.

Moreover, different glia may also become involved because of their proximity to electrical couplings between neurons called synapses, or because of how their activity is otherwise governed by neural activity.

The broader brain

That GENUS extends to the hippocampus, which is key for memory, and the prefrontal cortex, which is key for cognition, is likely a factor in how it preserves brain function. But again there are competing models for how increased gamma could facilitate multi-regional communication. In one, the authors write, coherence at the same frequency optimizes communication, while in the other model, one region’s gamma activity directly drives activity in regions downstream. New experiments that directly manipulate inter-regional circuits, they argue, could help resolve which model better explains gamma entrainment’s effects.

Finally, the effects of GENUS on brain function and behavior also aren’t fully explained. The Tsai lab’s has shown significant effects on spatial memory and some effects on other forms of memory, depending on the stimulation method. Other studies have shown that stimulating brain rhythms by other means, such as via genetic or optogenetic manipulations in mice, or via transcranial stimulation in humans, can also improve functions such as working memory. Adaikkan is interested in closing a gap between those studies and the Tsai lab’s work: Most studies measure cognitive performance during stimulation, while the Tsai lab has done so after the conclusion of repeated stimulation. He said he’d like to also test how mice perform while GENUS is actively underway.

“Our lab is excited to tackle these many hypotheses and to see how the field tackles many more,” Tsai said. “GENUS has created many intriguing new questions for neuroscience.”

The JPB Foundation, The Robert A. and Renee E. Belfer Foundation, and the Jeffrey and Nancy Halis Family Foundation have supported the work.

Li-Huei Tsai is shown in profile as she stands smiling at a podium

Tsai elected fellow of National Academy of Inventors

The National Academy of Inventors has selected MIT neuroscientist Li-Huei Tsai, Picower Professor of Neuroscience and director of The Picower Institute for Learning and Memory, as a member of its 2019 class of new fellows.

NAI fellows “have demonstrated a highly prolific spirit of innovation in creating or facilitating outstanding inventions that have made a tangible impact on the quality of life, economic development and welfare of society,” the organization stated in its announcement.

Tsai’s research focuses on neurodegenerative conditions such as Alzheimer’s disease. Her work has generated a dozen patents, many of which have been licensed by biomedical companies including two startups, Cognito Therapeutics and Souvien Bio Ltd., that have spun out from her and collaborator’s labs. Her team’s innovations include inhibiting an enzyme that affects the chromatin structure of DNA to rescue gene expression and restore learning and memory, and using light and sound stimulation to enhance the power and synchrony of 40Hz gamma rhythms in the brain to reduce Alzheimer’s pathology, prevent neuron death and preserve learning and memory. Each of these promising sets of findings in mice are now being tested in human trials.

“The goal of my lab is to improve our understanding of neurodegenerative disease mechanisms and to develop new therapies that could prevent the suffering of millions of people and their loved ones,” said Tsai who also directs MIT’s Aging Brain Initiative. “A crucial part of that effort is translating promising fundamental findings to the clinic and I’m honored that the NAI has recognized our work toward that goal.”

Tsai joins 22 colleagues from MIT as an NAI fellow, including Materials Science and Engineering Department Head Christopher Schuh, who was also elected this year. Among previously elected fellows are Tsai collaborators Emery N. Brown, a fellow Picower Institute faculty member and Edward Hood Taplin Professor of Computational Neuroscience and Health Sciences & Technology, and Ed Boyden, Y. Eva Tan Professor of Neurotechnology.

A microscope image showing white dots of amyloid built up in a cluster within a mouse brain

Study pinpoints Alzheimer’s plaque emergence early and deep in the brain

Long before symptoms like memory loss even emerge, the underlying pathology of Alzheimer’s disease, such as an accumulation of amyloid protein plaques, is well underway in the brain. A longtime goal of the field has been to understand where it starts so that future interventions could begin there.

A new study by MIT neuroscientists at The Picower Institute for Learning and Memory could help those efforts by pinpointing the regions with the earliest emergence of amyloid in the brain of a prominent mouse model of the disease. Notably, the study also shows that the degree of amyloid accumulation in one of those same regions of the human brain correlates strongly with the progression of the disease.

