Nature Communications

Building embryo-like cells in the lab

/ Kevin McCormack / 1 Comment
Dr. Magdalena Zernicka-Goetz: Photo courtesy Caltech

Human embryonic stem cells (hESCs) have many remarkable properties, not the least of which is their ability to turn into every other kind of cell in our body. But there are limits to what researchers can do with embryonic stem cells. One issue is that there aren’t always hESCs available – they come from eggs donated by couples who have undergone in vitro fertilization. Another is that researchers can only develop these cells in the laboratory for 14 days (though that rule may be changing).

Now researchers at Caltech have developed a kind of hESC-in-a-dish that could help make it easier to answer questions about human development without the need to wait for a new line of hESCs.

The team, led by Magdalena Zernicka-Goetz, used a line of expanded pluripotent cells (EPSCs), originally derived from a human embryo, to create a kind of 3D model that mimics some of the activities of an embryo.

The cool thing about these cells is that, because they were originally derived from an embryo, they retain some “memory” of how they are supposed to work. In a news release Zernicka-Goetz says this enables them to display elements of both polarization and cavitation, early crucial phases in the development of a human embryo.

“The ability to assemble the basic structure of the embryo seems to be a built-in property of these earliest embryonic cells that they are simply unable to ‘forget.’ Nevertheless, either their memory is not absolutely precise or we don’t yet have the best method of helping the cells recover their memories. We still have further work to do before we can get human stem cells to achieve the developmental accuracy that is possible with their equivalent mouse stem cell counterparts.”

Being able to create these embryo-like elements means researchers can generate cells in large numbers and won’t be so dependent on donated embryos.

In the study, published in the journal Nature Communications, the researchers say this could help them develop a deeper understanding of embryonic development.

“Understanding human development is of fundamental biological and clinical importance. Despite its significance, mechanisms behind human embryogenesis remain largely unknown…. this stem cell platform provides insights into the design of stem cell models of embryogenesis.

Gene therapy is life-changing for children with a life-threatening brain disorder

/ Kevin McCormack / 9 Comments

If you have never heard of AADC deficiency count yourself lucky. It’s a rare, incurable condition that affects only around 135 children worldwide but it’s impact on those children and their families is devastating. The children can’t speak, can’t feed themselves or hold up their head, they have severe mood swings and often suffer from insomnia.

But Dr. Krystof Bankiewicz, a doctor and researcher at the University of California San Francisco (UCSF), is using techniques he developed treating Parkinson’s disease to help those children. Full disclosure here, CIRM is funding Dr. Bankiewicz’s Parkinson’s clinical trial.

In AADC deficiency the children lack a critical enzyme that helps the brain make serotonin and dopamine, so called “chemical messengers” that help the cells in the brain communicate with each other. In his AADC clinical trial Dr. Bankiewicz and his team created a tiny opening in the skull and then inserted a functional copy of the AADC gene into two regions of the brain thought to have most benefit – the substantia nigra and ventral tegmental area of the brainstem.

Image showing target areas for AADC gene insertion: Courtesy UCSF

When the clinical trial began none of the seven children were able to sit up on their own, only two had any ability to control their head movement and just one could grasp an object in their hands. Six of the seven were described as moody or irritable and six suffered from insomnia.

In a news release Dr. Bankiewicz says the impact of the gene therapy was quite impressive: “Remarkably, these episodes were the first to disappear and they never returned. In the months that followed, many patients experienced life-changing improvements. Not only did they begin laughing and have improved mood, but some were able to start speaking and even walking.”

Those weren’t the only improvements, at the end of one year:

  • All seven children had better control of their head and body.
  • Four of the children were able to sit up by themselves.
  • Three patients could grasp and hold objects.
  • Two were able to walk with some support.

Two and a half years after the surgery:

  • One child was able to walk without any support.
  • One child could speak with a vocabulary of 50 words.
  • One child could communicate using an assistive device.

The parents also reported big improvements in mood and ability to sleep.

UCSF posted some videos of the children before and after the surgery and you can see for yourself the big difference in the children. It’s not a cure, but for families that had nothing in the past, it is a true gift.

The study is published in the journal Nature Communications.

