Stem cell stories that caught our eye: Horse patients, Brain cancer stem cells, and a Bony Heart

Horsing around at the World Stem Cell Summit
The World Stem Cell Summit (WSCS) is coming up very shortly (December 6-9) in lovely downtown West Palm Beach, Florida. And this year it has an added attraction; horses.

For my money the WSCS is the most enjoyable of the many conferences held around the US focusing on stem cells. Most conferences have either scientists or patients and patient advocates. This brings them both together creating an event that highlights the science, the people doing it, and the people who hope to benefit from it.

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Eadweard Muybridge’s Galloping Horse
Image: Wikimedia Commons

And this year it’s not just about people, it’s also about horses. For the first time the event will feature the Equine World Stem Cell Summit. This makes sense on so many levels. Animals, large and small, have always been an important element in advancing scientific research, enabling us to test treatments and make sure they are safe before trying them out on people.

But horses are also athletes and sports has always been a powerful force in accelerating research. When you think about the “Sport of Kings” and how much money is involved in breeding and racing horses it’s not surprising that rich owners are always looking for new treatments that can help their thoroughbreds recover from injuries.

And if they help repair damaged bones and tendons in thoroughbreds, who’s to say those techniques and that research couldn’t help the rest of us.

Loss of gene allows cancer stem cells to invade the brain
A fundamental property of stem cells is their ability to self-renew and make unlimited copies of themselves. That ability is great for repairing the body but in the case of cancer stem cells, it is thought to be responsible for the uncontrolled, lethal growth of tumors.

Both stem cells and cancer stem cells rely on special cellular neighborhoods, or “niches”, to support their function. Outside of those niches, the cells don’t survive well. But cancer stem cells somehow overcome this barrier which allows them to spread and do damage to whole organs.

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Brain MRI showing glioblastoma tumor
Image: Wikimedia Commons

A study this week at The University of Texas MD Anderson Cancer Center zeroed in on the gene QK1 that, when deleted in mice, provides cancer stem cells in the brain the ability to thrive outside their niches.  They team also showed that the loss of the gene slowed a cell process called endocytosis, which normally acts to break down and recycle protein receptors on the cell surface. Those receptors are critical for the cancer stem cell’s self-renew function. So by blocking endocytosis, the gene deletion leads to an accumulation of receptors on the cell surface and in turn that boosts the cancer stem cells’ ability to divide and grow outside of its niche.

In a university press release picked up by Science Daily, team lead Jian Hu talked about exploiting this result to find new ways to defeat glioblastoma, the deadliest form of brain cancer:

“This study may lead to cancer therapeutic opportunities by targeting the mechanisms involved in maintaining cancer stem cells. Although loss of QKI allows glioma stem cells to thrive, it also renders certain vulnerabilities to the cancer cells. We hope to design new therapies to target these.”

CIRM-funded scientists uncover mystery of bone growth in the heart
Calcium helps keep our bones strong but a build-up of the mineral in our soft tissues, like the heart, is nothing but bad news for our health. The origins of this abnormal process called ectopic calcification have been a mystery to scientists because the cells responsible for forming bone and secreting calcium, called osteoblasts, are not found in the heart. So where is the calcium coming from?

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Bone-forming osteoblasts. They’re bad news when found in the heart.
Image: Amgen

This week, a CIRM-funded team at UCLA found the answer: cardiac fibroblasts. The researchers suspected that this most abundant cell in the heart was the culprit behind ectopic calcification. So, using some genetic engineering tricks, they were able to track cardiac fibroblasts with a red fluorescent tag inside mice after a heart injury.

Within a week or so after injury, the team observed that cardiac fibroblasts had clustered around the areas of calcium deposits in the heart. It turns out that those cardiac fibroblasts had taken on the properties of heart stem cells and then became bone-forming osteoblasts. To prove this finding, they took some of those cells and transplanted them into healthy mice. Sure enough, the injection sites where the cells were located began to accumulate calcium deposits.

A comparison of gene activity in these abnormal cells versus healthy cells identified a protein called EPPN1 whose levels were really elevated when these calcium deposits occurred. Blocking EPPN1 put a stop to the calcification in the heart. In a university press release, lead author Arjun Deb explained that this detective work may lead to long sought after therapies:

Everyone recognizes that calcification of the heart and blood vessels and kidneys is abnormal, but we haven’t had a single drug that can slow down or reverse calcification; our study points to some therapeutic targets.

