Rhythmic brain circuits built from stem cells

The TV commercial is nearly 20 years old but I remember it vividly: a couple is driving down a street when they suddenly realize the music on their tape deck is in sync with the repetitive activity on the street. From the guy casually dribbling a basketball to people walking along the sidewalk to the delivery people passing packages out of their truck, everything and everyone is moving rhythmically to the beat.

The ending tag line was, “Sometimes things just come together,” which is quite true. Many of our basic daily activities like breathing and walking just come together as a result of repetitive movement. It’s easy to take them for granted but those rhythmic patterns ultimately rely on very intricate, interconnected signals between nerve cells, also called neurons, in the brain and spinal cord.

Circuitoids: a neural network in a lab dish

A CIRM-funded study published yesterday in eLife by Salk Institute scientists reports on a method to mimic these repetitive signals in a lab dish using neurons grown from embryonic stem cells. This novel cell circuitry system gives the researchers a tool for gaining new insights into neurodegenerative diseases, like Parkinson’s and ALS, and may even provide a means to fix neurons damaged by injury or disease.

The researchers changed or specialized mouse embryonic stem cells into neurons that either stimulate nerve signals, called excitatory neurons, or neurons that block nerve signals, called inhibitory neurons. Growing these groups of cells together led to spontaneous rhythmic nerve signals. These clumps of cells containing about 50,000 neurons each were dubbed circuitoids by the team.

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Confocal microscope immunofluorescent image of a spinal cord neural circuit made entirely from stem cells and termed a “circuitoid.” Credit: Salk Institute.

Making neural networks dance to a different beat

A video produced by the Salk Institute (see below), shows some fascinating microscopy visualizations of these circuitoids’ repetitive signals. In the video, team leader Samuel Pfaff explains that changing the ratio of excitatory vs inhibitory neurons had noticeable effects on the rhythm of the nerve impulses:

“What we were able to do is combine different ratios of cell types and study properties of the rhythmicity of the circuitoid. And that rhythmicity could be very tightly control depending on the cellular composition of the neural networks that we were forming. So we could regulate the speed [of the rhythmicity] which is kind of equivalent to how fast you’re walking.”

It’s possible that the actual neural networks in our brains have the flexibility to vary the ratio of the active excitatory to inhibitory neurons as a way to allow adjustments in the body’s repetitive movements. But the complexity of those networks in the human brain are staggering which is why these circuitoids could help:

Samuel Pfaff. (Salk Institute)

Samuel Pfaff. (Salk Institute)

“It’s still very difficult to contemplate how large groups of neurons with literally billions if not trillions of connections take information and process it,” says Pfaff in a press release. “But we think that developing this kind of simple circuitry in a dish will allow us to extract some of the principles of how real brain circuits operate. With that basic information maybe we can begin to understand how things go awry in disease.”

Using stem cells to fix bad behavior in the brain

 

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Gladstone Institutes Steven Finkbeiner and Gaia Skibinski: Photo courtesy Chris Goodfellow, Gladstone Institutes

Diseases of the brain have many different names, from Alzheimer’s and Parkinson’s to ALS and Huntington’s, but they often have similar causes. Researchers at the Gladstone Institutes in San Francisco are using that knowledge to try and find an approach that might be effective against all of these diseases. In a new CIRM-funded study, they have identified one protein that could help do just that.

Many neurodegenerative diseases are caused by faulty proteins, which start to pile up and cause damage to neurons, the brain cells that are responsible for processing and transmitting information. Ultimately, the misbehaving proteins cause those cells to die.

The researchers at the Gladstone found a way to counter this destructive process by using a protein called Nrf2. They used neurons from humans (made from induced pluripotent stem cells – iPSCs – hence the stem cell connection here) and rats. They then tested these cells in neurons that were engineered to have two different kinds of mutations found in  Parkinson’s disease (PD) plus the Nrf2 protein.

Using a unique microscope they designed especially for this study, they were able to track those transplanted neurons and monitor what happened to them over the course of a week.

The neurons that expressed Nrf2 were able to render one of those PD-causing proteins harmless, and remove the other two mutant proteins from the brain cells.

In a news release to accompany the study in The Proceedings of the National Academy of Sciences, first author Gaia Skibinski, said Nrf2 acts like a house-cleaner brought in to tidy up a mess:

“Nrf2 coordinates a whole program of gene expression, but we didn’t know how important it was for regulating protein levels until now. Over-expressing Nrf2 in cellular models of Parkinson’s disease resulted in a huge effect. In fact, it protects cells against the disease better than anything else we’ve found.”

