Author: davidjo

A pink cartoon brain is superposed over a background of DNA double-helixes. Toward the right side of the image, the brain is crumbling to dust.

Decoding the complexity of Alzheimer’s disease

By analyzing epigenomic and gene expression changes that occur in Alzheimer’s disease, researchers identify cellular pathways that could become new drug targets

Alzheimer’s disease affects more than 6 million people in the United States, and there are very few FDA-approved treatments that can slow the progression of the disease.

In hopes of discovering new targets for potential Alzheimer’s treatments, MIT researchers have performed the broadest analysis yet of the genomic, epigenomic, and transcriptomic changes that occur in every cell type in the brains of Alzheimer’s patients.

Using more than 2 million cells from more than 400 postmortem brain samples, the researchers analyzed how gene expression is disrupted as Alzheimer’s progresses. They also tracked changes in cells’ epigenomic modifications, which help to determine which genes are turned on or off in a particular cell. Together, these approaches offer the most detailed picture yet of the genetic and molecular underpinnings of Alzheimer’s.

The researchers report their findings in a set of four papers appearing today in Cell. The studies were led by Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory, and Manolis Kellis, a professor of computer science in MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) and a member of the Broad Institute of MIT and Harvard.

“What we set out to do was blend together our computational and our biological expertise and take an unbiased look at Alzheimer’s at an unprecedented scale across hundreds of individuals — something that has just never been undertaken before,” Kellis says.

The findings suggest that an interplay of genetic and epigenetic changes feed on each other to drive the pathological manifestations of the disease.

“It’s a multifactorial process,” said Tsai, who leads MIT’s Aging Brain Initiative. “These papers together use different approaches that point to a converging picture of Alzheimer’s disease where the affected neurons have defects in their 3D genome, and that is causal to a lot of the disease phenotypes we see.”

A complex interplay

Many efforts to develop drugs for Alzheimer’s disease have focused on the amyloid plaques that develop in patients’ brains. In their new set of studies, the MIT team sought to uncover other possible approaches by analyzing the molecular drivers of the disease, the cell types that are the most vulnerable, and the underlying biological pathways that drive neurodegeneration.

To that end, the researchers performed transcriptomic and epigenomic analyses on 427 brain samples from the Religious Orders Study/Memory and Aging Project (ROSMAP), a longitudinal study that has tracked memory, motor, and other age-related changes in older people since 1994. These samples included 146 people with no cognitive impairment, 102 with mild cognitive impairment, and 144 diagnosed with Alzheimer’s-linked dementia.

In the first Cell paper, focused on gene expression changes, the researchers used single-cell RNA-sequencing to analyze the gene expression patterns of 54 types of brain cells from these samples, and identified cellular functions that were most affected in Alzheimer’s patients. Among the most prominent, they found impairments in the expression of genes involved in mitochondrial function, synaptic signaling, and protein complexes needed to maintain the structural integrity of the genome.

This gene expression study, which was led by former MIT postdoc Hansruedi Mathys, graduate student Zhuyu (Verna) Peng, and former graduate student Carles Boix, also found that genetic pathways related to lipid metabolism were highly disrupted. In work published in Nature last year, the Tsai and Kellis labs showed that the strongest genetic risk for Alzheimer’s, called APOE4, interferes with normal lipid metabolism, which can then lead to defects in many other cell processes.

In the study led by Mathys, the researchers also compared gene expression patterns in people who showed cognitive impairments and those who did not, including some who remained sharp despite having some degree of amyloid buildup in the brain, a phenomenon known as cognitive resilience. That analysis revealed that cognitively resilient people had larger populations of two subsets of inhibitory neurons in the prefrontal cortex. In people with Alzheimer’s-linked dementia, those cells appear to be more vulnerable to neurodegeneration and cell death.

“This revelation suggests that specific inhibitory neuron populations might hold the key to maintaining cognitive function even in the presence of Alzheimer’s pathology,” Mathys says. “Our study pinpoints these specific inhibitory neuron subtypes as a crucial target for future research and has the potential to facilitate the development of therapeutic interventions aimed at preserving cognitive abilities in aging populations.”


In the second Cell paper, led by former MIT postdoc Xushen Xiong, graduate student Benjamin James, and former graduate student Carles Boix PhD ’22, the researchers examined some of the epigenomic changes that occurred in 92 people, including 48 healthy individuals and 44 with early or late-stage Alzheimer’s. Epigenomic changes are alterations in the chemical modifications or packaging of DNA that affect the usage of a particular gene within a given cell.

To measure those changes, the researchers used a technique called ATAC-Seq, which measures the accessibility of sites across the genome at single-cell resolution. By combining this data with single-cell RNA-sequencing data, the researchers were able to link information about how much a gene is expressed with data on how accessible that gene is. They could also start to group genes into regulatory circuits that control specific cell functions such as synaptic communication — the primary way that neurons transmit messages throughout the brain.

Using this approach, the researchers were able to track changes in gene expression and epigenomic accessibility that occur in genes that have previously been linked with Alzheimer’s. They also identified the types of cells that were most likely to express these disease-linked genes, and found that many of them occur most often in microglia, the immune cells responsible for clearing debris from the brain.

This study also revealed that every type of cell in the brain undergoes a phenomenon known as epigenomic erosion as Alzheimer’s disease progresses, meaning that the cells’ normal pattern of accessible genomic sites is lost, which contributes to loss of cell identity.

The role of microglia

In a third Cell paper, led by MIT graduate student Na Sun and research scientist Matheus Victor, the researchers focused primarily on microglia, which make up 5 to 10 percent of the cells in the brain. In addition to clearing debris from the brain, these immune cells also respond to injury or infection and help neurons communicate with each other.

In two panels red microglia surround a bluish blob. In the left panel the microglia are more slender whereas they are more bloated on the right. The blue blub is more compact on the left and more diffuse on the right.
Researchers tracked changes in microglia early (left) and late (right) in Alzheimer’s disease. Microglia (red) surround an amyloid plaque (blue). The microglia are noticeably more activated, with larger cell bodies, on the right. The amyloid plaque, meanwhile, is more diffused. Images by Mat Victor.

This study builds on a 2015 paper from Tsai and Kellis in which they found that many of the genome-wide association study (GWAS) variants associated with Alzheimer’s disease are predominantly active in immune cells like microglia, much more than in neurons or other types of brain cells.

In the new study, the researchers used RNA sequencing to classify microglia into 12 different states, based on hundreds of genes that are expressed at different levels during each state. They also showed that as Alzheimer’s disease progresses, more microglia enter inflammatory states. The Tsai lab has also previously shown that as more inflammation occurs in the brain, the blood-brain barrier begins to degrade and neurons begin to have difficulty communicating with each other.

At the same time, fewer microglia in the Alzheimer’s brain exist in a state that promotes homeostasis and helps the brain function normally. The researchers identified transcription factors that turn on the genes that keep microglia in that homeostatic state, and the Tsai lab is now exploring ways to activate those factors, in hopes of treating Alzheimer’s disease by programming inflammation-inducing microglia to switch back to a homeostatic state.

DNA damage

In the fourth Cell study, led by MIT research scientist Vishnu Dileep and Boix, the researchers examined how DNA damage contributes to the development of Alzheimer’s disease. Previous work from Tsai’s lab has shown that DNA damage can appear in neurons long before Alzheimer’s symptoms appear. This damage is partly a consequence of the fact that during memory formation, neurons create many double-stranded DNA breaks. These breaks are promptly repaired, but the repair process can become faulty as neurons age.

This fourth study found that as more DNA damage accumulates in neurons, it becomes more difficult for them to repair the damage, leading to genome rearrangements and 3D folding defects.

“When you have a lot of DNA damage in neurons, the cells, in their attempt to put the genome back together, make mistakes that cause rearrangements,” Dileep says. “The analogy that I like to use is if you have one crack in an image, you can easily put it back together, but if you shatter an image and try to piece it back together, you’re going to make mistakes.”

