CRISPR

Machine learning used to pattern stem cells – a vital step in organ modeling

/ Yimy Villa / Leave a comment
Gladstone researchers discovered a method to control the patterns stem cells form in a dish. The work was led by Senior Investigator Todd McDevitt (left) and his team, including (pictured) David Joy and Ashley Libby.

When someone thinks of machine learning, the first thing that comes to mind might be the technology used by Netflix or Hulu to suggest new shows based on their viewing history. But what if this technology could be applied towards advancing the field of regenerative medicine?

Thanks to a CIRM funded study, a team of scientists lead by Dr. Todd McDevitt at the Gladstone Institutes have found a way to to use machine learning to control the spacial organization of stem cells, a key process that plays a vital role in organ development. This new understanding of how stem cells organize themselves in 3D is an important step towards being able to create functional and/or personalized organs for research or organ transplants.

“We’ve shown how we can leverage the intrinsic ability of stem cells to organize,” said Dr. McDevitt in a news release from Gladstone Institutes. “This gives us a new way of engineering tissues, rather than a printing approach where you try to physically force cells into a specific configuration.”

In their normal environment, stem cells are able to form patterns as they mature and over time morph into the tissues seen in an adult organism. One type of stem cell, called an induced pluripotent stem cell (iPSC), can become nearly every cell type of the body. In fact, researchers have already found ways to direct iPSCs to become various cell types such as those in the heart or brain.

Unfortunately, attempting to replicate the pattern formation of stem cells as they mature has been challenging. Some have used 3D printing to lay out stem cells in a desired shape, but the cells often migrated away from their initial locations.

In the same news release mentioned above, Ashley Libby, a graduate student at Gladstone and co-first author of this study, said that,

“Despite the importance of organization for functioning tissues, we as scientists have had difficulty creating tissues in a dish with stem cells. Instead of an organized tissue, we often get a disorganized mix of different cell types.”

To solve this problem, the scientists used a computational model to learn how to influence stem cells into forming new arrangements, such as those that might be useful in generating personalized organs.

Previous studies conducted by Dr. McDevitt showed that blocking the expression of two genes, called ROCK1 and CDH1, affected the layout of iPS cells grown in a petri dish.

In this current study, the scientists used CRISPR/Cas9 gene editing (you can read about this technology in more detail here) to block expression of ROCK1 and CDH1 at any time by adding a drug to the iPSCs. This was done to see if they could predict stem cell arrangement based on the alterations made to ROCK1 and CDH1 at different drug doses and time periods.

The team carried out various experiments with different doses and timing. Then, the data was input into a machine-learning program designed to identify patterns, something that could take a human months to identify.

(Left) video showing simulated interactions between different stem cell populations. (Right) image of stem cells grown in conditions dictated by the machine-learning program generate a colony that forms a bull’s-eye pattern, as predicted.

The machine-learning program used the data to predict ways that ROCK1 and CDH1 affect iPSC organization. The scientists then began to see whether the program could compute how to make entirely new patterns, like a bull’s-eye or an island of cells. The team says the results were little short of astounding. Machine learning was able to accurately predict conditions that will cause stem cell colonies to form desired patterns.

The full study was published in the journal Cell Systems.

Stanford and University of Tokyo researchers crack the code for blood stem cells

/ Yimy Villa / 1 Comment
Blood stem cells grown in lab

Blood stem cells offer promise for a variety of immune and blood related disorders such as sickle cell disease and leukemia. Like other stem cells, blood stem cells have the ability to generate additional blood stem cells in a process called self-renewal. Additionally, they are able to generate blood cells in a process called differentiation. These newly generated blood cells have the potential to be utilized for transplantations and gene therapies.

However, two limitations have hindered the progress made in this field. One problem relates to the amount of blood stem cells needed to make a potential transplantation or gene therapy viable. Unfortunately, it has been challenging to isolate and grow blood stem cells in large quantity needed for these approaches. A part of this reason relates to getting the blood stem cells to self-renew rather than differentiate.