Steven Finkbeiner, the senior author on the study and a Gladstone professor, said this model doesn’t just hold out hope for treating Parkinson’s disease but for treating a number of other neurodegenerative problems:

“I am very enthusiastic about this strategy for treating neurodegenerative diseases. We’ve tested Nrf2 in models of Huntington’s disease, Parkinson’s disease, and ALS, and it is the most protective thing we’ve ever found. Based on the magnitude and the breadth of the effect, we really want to understand Nrf2 and its role in protein regulation better.”

The next step is to use this deeper understanding to identify other proteins that interact with Nrf2, and potentially find ways to harness that knowledge for new therapies for neurodegenerative disorders.

Measuring depression with non-invasive imaging of new brain cells

For most of the 20th century, scientists thought you’re basically stuck with the brain cells you’re born with. “Everything may die, nothing may be regenerated”, is how Santiago Ramón y Cajal, the father of modern neuroscience, described nerve cells, aka neurons, in the adult brain. But, over the past few decades, it’s become clear that stem cells are present in the brain and produce new neurons over the course of our lives.

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Hippocampus (in red)
Image: Life Science Databases

This better understanding of brain biology opened up new insights into brain function. For instance, a reduced volume of the hippocampus, an area of the brain important for learning and memory, is linked to depression and the use of anti-depressant drugs like Prozac have been shown to trigger the growth of new neurons in this part of the brain.

Now, researchers at the RIKEN institute in Japan have developed a non-invasive imaging method – so far, just in rats – to track the generation of new neurons from brain stem cells.  This study, reported in the Journal of Neuroscience, may provide new means to diagnose depression and to monitor the effectiveness of drugs in ways that aren’t currently possible.

A PET project to track new brain cells

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PET scan of human brain
Image: Wikipedia

The scientists focused on the use of positron emitting tomography (PET) imaging, which involves the injecting a radioactive tracer, designed to target an organ or a specific area of an organ, into the blood. The use of this type of tracer is routine in medical imaging and the radioactivity decays so fast that it’s essentially gone within 24 hours. The radioactive signal that’s emitted out from the body is then detected with PET scanning and reveals the precise location of the tracer within the body or organ. But PET scanning of neurogenesis in the brain had proved to be difficult – no definitive signals were observed. Magnetic resonance imaging (MRI) is also a no-go because it requires the risky injection of a tracer directly into the brain.

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PET scanner. Image: Jacoby Werther

The RIKEN team pinpointed the stumbling block: the lack of signal was due to the presence of proteins, called drug transporters, that continually pump the radioactive tracers out of the brain and back into the blood. When they re-ran the PET scan using a clinically available drug that blocks the transporter proteins, a neurogenesis signal was picked up.

Prozac helps stimulate new brain cell growth
With this obstacle overcome, the team tested out their technique. They gave one group of rats corticosterone, a stress hormone, for a month. This hormone is known to reduce neurogenesis and create depression-like behavior in the animals. They gave a second group of rats corticosterone plus Prozac. Sure enough, the PET scan signal was able to measure a decrease in neurogenesis in the corticosterone only group but also a recovery in neurogenesis in the group that received the hormone plus Prozac. Follow up analysis of rat brain slices confirmed that compared to untreated animals, neurogenesis was reduced 45% in the corticosterone group but no reduction was observed when Prozac was also included.

In a news release picked up by Nanowerk, team lead Yosky Kataoka discussed the game-changer possibilities of their new method:

“This is a very interesting finding because it has been a long-time dream to find a noninvasive test that can give objective evidence of depression and simultaneously show whether drugs are working in a given patient. We have shown that it is possible, at least in experimental animals, to use PET to show the presence of depression and the effectiveness of drugs… Since it is known that these same brain regions are involved in depression in the human brain, we would like to try this technique in the clinic and see whether it turns out to be effective in humans as well.”

Salk scientists explain why brain cells are genetically diverse

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I’ve always wondered why some sets of genetically identical twins become not so identical later in life. Sometimes they differ in appearance. Other times, one twin is healthy while the other is plagued with a serious disease. These differences can be explained by exposure to different environmental factors over time, but there could also be a genetic explanation involving our brains.