These repair mistakes also lead to a phenomenon known as gene fusion, which occurs when rearrangements take place between genes, leading to dysregulation of genes. Alongside defects in genome folding, these changes appear to predominantly impact genes related to synaptic activity, likely contributing to the cognitive decline seen in Alzheimer’s disease.

The findings raise the possibility of seeking ways to enhance neurons’ DNA repair capabilities as a way to slow down the progression of Alzheimer’s disease, the researchers say.

In addition, Kellis’ lab now hopes to use artificial intelligence algorithms such as protein language models, graph neural networks, and large language models to discover drugs that might target some of the key genes that the researchers identified in these studies.

The researchers also hope that other scientists will make use of their genomic and epigenomic data. “We want the world to use this data,” Kellis says. “We’ve created online repositories where people can interact with the data, can access it, visualize it, and conduct analyses on the fly.”

The research was funded, in part, by the National Institutes of Health and the Cure Alzheimer’s Foundation CIRCUITS consortium.

Research papers:
–Story by MIT News. Lead image by Christine Daniloff
A square panel shows tall yellow streaks. At the very bottom is a black field with a few blue dots. Almost across the top there is a strip of many blue dots.

Molecule reduces inflammation in Alzheimer’s models

A potential new Alzheimer’s drug represses the harmful inflammatory response of the brain’s immune cells, reducing disease pathology, preserving neurons and improving cognition in preclinical tests

Though drug developers have achieved some progress in treating Alzheimer’s disease with medicines that reduce amyloid-beta protein, other problems of the disease including inflammation, continue unchecked. In a new study, scientists at The Picower Institute for Learning and Memory at MIT describe a candidate drug that in human cell cultures and Alzheimer’s mouse models reduced inflammation and improved memory.

The target of the new “A11” molecule is a genetic transcription factor called PU.1. Prior research has shown that amid Alzheimer’s disease, PU.1 becomes an overzealous director of inflammatory gene expression in the brain’s microglia immune cells. A11 suppresses this problematic PU.1 activity, the new research shows, by recruiting other proteins that repress the inflammatory genes PU.1 works to express. But because A11 concentrates mostly in the brain and does not reduce PU.1 levels, it does not appear to disrupt PU.1’s other job, which is to ensure the production of a wide variety of blood cells.

“Inflammation is a major component of Alzheimer’s disease pathology that has been especially hard to treat,” said study senior author Li-Huei Tsai, Picower Professor of Neuroscience at MIT and director of The Picower Institute and MIT’s Aging Brain Initiative. “This preclinical study demonstrates that A11 reduces inflammation in human microglia-like cells as well as in multiple mouse models of Alzheimer’s disease and significantly improves cognition in the mice. We believe A11 therefore merits further development and testing.”

Tsai and Elizabeta Gjoneska of the National Institutes of Health are co-corresponding authors of the study published in the Journal of Experimental Medicine.

As a postdoc, Gjoneska co-led a 2015 study that implicated PU.1 as a regulator of errant microglia inflammation in a mouse model of Alzheimer’s disease. That research was a collaboration between Tsai’s lab and that of MIT Computer Science Professor Manolis Kellis, co-led by former postdoc Andreas Pfenning, now a faculty member at Carnegie Mellon University. Ever since then, Tsai has been seeking a safe way to restore PU.1 activity to healthier levels.

The work described in the new paper, led by Picower Institute research scientist William Ralvenius, starts with experiments to further validate that PU.1 would be a therapeutically meaningful target. To do that the scientists compared gene expression in immune cells of postmortem brain samples from Alzheimer’s patients and mouse models and matching non-Alzheimer’s controls. The comparisons showed that Alzheimer’s effects major changes in microglial gene expression and that an increase in PU.1 binding to inflammatory gene targets was a significant component of that change. Moreover, they showed that reducing PU.1 activity in a mouse model of Alzheimer’s reduced inflammation and neurodegeneration, the death of neurons.

Screening success

Genetically knocking down PU.1 in the body is not a viable therapeutic strategy given its importance in normal healthy function. The team therefore screened more than 58,000 small molecules from libraries of FDA-approved drugs and novel chemicals to see if any could safely and significantly reduce key inflammation and Alzheimer’s related genes regulated by by PU.1 in cell cultures. After several rounds of increasingly stringent screening, they narrowed the field down to six chemicals. A11 was by far the most potent among them.

They tested the effects of A11 doses on the function of human microglia-like cells cultured from patient stem cells. When they exposed the microglia-like cells to immune molecules that typically trigger inflammation, cells dosed with A11 exhibited reduced expression and secretion of inflammatory cytokines and less of the cell body shape changes associated with microglia inflammatory responses. The cells also showed less accumulation of lipid molecules, another sign of inflammatory activation. Looking at gene expression patterns, the scientists observed that A11-treated cells exposed to inflammatory triggers behaved much like unperturbed microglia, suggesting that A11 helps prevent microglia from overreacting to inflammatory cues.

Two more lab tests aimed at understanding how A11 exerts its effects revealed that it doesn’t change PU.1 levels. Instead it counteracts PU.1 activity by recruiting several proteins including MECP2, HDAC1, SIN3A and DMNT3A, known to repress expression of its targets. Essentially amid Alzheimer’s disease, A11 tamps down what PU.1 amps up.

“A11 represents a first-in-class molecule that converts PU.1 from a transcriptional activator to a transcriptional repressor, resulting in a controlled state of microglial inflammation,” the authors wrote.

Two square panels side by side show a stripe of many blue dots near the top. The panel on the left has a few yellow stripes extending down from the blue dots. The panel on the right has many more of the yellow vertical lines.
The brains of Alzheimer’s model mice treated with A11 (right) showed more tubulin (yellow), a marker of neuronal health, than untreated controls (left).

Mice in mazes

Having established that A11 reduced inflammatory activity in microglia and determined how that happens, the team focused on whether it worked as a medicine in mouse models of Alzheimer’s disease.

Pharmacological tests indicated that A11 is readily cleared from tissues and is capable of reaching brain cells.  Moreover, in healthy mice the chemical successfully crossed the blood-brain barrier and remained in brain cells much longer than anywhere else.

Finally the team tested the effects of the drugs on Alzheimer’s disease pathology and symptoms in three mouse strains that each model different aspects of Alzheimer’s disease: CK-p25 mice (severe neurodegeneration), Tau P301S transgenic mice (tauopathy), and 5XFAD mice (amyloid pathology).

Male and female CK-p25 mice dosed with A11 showed less inflammatory response among microglia and astrocyte cells and lost fewer neurons than untreated controls. TauP301S Tg mice responded similarly, also exhibiting a significant reduction of phosphorylated tau protein in the hippocampus region of the brain, which is an essential area for memory. In 5XFAD mice, amyloid was significantly reduced.

Two square panels side by side show brain tissue with green staining. The panel on the left shows much more green than the panel on the right.
A11 treated Alzheimer’s model mice (right) showed much less tau (green staining) than untreated controls (left).

The team subjected the Tau P301S Tg and CK-p25 mice to mazes designed to test their short-term working memory and longer-term learning. In both models and on both tests, A11-treated mice performed significantly better than untreated controls. For example, in the “Morris Water Maze,” where mice have to learn the location of a submerged platform that allows them to rest, treated CK-p25 mice learned much faster than untreated ones.

Much more testing needs to be done before A11 could become an approved medicine, Tsai said, but she noted that it could complement the new treatments that target amyloid.

“Given that A11 acts via a distinct mechanism from existing AD therapeutics, A11 could be used alone or in combination with approved therapeutics to provide improved treatment options for neurodegenerative diseases,” the authors concluded.