“Alzheimer’s is a neurodegenerative disease so in the end you can see a lot of neuron loss,” said Wen-Chin “Brian” Huang, co-lead author of the study and a postdoc in the lab of co-senior author Li-Huei Tsai, Picower Professor of Neuroscience and director of the Picower Institute. “At that point it would be hard to cure the symptoms. It’s really critical to understand what circuits and regions show neuronal dysfunction early in the disease. This will in turn facilitate the development of effective therapeutics.”

In addition to Huang, the study’s co-lead authors are Rebecca Canter, a former member of the Tsai lab, and Heejin Choi, a former member of the lab of co-senior author Kwanghun Chung, associate professor of chemical engineering and a member of the Picower Institute and the Institute for Medical Engineering and Science.

Tracking plaques

Many research groups have made progress in recent years by tracing amyloid’s path in the brain using technologies such as positron emission tomography and by looking at brains post-mortem, but the new study in Communications Biology adds substantial new evidence from the 5XFAD mouse model because it presents an unbiased look at the entire brain as early as one month of age. The study reveals that amyloid begins its terrible march in deep brain regions such as the mammillary body, the lateral septum and the subiculum before making its way along specific brain circuits that ultimately lead it to the hippocampus, a key region for memory, and the cortex, a key region for cognition.

The team used SWITCH, a technology developed by Chung, to label amyloid plaques and to clarify the whole brains of 5XFAD mice so that they could be imaged in fine detail at different ages. The team was consistently able to see that plaques first emerged in the deep brain structures and then tracked along circuits such as the Papez memory circuit to spread throughout the brain by 6-12 months (a mouse’s lifespan is up to three years).

The findings help to cement an understanding that has been harder to obtain from human brains, Huang said, because post-mortem dissection cannot easily account for how the disease developed over time and PET scans don’t offer the kind of resolution the new study provides from the mice.

Key validations

Importantly, the team directly validated a key prediction of their mouse findings in human tissue: If the mammillary body is indeed a very early place that amyloid plaques emerge, then the density of those plaques should increase in proportion with how far advanced the disease is. Sure enough, when the team used SWITCH to examine the mammillary bodies of post-mortem human brains at different stages of the disease, they saw exactly that relationship: The later the stage, the more densely plaque-packed the mammillary body was.

“This suggests that human brain alterations in Alzheimer’s disease look similar to what we observe in mouse,” the authors wrote. “Thus we propose that amyloid-beta deposits start in susceptible subcortical structures and spread to increasingly complex memory and cognitive networks with age.”

The team also performed experiments to determine whether the accumulation of plaques they observed were of real disease-related consequence for neurons in affected regions. One of the hallmarks of Alzheimer’s disease is a vicious cycle in which amyloid makes neurons too easily excited and overexcitement causes neurons to produce more amyloid. The team measured the excitability of neurons in the mammillary body of 5XFAD mice and found they were more excitable than otherwise similar mice that did not harbor the 5XFAD set of genetic alterations.

In a preview of a potential future therapeutic strategy, when the researchers used a genetic approach to silence the neurons in the mammillary body of some 5XFAD mice but left neurons in others unaffected, the mice with silenced neurons produced less amyloid.

While the study findings help explain much about how amyloid spreads in the brain over space and time, they also raise new questions, Huang said. How might the mammillary body affect memory and what types of cells are most affected there?

“This study sets a stage for further investigation of how dysfunction in these brain regions and circuits contributes to the symptoms of Alzheimer’s disease,” he said.

In addition to Huang, Canter, Choi, Tsai and Chung, the paper’s other authors are Jun Wang, Lauren Ashley Watson, Christine Yao, Fatema Abdurrob, Stephanie Bousleiman, Jennie Young, David Bennett and Ivana Dellalle.

The National Institutes of Health, the JPB Foundation, Norman B. Leventhal and Barbara Weedon fellowships, The Burroughs Wellcome Fund, the Searle Scholars Program, a Packard Award, a NARSAD Young Investigator Award and the NCSOFT Cultural Foundation funded the research.