The brain is composed of approximately 100 billion cells called neurons, each with a DNA blueprint that contains instructions that determine the function of these neurons in the brain. Originally it was thought that all cells, including neurons, have the same DNA. But more recently, scientists discovered that the brain is genetically diverse and that neurons within the same brain can have slightly different DNA blueprints, which could give them slightly different functions.

Jumping genes and genetic diversity

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Fred “Rusty” Gage: Photo courtesy Salk Institute

Why and how neurons have differences in their DNA are questions that Salk Institute professor Fred Gage has pursued for more than a decade. In 2005, his lab discovered a mechanism during neural development that causes differences in the DNA of neurons. As a brain stem cell develops into a neuron, long interspersed nuclear elements (L1s), which are small pieces of DNA, copy and paste themselves, seemingly at random, throughout a neuron’s genome.

These elements were originally dubbed “jumping genes” because of their ability to hop around and insert themselves into DNA. It turns out that L1s do more than copy and paste themselves to create changes in DNA, they also can delete chunks of DNA. In a CIRM-funded study published this week in the journal Nature Neuroscience, Gage and colleagues at the Salk Institute reported new insights into L1 activity and how it creates genetic diversity in the brain.

Copy, paste, delete

Gage and his team had clues that L1s can cause DNA deletions in neurons back in 2013. They used a technique called single-cell sequencing to record the sequence of individual neuronal genomes and saw that some of their genomes had large sections of DNA added or missing.

They thought that L1s could be the reason for these insertions and deletions, but didn’t have proof until their current study, which used an improved method to identify areas of the neuronal genome modified by L1s. This method, combined with a computer algorithm that can easily tell the difference between various types of L1 modifications, revealed that areas of the genome with L1s were susceptible to DNA cutting caused by enzymes that home in on the L1 sequences. These breaks in the DNA then cause the observed deletions.

Gage explained their findings in a news release:

“In 2013, we discovered that different neurons within the same brain have various complements of DNA, suggesting that they function slightly differently from each other even within the same person. This recent study reveals a new and surprising form of variation that will help us understand the role of L1s, not only in healthy brains but in those affected by schizophrenia and autism.”

Jennifer Erwin, first author on the study, further elaborated:

“The surprising part was that we thought all L1s could do was insert into new places. But the fact that they’re causing deletions means that they’re affecting the genome in a more significant way,” says Erwin, a staff scientist in Gage’s group.”

Insights into brain disorders

It’s now known that L1s are important for the brain’s genetic diversity, but Gage also believes that L1s could play a role in causing brain disorders like schizophrenia and autism where there is heightened L1 activity in the neurons of these patients. In future work, Gage and his team will study how L1s can cause changes in genes associated with schizophrenia and autism and how these changes can effect brain function and cause disease.

Stem cell transplant offers Jake a glimpse of hope

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Jake Javier surrounded by friends; Photo courtesy Julie Haener KTVU

On Thursday, July 7th, Jake Javier became the latest member of a very select group. Jake underwent a stem cell transplant for a spinal cord injury at Santa Clara Valley Medical Center here in the San Francisco Bay Area.

The therapy is part of the CIRM-funded clinical trial run by Asterias Biotherapeutics. For Asterias it meant it had hit a significant milestone (more on that later). But for Jake, it was something far more important. It was the start of a whole new phase in his life.

Jake seriously injured his spinal cord in a freak accident after diving into a swimming pool just one day before he was due to graduate from San Ramon Valley high school. Thanks, in part, to the efforts of the tireless patient advocate and stem cell champion Roman Reed, Jake was able to enroll in the Asterias trial.

astopc1The goal of the trial is to test the safety of transplanting three escalating doses of AST-OPC1 cells. These are a form of cell called oligodendrocyte progenitors, which are capable of becoming several different kinds of brain cells, some of which play a supporting role and help protect nerve cells in the central nervous system – the area damaged in spinal cord injury.

To be eligible, individuals have to have experienced a severe neck injury in the last 30 days, one that has left them with no sensation or movement below the level of their injury, and that means they have typically lost all lower limb function and most hand and arm function.

The first group of three patients was completed in August of last year. This group was primarily to test for safety, to make sure this approach was not going to cause any harm to patients. That’s why the individuals enrolled were given the relatively small dose of 2 million cells. So far none of the patients have experienced any serious side effects, and some have even shown some small improvements.

In contrast, the group Jake is in were given 10 million cells each. Jake was the fifth person treated in this group. That means Asterias can now start assessing the safety data from this group and, if there are no problems, can plan on enrolling people for group 3 in about two months. That group of patients will get 20 million cells.