Stem cell agency funds clinical trials in three life-threatening conditions

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A year ago the CIRM Board unanimously approved a new Strategic Plan for the stem cell agency. In the plan are some rather ambitious goals, including funding ten new clinical trials in 2016. For much of the last year that has looked very ambitious indeed. But today the Board took a big step towards reaching that goal, approving three clinical trials focused on some deadly or life-threatening conditions.

The first is Forty Seven Inc.’s work targeting colorectal cancer, using a monoclonal antibody that can strip away the cancer cells ability to evade  the immune system. The immune system can then attack the cancer. But just in case that’s not enough they’re going to hit the tumor from another side with an anti-cancer drug called cetuximab. It’s hoped this one-two punch combination will get rid of the cancer.

Finding something to help the estimated 49,000 people who die of colorectal cancer in the U.S. every year would be no small achievement. The CIRM Board thought this looked so promising they awarded Forty Seven Inc. $10.2 million to carry out a clinical trial to test if this approach is safe. We funded a similar approach by researchers at Stanford targeting solid tumors in the lung and that is showing encouraging results.

Our Board also awarded $7.35 million to a team at Cedars-Sinai in Los Angeles that is using stem cells to treat pulmonary hypertension, a form of high blood pressure in the lungs. This can have a devastating, life-changing impact on a person leaving them constantly short of breath, dizzy and feeling exhausted. Ultimately it can lead to heart failure.

The team at Cedars-Sinai will use cells called cardiospheres, derived from heart stem cells, to reduce inflammation in the arteries and reduce blood pressure. CIRM is funding another project by this team using a similar  approach to treat people who have suffered a heart attack. This work showed such promise in its Phase 1 trial it’s now in a larger Phase 2 clinical trial.

The largest award, worth $20 million, went to target one of the rarest diseases. A team from UCLA, led by Don Kohn, is focusing on Adenosine Deaminase Severe Combined Immune Deficiency (ADA-SCID), which is a rare form of a rare disease. Children born with this have no functioning immune system. It is often fatal in the first few years of life.

The UCLA team will take the patient’s own blood stem cells, genetically modify them to fix the mutation that is causing the problem, then return them to the patient to create a new healthy blood and immune system. The team have successfully used this approach in curing 23 SCID children in the last few years – we blogged about it here – and now they have FDA approval to move this modified approach into a Phase 2 clinical trial.

So why is CIRM putting money into projects that it has either already funded in earlier clinical trials or that have already shown to be effective? There are a number of reasons. First, our mission is to accelerate stem cell treatments to patients with unmet medical needs. Each of the diseases funded today represent an unmet medical need. Secondly, if something appears to be working for one problem why not try it on another similar one – provided the scientific rationale and evidence shows it is appropriate of course.

As Randy Mills, our President and CEO, said in a news release:

“Our Board’s support for these programs highlights how every member of the CIRM team shares that commitment to moving the most promising research out of the lab and into patients as quickly as we can. These are very different projects, but they all share the same goal, accelerating treatments to patients with unmet medical needs.”

We are trying to create a pipeline of projects that are all moving towards the same goal, clinical trials in people. Pipelines can be horizontal as well as vertical. So we don’t really care if the pipeline moves projects up or sideways as long as they succeed in moving treatments to patients. And I’m guessing that patients who get treatments that change their lives don’t particularly

Stem cell stories that caught our eye: Blood stem cells on a diet, Bladder control after spinal cord injuries, new ALS insights

Putting blood stem cells on a diet. (Karen Ring)

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Valine. Image: BMRB

Scientists from Stanford and the University of Tokyo have figured out a new way to potentially make bone marrow transplants more safe. Published yesterday in the journal Science, the teams discovered that removing an essential amino acid, called valine, from the diets of mice depleted their blood stem cells and made it easier for them to receive bone marrow transplants from other mice without the need for radiation or chemotherapy. Removing valine from human blood stem cells yielded similar results suggesting that this therapeutic approach could potentially change and improve the way that certain cancer patients are treated.

In an interview with Science Magazine, senior author Satoshi Yamazaki explained how current bone marrow transplants are toxic to patients and that an alternative, safer form of treatment is needed.

“Bone marrow transplantation is a toxic therapy. We have to do it to treat diseases that would otherwise be fatal, but the quality of life afterward is often not good. Relative to chemotherapy or radiation, the toxicity of a diet deficient in valine seems to be much, much lower. Mice that have been irradiated look terrible. They can’t have babies and live for less than a year. But mice given a diet deficient in valine can have babies and will live a normal life span after transplantation.”