Stem cell gene therapy for Fabry disease shows positive results in patients

/ Yimy Villa / Leave a comment
Darren Bidulka rests after his modified blood stem cells were transplanted into him at the Foothills Medical Centre in Calgary in 2017, allowing him to stop his enzyme therapy. (From left): Dr. Jeffrey Medin, Medical College of Wisconsin, Dr. Aneal Khan, the experimental trial lead in Calgary, and Darren Bidulka. Image Credit: Darren Bidulka

Fabry disease is an X-linked genetic disorder that can damage major organs and shorten lifespan. Without a functional version of a gene called GLA, our bodies are unable to make the correct version of an enzyme that breaks down a fat, and that in turn can lead to problems in the kidneys, heart and brain. It is estimated that one person in 40,000 to 60,000 has the disease and it affects men more severely than women since men only have one copy of the X chromosome. Current treatment consists of enzyme therapy infusions every two weeks but there is currently no cure for Fabry disease. 

However, a Canadian research team is conducting the world’s first pilot study to treat Fabry disease using a stem cell gene therapy approach. The researchers collected the patient’s own blood stem cells and used gene therapy to insert copies of the fully functional gene into the stem cells, allowing them to make the correct version of the enzyme. The newly modified stem cells were then transplanted back into each patient.

Five men participated in this trial and the results so far have been very encouraging. After treatment with the stem cell gene therapy, all patients began producing the corrected version of the enzyme to near normal levels within one week. With these initial results, all five patients were allowed to stop their biweekly enzyme therapy infusions. So far, only three patients decided to do so and are stable.

In a news release, Darren Bidulka, the first patient to be treated in the study, talked about how life changing this stem cell gene therapy has been for him.

“I’m really happy that this worked. What an amazing result in an utterly fascinating experience. I consider this a great success. I can lead a more normal life now without scheduling enzyme therapy every two weeks. This research is also incredibly important for many patients all over the world, who will benefit from these findings.”

CIRM is no stranger to stem cell gene therapy and its potential having funded clinical trials in various areas such as severe combined immunodeficiency (bubble baby disease), cystinosis, sickle cell disease, and various others. The broad range of genetic diseases it has been used in to treat patients further highlights its importance in scientific research.

The full results of this study were published in Nature Communications.

Stem cells used to promote quick and precise bone healing

/ Yimy Villa / 2 Comments
A close-up view of the intricate microarchitecture of the pluripotent stem-cell-derived extracellular matrix. Image Credit: Carl Gregory/Texas A&M

Although some broken bones can be mended with the help of a cast, others require more complex treatments. Bone grafts, which can come from the patient’s own body or a donor, are used to transplant bone tissue to the injury site. However, these procedures can have setbacks such as increased recovery time and chronic pain. Each year approximately 600,000 people in the United States alone experience complications from bone healing.

Researchers at Texas A&M University found a way to use induced pluripotent stem cells (iPSCs), a type of stem cell that can turn into any cell type and can be derived from adults cells (e.g. skin cells), to create superior bone grafts. The team of researchers said these grafts could potentially be used to promote swift and precise bone healing, enabling patients to optimally benefit from surgical intervention.

The Texas A&M team used iPSCS to make mesenchymal stem cells (MSCs), which make the extracellular matrix needed for bone grafts. MSCs can be obtained from bone marrow, but they have a relatively shorter life span and are not as biologically active when compared to MSCs generated from iPSCs.

To test the effectiveness of their iPSC generated bone grafts, they implanted the extracellular matrix at a site of bone defects. After a few weeks, they found that their iPSC generated matrix was five to sixfold more effective than the best FDA-approved graft stimulator.

In a news release from Texas A&M, Dr. Roland Kaunas discusses the potential benefits of using iPSC generated bone grafts.

“Our material is very promising because the pluripotent stem cells can ideally generate many batches of the extracellular matrix from just a single donor which will greatly simplify the large-scale manufacturing of these bone grafts.”

Additionally, the Texas A&M team said this approach has the potential to be incorporated into numerous engineered implants, such as 3D-printed implants or metal screws, so that these parts integrate better with the surrounding bone.

The full results of this study were published in Nature Communications.

A brief video on bone grafts from Texas A&M is available below.

Boosting the blood system after life-saving therapy

/ Kevin McCormack / Leave a comment
Following radiation, the bone marrow shows nearly complete loss of blood cells in mice (left). Mice treated with the PTP-sigma inhibitor displayed rapid recovery of blood cells (purple, right): Photo Courtesy UCLA

Chemotherapy and radiation are two of the front-line weapons in treating cancer. They can be effective, even life-saving, but they can also be brutal, taking a toll on the body that lasts for months. Now a team at UCLA has developed a therapy that might enable the body to bounce back faster after chemo and radiation, and even make treatments like bone marrow transplants easier on patients.