It’s these two groups, Jakes and group 3, that are getting enough cells that it’s hoped they will see some therapeutic benefits.

In a news release, Steve Cartt, President and CEO of Asterias, said they are encouraged by the progress of the trial so far:

“Successful completion of enrollment and dosing of our first efficacy cohort receiving 10 million cells in our ongoing Phase 1/2a clinical study represents a critically important milestone in our AST-OPC1 clinical program for patients with complete cervical spinal cord injuries. In addition, while it is still very early in the development process and the patient numbers are quite small, we are encouraged by the upper extremity motor function improvements we have observed so far in patients previously enrolled and dosed in the very low dose two million cell cohort that had been designed purely to evaluate safety.”

 

jake and familyJake and his family are well aware that this treatment is not going to be a cure, that he won’t suddenly get up and walk again. But it could help him in other, important ways, such as possibly getting back some ability to move his hands.

The latest news is that Jake is doing well, that he experienced some minor problems after the surgery but is bouncing back and is in good spirits.

Jake’s mother Isabelle said this has been an overwhelming experience for the family, but they are getting through it thanks to the love and support of everyone who hears Jake’s story. She told CIRM:

 “We are all beyond thrilled to have an opportunity of this magnitude. Just the thought of Jake potentially getting the use of his hands back gives him massive hope. Jake has a strong desire to recover to the highest possible level. He is focused and dedicated to this process. You have done well to choose him for your research. He will make you proud.”

He already has.

Jake and Brady gear

New England Patriots star quarterback Tom Brady signed a ball and jersey for Jake after hearing about the accident


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Adding new stem cell tools to the Parkinson’s disease toolbox

Understanding a complicated neurodegenerative disorder like Parkinson’s disease (PD) is no easy task. While there are known genetic risk factors that cause PD, only about 10 percent of cases are linked to a genetic cause. The majority of patients suffer from the sporadic form of PD, where the causes are unknown but thought to be a combination of environmental, lifestyle and genetic factors.

Unfortunately, there is no cure for PD, and current treatments only help PD patients manage the symptoms of their disease and inevitably lose their effectiveness over time. Another troubling issue is that doctors and scientists don’t have good ways to predict who is at risk for PD, which closes an important window of opportunity for delaying the onset of this devastating disease.

Scientists have long sought relevant disease models that mimic the complicated pathological processes that occur in PD. Current animal models have failed to truly represent what is going on in PD patients. But the field of Parkinson’s research is not giving up, and scientists continue to develop new and improved tools, many of them based on human stem cells, to study how and why this disease happens.

New Stem Cell Tools for Parkinson’s

Speaking of new tools, scientists from the Buck Institute for Research on Aging published a study that generated 10 induced pluripotent stem cell (iPS cell) lines derived from PD patients carrying well known genetic mutations linked to PD. These patient cell lines will be a useful resource for studying the underlying causes of PD and for potentially identifying therapeutics that prevent or treat this disorder. The study was partly funded by CIRM and was published today in the journal PLOS ONE.

Dr. Xianmin Zeng, the senior author on the study and Associate Professor at Buck Institute, developed these disease cell lines as tools for the larger research community to use. She explained in a news release:

Xianmin Zeng, Buck Institute

Xianmin Zeng, Buck Institute

“We think this is the largest collection of patient-derived lines generated at an academic institute. We believe the [iPS cell] lines and the datasets we have generated from them will be a valuable resource for use in modeling PD and for the development of new therapeutics.”

 

The datasets she mentions are part of a large genomic analysis that was conducted on the 10 patient stem cell lines carrying common PD mutations in the SNCA, PARK2, LRRK2, or GBA genes as well as control stem cell lines derived from healthy patients of the same age. Their goal was to identify changes in gene expression in the Parkinson’s stem cell lines as they matured into the disease-affected nerve cells of the brain that could yield clues into how PD develops at the molecular level.

Using previous methods developed in her lab, Dr. Zeng coaxed the iPS cell lines into neural stem cells (brain stem cells) and then further into dopaminergic neurons – the nerve cells that are specifically affected and die off in Parkinson’s patients. Eight of the ten patient lines were able to generate neural stem cells, and all of the neural stem cell lines could be coaxed into dopaminergic neurons – however, some lines were better at making dopaminergic neurons than others.