The scientists found that the effects of a valine-deficient diet were mostly specific to blood stem cells in the mice, but also did affect hair stem cells and some T cells. The effects on these other populations of cells were not as dramatic however as the effects on blood stem cells.

Going forward, the teams are interested to find out whether valine deficiency will be a useful treatment for leukemia stem cells, which are stem cells that give rise to a type of blood cancer. As mentioned before, this alternative form of treatment would be very valuable for certain cancer patients in comparison to the current regimen of radiation treatment before bone marrow transplantation.

Easing pain and improving bladder control in spinal cord injury (Kevin McCormack)
When most people think of spinal cord injuries (SCI) they focus on the inability to walk. But for people with those injuries there are many other complications such as intense nerve or neuropathic pain, and inability to control their bladder. A CIRM-funded study from researchers at UCSF may help point at a new way of addressing those problems.

The study, published in the journal Cell Stem Cell, zeroed in on the loss in people with SCI of a particular amino acid called GABA, which acts as a neurotransmitter in the central nervous system and inhibits nerve transmission in the brain, calming nervous activity.

Here’s where we move into alphabet soup, but stick with me. Previous studies showed that using cells called inhibitory interneuron precursors from the medial ganglionic eminence (MGE) helped boost GABA signaling in the brain and spinal cord. So the researchers turned some human embryonic stem cells (hESCs) into MGEs and transplanted those into the spinal cords of mice with SCI.

Six months after transplantation those cells had integrated into the mice’s spinal cord, and the mice not only showed improved bladder function but they also seemed to have less pain.

Now, it’s a long way from mice to men, and there’s a lot of work that has to be done to ensure that this is safe to try in people, but the researchers conclude: “Our findings, therefore, may have implications for the treatment of chronically spinal cord-injured patients.”

CIRM-funded study reveals potential new ALS drug target (Todd Dubnicoff)
Of the many diseases CIRM-funded researchers are tackling, Amyotrophic Lateral Sclerosis (ALS), also known as Lou Gehrig’s Disease, has got to be one of the worst.

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Motor neurons derived from skin cells of a healthy donor
Image: UC San Diego

This neurodegenerative disorder attacks and kills motor neurons, the nerve cells that control voluntary muscle movement. People diagnosed with ALS, gradually lose the ability to move their limbs, to swallow and even to breathe. The disease is always fatal and people usually die within 3 to 5 years after initial diagnosis. There’s no cure for ALS mainly because scientists are still struggling to fully understand what causes it.

Stem cell-derived “disease in a dish” experiments have recently provided many insights into the underlying biology of ALS. In these studies, skin cells from ALS patients are reprogrammed into an embryonic stem cell-like state called induced pluripotent stem cells (iPSCS). These iPS cells are grown in petri dishes and then specialized into motor neurons, allowing researchers to carefully look for any defects in the cells.

This week, a UC San Diego research team using this disease in a dish strategy reported they had uncovered a cellular process that goes haywire in ALS cells. The researchers generated motor neurons from iPS cells that had been derived from the skin samples of ALS patients with hereditary forms of the disease as well as samples from healthy donors. The team then compared the activity of thousands of genes between the ALS and healthy motor neurons. They found that a particular hereditary mutation doesn’t just impair a protein called hnRNP A2/B1, it actually gives the protein new toxic activities that kill off the motor neurons.

Fernando Martinez, the first author on this study in Neuron, told the UC San Diego Health newsroom that these news results reveal an important context for their on-going development of therapeutics that target proteins like hnRNP:

“These … therapies [targeting hnRNP] can eliminate toxic proteins and treat disease. But this strategy is only viable if the proteins have gained new toxic functions through mutation, as we found here for hnRNP A2/B1 in these ALS cases.”

Buildup of random mutations in adult stem cells doesn’t explain varying frequency of cancers

To divide or not to divide?

 It’s a question every cell in your body must constantly ask itself. Cells in your small intestine, for instance, replace themselves about every three days so the cells in that tissue must divide frequently to replenish the tissue. Liver cell are less active and turn over about once a year. And on the other extreme, the cells in the lens of the eye are kept over a life time.

The cell cycle, an exquisitely controlled process.