First a little background. Some cancer treatments use chemotherapy and radiation to kill the cancer, but they can also damage other cells, including those in the bone marrow responsible for making blood stem cells. Those cells eventually recover but it can take weeks or months, and during that time the patient may feel fatigue and be more susceptible to infections and other problems.

In a CIRM-supported study, UCLA’s Dr. John Chute and his team developed a drug that speeds up the process of regenerating a new blood supply. The research is published in the journal Nature Communications.

They focused their attention on a protein called PTP-sigma that is found in blood stem cells and acts as a kind of brake on the regeneration of those cells. Previous studies by Dr. Chute showed that, after undergoing radiation, mice that have less PTP-sigma were able to regenerate their blood stem cells faster than mice that had normal levels of the protein.

John Chute: Photo courtesy UCLA

So they set out to identify something that could help reduce levels of PTP-sigma without affecting other cells. They first identified an organic compound with the charming name of 6545075 (Chembridge) that was reported to be effective against PTP-sigma. Then they searched a library of 80,000 different small molecules to find something similar to 6545075 (and this is why science takes so long).

From that group they developed more than 100 different drug candidates to see which, if any, were effective against PTP-sigma. Finally, they found a promising candidate, called DJ009. In laboratory tests DJ009 proved itself effective in blocking PTP-sigma in human blood stem cells.

They then tested DJ009 in mice that were given high doses of radiation. In a news release Dr. Chute said the results were very encouraging:

“The potency of this compound in animal models was very high. It accelerated the recovery of blood stem cells, white blood cells and other components of the blood system necessary for survival. If found to be safe in humans, it could lessen infections and allow people to be discharged from the hospital earlier.”

Of the radiated mice, most that were given DJ009 survived. In comparison, those that didn’t get DJ009 died within three weeks.

They saw similar benefits in mice given chemotherapy. Mice with DJ009 saw their white blood cells – key components of the immune system – return to normal within two weeks. The untreated mice had dangerously low levels of those cells at the same point.

It’s encouraging work and the team are already getting ready for more research so they can validate their findings and hopefully take the next step towards testing this in people in clinical trials.

HIV eliminated from mice using CRISPR and LASER ART

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Dr. Kamel Khalili

In the United States alone, there are approximately 1.1 million people living with Human immunodeficiency virus (HIV), a virus that weakens the immune system by destroying important cells that fight off disease and infection. This number is much larger on a global scale, with 36.9 million people living with HIV as of 2017. If left untreated, the immune system becomes so weakened that the condition worsens into acquired immunodeficiency syndrome (AIDS), which is usually fatal.

Current treatment for HIV focuses on the use of antiretroviral therapy (ART). This treatment is able to suppress replication of the virus, but it does not eliminate it from the body entirely. In order to be sustainable, ART must be taken throughout the course of a lifetime, otherwise HIV rebounds and the replication of the virus renews, fueling the development of AIDS.

The ability of HIV to rebound is related to the fact that it is able to integrate its DNA into various cells inside the body and beyond the reach of ART. Here they are able to remain dormant and ready to replicate as soon as ART is not interfering. It is because of this that ART is not sufficient on its own to cure HIV, but a group of scientists have uncovered a promising breakthrough to change that.

In a major collaboration, researchers at the Lewis Katz School of Medicine at Temple University and the University of Nebraska Medical Center (UNMC) have for the first time eliminated HIV from the DNA of living mice. This study marks a critical step toward the development of a possible cure for human HIV infection.

The team of researchers was able to do this with the help of a new technology called long-acting slow-effective release (LASER) ART. LASER ART is able to target HIV sanctuaries and maintain replication at low levels for extended periods of time. Immediately after administering LASER ART, the team used a gene editing technology known as CRISPR to remove the final remnants of HIV DNA hidden inside cells.

In a press release, Dr. Kamel Khalili, senior investigator for this study, was quoted as saying,

“Our study shows that treatment to suppress HIV replication and gene editing therapy, when given sequentially, can eliminate HIV from cells and organs of infected animals…We now have a clear path to move ahead to trials in non-human primates and possibly clinical trials in human patients within the year.”

The full results of this study were published in Nature Communications.

To learn more about how CRISPR technology works, you can read more about it on a previous blog post.