The second problem involves the existing blood stem cells in the patient’s body prior to transplantation. In order for the procedure to work, the patient’s own blood stem cells must be eliminated to make space for the transplanted blood stem cells. This is done through a process known as conditioning, which typically involves chemotherapy and/or radiation. Unfortunately, chemotherapy and radiation can cause life-threatening side effects due to its toxicity, particularly in pediatric patients, such as growth retardation, infertility and secondary cancer in later life. Very sick or elderly patients are unable to tolerate this conditioning process, making them ineligible for transplants.

A CIRM funded study by a team at Stanford and the University of Tokyo has unlocked the code related to the generation of blood stem cells.

The collaborative team was able to modify the components used to grow blood stem cells. By making these modifications, which effects the growth and physical conditions of blood stem cells, the researchers have shown for the first time that it’s possible to get blood stem cells from mice to renew themselves hundreds or even thousands of times within a period of just 28 days. 

Furthermore, the team showed that when they transplanted the newly grown cells into mice that had not undergone conditioning, the donor cells had engrafted and remained functional.

The team also found that gene editing technology such as CRISPR could be used while growing an adequate supply of blood stem cells for transplantation. This opens the possibility of obtaining a patient’s own blood stem cells, correcting the problematic gene, and reintroducing these back to the patient.

The complete study was published in Nature.

In a news release, Dr. Hiromitsu Nakauchi, a senior author of the study, is quoted as saying,

“For 50 years, researchers from laboratories around the world have been seeking ways to grow these cells to large numbers. Now we’ve identified a set of conditions that allows these cells to expand in number as much as 900-fold in just one month. We believe this approach could transform how [blood] stem cell transplants and gene therapy are performed in humans.” 

Stanford scientist uses CRISPR-Cas9 and stem cells to develop potential “bubble baby” therapy

/ Yimy Villa / 1 Comment
Dr. Matthew Porteus, professor of pediatrics at Stanford University.
Photo courtesy of Stanford Medicine.

Our immune system is an important and essential part of everyday life. It is crucial for fighting off colds and, with the help of vaccinations, gives us immunity to potentially lethal diseases. Unfortunately, for some infants, this innate bodily defense mechanism is not present or is severely lacking in function.

This condition is known as severe combined immunodeficiency (SCID), commonly nicknamed “bubble baby” disease because of the sterile plastic bubble these infants used to be placed in to prevent exposure to bacteria, viruses, and fungi that can cause infection. There are several forms of SCID, one of which involves a single genetic mutation on the X chromosome and is known as SCID-X1

Many infants with SCID-X1 develop chronic diarrhea, a fungal infection called thrush, and skin rashes. Additionally, these infants grow slowly in comparison to other children. Without treatment, many infants with SCID-X1 do not live beyond infancy.

SCID-X1 occurs almost predominantly in males since they only carry one X chromosome, with at least 1 in 50,000 baby boys born with this condition. Since females carry two X chromosomes, one inherited from each parent, they are unlikely to inherit two X chromosomes with the mutation present since it would require the father to have SCID-X1.

What if there was a way to address this condition by correcting the single gene mutation? Dr. Matthew Porteus at Stanford University is leading a study that has developed an approach to treat SCID-X1 that utilizes this concept.

By using CRISPR-Cas9 technology, which we have discussed in detail in a previous blog post, it is possible to delete a problematic gene and insert a corrected gene. Dr. Porteus and his team are using CRISPR-Cas9 to edit blood stem cells, which give rise to immune cells, which are the foundation of the body’s defense mechanism. In a study published in Nature, Dr. Porteus and his team have demonstrated proof of concept of this approach in an animal model.

The Stanford team was able to take blood stem cells from six infants with SCID-X1 and corrected them with CRISPR-Cas9. These corrected stem cells were then introduced into mice modeled to have SCID-X1. It was found that these mice were not only able to make immune cells, but many of the edited stem cells maintained their ability to continuously create new blood cells.

In a press release, Dr. Mara Pavel-Dinu, a member of the research team, said:

“To our knowledge, it’s the first time that human SCID-X1 cells edited with CRISPR-Cas9 have been successfully used to make human immune cells in an animal model.”

CIRM has previously awarded Dr. Porteus with a preclinical development award aimed at developing gene correction therapy for blood stem cells for SCID-X1. In addition to this, CIRM has funded two other projects conducted by Dr. Porteus related to CRISPR-Cas9. One of these projects used CRISPR-Cas 9 to develop a treatment for chronic sinusitis due to cystic fibrosis and the second project used the technology to develop an approach for treating sickle cell disease.