The cell cycle, an exquisitely controlled process. (Source wikipedia)

It’s no wonder that the process of cell division, also called the cell cycle, is exquisitely controlled by many different proteins and signaling molecules. It also makes sense that mutations in genes that produce the cell cycle proteins, could cause the regulation of cell division to go awry.

Mutations pave a path to cancer

Accumulation of enough mutations over a lifetime can lead to uncontrolled cell growth and eventually cancer. Adult stem cells are thought to be especially vulnerable to cell cycle mutations since these cells already have the capacity to self-renew and can pass mutations to their daughter cells.

Now, gene mutations can be inherited from one’s parents or caused by environmental factors like UV rays from the sun or acquired by random mistakes that occur as DNA replicates itself during cells division. Studying how the accumulation of these different mutation types impact cell division is important for understanding the formation of cancers. Results from a study in early 2015 indicated that mutations caused by random mistakes in DNA replication had a bigger impact on many cancers than mutations arising from lifestyle and environmental factors.

“Bad luck” mutations may not be the most harmful

But a new research publication in Nature suggests that, while these “bad luck” mutations can drive the development of cancer, they probably are not the main contributors. To reach this conclusion, the research team – which hails from the University Medical Center Utrecht in the Netherlands – directly measured mutation rates in human adult stem cells collected from donors as young as three years and as old as 87. In particular, stem cells from the liver, small intestine and colon were obtained. Individual stem cells were grown in the lab into mini-organs, or organoids, that resemble the structures of the source tissue. After studying these organoids, they determined that the frequency of cancer is very different in these organs, with the incidence cancer in the colon being much higher than in the other two organs.

Mutation rate the same, despite age, despite organ type

Through a various genetic analyses, the team found that an interesting pattern: the mutation rate was the same – about 40 mutations per year – for all organ types and all ages despite the higher incidence of colon cancer and older age-related cancers. Dr. Ruben van Boxtel, the team leader, expressed his reaction to these results in an interview with Medical News Today:

“We were surprised to find roughly the same mutation rate in stem cells from organs with different cancer incidence. This suggests that simply the gradual accumulation of more and more ‘bad luck’ DNA errors over time cannot explain the difference we see in cancer incidence – at least for some cancers.”

Still, the team did observe that different types of random mutations were specific to one organ over the other. These differences may help explain why the colon, for example, has a higher cancer incidence than the liver or small intestine. Van Boxtel and his team are interested in examining this result further:

“It seems ‘bad luck’ is definitely part of the story but we need much more evidence to find out how, and to what extent. This is what we want to focus on next.”

Stem cell stories that caught our eye: Salamander limb regrowth, mass producing cells for kidneys and halting cancer stem cells

Here are some stem cell stories that caught our eye this past week. Some are groundbreaking science, others are of personal interest to us, and still others are just fun.

Fun with axolotls.  Axolotls, the albino aquatic critters that look like they have feathers growing out of the backs of their heads, have long been a favorite model for studying how they and their salamander cousins regrow limbs. But only recently, with refined methods for turning specific genes on and off, have we begun to really understand this amazing feat.

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Carl Zimmer, national correspondent for the online publication STAT, interviewed Jessica Whited of Harvard-affiliated Brigham and Women’s Hospital about her work trying to understand the genetics of limb regrowth and posted both a four-minute video and a short story about the research. Part of the video series Zimmer calls “Science Happens,” the interview lets Whited explain that when a limb is cut off, the animal summons cells called blastemas to the stump. Those cells have properties like stem cells in that they can make different tissues like the bone, skin and muscle needed to grow a limb, but they seem to do this by selectively turning genes on and off.

With a mix of cartoon drawings and real lab images, the video provides an easy to follow explanation of how the researchers turn off individual genes and then look for the effect. And I have to say I agree with Zimmer when talking about the axolotls he declares “I think they’re creepy.”

 

Advance for kidney disease.  Often in stem cell research you don’t want the starting stem cell and you don’t want the end desired tissue, you want the middleman called a progenitor that has already decided it wants to become the end tissue, but can still mass produce itself. Instead of being handed a roll of 10 dollar bills, you have a printing press with Hamilton’s face already set on the printing plate.

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Progenitor cells (bright red) growing in a kidney

In CIRM-funded research published this week in Cell Stem Cell a team at the Salk Institute has found a way to configure that printing press for nephron progenitor cells, the cells that yield the vital nephrons that allow your kidneys to cleanse your blood. While many have tried to mass produce these vital cells to repair damaged kidneys, they have not had much luck. These cells do not like to stay in the progenitor state. Once they are on the path toward the end tissue they like to keep on moving in that direction.