Muscle stem cells provide insight into treatment of muscular dystrophies and aging muscles

/ Yimy Villa / 3 Comments
Dr. Alessandra Sacco, associate professor in the Development, Aging and Regeneration Program at Sanford Burnham Prebys.

Muscles are a vital part of the body that enable us to walk, run, lift, and do everyday activities. When muscles start to deteriorate, we start to have difficulty performing these activities, which severely limits quality of life and autonomy. Typically, this becomes more commonplace as we age and is known as sarcopenia, which affects nearly ten percent of adults over the age of 50 and nearly half of individuals in their 80s.

However, there are other instances where this happens much more rapidly and early on due to genetic disease. These are commonly known as muscular dystrophies, which consist of more than 30 genetic diseases characterized by progressive muscle weakness and degeneration. A cure does not currently exist.

Regardless of the cause of the muscle deterioration, scientists at Sanford Burnham Prebys have uncovered how to potentially promote growth inside stem cells found within the muscle, thereby promoting muscle growth. In a mouse model study funded in part by CIRM and published in Nature Communications, Dr. Alessandra Sacco, senior author of the paper, and her team describe how a signaling pathway, along with a specific protein, can help regulate what muscle stem cells do.

Muscle stem cells can do two things, they either become adult muscle cells or self-renew to replenish the stem cell population. The paper discusses how the signaling pathway and specific protein are crucial for muscle stem cell differentiation and muscle growth, both of which are needed to prevent deterioration. Their aim is to use this knowledge to develop therapeutic targets that can aid with muscle growth.

Dr. Alessandra Sacco is quoted in an article as saying,

“Muscle stem cells can ‘burn out’ trying to regenerate tissue during the natural aging process or due to chronic muscle disease. We believe we have found promising drug targets that direct muscle stem cells to ‘make the right decision’ and stimulate muscle repair, potentially helping muscle tissue regeneration and maintaining tissue function in chronic conditions such as muscular dystrophy and aging.”

Targeted treatment for pediatric brain tumors shows promising results

/ Yimy Villa / Leave a comment
Image of medulloblastoma

Imagine sitting in the doctor’s office and being told the heartbreaking news that your child has been diagnosed with a malignant brain tumor. As one might expect, the doctor states that the most effective treatment option is typically a combination of chemotherapy and radiation. However, the doctor reveals that there are additional risks to take into account that apply to children. Since children’s tiny bodies are still growing and developing, chemotherapy and radiation can cause long-term side effects such as intellectual disabilities. As a parent, it is painful enough to have to watch a child go through chemotherapy and radiation without adding permanent damage into the fold.

Sadly, this scenario is not unique. Medulloblastoma is the most prevalent form of a pediatric brain tumor with more than 350 children diagnosed with cancer each year. There are four distinct subtypes of medulloblastoma, with the deadliest being known as Group 3.

Researchers at Sanford Burnham Prebys Medical Discovery Institute (SBP) are trying to minimize the collateral damage by finding personalized treatments that reduce side effects while remaining effective. Scientists at SBP are working with an inhibitor known as LSD1 that specifically targets Group 3 medulloblastoma in a mouse model. The study, published in Nature Communications, showed that the drug dramatically decreased the size of tumors grown under the mouse’s skin by shrinking the cancer by more than 80 percent. This suggested that it could also be effective against patients’ tumors if it could be delivered to the brain. The LSD1 inhibitor has shown promise in clinical trials, where it has been tested for treating other types of cancer.

According to Robert Wechsler-Reya, Ph.D., senior author of the paper and director of the Tumor Initiation and Maintenance Program at SBP: “Our lab is working to understand the genetic pathways that drive medulloblastoma so we can find better ways to intervene and treat tumors. This study shows that a personalized treatment based upon a patient’s specific tumor type might be within our reach.”

Dr. Wechsler-Reya’s work on medulloblastoma was, in part, funded by the CIRM (LA1-01747) in the form of a Research Leadership Award for $5,226,049.

Stories that Caught Our Eye: New ways to heal old bones; and keeping track of cells once they are inside you

/ Kevin McCormack / Leave a comment

broken bones

How Youth Factor Can Help Repair Old Bones

As we get older things that used to heal quickly tend to take a little longer to get better. In some cases, a lot longer. Take bones for example. A fracture in someone who is in their 70’s often doesn’t heal as quickly, or completely, as in someone much younger. For years researchers have been working on ways to change that. Now we may be one step closer to doing just that.