CIRM has also funded four clinical trials related to SCID. Two of these trials are related to SCID-X1, one being conducted at St. Jude Children’s Research Hospital and the other at Stanford University. The third trial is related to a different form of SCID known as ADA-SCID and is being conducted at UCLA in partnership with Orchard Therapeutics. Finally, the last of the four trials is related to an additional form of SCID known as ART-SCID and is being conducted at UCSF.

CRISPR-Cas9 101: an overview and the role it plays in developing therapies

/ Yimy Villa / 3 Comments
Illustration courtesy of TED website

There has been a lot of conversation surrounding CRISPR-Cas9 in these recent months as well as many sensational news stories. Some of these stories highlight the promise this technology holds, while others emphasize a word of caution. But what exactly does this technology do and how does it work? Here is a breakdown that will help you better understand.

To start off, CRISPR is a naturally occurring process found in bacteria used as an immune system to defend against viruses. CRISPR simply put, are strands of DNA segments that contain repeating patterns. There are “scissor like” CRISPR proteins that have the ability to cut DNA segments. When a copy of a virus enters the bacteria, these “scissor like” proteins cut a segment of DNA from the virus and insert it into CRISPR. A copy of the viral DNA is made and another “attack” protein known as Cas9 attaches to it. By binding to the viral copy, Cas9 is able to sense that virus. When the same virus tries to enter the bacteria, Cas9 is able to seek and destroy it.

You can view a more detailed video explaining this concept below.

Many scientists analyzed this process in detail and it was eventually discovered that this CRISPR-Cas9 complex could be used to removed unwanted genes and insert a corrected copy, revolutionizing the way that we view the approach towards treating a wide variety of genetic diseases.

In fact, researchers at the Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and the University of Massachusetts Medical School have developed a strategy using this complex to treat two inherited, lethal blood disorders, sickle cell disease (SCD) and beta thalassemia. Both of these diseases involve a mutation that effects production of red blood cells, which are produced by blood stem cells. In beta-thalassemia, the mutation prevent red blood cells from being able to carry enough oxygen, leading to anemia. In SCD, the mutations cause red blood cells to take on a “sickle” shape which can block blood vessels.

By using CRISPR-Cas9 to insert a corrected copy of the gene into a patient’s own blood stem cells, this team demonstrated that functional red blood cells can then be produced. These results pay the way for other blood disorders as well.

In a press release , Dr. Daniel Bauer, an attending physician with Dana-Farber and a senior author on both of these studies stated that,

“Combining gene editing with an autologous stem-cell transplant could be a therapy for sickle-cell disease, beta-thalassemia and other blood disorders.”

In a separate study, scientists at University of Massachusetts Medical School have developed a strategy that could be used to treat genetic disorders associated with unintentional repeats or copies of small DNA segments. These problematic small segments of DNA are called microduplications and cause as many as 143 different diseases, including limb-girdle muscular dystrophy, Hermansky-Pudlak syndrome, and Tay-Sachs.

Because these are issues caused by repeats or copies of small DNA segments, the CRISPR-Cas9 complex can be used to remove microduplications without having to insert any additional genetic material.

Dr. Scot A. Wolfe, a co-investigator of this study, stated that,

“It’s like hitting the reset button. We don’t have to add any corrective genetic material, instead the cell stitches the DNA back together minus the duplication. It’s a shortcut for gene correction with potential therapeutic appeal.”

Although there has been a lot progress made with this technology, there are still concerns that need to be addressed. An article in Science mentions how two studies have shown that CRISPR can still make unintended changes to DNA, which can be potentially dangerous. In the article, Dr. Jin-Soo Kim, a CRISPR researcher at Seoul National University is quoted as saying,

“It is now important to determine which component is responsible for the collateral mutations and how to reduce or avoid them.”

Overall, CRISPR-Cas9 has revolutionized the approach of precision medicine. A wide variety of diseases are caused by small, unexpected segments of DNA. By applying this approach found in bacteria to humans, we have uncovered a way to correct these segments at the microscopic level. However, there is still much that needs to be learned and perfected before it can be utilized in patients.

Researcher claims to have made first gene-edited baby. But did it really happen?