In addition to Tsai, Gjoneska and Ralvenius, the paper’s other authors are Alison E. Mungenast, Hannah Woolf, Margaret M. Huston, Tyler Z. Gillingham, Stephen K. Godin, Jay Penney, Hugh P. Cam, Fan Gao, Celia G. Fernandez, Barbara Czako, Yaima Lightfoot, William J. Ray, Adrian Beckmann, Alison M. Goate, Edoardo Marcora, Carmen Romero-Molina, Pinar Ayata, and Anne Schaefer.

The Robert A. and Renee E. Belfer Family Foundation and the National Institutes of Health funded the research. Additional support came from The JPB Foundation and The Picower Institute for Learning and Memory, The Halis Family Foundation, Lester A. Gimpelson and Jay L. and Caroll Miller.

Two panels show sections of mouse brain tissue with a dull magenta glow. In the panel on the left many cells are lit up brightly in magenta. In the panel on the right, only one cell is lit up brightly.

40 Hz vibrations reduce Alzheimer’s pathology, symptoms in mouse models

Tactile stimulation improved motor performance, reduced phosphorylated tau, preserved neurons and synapses and reduced DNA damage, a new study shows

Evidence that non-invasive sensory stimulation of 40 Hz gamma frequency brain rhythms can reduce Alzheimer’s disease pathology and symptoms, already shown with light and sound by multiple research groups in mice and humans, now extends to tactile stimulation. A new study by MIT scientists shows that Alzheimer’s model mice exposed to 40 Hz vibration an hour a day for several weeks showed improved brain health and motor function compared to untreated controls.

The MIT group is not the first to show that gamma frequency tactile stimulation can affect brain activity and improve motor function, but they are the first to show that the stimulation can also reduce levels of the hallmark Alzheimer’s protein phosphorylated tau, keep neurons from dying or losing their synapse circuit connections, and reduce neural DNA damage.

“This work demonstrates a third sensory modality that we can use to increase gamma power in the brain,” said Li-Huei Tsai, corresponding author of the study, director of The Picower Institute for Learning and Memory and the Aging Brain Initiative at MIT, and Picower Professor in the Department of Brain and Cognitive Sciences (BCS). “We are very excited to see that 40 Hz tactile stimulation benefits motor abilities, which has not been shown with the other modalities. It would be interesting to see if tactile stimulation can benefit human subjects with impairment in motor function.”

Ho-Jun Suk, Nicole Buie, Guojie Xu and Arit Banerjee are lead authors of the study in Frontiers in Aging Neuroscience and Ed Boyden, Y. Eva Tan Professor of Neurotechnology at MIT, is a co-senior author of the paper. Boyden, an affiliate member of The Picwoer Institute, is also appointed in BCS as well as the Departments of Bioengineering and Media Arts and Sciences, the McGovern Institute for Brain Research, and the K. Lisa Yang Cener for Bionics.

Feeling the vibe

In a series of papers starting in 2016, a collaboration led by Tsai’s lab has demonstrated that light flickering and/or sound clicking at 40 Hz (a technology called GENUS for Gamma Entrainment Using Sensory stimuli), reduces levels of amyloid-beta and tau proteins, prevents neuron death and preserves synapses and even sustains learning and memory in a variety of Alzheimer’s disease mouse models. Most recently in pilot clinical studies the team showed that 40 Hz light and sound stimulation was safe, successfully increased brain activity and connectivity and appeared to produce significant clinical benefits in a small cohort of human volunteers with early-stage Alzheimer’s disease. Other groups have replicated and corroborated health benefits of 40 Hz sensory stimulation and an MIT spin-off company, Cognito Therapeutics, has launched stage III clinical trials of light and sound stimulation as an Alzheimer’s treatment.

The new study tested whether whole-body 40 Hz tactile stimulation produced meaningful benefits in two commonly used mouse models of Alzheimer’s neurodegeneration, the Tau P301S mouse, which recapitulates the disease’s tau pathology, and the CK-p25 mouse, which recapitulates the synapse loss and DNA damage seen in human disease. The team focused its analyses in two areas of the brain: the primary somatosensory cortex (SSp), where tactile sensations are processed, and the primary motor cortex (MOp), where the brain produces movement commands for the body.

To produce the vibration stimulation, the researchers placed mouse cages over speakers playing 40 Hz sound, which vibrated the cages. Non-stimulated control mice were in cages interspersed in the same room so that all the mice heard the same 40 Hz sound. The differences measured between the stimulated and control mice were therefore made by the addition of tactile stimulation.

First the researchers confirmed that 40 Hz vibration made a difference in neural activity in the brains of healthy (i.e. non-Alzheimer’s) mice. As measured by expression of c-fos protein, activity increased two-fold in the SSp and more than 3-fold in the MOp, a statistically significant increase in the latter case.

Once the researchers knew that 40 Hz tactile stimulation could increase neural activity, they assessed the impact on disease in the two mouse models. To ensure both sexes were represented, the team used male P301S mice and female CK-p25 mice.

P301S mice stimulated for three weeks showed significant preservation of neurons compared to unstimulated controls in both brain regions. Stimulated mice also showed significant reductions in tau in the SSp by two measures, and exhibited similar trends in the MOp.

CK-p25 mice received six weeks of vibration stimulation. These mice showed higher levels of synaptic protein markers in both brain regions compared to unvibrated control mice. They also showed reduced levels of DNA damage.

Finally the team assessed the motor abilities of mice exposed to the vibration vs. not exposed. They found that both mouse models were able to stay on a rotating rod significantly longer. P301S mice also hung on to a wire mesh for significantly longer than control mice while CK-p25 mice showed a positive, though non-significant trend.

“The current study, along with our previous studies using visual or auditory GENUS demonstrates the possibility of using non-invasive sensory stimulation as a novel therapeutic strategy for ameliorating pathology and improving behavioral performance in neurodegenerative diseases,” the authors concluded.

Support for the study came from The JPB Foundation, The Picower Institute for Learning and Memory, Eduardo Eurnekian, The DeGroof-VM Foundation, Halis Family Foundation, Melissa and Doug Ko Hahn, Lester Gimpelson, Eleanor Schwartz Charitable Foundation, The Dolby Family, Kathleen and Miguel Octavio, Jay and Carroll Miller, Anne Gao and Alex Hu and Charles Hieken.

A mouse brain cross section is highlighted n blue. At the bottom center a football-shaped patch is highlighted in green

Neuroscientists identify cells especially vulnerable to Alzheimer’s

Neurons that form part of a memory circuit are among the first brain cells to show signs of neurodegeneration in Alzheimer’s disease.

Neurodegeneration, or the gradual loss of neuron function, is one of the key features of Alzheimer’s disease. However, it doesn’t affect all parts of the brain equally.

One of the first brain regions to show neurodegeneration in Alzheimer’s disease is a part of the hypothalamus called the mammillary body. In a new study, MIT researchers have identified a subset of neurons within this body that are most susceptible to neurodegeneration and hyperactivity. They also found that this damage leads to memory impairments.

The findings suggest that this region may contribute to some of the earliest symptoms of Alzheimer’s disease, making it a good target for potential new drugs to treat the disease, the researchers say.

“It is fascinating that only the lateral mammillary body neurons, not those in the medial mammillary body, become hyperactive and undergo neurodegeneration in Alzheimer’s disease,” says Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory and the senior author of the study. Tsai also directs MIT’s Aging Brain Initiative.

In a study of mice, the researchers showed that they could reverse memory impairments caused by hyperactivity and neurodegeneration in mammillary body neurons by treating them with a drug that is now used to treat epilepsy.

Former MIT postdoc Wen-Chin (Brian) Huang and MIT graduate students Zhuyu (Verna) Peng and Mitchell Murdock are the lead authors of the paper, which appears today in Science Translational Medicine.

Predisposed to degeneration

As Alzheimer’s disease progresses, neurodegeneration occurs along with the buildup of amyloid beta plaques and misfolded Tau proteins, which form tangles in the brain. One question that remains unresolved is whether this neurodegeneration strikes indiscriminately, or if certain types of neurons are more susceptible.