An animation shows a microglia cell gobbling an amyloid protein

New Video: An update about our gamma research

In a new video we summarize the recent developments in our GENUS research. We have found that sensory stimulation of 40Hz gamma-frequency rhythms in the brain can help reduce Alzheimer’s disease pathology and improve memory in multiple mouse models of the disease. We are continuing to study the mechanisms of how that works and whether these results can be translated to people.

In Neuron: Why visual stimulation may work against Alzheimer’s

Several years ago, MIT neuroscientists showed that they could dramatically reduce the amyloid plaques seen in mice with Alzheimer’s disease simply by exposing the animals to light flickering at a specific frequency.

In a new study, the researchers have found that this treatment has widespread effects at the cellular level, and it helps not just neurons but also immune cells called microglia. Overall, these effects reduce inflammation, enhance synaptic function, and protect against cell death, in mice that are genetically programmed to develop Alzheimer’s disease.

“It seems that neurodegeneration is largely prevented,” says Li-Huei Tsai, the director of MIT’s Picower Institute for Learning and Memory and the senior author of the study.

The researchers also found that the flickering light boosted cognitive function in the mice, which performed much better on tests of spatial memory than untreated mice did. The treatment also produced beneficial effects on spatial memory in older, healthy mice.

Chinnakkaruppan Adaikkan, an MIT postdoc, is the lead author of the study, which appears online in Neuron on May 7.

Beneficial brain waves

Tsai’s original study on the effects of flickering light showed that visual stimulation at a frequency of 40 hertz (cycles per second) induces brain waves known as gamma oscillations in the visual cortex. These brain waves are believed to contribute to normal brain functions such as attention and memory, and previous studies have suggested that they are impaired in Alzheimer’s patients.

Tsai and her colleagues later found that combining the flickering light with sound stimuli — 40-hertz tones — reduced plaques even further and also had farther-reaching effects, extending to the hippocampus and parts of the prefrontal cortex. The researchers have also found cognitive benefits from both the light- and sound-induced gamma oscillations.

In their new study, the researchers wanted to delve deeper into how these beneficial effects arise. They focused on two different strains of mice that are genetically programmed to develop Alzheimer’s symptoms. One, known as Tau P301S, has a mutated version of the Tau protein, which forms neurofibrillary tangles like those seen in Alzheimer’s patients. The other, known as CK-p25, can be induced to produce a protein called p25, which causes severe neurodegeneration. Both of these models show much greater neuron loss than the model they used for the original light flickering study, Tsai says.

The researchers found that visual stimulation, given one hour a day for three to six weeks, had dramatic effects on neuron degeneration. They started the treatments shortly before degeneration would have been expected to begin, in both types of Alzheimer’s models. After three weeks of treatment, Tau P301S mice showed no neuronal degeneration, while the untreated Tau P301S mice had lost 15 to 20 percent of their neurons. Neurodegeneration was also prevented in the CK-p25 mice, which were treated for six weeks.

“I have been working with p25 protein for over 20 years, and I know this is a very neurotoxic protein. We found that the p25 transgene expression levels are exactly the same in treated and untreated mice, but there is no neurodegeneration in the treated mice,” Tsai says. “I haven’t seen anything like that. It’s very shocking.”

The researchers also found that the treated mice performed better in a test of spatial memory called the Morris water maze. Intriguingly, they also found that the treatment improved performance in older mice that did not have a predisposition for Alzheimer’s disease, but not young, healthy mice.

Genetic changes

To try to figure out what was happening at a cellular level, the researchers analyzed the changes in gene expression that occurred in treated and untreated mice, in both neurons and microglia — immune cells that are responsible for clearing debris from the brain.

In the neurons of untreated mice, the researchers saw a drop in the expression of genes associated with DNA repair, synaptic function, and a cellular process called vesicle trafficking, which is important for synapses to function correctly. However, the treated mice showed much higher expression of those genes than the untreated mice. The researchers also found higher numbers of synapses in the treated mice, as well as a greater degree of coherence (a measure of brain wave synchrony between different parts of the brain).