/ Kevin McCormack / Leave a comment

Raelians

Claude Vorilhorn, founder of Raelism; Photo: courtesy thoughtco.com

Remember the Raelians? Probably not. But way back in 2002 the group, some described them as a cult, claimed it had created the world’s first cloned baby. The news made headlines all around the world raising fears we were stepping into uncharted scientific territory. Several weeks later the scientist brought in by the Raelians to verify their claims called it an “elaborate hoax.”

hejiankui

He Jiankui: Photo courtesy MIT Technology Review

Fast forward 16 years and a Chinese scientist named He Jiankui of Shenzhen claims he has created the first genetically modified humans. Again, it is generating headlines around the world and alarming people. In an interview with CNBC, Hank Greely, a bioethicist at Stanford, said if it happened it was “criminally reckless and I unequivocally condemn the experiment.”

The question now is did it happen, or is this just another “elaborate hoax”?

The concerns about this story are real. The scientist claims he used CRISPR to modify embryos during fertility treatments, resulting in the birth of twin girls.

CRISPR has been making headlines all of its own in the last few years as a fast, cheap and efficient way of editing genes. CIRM supports research using CRISPR for problems such as sickle cell disease. The difference being that our research works with adults so any changes in their genes are just for them. Those changes are not passed on to future generations.

The work making headlines around the world used CRISPR on embryos, meaning a child born from one of those embryos would pass those changes on to future generations. In effect, creating a new kind of human being.

This approach raises all sorts of serious issues – scientific, ethical and moral – not the least of which is that the technique could create unknown mutations down the road that would be passed on to future generations.  That’s why in the US the editing of embryos for pregnancy is banned.

But almost as soon as the news was announced there were questions raised about it. The research was not published anywhere. A hospital that the researchers named in their ethical approval documents is denying any involvement.

If it did happen, it could open a new, and potentially frightening chapter in science. In an interview on CNN, Julian Savulescu, director of the Oxford Uehiro Centre for Practical Ethics at the University of Oxford, called the use of CRISPR in this manner as “genetic Russian Roulette.”

“If true, this experiment is monstrous. Gene editing itself is experimental and is still associated with off-target mutations, capable of causing genetic problems early and later in life, including the development of cancer.”

And in an interview on the BBC, Prof Robert Winston, Professor of Science and Society at Imperial College London, said: “If this is a false report, it is scientific misconduct and deeply irresponsible. If true, it is still scientific misconduct.”

Our best hope right now is that this is just a repeat of the Raelians. Our worst fear, is that it’s not.

Has Regenerative Medicine Come of Age?

/ Kevin McCormack / 1 Comment

Signals logo

For the past few years the Signals blog site –  which offers an insiders’ perspectives on the world of regenerative medicine and stem cell research – has hosted what it calls a “Blog Carnival”. This is an event where bloggers from across the stem cell field are invited to submit a piece based on a common theme. This year’s theme is “Has Regenerative Medicine Come of Age?” Here’s my take on that question:

Many cultures have different traditions to mark when a child comes of age. A bar mitzvah is a Jewish custom marking a boy reaching his 13th birthday when he is considered accountable for his own actions. Among Latinos in the US a quinceañera is the name given to the coming-of-age celebration on a girl’s 15th birthday.

Regenerative Medicine (RM) doesn’t have anything quite so simple or obvious, and yet the signs are strong that if RM hasn’t quite come of age, it’s not far off.

For example, look at our experience at the California Institute for Regenerative Medicine (CIRM). When we were created by the voters of California in 2004 the world of stem cell research was still at a relatively immature phase. In fact, CIRM was created just six years after scientists first discovered a way to derive stem cells from human embryos and develop those cells in the laboratory. No surprise then that in the first few years of our existence we devoted a lot of funding to building world class research facilities and investing in basic research, to gain a deeper understanding of stem cells, what they could do and how we could use them to develop therapies.

Fast forward 14 years and we now have funded 49 projects in clinical trials – everything from stroke and cancer to spinal cord injury and HIV/AIDS – and our early funding also helped another 11 projects get into clinical trials. Clearly the field has advanced dramatically.

In addition the FDA last year approved the first two CAR-T therapies – Kymriah and Yescarta – another indication that progress is being made at many levels.