Dopaminergic neurons derived from induced pluripotent stem cells. (Xianmin Zeng, Buck Institute)

Dopaminergic neurons derived from induced pluripotent stem cells. (Xianmin Zeng, Buck Institute)

When they analyzed these lines, surprisingly they found that the overall gene expression patterns were similar between diseased and healthy cell lines no matter what cell stage they were at (iPS cells, neural stem cells, and neurons). They next stressed the cells by treating them with a drug called MPTP that is known to cause Parkinson’s like symptoms in humans. MPTP treatment of dopaminergic neurons derived from PD patient iPS cell lines did cause changes in gene expression specifically related to mitochondrial function and death, but these changes were also seen in the healthy dopaminergic neurons.

Parkinson’s, It’s complicated…

These interesting findings led the authors to conclude that while their new stem cell tools certainly display some features of PD, individually they are not sufficient to truly model all aspects of PD because they represent a monogenic (caused by a single mutation) form of the disease.

They explain in their conclusion that the power of their PD patient iPS cell lines will be achieved when combined with additional patient lines, better controls, and more focused data analysis:

“Our studies suggest that using single iPSC lines for drug screens in a monogenic disorder with a well-characterized phenotype may not be sufficient to determine causality and mechanism of action due to the inherent variability of biological systems. Developing a database to increase the number of [iPS cell] lines, stressing the system, using isogenic controls [meaning the lines have identical genes], and using more focused strategies for analyzing large scale data sets would reduce the impact of line-to-line variations and may provide important clues to the etiology of PD.”

Brian Kennedy, Buck Institute President and CEO, also pointed out the larger implications of this study by commenting on how these stem cell tools could be used to identify potential drugs that specifically target certain Parkinson’s mutations:

Brian Kennedy, Buck Institute

Brian Kennedy, Buck Institute

“This work combined with dozens of other control, isogenic and reporter iPSC lines developed by Dr. Zeng will enable researchers to model PD in a dish. Her work, which we are extremely proud of, will help researchers dissect how genes interact with each other to cause PD, and assist scientists to better understand what experimental drugs are doing at the molecular level to decide what drugs to use based on mutations.”

Overall, what inspires me about this study is the author’s mission to provide a substantial number of PD patient stem cell lines and genomic analysis data to the research community. Hopefully their efforts will inspire other scientists to add more stem cell tools to the Parkinson’s tool box. As the saying goes, “it takes an army to move a mountain”, in the case of curing PD, the mountain seems more like Everest, and we need all the tools we can get.


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Approach that inspires DREADD could create new way to treat Parkinson’s disease

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Dopamine producing brain nerve cells, made from embryonic stem cells

Imagine having a treatment for Parkinson’s that acts like a light switch, enabling you to turn it on or off depending on your needs. Well, that’s what researchers at the University of Wisconsin-Madison have come up with. And if it works, it might help change the way we treat many other diseases.

For years researchers have been trying to come up with a way of replacing the dopamine-producing brain nerve cells, or neurons, that are attacked and destroyed by Parkinson’s. Those cells regulate movement and as they are destroyed they diminish a person’s ability to control their body, their movement and even their emotions.

Attempts to transplant dopamine-producing cells into the brains of people with Parkinson’s disease have met with mixed results. In some cases the transplanted cells have worked. In many cases the cells don’t make enough dopamine to control movement. In about 10 percent of cases the cells make too much dopamine, causing uncontrolled movements called graft-induced dyskinesia.

But now the researchers at UW Madison have found a new approach that might change that. Using the gene-editing tool CRISPR (you can read about that here) they reprogrammed embryonic stem cells to become two different types of neurons containing a kind of genetic switch called a DREADD, which stands for designer receptor exclusively activated by designer drug. When they gave mice the designer drug they created to activate DREADD, one group of cells boosted production of dopamine, the other group shut down its dopamine production.

In a news release about the study, which is published in the journal Cell Stem Cell, lead author Su-Chun Zhang says this kind of control is essential in developing safe, effective therapies:

“If we are going to use cell therapy, we need to know what the transplanted cell will do. If its activity is not right, we may want to activate it, or we may need to slow or stop it.”

Zhang says the cells developed using this approach have another big advantage:

“We can turn them on or off, up or down, using a designer drug that can only act on cells that express the designer receptor. The drug does not affect any host cell because they don’t have that specialized receptor. It’s a very clean system.”

Tests in mice showed that the cells, and the designer drug, worked as the researchers hoped they would with some cells producing more dopamine, and others halting production.