“If we could identify specific molecular properties of classes of neurons that are predisposed to dysfunction and degeneration, then we would have a better understanding of neurodegeneration,” Murdock says. “This is clinically important because we could find ways to therapeutically target these vulnerable populations and potentially delay the onset of cognitive decline.”

In a 2019 study using a mouse model of Alzheimer’s disease, Tsai, Huang, and others found that the mammillary bodies — a pair of structures found on the left and right underside of the hypothalamus — had the highest density of amyloid beta. These bodies are known to be involved in memory, but their exact role in normal memory and in Alzheimer’s disease is unknown.

To learn more about the mammillary body’s function, the researchers used single-cell RNA-sequencing, which can reveal the genes that are active within different types of cells in a tissue sample. Using this approach, the researchers identified two major populations of neurons: one in the medial mammillary body and the other in the lateral mammillary body. In the lateral neurons, genes related to synaptic activity were very highly expressed, and the researchers also found that these neurons had higher spiking rates than medial mammillary body neurons.

Based on those differences, the researchers wondered if the lateral neurons might be more susceptible to Alzheimer’s disease. To explore that question, they studied a mouse model with five genetic mutations linked to early-onset Alzheimer’s in humans. The researchers found that these mice showed much more hyperactivity in lateral mammillary body neurons than healthy mice. However, the medial mammillary body neurons in healthy mice and the Alzheimer’s model did not show any such differences.

The researchers found that this hyperactivity emerged very early — around two months of age (the equivalent of a young human adult), before amyloid plaques begin to develop. The lateral neurons became even more hyperactive as the mice aged, and these neurons were also more susceptible to neurodegeneration than the medial neurons.

“We think the hyperactivity is related to dysfunction in memory circuits and is also related to a cellular progression that might lead to neuronal death,” Murdock says.

The Alzheimer’s mouse model showed impairments in forming new memories, but when the researchers treated the mice with a drug that reduces neuronal hyperactivity, their performance on memory tasks was significantly improved. This drug, known as levetiracetam, is used to treat epileptic seizures and is also in clinical trials to treat epileptiform activity — hyperexcitability in the cortex, which increases the risk of seizures — in Alzheimer’s patients.

Comparing mice and humans

The researchers also studied human brain tissue from the Religious Orders Study/Memory and Aging Project (ROSMAP), a longitudinal study that has tracked memory, motor, and other age-related issues in older people since 1994. Using single-cell RNA-sequencing of mammillary body tissue from people with and without Alzheimer’s disease, the researchers found two clusters of neurons that correspond to the lateral and medial mammillary body neurons they found in mice.

Similar to the mouse studies, the researchers also found signatures of hyperactivity in the lateral mammillary bodies from Alzheimer’s tissue samples, including overexpression of genes that encode potassium and sodium channels. In those samples, they also found higher levels of neurodegeneration in the lateral neuron cluster, compared to the medial cluster.

Other studies of Alzheimer’s patients have found a loss of volume of the mammillary body early in the disease, along with deposition of plaques and altered synaptic structure. All of these findings suggest that the mammillary body could make a good target for potential drugs that could slow down the progression of Alzheimer’s disease, the researchers say.

Tsai’s lab is now working on further defining how the lateral neurons of the mammillary body are connected to other parts of the brain, to figure out how it forms memory circuits. The researchers also hope to learn more about what properties of the lateral neurons of the mammillary body make them more vulnerable to neurodegeneration and amyloid deposition.

The research was funded by The JPB Foundation, the Carol and Gene Ludwig Family Foundation, and the U.S. National Institutes of Health.

–From MIT News

Four panels in a 2x2 array. The top left shows a lot of purple staining of cells. The top right shows much less purple. The bottom row shows two nearly idential stripes of blue with lots of blue spots above and below.

A new peptide may hold potential as an Alzheimer’s treatment

The peptide blocks a hyperactive brain enzyme that contributes to the neurodegeneration seen in Alzheimer’s and other diseases

MIT neuroscientists have found a way to reverse neurodegeneration and other symptoms of Alzheimer’s disease by interfering with an enzyme that is typically overactive in the brains of Alzheimer’s patients.

When the researchers treated mice with a peptide that blocks the hyperactive version of an enzyme called CDK5, they found dramatic reductions in neurodegeneration and DNA damage in the brain. These mice also showed improvements in their ability to perform tasks such as learning to navigate a water maze.

“We found that the effect of this peptide is just remarkable,” says Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory and the senior author of the study. “We saw wonderful effects in terms of reducing neurodegeneration and neuroinflammatory responses, and even rescuing behavior deficits.”

With further testing, the researchers hope that the peptide could eventually be used as a treatment for patients with Alzheimer’s disease and other forms of dementia that have CDK5 overactivation. The peptide does not interfere with CDK1, an essential enzyme that is structurally similar to CDK5, and it is similar in size to other peptide drugs that are used in clinical applications.

Picower Institute Research Scientist Ping-Chieh Pao is the lead author of the paper, which appears this week in the Proceedings of the National Academy of Sciences.

Targeting CDK5

Tsai has been studying CDK5’s role in Alzheimer’s disease and other neurodegenerative diseases since early in her career. As a postdoc, she identified and cloned the CDK5 gene, which encodes a type of enzyme known as a cyclin-dependent kinase. Most of the other cyclin-dependent kinases are involved in controlling cell division, but CDK5 is not. Instead, it plays important roles in the development of the central nervous system, and also helps to regulate synaptic function.

CDK5 is activated by a smaller protein that it interacts with, known as P35. When P35 binds to CDK5, the enzyme’s structure changes, allowing it to phosphorylate — add a phosphate molecule to — its targets. However, in Alzheimer’s and other neurodegenerative diseases, P35 is cleaved into a smaller protein called P25, which can also bind to CDK5 but has a longer half-life than P35.

When bound to P25, CDK5 becomes more active in cells. P25 also allows CDK5 to phosphorylate molecules other than its usual targets, including the Tau protein. Hyperphosphorylated Tau proteins form the neurofibrillary tangles that are one of the characteristic features of Alzheimer’s disease.

In previous work, Tsai’s lab has shown that transgenic mice engineered to express P25 develop severe neurodegeneration. In humans, P25 has been linked to several diseases, including not only Alzheimer’s but also Parkinson’s disease and frontotemporal dementia.

Pharmaceutical companies have tried to target P25 with small-molecule drugs, but these drugs tend to cause side effects because they also interfere with other cyclin-dependent kinases, so none of them have been tested in patients.

The MIT team decided to take a different approach to targeting P25, by using a peptide instead of a small molecule. They designed their peptide with a sequence identical to that of a segment of CDK5 known as the T loop, which is a structure critical to the binding of CDK5 to P25. The entire peptide is only 12 amino acids long — slightly longer than most existing peptide drugs, which are five to 10 amino acids long.

“From a peptide drug point of view, usually smaller is better,” Tsai says. “Our peptide is almost within that ideal molecular size.”

Dramatic effects

In tests in neurons grown in a lab dish, the researchers found that treatment with the peptide led to a moderate reduction in CDK5 activity. Those tests also showed that the peptide does not inhibit the normal CDK5-P35 complex, nor does it affect other cyclin-dependent kinases.

When the researchers tested the peptide in a mouse model of Alzheimer’s disease that has hyperactive CDK5, they saw a myriad of beneficial effects, including reductions in DNA damage, neural inflammation, and neuron loss. These effects were much more pronounced in the mouse studies than in tests in cultured cells.

The peptide treatment also produced dramatic improvements in a different mouse model of Alzheimer’s, which has a mutant form of the Tau protein that leads to neurofibrillary tangles. After treatment, those mice showed reductions in both Tau pathologies and neuron loss. Along with those effects in the brain, the researchers also observed behavioral improvements. Mice treated with the peptide performed much better in a task that required learning to navigate a water maze, which relies on spatial memory, than mice that were treated with a control peptide (a scrambled version of the peptide used to inhibit CDK5-P25).