But there is still a lot of work to do. Many of the trials we are funding at the Stem Cell Agency are either Phase 1 or 2 trials. We have only a few Phase 3 trials on our books, a pattern reflected in the wider RM field. For some projects the results are very encouraging – Dr. Gary Steinberg’s work at Stanford treating people recovering from a stroke is tremendously promising. For others, the results are disappointing. We have cancelled some projects because it was clear they were not going to meet their goals. That is to be expected. These clinical trials are experiments that are testing, often for the first time ever in people, a whole new way of treating disease. Failure comes with the territory.

As the number of projects moving out of the lab and into clinical trials increases so too are the other signs of progress in RM. We recently held a workshop bringing together researchers and regulators from all over the world to explore the biggest problems in manufacturing, including how you go from making a small batch of stem cells for a few patients in an early phase clinical trial to mass producing them for thousands, if not millions of patients. We are also working with the National Institutes of Health and other stakeholders in discussing the idea of reimbursement, figuring out who pays for these therapies so they are available to the patients who need them.

And as the field advances so too do the issues we have to deal with. The discovery of the gene-editing tool CRISPR has opened up all sorts of possible new ways of developing treatments for deadly diseases. But it has also opened up a Pandora’s box of ethical issues that the field as a whole is working hard to respond to.

These are clear signs of a maturing field. Five years ago, we dreamed of having these kinds of conversations. Now they are a regular feature of any RM conference.

The simple fact that we can pose a question asking if RM has come of age is a sign all by itself that we are on the way.

Like little kids sitting in the back of a car, anxious to get to their destination, we are asking “Are we there yet?” And as every parent in the front seat of their car responds, “Not yet. But soon.”

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…”

 

Stem Cell Roundup: New understanding of Huntington’s; how stem cells can double your DNA; and using “the Gary Oldman of cell types” to reverse aging

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This week’s roundup highlights how we are constantly finding out new and exciting ways that stem cells could help change the way we treat disease.

Our Cool Stem Cell Image of the Week comes from our first story, about unlocking some of the secrets of Huntington’s disease. It comes from the Laboratory of Stem Cell Biology and Molecular Embryology at The Rockefeller University

Huntington's neurons

A new approach to studying and developing therapies for Huntington’s disease

Researchers at Rockefeller University report new findings that may upend the way scientists study and ultimately develop therapies for Huntington’s disease, a devastating, inherited neurodegenerative disorder that has no cure. Though mouse models of the disease are well-established, the team wanted to focus on human biology since our brains are more complex than those of mice. So, they used CRISPR gene editing technology in human embryonic stem cells to introduce the genetic mutations that cause HD.

Though symptoms typically do not appear until adulthood, the researchers were surprised to find that in their human cell-based model of HD, abnormalities in nerve cells occur at the earliest steps in brain development. These results suggest that HD therapies should focus on treatments much earlier in life.

The researchers observed another unexpected twist: cells that lack Huntingtin, the gene responsible for HD, are very similar to cells found in HD. This suggests that too little Huntingtin may be causing the disease. Up until now, the prevailing idea has been that Huntington’s symptoms are caused by the toxicity of too much mutant Huntingtin activity.

We’ll certainly be keeping an eye on how further studies using this new model affect our understanding of and therapy development for HD.

This study was published in Development and was picked by Science Daily.

How you can double your DNA

dna

As you can imagine we get lots of questions about stem cell research here at CIRM. Last week we got an email asking if a stem cell transplant could alter your DNA? The answer is, under certain circumstances, yes it could.

A fascinating article in the Herald Review explains how this can happen. In a bone marrow transplant bad blood stem cells are killed and replaced with healthy ones from a donor. As those cells multiply, creating a new blood supply, they also carry the DNA for the donor.

But that’s not the only way that people may end up with dual DNA. And the really fascinating part of the article is how this can cause all sorts of legal and criminal problems.

One researcher’s efforts to reverse aging

gary-oldman

Gary Oldman: Photo courtesy Variety

“Stem cells are the Gary Oldman of cell types.” As a fan of Gary Oldman (terrific as Winston Churchill in the movie “Darkest Hour”) that one line made me want to read on in a profile of Stanford University researcher Vittorio Sebastiano.