In their analysis of microglia, the researchers found that cells in untreated mice turned up their expression of inflammation-promoting genes, but the treated mice showed a striking decrease in those genes, along with a boost of genes associated with motility. This suggests that in the treated mice, microglia may be doing a better job of fighting off inflammation  and clearing out molecules that could lead to the formation of amyloid plaques and neurofibrillary tangles, the researchers say. They also found lower levels of the version of the Tau protein that tends to form tangles.

A key unanswered question, which the researchers are now investigating, is how gamma oscillations trigger all of these protective measures, Tsai says.

“A lot of people have been asking me whether the microglia are the most important cell type in this beneficial effect, but to be honest, we really don’t know,” she says. “After all, oscillations are initiated by neurons, and I still like to think that they are the master regulators. I think the oscillation itself must trigger some intracellular events, right inside neurons, and somehow they are protected.”

The researchers also plan to test the treatment in mice with more advanced symptoms, to see if neuronal degeneration can be reversed after it begins. They have also begun phase 1 clinical trials of light and sound stimulation in human patients.

The research was funded by the National Institutes of Health, the Halis Family Foundation, the JPB Foundation, and the Robert A. and Renee E. Belfer Family Foundation.

From MIT News

In Nature: A comprehensive map of how Alzheimer’s affects the brain

MIT researchers have performed the first comprehensive analysis of the genes that are expressed in individual brain cells of patients with Alzheimer’s disease. The results allowed the team to identify distinctive cellular pathways that are affected in neurons and other types of brain cells.

This analysis could offer many potential new drug targets for Alzheimer’s, which afflicts more than 5 million people in the United States.

“This study provides, in my view, the very first map for going after all of the molecular processes that are altered in Alzheimer’s disease in every single cell type that we can now reliably characterize,” says Manolis Kellis, a professor of computer science and a member of MIT’s Computer Science and Artificial Intelligence Laboratory and of the Broad Institute of MIT and Harvard. “It opens up a completely new era for understanding Alzheimer’s.”

The study revealed that a process called axon myelination is significantly disrupted in patients with Alzheimer’s. The researchers also found that the brain cells of men and women vary significantly in how their genes respond to the disease.

Kellis and Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory, are the senior authors of the study, which appears in the May 1 online edition of Nature. MIT postdocs Hansruedi Mathys and Jose Davila-Velderrain are the lead authors of the paper.

Single-cell analysis

The researchers analyzed postmortem brain samples from 24 people who exhibited high levels of Alzheimer’s disease pathology and 24 people of similar age who did not have these signs of disease. All of the subjects were part of the Religious Orders Study, a longitudinal study of aging and Alzheimer’s disease. The researchers also had data on the subjects’ performance on cognitive tests.

The MIT team performed single-cell RNA sequencing on about 80,000 cells from these subjects. Previous studies of gene expression in Alzheimer’s patients have measured overall RNA levels from a section of brain tissue, but these studies don’t distinguish between cell types, which can mask changes that occur in less abundant cell types, Tsai says.

“We wanted to know if we could distinguish whether each cell type has differential gene expression patterns between healthy and diseased brain tissue,” she says. “This is the power of single-cell-level analysis: You have the resolution to really see the differences among all the different cell types in the brain.”

Using the single-cell sequencing approach, the researchers were able to analyze not only the most abundant cell types, which include excitatory and inhibitory neurons, but also rarer, non-neuronal brain cells such as oligodendrocytes, astrocytes, and microglia. The researchers found that each of these cell types showed distinct gene expression differences in Alzheimer’s patients.

Some of the most significant changes occurred in genes related to axon regeneration and myelination. Myelin is a fatty sheath that insulates axons, helping them to transmit electrical signals. The researchers found that in the individuals with Alzheimer’s, genes related to myelination were affected in both neurons and oligodendrocytes, the cells that produce myelin.

Most of these cell-type-specific changes in gene expression occurred early in the development of the disease. In later stages, the researchers found that most cell types had very similar patterns of gene expression change. Specifically, most brain cells turned up genes related to stress response, programmed cell death, and the cellular machinery required to maintain protein integrity.