In those mouse studies, the researchers injected the peptide and found that it was able to cross the blood-brain barrier and reach neurons of the hippocampus and other parts of the brain.

The researchers also analyzed the changes in gene expression that occur in mouse neurons following treatment with the peptide. Among the changes they observed was an increase in expression of about 20 genes that are typically activated by a family of gene regulators called MEF2. Tsai’s lab has previously shown that MEF2 activation of these genes can confer resilience to cognitive impairment in the brains of people with Tau tangles, and she hypothesizes that the peptide treatment may have similar effects.

“Further development of such peptide inhibitors toward a lead therapeutic candidate, if proven to be selective for the target and relatively free of clinical side effects, may eventually lead to novel treatments for neurodegenerative disorders ranging from Alzheimer’s disease to Frontotemporal dementia to Parkinson’s disease,” says Stuart Lipton, a professor of neuroscience at Scripps Research, who was not involved in the study.

Tsai now plans to do further studies in other mouse models of diseases that involve P25-associated neurodegeneration, such as frontotemporal dementia, HIV-induced dementia, and diabetes-linked cognitive impairment.

“It’s very hard to say precisely which disease will most benefit, so I think a lot more work is needed,” she says.

The research was funded by the National Institutes of Health.


New technologies revealing cross-cutting breakdowns in Alzheimer’s disease

‘Single-cell profiling’ is helping neuroscientists see how disease affects major brain cell types and identify common, potentially targetable pathways

After decades of fundamental scientific and drug discovery research, Alzheimer’s disease has remained inscrutable and incurable, with a bare minimum of therapeutic progress. But in a new review article in Nature Neuroscience, MIT scientists write that by employing the new research capability of single-cell profiling, the field has rapidly achieved long-sought insights with strong potential for both explaining Alzheimer’s disease and doing something meaningful about it. By analyzing this new evidence, for instance, the authors show that the disease’s disruptions converge on five main areas of cellular function, or “pathways,” in each of five major brain cell types.

Single-cell profiling technologies produce comprehensive measurements of genetic activity in individual cells, such as levels of RNA which is transcribed from DNA, so that the cell’s functions and roles of in the biology of the brain, and the pathology of disease, can be assessed. Single-cell profiling technologies go beyond genome sequencing, which catalogs the DNA present in most every cell of a person, by revealing how each cell is uniquely making use of that common set of instructions. In studying Alzheimer’s disease, scientists have been using single-cell profiling to see how various brain cells, such as distinct types of neurons and microglia and astrocytes act differently in disease compared to how they behave in a healthy brain.

In the article, MIT Brain and Cognitive Sciences doctoral student Mitch Murdock and Picower Professor Li-Huei Tsai, Director of MIT’s Picower Institute for Learning and Memory and Aging Brain Initiative, write that while the findings of single-cell profiling studies confirm that the disease’s terrible effects are complex and far-reaching, there appear to also be five pathways that become perturbed in each of five major cell types. Investigating these pathways, they write, could produce valuable biomarkers of disease and yield meaningful targets for therapeutic intervention:

  • Inflammation and immune response
  • Lipid (fat molecule) signaling and metabolism
  • Metabolic stress and protein folding
  • DNA damage and cellular senescence (aging)
  • Interactions with brain vasculature (blood vessels)
Five panels offer cartoon schematics of a wide variety of cell and molecular interactions. The graphic is headed by this text: "single-cell genomics highlght common signaling pathways perturbed across multiple cell types in AD"
A figure from the paper depicts pathways perturbed in Alzheimer’s disease. Below examples are listed for each pathway by major brain cell type.

For each of these pathways in neurons, microglia, astrocytes, oligodendrocytes and oligodendrocyte precursor cells, Tsai and Murdock identify specific differences in gene regulation, found in single-cell studies, that significantly occur in brains of Alzheimer’s patients or mouse models compared to healthy control samples.

For example, Tsai and Murdock highlight more than a dozen genes all intimately involved in lipid processing whose expression is altered in various ways in various cells in the brain’s prefrontal cortex. For another example they show that all five cell types show impairments in DNA repair, albeit by changed expression of different genes in each.

“By identifying vulnerable cell types and the molecular programs that give rise to them, therapeutic interventions might reverse aberrant cellular trajectories,” Murdock and Tsai wrote in Nature Neuroscience. “While many transcriptional alterations are cell-type specific, these changes ultimately might converge on shared signaling pathways across cell types that might represent targets for new therapeutic strategies.”

To be sure, the authors note, there is still plenty of work to be done, both in refining and improving on single-cell techniques and also exploiting newer related opportunities. The paper notes a number of issues that must be carefully considered in producing valid single-cell profiling results, including where cells are sampled in the brain for sequencing, from whom, and in what condition. Moreover, it’s not always straightforward to show how changes in gene expression necessarily affect biology and it’s even harder to know whether any particular intervention, for instance to target altered inflammation pathways, will prove safe and effective as a therapy.

Future directions, meanwhile could include making greater use of “spatial transcriptomics,” which measures gene transcription in cells where they are situated within the brain, rather than removing them for analysis. Studies should be expanded to incorporate more human samples so that varying disease and demographic differences can be fully accounted for. Datasets should be shared and integrated, the authors write, and better comparisons between human and mouse samples are necessary to better understand how well, or not, they overlap.

“Single-cell profiling facilitates a nuanced portrait of the diverse cellular processes perturbed in the AD brain,” Tsai and Murdock conclude. “These varied molecular programs help explain the divergence between healthy aging and cognitive decline, and highlight cell-type-specific molecular programs involved in AD. Core signaling modules are disrupted across multiple cell types, and manipulating disrupted cellular states will pave the way for new therapeutic opportunities.”

The foreground shows a computer monitor with multiple views inside a brain. The background shows a person lying inside the tube of an MRI machine.

Small studies of 40Hz sensory stimulation confirm safety, suggest Alzheimer’s benefits

MIT researchers report early stage clinical study results of tests with non-invasive 40Hz light and sound treatment

A pair of early stage clinical studies testing the safety and efficacy of 40Hz sensory stimulation to treat Alzheimer’s disease has found that the potential therapy was well tolerated, produced no serious adverse effects and was associated with some significant neurological and behavioral benefits among a small cohort of participants.

“In these clinical studies we were pleased to see that volunteers did not experience any safety issues and used our experimental light and sound devices in their homes consistently,” said Li-Huei Tsai, Picower Professor in the The Picower Institute for Learning and Memory at MIT and senior author of the paper describing the studies in PLOS ONE Dec. 1. “While we are also encouraged to see some significant positive effects on the brain and behavior, we are interpreting them cautiously given our study’s small sample size and brief duration. These results are not sufficient evidence of efficacy, but we believe they clearly support proceeding with more extensive study of 40Hz sensory stimulation as a potential non-invasive therapeutic for Alzheimer’s disease.”

In three studies spanning 2016-2019, Tsai’s lab discovered that exposing mice to light flickering or sound clicking at the gamma-band brain rhythm frequency of 40Hz – or employing the light and sound together – produced widespread beneficial effects. Treated mice modeling Alzheimer’s disease pathology experienced improvements in learning and memory; reduced brain atrophy, neuron and synapse loss; and showed lower levels of the hallmark Alzheimer’s proteins amyloid beta and phosphorylated tau compared to untreated controls. The stimulation appears to produce these effects by increasing the power and synchrony of the 40Hz brain rhythm, which the lab has shown profoundly affects the activity of several types of brain cells, including the brain’s vasculature.Study designs

Based on those encouraging results, Diane Chan, a neurologist at Massachusetts General Hospital and a postdoctoral clinical fellow in Tsai’s lab, led the two new clinical studies at MIT. One set of tests, a “Phase 1” study, enrolled 43 volunteers of various ages including 16 people with early stage Alzheimer’s to confirm that exposure to 40Hz light and sound was safe and test whether it increased 40Hz rhythm and synchrony after a few minutes of exposure, as measured with EEG electrodes. The study also included two patients with epilepsy at the University of Iowa who consented to having measurements taken in deeper brain structures during exposure to 40Hz sensory stimulation while undergoing epilepsy-related surgery.