It’s an encouraging start but a lot more work needs to be done to make sure the the genetically engineered stem cells, and the designer drug, are safe and that they can get the cells to go to the part of the brain that needs increased dopamine production.

As Zhang says, having a method of remotely controlling the action of transplanted cells, one that is reversible, could create a whole new way of treating diseases.

“This is the first proof of principle, using Parkinson’s disease as the model, but it may apply to many other diseases, and not just neurological diseases.”

An inside look reveals the adult brain prunes its own branches

Did you know that when you’re born, your brain contains around 100 billion nerve cells? This is impressive considering that these nerve cells, also called neurons, are already connected to each other through an intricate, complex neural network that is essential for brain function.

Here’s how the brain does it. During development, neural stem cells produce neurons that navigate their way through the brain. Once at their destination, neurons set up shop and send out long extensions called axons and branched extensions called dendrites that allow them to form what are called synaptic connections through which they can communicate through electrical and chemical signals.

Studies of early brain development revealed that neurons in the developing brain go on overdrive and make more synaptic connections than they need. Between birth and early adulthood, the brain carefully prunes away weak or unnecessary connections, and by your mid-twenties, your brain has eliminated almost half of the synaptic connections you started out with as a baby.

This synaptic pruning process allows the brain to fine-tune its neural network and strengthen the connections between neurons that are important for brain function. It’s similar to how a gardener prunes away excess branches on fruit trees so that the resulting branches can produce healthier and better tasting fruit.

The brain can make new neurons

It was thought that by adulthood, this process of pruning excess connections between neurons was over. However, a new study from the Salk Institute offers visual proof that synaptic pruning occurs during adulthood similarly to how it does during development. The work was published today in the journal Nature Neuroscience, and it was funded in part by CIRM.

Rusty Gage, Salk Institute.

Rusty Gage, Salk Institute.

The study was led by senior author and Salk Professor Rusty Gage. Gage is well known for his earlier work on adult neurogenesis. In the late 90’s, he discovered that the adult brain can in fact make new neurons, a notion that overturned the central dogma that the brain doesn’t contain stem cells and that we’re born with all the neurons we will ever have.

There are two main areas of the adult brain that harbor neural stem cells that can generate new neurons. One area is called the dentate gyrus, which is located in the memory forming area of the brain called the hippocampus. Gage and his team were curious to know whether the new neurons generated from stem cells in the dentate gyrus also experienced the same synaptic overgrowth and pruning that the neurons in the developing brain did.

Pruning the Adult Brain

They developed a special microscope technique that allowed them to visually image the development of new neurons from stem cells in the dentate gyrus of the mouse brain. Every day, they would image the growing neurons and monitor how many dendritic branches they sent out.

Newly generated neurons (green) send out branched dendritic extensions to make connections with other neurons. (Image credit: Salk Institute)

Newly generated neurons (green) send out branched dendritic extensions to make connections with other neurons. (Image credit: Salk Institute)

After observing the neurons for a few weeks, they were amazed to discover that these new neurons behaved similarly to neurons in the developing brain. They sent out dozens of dendritic branches and formed synaptic connections with other neurons, some of which were eventually pruned away over time.

This phenomenon was observed more readily when they made the mice exercise, which stimulated the stem cells in the dentate gyrus to divide and produce more neurons. These exercise-induced neurons robustly sent out dendritic branches only to have them pruned back later.

First author on the paper, Tiago Gonçalves commented on their observations:

“What was really surprising was that the cells that initially grew faster and became bigger were pruned back so that, in the end, they resembled all the other cells.”

Rusty Gage was also surprised by their findings but explained that developing neurons, no matter if they are in the developing or adult brain, have evolved this process in order to establish the best connections.

“We were surprised by the extent of the pruning we saw. The results suggest that there is significant biological pressure to maintain or retain the dendrite tree of these neurons.”

A diagram showing how the adult brain prunes back the dendritic branches of newly developing neurons over time. (Image credit: Salk Institute).

A diagram showing how the adult brain prunes back the dendritic branches of newly developing neurons over time. (Image credit: Salk Institute).

Potential new insights into brain disorders

This study is important because it increases our understanding of how neurons develop in the adult brain. Such knowledge can help scientists gain a better understanding of what goes wrong in brain disorders such as autism, schizophrenia, and epilepsy, where defects in how neurons form synaptic connections or how these connections are pruned are to blame.

Gonçalves also mentioned that this study raises another important question related to the regenerative medicine applications of stem cells for neurological disease.