The Salk team, led by Juan Carlos Izpisua Belmonte, got around this by changing the progenitor cells’ environment. Instead of a flat lab dish, they grew them in 3D cultures and gave them a new mix of signaling molecules.

“We provide a proof-of-principle for how to make and maintain unlimited numbers of precursor kidney cells,” said Izpisua Belmonte in an institute press release posted by HealthMedicineNet. “Having a supply of these cells could be a starting point to grow functional organs in the laboratory as well as a way to begin applying cell therapy to kidneys with malfunctioning genes.”

Their system worked first in mouse cells and then in human cells. They predicted that the methods could be used to grow progenitor cells for many other tissues.

 

Halting cancer stem cells. The bad guys of the stem cell world, cancer stem cells (CSCs), are turning out to have a number of vulnerabilities, and many companies around the world have staked their fortunes on attacking one of those weak spots. While we have known for some time that CSCs require proteins in the Wnt family to grow, we haven’t had a good way of blocking that path. Now researchers at the Riken Center and National Cancer Center in Japan claim they have a candidate drug, at least for colon cancer.

They screened a library of compounds likely to inhibit the Wnt pathway and tested them in mice that had received transplants of human colon cancer. They found one, NCB-0846 that can be administered orally, that was able to suppress the cancer grafts.

 “We’re very encouraged by our promising preclinical data for NCB-0846, especially considering the difficulty in targeting this pathway to date, and shortly we hope to conduct a clinical trial at the NCC hospitals” said Dr. Tesshi Yamada of the National Cancer Center in a Riken release posted by ScienceCodex.

CIRM funds several team trying to halt CSCs, each team targeting a different vulnerability on the CSCs, including teams at Stanford, and at University of California campuses in San Diego and Los Angeles.

Sleep inducing hormone puts breast cancer cells to rest  

It’s pretty easy to connect the dots between a lack of sleep and an increased risk of a deadly car crash. But what about an increased risk of cancer? A 2012 study of 101 women newly diagnosed with breast cancer found that those with inadequate sleep were more likely to have more aggressive tumors. Though the results of this survey were statistically significant, the biological connection between sleep and breast cancer is not well understood.

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Melatonin, the sleep hormone, may help fight cancer. Image Credit

Now, a report in Genes and Cancer by a Michigan State University research team shows that the interplay between melatonin, a hormone involved in sleep-wake cycles, and breast cancer stem cells may provide an explanation. And, more importantly, the study points to melatonin’s potential use as a cancer therapeutic.

Mammospheres: cancer in a more natural environment
To carry out their lab experiments, the researchers grew breast cancer cells into three-dimensional aggregates, called mammospheres, that resemble the tumor cell composition seen in an actual tumor in the body. This cell mix includes breast cancer stem cells which are thought to drive the uncontrolled tumor growth and reccurrence. David Arnosti, a MSU professor and co-author on the study, used a helpful analogy in a university press release to explain the importance of using the mammosphere technique:

“You can watch bears in the zoo, but you only understand bear behavior by seeing them in the wild. Similarly, understanding the expression of genes in their natural environment reveals how they interact in disease settings. That’s what is so special about this work.”

 

Melatonin fighting cancer cells via their stem cell-like properties
The cancer cells used in this study are also categorized as so-called estrogen receptor (ER) -positive cells. This classification means that the cancer growth is largely stimulated by the hormone estrogen.  The first round of experiments analyzed melatonin’s effects on estrogen’s ability to increase the growth and size of the mammospheres. The team also tested Bisphenol A (BPA), a chemical used in the plastics industry that mimics estrogen’s effects. While estrogen or BPA alone caused a large increase in mammosphere size and number, addition of melatonin stunted these effects.

Next, the team went deeper and looked at melatonin’s impact from a genes and proteins perspective. Estrogen is a steroid hormone that acts by passing through the cell wall and binding to the estrogen receptor inside the cell. Once bound by estrogen, the receptor travels to a cell’s nucleus and binds particular regions of DNA which can activate genes. One of those activated genes is responsible for producing OCT4, a protein that plays a critical role in a stem cell’s ability to indefinitely makes copies of itself and to maintain its unspecialized, stem cell state. This cellular pathway is how estrogen helps drives the growth of ER-positive breast cancer cells. The researchers showed that estrogen- and BPA-stimulated binding of the estrogen receptor to the OCT4 gene in the mammospheres was inhibited when melatonin was added to the cells.