The second set of tests, a “Phase 2A” pilot study, enrolled 15 people with early stage Alzheimer’s disease in a single-blinded, randomized, controlled study to receive exposure to 40Hz light and sound (or non-40Hz “sham” stimulation for experimental controls) for an hour a day for at least three months. They underwent baseline and follow-up visits including EEG measurements during stimulation, MRI scans of brain volume, and cognitive testing. The stimulation device the volunteers used in their homes (a light panel synchronized with a speaker) was equipped with video cameras to monitor device usage. Participants also wore sleep-monitoring bracelets during their participation in the trial.

The Phase 2A trial launched just before the onset of the Covid-19 pandemic in 2020, causing some participants to become unable to undergo follow ups after three months. The study therefore only reports results through a four-month period.

Study results

In the Phase 1 study volunteers filled out a questionnaire on side effects, reporting a few minor but no major adverse effects. The most common was feeling “sleepy or drowsy.” Meanwhile, measurements taken with EEG scalp electrodes clustered at frontal and occipital sites showed significant increases in 40Hz rhythm power at each cortical site among cognitively normal younger and older participants as well as volunteers with mild Alzheimer’s. The readings also demonstrated significant increase in coherence at the 40Hz frequency between the two sites. Between the two volunteers with epilepsy, measurements showed significant increases in 40Hz power in deeper brain regions such as the gyrus rectus, amygdala, hippocampus and insula with no adverse events including seizures.

In the Phase 2A study, neither treated nor control volunteers reported serious adverse events. Both groups used their devices 90 percent of the time. The eight volunteers treated with 40Hz stimulation experienced several beneficial effects that reached statistical significance compared to the seven volunteers in the control condition. Control participants exhibited two signs of brain atrophy as expected with disease progression: reduced volume of the hippocampus and increased volume of open spaces, or ventricles. Treated patients did not experience significant changes in these measures. Treated patients also exhibited better connectivity across brain regions involved in the brain’s default mode and medial visual networks, which are related to cognition and visual processing respectively. Treated patients also exhibited more consistent sleep patterns than controls.

“Overall, these findings suggest that 40Hz GENUS has positive effects on AD-related pathology and symptoms and should be studied more extensively to evaluate its potential as a disease-modifying intervention for AD.”

Neither the treatment and control groups showed any differences after just three months on most cognitive tests, but the treatment group did perform significantly better on a face-name association test, a memory task with a strong visual component. The two groups, which were evenly matched by age, gender, APOE risk gene status, and cognitive scores, differed by years of education but that difference had no relationship to the results, the researchers wrote.

“After such a short time we didn’t expect to see significant effects on cognitive measures so it was encouraging to see that at least on face-name association the treatment group did perform significantly better,” Chan said.

In PLOS ONE the researchers concluded: “Overall, these findings suggest that 40Hz GENUS has positive effects on AD-related pathology and symptoms and should be studied more extensively to evaluate its potential as a disease-modifying intervention for AD.”

After the study ended all participants were permitted to continue using the devices set to provide the 40Hz stimulation.

The MIT team is now planning new clinical studies to test whether 40Hz sensory stimulation may be effective in preventing the onset of Alzheimer’s in high-risk volunteers and is launching preliminary studies to determine its therapeutic potential for Parkinson’s disease and Down syndrome. Cognito Therapeutics, an MIT spin-off company co-founded by Tsai and co-author Ed Boyden, Y. Eva Tan Professor of Neurotechnology at MIT, has launched Phase 3 trials of 40Hz sensory stimulation as an Alzheimer’s treatment using a different device.

Tsai, Boyden and co-author Emery N. Brown, Edward Hood Taplin Professor of Computational Neuroscience and Medical Engineering at MIT, are among the co-founders of MIT’s Aging Brain Initiative, which has advanced this collaboration and other neurodegeneration research at MIT.

In addition to Tsai, Chan, Boyden and Brown, the study’s other authors are Ho-Jun Suk, Brennan Jackson, Noah Milman, Danielle Stark, Elizabeth Klerman, Erin Kitchener, Vanesa S. Fernandez Avalos, Gabrielle de Weck, Arit Banerjee, Sara D. Beach, Joel Blanchard, Colton Stearns, Aaron D. Boes, Brandt Uitermarkt, Phillip Gander, Matthew Howard III, Eliezer J. Sternberg, Alfonso Nieto-Castanon, Sheeba Anteraper, Susan Whitfield-Gabrieli, and Bradford C. Dickerson.

Funding for the study came from sources including the Robert A. and Renee E. Belfer Family Foundation, Ludwig Family Foundation, JPB Foundation, Eleanor Schwartz Charitable Foundation, the Degroof-VM Foundation, Halis Family Foundation, and David B Emmes, Gary Hua and Li Chen, the Ko Han Family, Lester Gimpelson, Elizabeth K. and Russell L. Siegelman, Joseph P. DiSabato and Nancy E. Sakamoto, Alan and Susan Patricof, Jay L. and Carroll D Miller, Donald A. and Glenda G. Mattes, the Marc Haas Foundation, Alan Alda, and Dave Wargo.

A 3x2 array of squares shows a top row of three pinkish brain tissue samples with clear dark streaks. On the bottom row the pinkish squares of brain tissue don't show such a clear pattern

Alzheimer’s risk gene undermines insulation of brain’s “wiring”

In people carrying the APOE4 risk variant, a key brain cell type mismanages cholesterol needed to insulate neurons properly—another sign that APOE4 contributes to disease by disrupting lipids in the brain.

It’s well known that carrying one copy of the APOE4 gene variant increases one’s risk for Alzheimer’s disease threefold and two copies about tenfold, but the fundamental reasons why and what can be done to help patients remain largely unknown. A study published by an MIT-based team Nov. 16 in Nature provides some new answers as part of a broader line of research that has demonstrated APOE4’s consequences cell type by cell type in the brain.

The new study combines evidence from postmortem human brains, lab-based human brain cell cultures, and Alzheimer’s model mice to show that when people have one or two copies of APOE4, rather than the more common and risk-neutral APOE3 version, cells called oligodendrocytes mismanage cholesterol, failing to transport the fat molecule to wrap the long vine-like axon “wiring” that neurons project to make brain circuit connections. Deficiency of this fatty insulation, called myelin, may be a significant contributor to the pathology and symptoms of Alzheimer’s disease because without proper myelination, communications among neurons are degraded.

Recent studies by the research group, led by Picower Professor Li-Huei Tsai, director of The Picower Institute for Learning and Memory and the Aging Brain Initiative at MIT, have found distinct ways that APOE4 disrupts how fat molecules, or lipids, are handled by key brain cell types including neurons, astrocytes and microglia. In the new study as well as in those, the team has identified compounds that appear in the lab to correct these different problems, yielding potential pharmaceutical-based treatment strategies.

The new study extends that work not only by discovering how APOE4 disrupts myelination, but also by providing the first systematic analysis across major brain cell types using single nucleus RNA sequencing (snRNAseq) to compare how gene expression differs in people with APOE4 compared to APOE3.

“This paper shows very clearly from the snRNAseq of postmortem human brains in a genotype specific manner that APOE4 influences different brain cell types very distinctly,” said Tsai, a member of MIT’s Brain and Cognitive Sciences faculty. “We see convergence of lipid metabolism being disrupted, but when you really look into further detail at the kind of lipid pathways being disturbed in different brain cell types, they are all different.

“I feel that lipid dysregulation could be this very fundamental biology underlying a lot of the pathology we observe,” she said.