We know that using blood stem cells can help speed up healing for bone fractures (CIRM is funding work on that) and now researchers at Duke Health believe they have figured out how that works.

The research, published in the journal Nature Communications, identifies what the Duke team call the “youth factor” inside bone marrow stem cells. It’s a type of white blood cell called a macrophage. They say the proteins these macrophages produce help stimulate bone repair.

In a news story in Medicine News Line  Benjamin Alman, senior author on the study, says:

“While macrophages are known to play a role in repair and regeneration, prior studies do not identify secreted factors responsible for the effect. Here we show that young macrophage cells play a role in the rejuvenation process, and injection of one of the factors produced by the young cells into a fracture in old mice rejuvenates the pace of repair. This suggests a new therapeutic approach to fracture rejuvenation.”

Next step, testing this in people.

A new way to track stem cells in the body

It’s one thing to transplant stem cells into a person’s body. It’s another to know that they are going to go where you want them to and do what you want them to. University of Washington researchers have invented a device that doesn’t just track where the cells end up, but also what happens to them along the way.

The device is called “CellTagging”, and in an article in Health Medicine Network, Samantha Morris, one of the lead researchers says this could help in better understanding how to use stem cells to grow replacement tissues and organs.

“There is a lot of interest in the potential of regenerative medicine — growing tissues and organs in labs — to test new drugs, for example, or for transplants one day. But we need to understand how the reprogramming process works. We want to know if the process for converting skin cells to heart cells is the same as for liver cells or brain cells. What are the special conditions necessary to turn one cell type into any other cell type? We designed this tool to help answer these questions.”

In the study, published in the journal Nature, the researchers explain how they use a virus to insert tiny DNA “barcodes” into cells and that as the cells travel through the body they are able to track them.

Morris says this could help scientists better understand the conditions needed to more effectively program cells to do what we want them to.

“Right now, cell reprogramming is really inefficient. When you take one cell population, such as skin cells, and turn it into a different cell population — say intestinal cells — only about 1 percent of cells successfully reprogram. And because it’s such a rare event, scientists have thought it is likely to be a random process — there is some correct set of steps that a few cells randomly hit upon. We found the exact opposite. Our technology lets us see that if a cell starts down the right path to reprogramming very early in the process, all of its related sibling cells and their descendants are on the same page, doing the same thing.”

For the first time, scientists entirely reprogram human skin cells to iPSCs using CRISPR

/ Pallavi Penumetcha / Leave a comment

Picture1

CRISPR iPSC colony of human skin cells showing expression of SOX2 and TRA-1-60, markers of human embryonic pluripotent stem cells

Back in 2012, Shinya Yamanaka was awarded the Nobel Prize in Physiology or Medicine for his group’s identification of “Yamanaka Factors,” a group of genes that are capable of turning ordinary skin cells into induced pluripotentent stem cells (iPSCs) which have the ability to become any type of cell within the body. Discovery of iPSCs was, and has been, groundbreaking because it not only allows for unprecedented avenues to study human disease, but also has implications for using a patient’s own cells to treat a wide variety of diseases.

Recently, Timo Otonkoski’s group at the University of Helsinki along with Juha Kere’s group at the Karolinska Institutet and King’s College, London have found a way to program iPSCs from skin cells using CRISPR, a gene editing technology. Their approach allows for the induction, or turning on of iPSCs using the cells own DNA, instead of introducing the previously identified Yamanka Factors into cells of interest.

As detailed in their study, published in the journal Nature Communications, this is the first instance of mature human cells being completely reprogrammed into pluripotent cells using only CRISPR. Instead of using the canonical CRISPR system that allows the CAS9 protein (an enzyme that is able to cut DNA, thus rendering a gene of interest dysfunctional) to mutate any gene of interest, this group used a modified version of the CAS9 protein, which allows them to turn on or off the gene that CAS9 is targeted to.

The robustness of their approach lies in the researcher’s identification of a DNA sequence that is commonly found near genes involved in embryonic development. As CAS9 needs to be guided to genes of interest to do its job, identification of this common motif allows multiple genes associated with pluripotency to be activated in mature human skin cells, and greatly increased the efficiency and effectiveness of this approach.

In a press release, Dr. Otonkoski further highlights the novelty and viability of this approach:

“…Reprogramming based on activation of endogenous genes rather than overexpression of transgenes is…theoretically a more physiological way of controlling cell fate and may result in more normal cells…”