Bruce Yankner, a professor of genetics and neurology at Harvard Medical School, described the study as “a tour de force of molecular pathology.”

“This is the first comprehensive application of single-cell RNA sequencing technology to Alzheimer’s disease,” says Yankner, who was not involved in the research. “I anticipate this will be a very valuable resource for the field and will advance our understanding of the molecular basis of the disease.”

Sex differences

The researchers also discovered correlations between gene expression patterns and other measures of Alzheimer’s severity such as the level of amyloid plaques and neurofibrillary tangles, as well as cognitive impairments. This allowed them to identify “modules” of genes that appear to be linked to different aspects of the disease.

“To identify these modules, we devised a novel strategy that involves the use of an artificial neural network and which allowed us to learn the sets of genes that are linked to the different aspects of Alzheimer’s disease in a completely unbiased, data-driven fashion,” Mathys says. “We anticipate that this strategy will be valuable to also identify gene modules associated with other brain disorders.”

The most surprising finding, the researchers say, was the discovery of a dramatic difference between brain cells from male and female Alzheimer’s patients. They found that excitatory neurons and other brain cells from male patients showed less pronounced gene expression changes in Alzheimer’s than cells from female individuals, even though those patients did show similar symptoms, including amyloid plaques and cognitive impairments. By contrast, brain cells from female patients showed dramatically more severe gene-expression changes in Alzheimer’s disease, and an expanded set of altered pathways.

“That’s when we realized there’s something very interesting going on. We were just shocked,” Tsai says.

So far, it is unclear why this discrepancy exists. The sex difference was particularly stark in oligodendrocytes, which produce myelin, so the researchers performed an analysis of patients’ white matter, which is mainly made up of myelinated axons. Using a set of MRI scans from 500 additional subjects from the Religious Orders Study group, the researchers found that female subjects with severe memory deficits had much more white matter damage than matched male subjects.

More study is needed to determine why men and women respond so differently to Alzheimer’s disease, the researchers say, and the findings could have implications for developing and choosing treatments.

“There is mounting clinical and preclinical evidence of a sexual dimorphism in Alzheimer’s predisposition, but no underlying mechanisms are known. Our work points to differential cellular processes involving non-neuronal myelinating cells as potentially having a role. It will be key to figure out whether these discrepancies protect or damage the brain cells only in one of the sexes — and how to balance the response in the desired direction on the other,” Davila-Velderrain says.

The researchers are now using mouse and human induced pluripotent stem cell models to further study some of the key cellular pathways that they identified as associated with Alzheimer’s in this study, including those involved in myelination. They also plan to perform similar gene expression analyses for other forms of dementia that are related to Alzheimer’s, as well as other brain disorders such as schizophrenia, bipolar disorder, psychosis, and diverse dementias.

The research was funded by the National Institutes of Health, the JBP Foundation, and the Swiss National Science Foundation.

–From MIT News

In mouse brains stained for the presence of amyloid, much less is visible in the cortex of a mouse treated with sensory gamma stimulation (right) than in a mouse left untreated (left).

In Cell: Brain wave stimulation may improve Alzheimer’s symptoms

By exposing mice to a unique combination of light and sound, MIT neuroscientists have shown that they can improve cognitive and memory impairments similar to those seen in Alzheimer’s patients.

This noninvasive treatment, which works by inducing brain waves known as gamma oscillations, also greatly reduced the number of amyloid plaques found in the brains of these mice. Plaques were cleared in large swaths of the brain, including areas critical for cognitive functions such as learning and memory.

“When we combine visual and auditory stimulation for a week, we see the engagement of the prefrontal cortex and a very dramatic reduction of amyloid,” says Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory and the senior author of the study.

Further study will be needed, she says, to determine if this type of treatment will work in human patients. The researchers have already performed some preliminary safety tests of this type of stimulation in healthy human subjects.

MIT graduate student Anthony Martorell and Georgia Tech graduate student Abigail Paulson are the lead authors of the study, which appears in the March 14 issue of Cell.