The paper’s lead authors are Joel Blanchard, an assistant professor at Mt. Sinai’s Icahn School of Medicine who began the work as a postdoc in Tsai’s MIT lab, Djuna Von Maydell and Leyla Akay, who are graduate students in Tsai’s lab, and Jose Davila Velderrain, a research group leader at Human Technopole and former postdoc in the lab of co-corresponding author Manolis Kellis, Computer Science Professor at MIT.

Many methods to examine myelination

Postmortem human brain samples came from the Religious Orders Study and the Rush Memory and Aging Project. The team’s snRNAseq results, a dataset that von Maydell has made freely available, encompasses more than 160,000 individual cells of 11 different types from the prefrontal cortex of 32 people—12 with two APOE3 copies, 12 with one copy of each APOE3 and APOE4, and eight with two APOE4 copies. The APOE3/3 and APOE3/4 samples were balanced by Alzheimer’s diagnosis, gender, and age. All APOE4/4 carriers had Alzheimer’s and 5 of 8 were female.

Some results reflected known Alzheimer’s pathology, but other patterns were novel. One in particular showed that APOE4-carrying oligodendrocytes exhibited greater expression of cholesterol synthesis genes and disruptions to cholesterol transport. The more APOE4 copies people had, the greater the effect. This was especially interesting given results from a prior analysis by Tsai’s and Kellis’s labs in 2019 that linked Alzheimer’s disease to reduced expression of myelination genes among oligodendrocytes.

Using a variety of techniques to look directly at the tissue, the team saw that in APOE4 brains, aberrant amounts of cholesterol accumulated within cell bodies, especially of oligodendrocytes, but was relatively lacking around neural axons.

To understand why, the team used patient-derived induced pluripotent stem cells to create lab cell cultures of oligodendrocytes engineered to differ only by whether they had APOE4 or APOE3. Again APOE4 cells showed major lipid disruptions. In particular, the afflicted oligodendrocytes hoarded extra cholesterol within their bodies, showed signs that the extra internal fats were stressing organelles called the endoplasmic reticulum that have a role in cholesterol transport, and indeed transported less cholesterol out to their membranes. Later when they were co-cultured with neurons, the APOE4 oligodendrocytes failed to myelinate the neurons as well as APO3 cells did, regardless of whether the neurons carried APOE4 or APOE3.

The team also observed that in post-mortem brains there was less myelination in APOE4 carriers than APOE3 carriers. For instance, the sheaths around axons running through the corpus callosum (the structure that connects brain hemispheres) were notably thinner in APOE4 brains. The same was true in mice engineered to harbor human APOE4 vs. those engineered to have APOE3.

A productive intervention

Eager to find a potential intervention, the team focused on drugs that affect cholesterol including statins (which suppress synthesis) and cyclodextrin, which aids cholesterol transport. The statins didn’t help, but applying cyclodextrin to APOE4 oligodendrocyte cultured in a dish reduced accumulation of cholesterol within the cells and improved myelination in co-cultures with neurons. Moreover, it also had these effects in APOE4 mice.

Finally, the team treated some APOE4 mice with cyclodextrin, left others untreated, and subjected them all to two different memory tests.  The cyclodextrin-treated mice performed both tests significantly better, suggesting an association between improved myelination and improved cognition.

Tsai said a clear picture is emerging in which intervening to correct specific lipid dysregulations by cell type could potentially help counteract APOE4’s contributions to Alzheimer’s pathology.

“It’s encouraging that we’ve seen a way to rescue oligodendrocyte function and myelination in lab and mouse models,” Tsai said. “But in addition to oligodendrocytes, we may also need to find clinically effective ways to take care of microglia, astrocytes, and vasculature to really combat the disease.”

In addition to the lead authors, Tsai and Kellis, the paper’s other authors are Hansruedi Mathys, Shawn Davidson, Audrey EffenbergerChi0yu Chen, Kristan Maner-Smith, Ihab Jahhar, Eric Orlund, Michael Bula, Emre Agbas, Ayesha Ng., Xueqiao Jiang, Martin Kahn, Cristina Blanco-Duque, Nicolas Lavoie, Liwang Liu, Ricardo Reyes, Yuan-Ta lin, Tak Ko, Lea R’Bibo, William Ralvenius, David Bennet and Hugh Cam.

The Robert A. and Renee E. Belfer Foundation, the JPB Foundation, the Carol and Gene Ludwig Family Foundation the Cure Alzheimer’s Fund and the National Insitutes of Health funded the study.

ON a black background the M-shaped coronal cross section of a mouse brain featurse patches of magenta and teal dots

With fractured genomes, Alzheimer’s neurons call for help

Study indicates that ailing neurons may instigate an inflammatory response from the brain’s microglia immune cells

A new study by researchers in The Picower Institute for Learning and Memory at MIT provides evidence from both mouse models and postmortem human tissue of a direct link between two problems that emerge in Alzheimer’s disease: a buildup of double-stranded breaks (DSBs) in the DNA of neurons and the inflammatory behavior of microglia, the brain’s immune cells.

A key new finding is that neurons actively trigger an inflammatory response to their genomic damage. Neurons have not been known to signal the brain’s immune system in Alzheimer’s disease, said study lead author Gwyneth Welch, a former MIT Brain and Cognitive Sciences graduate student in the lab of senior author Li-Huei Tsai.

“This is a novel concept in neuroscience: the idea that neurons can be activating inflammatory activity in response to DNA damage,” Welch said. “The general idea was that neurons have a more passive relationship with microglia regarding age-associated neuroinflammation.”

Instead, what Welch, Tsai and co-authors report in Science Advances is that neurons coping with mounting DSBs go through stages of first trying to fix their fractured DNA and then, when it apparently fails, sending out via molecular signals to microglia, which responded by taking on a more inflammatory state. In experiments where the scientists interrupted the immune signaling, they prevented microglia from entering that state and degrading neural circuit connections, or synapses.

Members of Tsai’s lab have been studying DSBs in the context of Alzheimer’s for more than a decade. Tsai said the new findings add to the emerging understanding of the role they play in Alzheimer’s.

“We have a longstanding interest in understanding DNA breaks in neurons,” said Tsai, Picower Professor of Neuroscience and a founder of MIT’s Aging Brain Initiative. “We previously showed that DNA double stranded breaks are necessary for the induction of activity-regulated gene expression in neurons but we also observed profound DNA damage in neurons in the early stages of neurodegeneration.

“We now know that DNA-damaged neurons exhibit senescent phenotypes and play an active role in eliciting an immune response from microglia and perhaps astrocytes,” Tsai said. “This is mediated by the activation of the NFkappaB transcription factor. Moreover, we identified two cytokines secreted by damaged neurons to recruit microglia and elicit microglial response.  Importantly, we show that inhibition of NFkappaB rescued synaptic loss in neurodegeneration, further elucidating of impact of neuroimmune response on synaptic integrity and cognitive function.”

In her thesis research Welch used the lab’s “CK-p25” mouse model of Alzheimer’s, in which disease pathology can be induced, She observed a timeline in which neurons with DSBs appeared within a week, peaked in number after two weeks and then tapered off, becoming notably reduced by six weeks. Meanwhile, those neurons also lost their ability to express a standard marker of neuronal identity. Welch realized there seemed to be stages to the process of coping with DSBs. First neurons have few DSBs and strong identity (baseline), then high DSBs with no loss of identity (stage 1), then high DSBs and a loss of neuronal identity (stage 2).

Transcripts tell the tale

To understand what cells were doing differently in each stage, Welch and the team used multiple “transcriptomics” technologies, which tracks differences in gene expression. Her analyses revealed that neuronal identity genes were most strongly expressed at baseline, DNA repair genes were strong during stage 1, and immune signaling genes were particularly prominent during stage 2.

Among the immune signaling genes were ones governed by the master transcription regulator NFkappaB. These included the cytokines Ccl2 and Cxcl10.