“This also has big repercussions for regenerative medicine. Could we replace cells in this area of the brain with new stem cells and would they develop in the same way? We don’t know yet.”


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Unlocking the brain’s secrets: scientists find over 100 unique mutations in brain cells

Your brain is made up of approximately 100 billion neurons. These are the cells that process information and pass along electrical and chemical signals to their other neuron buddies throughout the body to coordinate thoughts, movement, and many other functions. It’s no small task to create the intricate neuronal network that is the backbone of the central nervous system. If any of these neurons or a group of neurons acquire genetic mutations that alter their function, a lot can go wrong.

The genetic makeup of neurons is particularly interesting because it appears that each neuron has its own unique genome. That means 100 billion different genomes in a single cell type in the brain. Scientists suggest that this “individuality” could explain why monozygotic, or identical, twins have different personalities and susceptibilities to neurological disorders or mental illnesses and why humans develop brain diseases or cancer over time.

To understand what a genome of a cell looks like, you need to sequence its genetic material, or the DNA, that’s housed in a cell’s nucleus. Sequencing the genome of an individual cell is hard to do accurately with our current technology, so scientists have developed clever alternatives to get a front-row view into the workings of neuronal genomes.

Cloning mouse neurons reveals 100+ unique genetic mutations

One such method was published recently in the journal Neuron by a CIRM-funded team from The Scripps Research Institute (TSRI). Led by senior author and Associate Professor at TSRI, Kristen Baldwin, the team took on the challenge of cloning individual mouse neurons to unlock the secrets of neuronal genomes. (For those who aren’t familiar with the term, cloning is a process that produces new cells or organisms that harbor identical genetic information from the originating cell.)

What they found from their cloning experiment was surprising: each neuron they sequenced had an average of more than 100 unique genetic mutations, and these mutations tended to appear in genes that were heavily used by neurons, something that is uncommon in cell types of other organs that tend to protect their frequently used genes. Their findings could help unravel the mystery behind some of the causes for diseases like Alzheimer’s and autism.

In a TSRI news release, Kristen Baldwin explained:

Kristen Baldwin

Kristen Baldwin

“Neuronal genomes have remained a mystery for a long time. The findings in this study and the extensive validation of genome sequencing-based mutation discovery that this method permits, open the door to additional studies of brain mutations in aging and disease, which may help us understand or treat cognitive decline in aging, neurodegeneration and neurodevelopmental diseases such as autism.”

Making mice with neuronal genomes

To clone individual neurons, the team took the nucleus of a single neuron and transplanted it into a mouse egg cell that lacked its own nucleus. The egg developed and matured all while copying and passing on the genetic information of the original mouse neuron. The team generated cloned embryonic stem cell lines from these eggs and were able to expand the stem cell lines to generate millions of stem cells that contained the same genetic material.

TSRI Research Assistant Alberto Rodriguez uses a tiny straw-like micropipette to pick up red fluorescent neurons and transfer their genomes into an egg.

TSRI scientists extract the nuclei of neurons and transfer their genomes into an egg. (Image courtesy of TSRI)

They made several different cloned stem cell lines representing different neuronal genomes and sequenced these lines to identify unique genetic mutations. They also were able to generate cloned stem cell lines from the neurons of older mice, and thus were able to track the accumulation of genetic mutations over time. Even more impressive, they made living mice that contained the cloned genomes of individual neurons in all of their cells, proving that neuronal genomes are compatible with development.

The team did report that not all neurons could be developed into cloned stem cell lines for reasons that they couldn’t fully explain, but they decided to focus on studying the cloned stem cell lines that were successful.

What does this mean for humans?

Baldwin explained that what was most surprising about their study was “that every neuron we looked at was unique – carrying more than 100 DNA changes or mutations that were not present in other cells.”

The next steps for their research are to explore why this diversity among neuronal genomes exists and how this could contribute to neurological disease in humans.

Co-first authors Jennifer Hazen and Gregory Faust.

Co-first authors Jennifer Hazen and Gregory Faust.

Co-first author Jennifer Hazen explains, “We need to know more about mutations in the brain and how they might impact cell function.”

Also mentioned in the news release, the team plans “to study neuronal genomes of very old mice and those with neurological diseases. They hope this work will lead to new insights and therapeutic strategies for treating brain aging and neurologic diseases caused by neuronal mutations.”