Continue reading…

Tsai earns Hans Wigzell Research Foundation Science Prize

The Hans Wigzell Research Foundation announced Jan. 23 that neuroscientist Li-Huei Tsai, Picower Professor and director of The Picower Institute for Learning and Memory at MIT, is the winner of Hans Wigzell´s Prize in Medicine for 2018. Tsai will travel to Stockholm to receive the prize and deliver a lecture on her research Feb. 14.

“The prize is given to professor Li-Huei Tsai for her innovative research in trying to understand the etiology and possible treatment of Alzheimer´s disease,” the Foundation stated in the announcement of the $100,000 prize. “Professor Tsai has in her research made a series of impressive findings with regard to this disease.”

In decades of research with collaborators, postdocs and students, Tsai has led several fundamental and translatable discoveries about biological mechanisms underlying neurodegeneration including specific aberrations in epigenetic gene regulation, enzyme pathways and repair of DNA damage. Tsai and collaborators have also uncovered substantial evidence that impaired neuronal synchrony may underlie Alzheimer’s progression, an insight that has allowed her to demonstrate a non-invasive treatment approach using light and sound stimuli to drive neural oscillations, engage the brain’s immune system, reduce pathology, and improve functionality in multiple mouse models. Testing of the technique has recently begun in humans.

“This treatment has resulted in dramatic improvements of the diseased animals both with regard to pathology and performance,” the foundation noted. “Her research has rapidly resulted in the start of advanced, clinical trials in Alzheimer’s patients.”

Tsai, who also directs the Aging Brain Initiative at MIT, said she was honored to earn the Wigzell Foundation’s recognition. Hans Wigzell is a former President of the Karolinska Institute and Chairman of the Nobel Prize Committee of the Institute.

“I am deeply grateful to Professor Wizgell and the Foundation for this award,” Tsai said. “The prize provides my team with great inspiration and resources to continue our work to understand the biology of neurodegeneration and to translate our findings to effective treatments for Alzheimer’s and other diseases.”

With fellowship, postdoc will work to solve Alzheimer’s myelin mystery

Growing up, Joel Blanchard watched his grandfather remain cognitively sharp past the age of 90 but his grandmother develop Alzheimer’s in her 70s. The difference sparked an interest in brain aging that motivates him today as a postdoc in MIT’s Picower Institute for Learning and Memory. As the new recipient of a 2018 Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research, he will embark on research that could help explain why myelin, the insulation that clads the brain’s neural wiring, breaks down in Alzheimer’s disease.

“As a teenager, I wondered why these two people with shared experiences and lives had such different outcomes,” said Blanchard, whose interest in Alzheimer’s disease helped bring him to the lab of Picower Professor and Institute Director Li-Huei Tsai.

One of the main mysteries of Alzheimer’s disease – and brain aging more generally – is why myelin degenerates, Blanchard said.

“Myelin and oligodendrocytes insulate neuronal axons supporting and reinforcing neuronal networks, cognition, learning, and memory,” he said. “In aging and Alzhiemer’s disease, myelin degenerates, but it is unknown why this occurs and how it contributes to disease pathogenesis.”

With the award of $60,000 provided by the American Federation for Aging Research (AFAR) and the Glenn Foundation for Medical Research, Blanchard plans to address the question by using three-dimensional cultures of brain tissue grown from human induced pluripotent stem cells.

“We have developed a 3D model of human myelination in a tissue culture dish,” Blanchard said. “This is allowing us to investigate how genetic and environmental factors associated with cognitive aging and Alzheimer’s disease influence myelinating cells and neuronal health.”

Using the cultures, he’ll be able to observe how they grow and change, and will even be able to edit their genes to see the difference that might be made by variations associated with Alzheimer’s disease.

Blanchard said his goal is not only to improve understanding but also to identify new approaches to diagnosing and treating the disease.

“By investigating how and why myelin degenerates in Alzheimer’s disease we hope to identify new strategies for therapeutic intervention and biomarkers for identifying people at risk for cognitive impairments later in life,” he said.