To see if these changes were due specifically to DSBs, Welch treated neurons in the absence of any induced pathology with a chemical called etoposide that causes DSBs. Similar gene expression patterns evident in the induced mice were recapitulated in the ones treated with etoposide. And when Welch also looked at gene expression in the brains of people with DSBs and with Alzheimer’s she also found many significant overlaps.

“We found that stage 1 and stage 2 gene signatures were active in human DSB-bearing neurons,” she and her co-authors wrote. “This neuronal immune signature was further amplified in the context of AD pathology, suggesting that it may serve a functional role in disease-associated neuroinflammation.”

A big role for microglia

Having established that DSB-afflicted neurons employ NFkappaB to send out immune signals such as Ccl2 and Cxcl10, Welch and the team then asked what the effect was. Given that the lab in 2017 had characterized a late-stage inflammatory response on the part of microglia in Alzheimer’s, they hypothesized that neurons might be responsible.

For this analysis Welch used spatial transcriptomics. She divided up both uninduced and induced mouse brains into many areas, and rated each area based on the strength of their DSB signal. Then she analyzed gene transcription in each area and found that locations with high DSBs also had many more microglia in an inflammatory state than locations with low DSBs. They were also able to directly image this relationship, yielding the observation that inflammatory microglia (evidenced by abnormally large cell bodies) were co-located with high-DSB neurons.

To further test the hypothesis, they disrupted NFkappaB regulated transcription in neurons by interfering with a key molecular cog in that machinery called p65. That step resulted in reduced proliferation of microglia and reduced microglia cell body size. It also induced beneficial changes in microglia gene expression, making them more consistent with their normal “homeostatic” state.

In other experiments they found that etoposide-treated neurons expressed Cxcl10 and Ccl2 but that disrupting NFkappaB reduced that expression. They also saw that depleting the two molecules from the brains also prevented microglia from becoming reactive.

And looking back at the neurons, they saw that while knocking down NFkappaB activity didn’t prevent them from dying, it did preserve circuit connections, or synapses, on the neurons that remained alive. That’s important because those circuit connections underlie brain function and microglia are known to prune those.

Because NFkappaB is known to help prevent cell death (which may be why knocking it down didn’t prevent neurons from dying), Welch said knocking it down is not likely to be a therapeutic strategy.

“Its more a proof of principle that that if you turn off a major switch for inflammation, that will change how microglia and neurons interact,” she said. “If your goal is to target inflammatory pathways, focusing on specific signaling molecules might be the more precise way to intervene.”

In addition to Welch and Tsai, the paper’s other authors are Carles Boix, Eloi Schmauch, Jose Davila-Velderrain, Matheus Victor, Vishnu Dileep, P. Lorenzo Bozzelli, Qiao Su, Jemmie D. Cheng, Audrey Lee, Noelle S. Leary, Andreas R. Pfenning, and Manolis Kellis.

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

A blue-hued cross-secction of a mouse;s brain highlights the visual cortex in red on the upper left and green on the upperright.

When Alzheimer’s degrades cells that cross hemispheres, visual memory suffers

New research reveals cells that span brain hemispheres to coordinate activity in visual processing centers and shows that Alzheimer’s degrades their structure and therefore their function

A new MIT study finds that Alzheimer’s disease disrupts at least one form of visual memory by degrading a newly identified circuit that connects the vision processing centers of each brain hemisphere.

The results of the study, published in Neuron by a research team based at The Picower Institute for Learning and Memory, come from experiments in mice, but provide a physiological and mechanistic basis for prior observations in human patients: the degree of diminished brain rhythm synchrony between counterpart regions in each hemisphere correlates with the clinical severity of dementia.

“We demonstrate that there is a functional circuit that can explain this phenomenon,” said lead author Chinnakkaruppan Adaikkan, a former Picower Institute postdoc who is now an assistant professor in the Centre for Brain Research at the Indian Institute of Science (IISc) in Bangalore. “In a way we uncovered a fundamental biology that was not known before.”

Specifically, Adaikkan’s work identified neurons that connect the primary visual cortex (V1) of each hemisphere and showed that when the cells are disrupted, either by genetic alterations that model Alzheimer’s disease or by direct laboratory perturbations, brain rhythm synchrony becomes reduced and mice become significantly less able to notice when a new pattern appeared on a wall in their enclosures. Such recognition of novelty, which requires visual memory of what was there the prior day, is an ability commonly disrupted in Alzheimer’s.

“This study demonstrates the propagation of gamma rhythm synchrony across the brain hemispheres via the cross hemispheric connectivity,” said study senior author Li-Huei Tsai, Picower Professor and director of The Picower Institute and MIT’s Aging Brain Initiative. “It also demonstrates that the disruption of this circuit in AD mouse models is associated with specific behavioral deficits.”

Cross-hemispheric cells

In the study, Adaikkan, Tsai, Thomas McHugh and co-authors discovered and traced V1 neurons that extended their axons all the way through the corpus callosum, which connects the brain’s hemispheres, to cells in the V1 on the brain’s other side. There, they found, the cross-hemispheric (CH) neurons forged connections, or synapses, with target cells, providing them with “excitatory” stimulation to drive their activity. Adaikkan also found that CH neurons were much more likely to be activated by a novelty discrimination task than V1 neurons in general or neurons in other regions heavily involved in memory such as the hippocampus or the prefrontal cortex.

Curious about how this might differ in Alzheimer’s disease, the team looked at the activity of the cells in two different Alzheimer’s mouse models. The found that CH cell activity was significantly lessened amid the disease. Unsurprisingly, Alzheimer’s mice fared much poorer in novelty discrimination tasks.

The team examined the CH cells closely and found that they gather incoming input from a variety of other cells within their V1 and other regions in their hemisphere that process visual information. When they compared the incoming connections of healthy CH neurons to those in CH cells afflicted with Alzheimer’s, they found that cells in the disease condition had significantly less infrastructure for hosting incoming connections (measured in terms of synapse-hosting spines protruding from the vine-like dendrites that sprawl out of the cell body).

Given the observations correlating reduced brain rhythm synchrony and memory performance in Alzheimer’s, the team wondered if that occurred in the mice, too. To find out, they custom-designed electrodes to measure rhythmic activity simultaneously in all cortical layers of each hemisphere’s V1. They observed that cross-hemispheric synchrony increased notably between the V1s when mice engaged in novelty discrimination but that the synchrony, both at high “gamma” and lower “theta” frequency rhythms, was significantly lower in the Alzheimer’s mice than it was in healthy mice.

Adaikkan’s evidence at that point was strong, but still only suggestive, that CH neurons provided the means by which the V1 regions on each side of the brain could coordinate to enable novelty discrimination, and that this ability became undermined by Alzheimer’s degradation of the CH cells’ connectivity. To more directly determine whether the CH circuit played such a causal, consequential role, the team directly intervened to disrupt them, testing what effect targeted perturbations had.

They found that chemically inhibiting CH cells disrupted rhythm synchrony between V1s, mirroring measures made in Alzheimer’s model mice. Moreover, disrupting CH activity undermined novelty discrimination ability. To further test whether it was the cells’ cross-hemispheric nature that mattered specifically, they engineered CH cells to be controllable with flashes of light (a technology called “optogenetics”). When they shined the light on the connections, they forged in the other hemisphere to inhibit those, they found that doing so again compromised visual discrimination ability.

All together, the study results show that CH cells in V1 connect with neurons in the counterpart area of the opposite hemisphere to synchronize neural activity needed for properly recognizing novelty, but that Alzheimer’s disease damages their ability to do that job.

Adaikkan said he is curious to now look at other potential cross-hemispheric connections and how they may be affected in Alzheimer’s disease, too. He said he also wants to study what happens to synchrony at other rhythm frequencies.

In addition to Adaikkan and Tsai, the study’s other authors are Jun Wang, Karim Abdelall, Steven Middleton, Lorenzo Bozzelli, and Ian Wickersham.

The JPB Foundation, The National Institutes of Health, and the Robert A. and Renee E. Belfer Foundation provided funding for the study.