Melatonin: putting cancer stems to bed?
Putting these observations together, melatonin appears to suppress breast tumor growth by directing inhibiting genes responsible for driving the stem cell-like properties of the breast cancer stem cells within the mammosphere. Melatonin is produced by the brain’s pineal gland which is only active at night. Once released, melatonin helps induce sleep. So a disrupted sleep pattern, like insomnia, would reduce melatonin levels and as a consequence the block on estrogen driven cancer growth is removed. ­

James Trosko, whose MSU lab perfected the mammosphere technique, sees these breast cancer results in a larger perspective:

“This work establishes the principal by which cancer stem cell growth may be regulated by natural hormones, and provides an important new technique to screen chemicals for cancer-promoting effects, as well as identify potential new drugs for use in the clinic.”

 

Keep in mind that these are very preliminary studies and more work is needed before a potential clinical application sees the light of day. In the meantime, have a good day and get a good night’s sleep.

 

 

Stem cell stories that caught our eye: screening for cancer drugs for kids, better CRISPR gene editing and funding for chimeras

Here are some stem cell stories that caught our eye this past week. Some are groundbreaking science, others are of personal interest to us, and still others are just fun.

Stem cells screen drugs for kids’ rare tumor.  A team at Johns Hopkins University in Baltimore has transformed stem cells into a particularly nasty form of pediatric brain cancer, medulloblastoma. They then used those cells to figure out what drugs might defeat the tumor and found one existing drug, approved for advanced breast cancer, that seemed to be a good candidate.

While about two-thirds of medulloblastoma patients do well with standard therapy, those in a class called “group 3” often do not survive. But the rarity of that condition, meant the researcher could not use what has become a common route to determining effective drugs: comparing the genetic profile of the cancer with the genetic profile of banks of cancer cells that have already have been tested against existing cancer drugs. There are not enough Group 3 samples in the banks to take that route.

So, the Hopkins team used a two-step process for the drug search. They first inserted genes associated with the Group 3 cancers into stem cells and let the cells begin to transform into tumors. After making sure their stem cell tumors genetically looked and behaved like medulloblastoma the researchers compared genetic “signatures” from those cells with the signatures of cells in the large databases of other cancers.

eric raabe hopkins

Raabe

“We wanted to find whether the cells we created matched any of these existing signatures, because if they did, then we would have some idea of what kinds of drugs are more or most likely to kill these cells,” said Eric Raabe in a university release posted by ScienceDaily. “We didn’t have to do the laborious screening to test 100,000 compounds against our own cells.”

Raabe suggested this system might work to create a short cut to finding best therapies for other rare tumors as well.

 

Combining tricks from two critters.  This article does not address stem cells directly, but rather a widely popular gene editing technique many hope to use with stem cell therapies, the system known as CRISPR.  But before that can happen, researchers need to figure out how to eliminate or minimize pesky “off-target” gene editing, when the genetic scissor slices the DNA in a spot that was not intended.

CRISPR technology borrows from bacteria. About 40 percent of bacteria immune systems use CRISPR’s genetic elements to recognize foreign genes such as phages, the viruses that can kill or tag along in bacteria. Scientists generally pair CRISPR’s ability to recognize specific gene segments, with great specificity, with the nuclease, or genetic scissor, called CAS9. But that scissor is not quite as precise. So, a team at Kobe University in Japan borrowed an immune system trick from a second critter, a sea lamprey, sometimes incorrectly called an eel. The result was a much more precise gene editing tool.

Lamprey

The lamprey gene editing tool they borrowed is based on an enzyme called a deaminase. The lamprey uses the enzyme to create breaks in the genes for its immune system’s antibodies in order to have a more diverse immune system able to recognize more outside pathogens. That deaminase tool turns out to go a long way toward making CRISPR precise enough to be considered for use in a therapy.

The Japanese work published in the journal Science, marks the second time researchers have recently published a way to use a deaminase tool to improve CRISPR. The prior work came from the lab of Harvard’s George Church, who is quoted extensively in an article about the latest study in The Scientist. Be warned, Church likes detail and this is a pretty technical article unless you are a science nerd like us at The Stem Cellar.