Sebastiano’s goal is, to say the least, rather ambitious. He wants to reverse aging in people. He believes that if you can induce a person’s stem cells to revert to a younger state, without changing their function, you can effectively turn back the clock.

Sebastiano says if you want to achieve big things you have to think big:

“Yes, the ambition is huge, the potential applications could be dramatic, but that doesn’t mean that we are going to become immortal in some problematic way. After all, one way or the other, we have to die. We will just understand aging in a better way, and develop better drugs, and keep people happier and healthier for a few more years.”

The profile is in the journal Nautilus.

UCLA scientists on track to develop a stem cell replacement therapy for Duchenne Muscular Dystrophy

/ Karen Ring / 2 Comments

Muscle cells generated by April Pyle’s Lab at UCLA.

Last year, we wrote about a CIRM-funded team at UCLA that’s on a mission to develop a stem cell treatment for patients with Duchenne muscular dystrophy (DMD). Today, we bring you an exciting update on this research just in time for the holidays (Merry Christmas and Happy Hanukkah and Kwanza to our readers!).

DMD is a deadly muscle wasting disease that primarily affects young boys and young men. The UCLA team is trying to generate better methods for making skeletal muscle cells from pluripotent stem cells to regenerate the muscle tissue that is lost in patients with the condition. DMD is caused by genetic mutations in the dystrophin gene, which codes for a protein that is essential for skeletal muscle function. Without dystrophin protein, skeletal muscles become weak and waste away.

In their previous study, the UCLA team used CRISPR gene editing technology to remove dystrophin mutations in induced pluripotent stem cells (iPSCs) made from the skin cells of DMD patients. These corrected iPSCs were then matured into skeletal muscle cells that were transplanted into mice. The transplanted muscle cells successfully produced dystrophin protein – proving for the first time that DMD mutations can be corrected using human iPSCs.

A Step Forward

The team has advanced their research a step forward and published a method for making skeletal muscle cells, from DMD patient iPSCs, that look and function like real skeletal muscle tissue. Their findings, which were published today in the journal Nature Cell Biology, address a longstanding problem in the field: not being able to make stem cell-derived muscle cells that are mature enough to model DMD or to be used for cell replacement therapies.

Dr. April Pyle, senior author on the study and Associate Professor at the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA explained in a news release:

April Pyle, UCLA.

“We have found that just because a skeletal muscle cell produced in the lab expresses muscle markers, doesn’t mean it is fully functional. For a stem cell therapy for Duchenne to move forward, we must have a better understanding of the cells we are generating from human pluripotent stem cells compared to the muscle stem cells found naturally in the human body and during the development process.”

By comparing the proteins expressed on the cell surface of human fetal and adult muscle cells, the team identified two proteins, ERBB3 and NGFR, that represented a regenerative population of skeletal muscle cells. They used these two markers to isolate these regenerative muscle cells, but found that the muscle fibers they created in a lab dish were smaller than those found in human muscle.

First author, Michael Hicks, discovered that using a drug to block a human developmental signaling pathway called TGF Beta pushed these ERBB3/NGFR cells past this intermediate stage and allowed them to mature into functional skeletal muscle cells similar to those found in human muscle.

Putting It All Together

In their final experiments, the team combined the new stem cell techniques developed in the current study with their previous work using CRISPR gene editing technology. First, they removed the dystrophin mutations in DMD patient iPSCs using CRISPR. Then, they coaxed the iPSCs into skeletal muscle cells in a dish and isolated the regenerative cells that expressed ERBB3 and NGFR. Mice that lacked the dystrophin protein were then transplanted with these cells and were simultaneously given an injection of a TGF Beta blocking drug.

The results were exciting. The transplanted cells were able to produce human dystrophin and restore the expression of this protein in the Duchenne mice.

Skeletal muscle cells isolated using the ERBB3 and NGFR surface markers (right) restore human dystrophin (green) after transplantation significantly greater than previous methods (left). (Image courtesy of UCLA)

Dr. Pyle concluded,

“The results were exactly what we’d hoped. This is the first study to demonstrate that functional muscle cells can be created in a laboratory and restore dystrophin in animal models of Duchenne using the human development process as a guide.”

In the long term, the UCLA team hopes to translate this research into a patient-specific stem cell therapy for DMD patients. In the meantime, the team will use funding from a recent CIRM Quest award to make skeletal muscle cells that can regenerate long-term in response to chronic injury in hopes of developing a more permanent treatment for DMD.