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Bringing down the gatekeeper for a stem cell-based Parkinson’s cure

Feng-dopamine-HI

University of Buffalo researchers converted these dopamine neurons directly from human skin cells. Image shows a protein found only in neurons (red) and an enzyme that synthesizes dopamine (green). Cell DNA is labeled in blue.

On the surface, a stem cell-based cure for Parkinson’s disease seems pretty straight-forward. This age-related neurodegenerative disorder, which leads to progressively worsening tremors, slowness of movement and muscle rigidity, is caused by the death of a specific type of nerve cell, or neuron, that produces the chemical dopamine in a specific region of the brain. So it would seem that simply transplanting stem cell-derived dopamine-producing neurons (DA neurons) in the brains of Parkinson’s patients to replace the lost cells would restore dopamine levels and alleviate Parkinson’s symptoms.

Easier said than done
Well, it hasn’t turned out to be that easy. After initial promising results using fetal brain stem cell transplants in the 80’s and 90’s, larger clinical trials showed no significant benefit and even led to a worsening of symptoms in some patients. One potential issue with those early trials could have been variable cell composition of the fetal cell-based therapy. On top of that, the availability of fetal tissue is limited and the quantities of transplantable cells obtained from these samples are very low.

More recently, researchers have been busy at generating more pure populations of DA neurons from human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs). Great progress has been made so far, but the field is still hampered by not being able to make enough DA neurons from hESCs and iPSCs in a timely manner.

Cutting out the pluripotent “middle man”
This week a research team at the University of Buffalo reported in Nature Communications about a much more efficient method for producing DA neurons. It’s a finding that could provide a strong push towards stem cell-based therapy development for Parkinson’s disease.

The team bypassed the need to start with hESCs or iPSCs and instead converted skin cells directly into DA neurons. A thorough analysis of the cells confirmed that they were functional and matched that characteristics of the specific dopamine neurons that are lost in Parkinson’s.

This direct reprogramming of skin cells into DA neurons as well as other cells is a technique pioneered by several independent researchers including some of our own grantees. This method is thought to have a few advantages over the specialization of immature hESCs or iPSCs into tissue-specific cells. Not only is the direct reprogramming process faster it also doesn’t require cell division so there’s less concern about the introduction of DNA mutations and the potential of tumor formation. Another plus for direct reprogramming is the possibility of inducing the direct conversion of one cell type into another inside the body rather than relying on the manipulation of hESCs and iPSCs in the lab. Still, despite these advantages the efficiency of direct reprogramming is still very low. That’s where the University of Buffalo team comes into the picture.

Bringing down the gatekeeper
The researchers led by physiology and biophysics professor Jian Feng, made a few key modifications to increase the efficiency of the current skin cell to DA neuron direct reprogramming methods. They first reduced the level of a protein call p53. This protein has several nicknames like “guardian of our genes” and “tumor suppressor” because it plays critical roles in controlling cell division and DNA repair and, in turn, helps keep a clamp on cell growth.

Reducing the presence of p53 during the direct reprogramming process led to a much more efficient conversion of skin cells to DA neurons. And because the conversion from a skin cell to a neuron happens quickly – just a couple days – timing the introduction of cell nutrients specific to neurons had to be carefully watched. Together, these tweaks improved upon previous studies as Feng mentioned in a University of Buffalo press release:

“The best previous method could take two weeks to produce 5 percent dopamine neurons. With ours, we got 60 percent dopamine neurons in ten days.”

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Jian Feng, PhD, professor of physiology and biophysics, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo

IMHO (In my humble opinion)
I imagine there’s a lot more work ahead to get this method of deriving DA neurons from skin ready for the clinic. This reprogramming technique relied on the introduction of neuron-specific genes into the skin cells using a deactivated virus as the means of delivery. Even though the virus is inactive, its viral DNA randomly inserts into the cells’ chromosomes which can turn on genes that cause cancer. Therefore, a non-viral version of this method would need to be developed for clinical use.

Also, as mentioned earlier, since p53 inhibits tumors by suppressing uncontrolled cell division, it would be important to make sure that a reduction of p53 didn’t lead to any long-term negative consequences, like the transplantation of potentially cancerous cells into the patient.

Still, this dramatic increase in efficiency for making functional DA neurons and the identification of p53 as a key control point for direct reprogramming are very exciting developments for a disease field that is committed to finding cures for its patients.

Related links:

From the Stem Cellar archives: blogs about direct reprogramming
Video: CIRM Grantee Marius Wernig discusses direct reprogramming
Video: Thirty second elevator pitch describing direct reprogramming