 

Animals with bits of human get green light.  A flurry of stories came out a few months ago when a reporter realized that while the National Institutes of Health (NIH) had a moratorium on creating chimeras—animal embryos that are partly human—CIRM was still funding the work. Now, NIH has announced plans to lift that moratorium with several safeguards in place to make sure certain projects that raise ethical issues don’t get approved. We are glad to have company in funding this potentially life-saving research.

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Researchers working in the area have two main goals. They want to create better models of human disease, and they want to grow human organs in animals such as pigs to alleviate the current shortage of donor organs and help the thousands of patients who die each year waiting for a donor.

NPR aired a story that did a good job describing the safeguards and the types of projects that would not be allowed. It quoted Carrie Wolinetz, the NIH associate director for science policy:

 “At the end of the day, we want to make sure this research progresses because it’s very important to our understanding of disease. It’s important to our mission to improve human health. But we also want to make sure there’s an extra set of eyes on these projects because they do have this ethical set of concerns associated with them.”

Forbes posted a story online that took great liberty with comparisons to science fiction, but had fun with it and in the end valued the potential for the work. And the public does have a chance to weigh in on the ethical issues as NIH has published a call for comments in the Federal Register.

T cell fate and future immunotherapies rely on a tag team of genetic switches

Imagine if scientists could build microscopic smart missiles that specifically seek out and destroy deadly, hard-to-treat cancer cells in a patient’s body? Well, you don’t have to imagine it actually. With techniques such as chimeric antigen receptor (CAR) T therapy, a patient’s own T cells – immune system cells that fight off viruses and cancer cells – can be genetically modified to produce customized cell surface proteins to recognize and kill the specific cancer cells eluding the patient’s natural defenses. It is one of the most exciting and promising techniques currently in development for the treatment of cancer.

Human T Cell (Wikipedia)

Human T Cell (Wikipedia)

Although there have been several clinical trial success stories, it’s still early days for engineered T cell immunotherapies and much more work is needed to fine tune the approach as well as overcome potential dangerous side effects. Taking a step back and gaining a deeper understanding of how stem cells specialize into T cells in the first place could go a long way into increasing the efficiency and precision of this therapeutic strategy.

Enter the CIRM-funded work of Hao Yuan Kueh and others in Ellen Rothenberg’s lab at CalTech. Reporting yesterday in Nature Immunology, the Rothenberg team uncovered a time dependent array of genetic switches – some with an ON/OFF function, others with “volume” control – that together control the commitment of stem cells to become T cells.

Previous studies have shown that the protein encoded by the Bcl11b gene is the key master switch that when activated sets a “no going back” path toward a T cell fate. A group of other genes, including Runx1, TCF-1 and GATA-3 are known to play a role in activating Bcl11b. The dominant school of thought is that these proteins gradually accumulate at the Bcl11b gene and once a threshold level is achieved, the proteins combine to enable the Bcl11b activation switch to flip on. However, other studies suggest that some of these proteins may act as “pioneer” factors that loosen up the DNA structure and allow the other proteins to readily access and turn on the Bcl11b gene. Figuring out which mechanism is at play is critical to precisely manipulating T cell development through genetic engineering.

To tease out the answer, the CalTech team engineered mice such that cells with activated Bcl11b would glow which allows visualizing the fate of single cells. We reached out to Dr. Kueh on the rationale for this experimental approach:

Hao Yuan Kueh, CalTech

Hao Yuan Kueh, CalTech

“To fully understand how genes are controlled, we need to watch them turn on and off in single, living cells over time.  As cells in our body are unique and different from one another, standard measurement methods, which average over millions of cells, often do not tell us the entire picture.”

The team examined the impact of inhibiting the T cell specific proteins GATA-3 and TCF-1 at different stages in T cell development in single cells. When the production of these two proteins were blocked in very early T cell progenitor (ETPs) cells, activation of Bcl11b was dramatically reduced. But that’s not what they observed when the experiment was repeated in a later stage of T cell development. In this case, blocking GATA-3 and TCF-1 had a much weaker impact on Bcl11b. So GATA-3 and TCF-1 are important for turning on Bcl11b early in T cell development but are not necessary for maintaining Bcl11b activation at later stages.

Inhibition of Runx1, on the other hand, did lead to a reduction in Bcl11b in these later T cell development stages. Making Runx1 levels artificially high conversely led to elevated Bcl11b in these cells.