The UCLA study discussed in this blog received funding from Discovery stage CIRM awards, which you can read more about here and here.

Turning the corner with the FDA and NIH; CIRM creates new collaborations to advance stem cell research

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FDAThis blog is part of the Month of CIRM series on the Stem Cellar

A lot can change in a couple of years. Just take our relationship with the US Food and Drug Administration (FDA).

When we were putting together our Strategic Plan in 2015 we did a survey of key players and stakeholders at CIRM – Board members, researchers, patient advocates etc. – and a whopping 70 percent of them listed the FDA as the biggest impediment for the development of stem cell treatments.

As one stakeholder told us at the time:

“Is perfect becoming the enemy of better? One recent treatment touted by the FDA as a regulatory success had such a high clinical development hurdle placed on it that by the time it was finally approved the standard of care had evolved. When it was finally approved, five years later, its market potential had significantly eroded and the product failed commercially.”

Changing the conversation

To overcome these hurdles we set a goal of changing the regulatory landscape, finding a way to make the system faster and more efficient, but without reducing the emphasis on the safety of patients. One of the ways we did this was by launching our “Stem Cell Champions” campaign to engage patients, patient advocates, the public and everyone else who supports stem cell research to press for change at the FDA. We also worked with other organizations to help get the 21st Century Cures Act passed.

21 century cures

Today the regulatory landscape looks quite different than it did just a few years ago. Thanks to the 21st Century Cures Act the FDA has created expedited pathways for stem cell therapies that show promise. One of those is called the Regenerative Medicine Advanced Therapy (RMAT) designation, which gives projects that show they are both safe and effective in early-stage clinical trials the possibility of an accelerated review by the FDA. Of the first projects given RMAT designation, three were CIRM-funded projects (Humacyte, jCyte and Asterias)

Partnering with the NIH

Our work has also paved the way for a closer relationship with the National Institutes of Health (NIH), which is looking at CIRM as a model for advancing the field of regenerative medicine.

In recent years we have created a number of innovations including introducing CIRM 2.0, which dramatically improved our ability to fund the most promising research, making it faster, easier and more predictable for researchers to apply. We also created the Stem Cell Center  to make it easier to move the most promising research out of the lab and into clinical trials, and to give researchers the support they need to help make those trials successful. To address the need for high-quality stem cell clinical trials we created the CIRM Alpha Stem Cell Clinic Network. This is a network of leading medical centers around the state that specialize in delivering stem cell therapies, sharing best practices and creating new ways of making it as easy as possible for patients to get the care they need.

The NIH looked at these innovations and liked them. So much so they invited CIRM to come to Washington DC and talk about them. It was a great opportunity so, of course, we said yes. We expected them to carve out a few hours for us to chat. Instead they blocked out a day and a half and brought in the heads of their different divisions to hear what we had to say.

A model for the future

We hope the meeting is, to paraphrase Humphrey Bogart at the end of Casablanca, “the start of a beautiful friendship.” We are already seeing signs that it’s not just a passing whim. In July the NIH held a workshop that focused on what will it take to make genome editing technologies, like CRISPR, a clinical reality. Francis Collins, NIH Director, invited CIRM to be part of the workshop that included thought leaders from academia, industry and patients advocates. The workshop ended with a recommendation that the NIH should consider building a center of excellence in gene editing and transplantation, based on the CIRM model (my emphasis).  This would bring together a multidisciplinary disease team including, process development, cGMP manufacturing, regulatory and clinical development for Investigational New Drug (IND) filing and conducting clinical trials, all under one roof.

dr_collins

Dr. Francis Collins, Director of the NIH

In preparation, the NIH visited the CIRM-funded Stem Cell Center at the City of Hope to explore ways to develop this collaboration. And the NIH has already begun implementing these suggestions starting with a treatment targeting sickle cell disease.

There are no guarantees in science. But we know that if you spend all your time banging your head against a door all you get is a headache. Today it feels like the FDA has opened the door and that, together with the NIH, they are more open to collaborating with organizations like CIRM. We have removed the headache, and created the possibility that by working together we truly can accelerate stem cell research and deliver the therapies that so many patients desperately need.