Together, these results point to GATA-3 and TCF-1 as the key factors for turning on Bcl11b to commit cells to a T cell fate and then they hand off their duties to Runx1 to keep Bcl11b on and maintaining the T cell identity. Dr. Kuhn sums up the results and their implications this way:

“Our work shows that control of gene expression is very much a team effort, where some proteins flip the gene’s master ON-OFF switch, and others set its expression levels after it turns on…These results will help us generate customized T-cells to fight cancer and other diseases.  As T-cells are specialized to recognize and fight foreign agents in our body, this therapy strategy holds much promise for diseases that are difficult to treat with standard drug-based methods.  Also, these intricate gene regulation mechanisms are likely to be in play in other cell types in our body, not just T-cells, and so we believe our results will be widely relevant.”

Circular RNAs: the Mind-Boggling Dark Matter of the Human Genome

We were just a few hours into the 2016 annual meeting of the International Society for Stem Cell Research (ISSCR) yesterday afternoon and my mind was already blown away. Pier Paolo Pandolfi of the Beth Israel Deaconess Medical Center at Harvard, spoke during the first plenary session about circular RNAs, which he dubbed, “the mind-boggling dark matter of the human genome” because their existence wasn’t confirmed until just four years ago.

To introduce the topic, Pandolfi compared human DNA to that of bacteria. Both species contain stretches of DNA sequence called genes that contain the instructions for making proteins which collectively form our bodies. Each gene is first transcribed into messenger RNA (mRNA) which in turn is translated into a protein.

Iceberg

Our DNA contains 20,000 genes. But that genetic material is just the tip of the iceberg.

But with the ability to sequence all the mRNA transcripts of an organism, or its transcriptome, came a startling fact about how differently our genetic structure is organized compared to bacteria. It turns out that 88% of DNA sequence in bacteria make up genes that code for proteins but only 2% of human DNA sequence directly codes for proteins. So what’s going with the other 98%? Scientist typically call this 98% chunk of the genome “regulatory DNA” because it contains sequences that act as control switches for turning genes on or off. But Pandolfi explained that more recent studies suggest that a whopping 70% of our genome (maybe even 95%) is transcribed into RNA but those RNA molecules just don’t get translated into protein.

 

One type of this “non-coding” RNA which we’ve blogged about plenty of times is called microRNA (miRNA). So far, about 5,000 human miRNAs have been identified compared to the 20,000 messenger RNAs that code for proteins. But by far the most abundant non-coding RNA in our transcriptome is the mysterious circular RNA (circRNA) with at least 100,000 different transcripts. circRNA was first observed as cellular structures in the 1980’s via electronic microscope images. Then in the 1990’s a scientist published DNA sequencing data suggesting the existence of circRNA. But the science community at that time panned the results, discrediting it as merely background noise of the experiments.

Pandolfi_2

Pier Paolo Pandolfi
Image: Beth Israel Deaconess Medical Center

But four years ago, the circRNAs were directly sequenced and their existence confirmed. The circRNAs are formed when messenger RNA goes through a well-described trimming process of its sequence. Some of the excised pieces of RNA form into the circular RNAs. It would seem that these circRNAs are just throw away debris but Pandolfi’s lab has found evidence that they directly play a role in cellular functions and even cancer.

His team studies a gene called Pokemon which, when genetically “knocked out” or removed from a mouse’s genome, leads to cancer. Now, it turns out this knockout not only removes the Pokemon protein but also a Pokemon circRNA (circPok). When the lab added back just the Pokemon gene, as you might expect, it acted to suppress cancer in the mice. But when just the circPok was added back, stunningly, it increased the formation of cancer in the mice. Given that genetic knockouts are one of the most pervasive techniques in biomedical science, a closer look at circRNAs that may have been overlooked in all of those results is clearly warranted.

Though this finding is somewhat scary in the fact that it’s a whole aspect of our genome that we’ve been unaware of, one fortunate aspect of circRNA is that they all carry a particular sequence which could be used as a target for a new class of drugs.

This data may extend to stem cells as well. We know that microRNAs have critical roles in regulating the maturation of stem cells into specialized cell types. Since circRNAs are thought to act by competing microRNA, it may not be long before we learn about circRNA’s role in stem cell function.

The other speakers at the first plenary session of the ISSCR annual meeting all gave high caliber talks. Luckily, Paul Knoepfler live blogged on two of those presentations. Here are the links:

 

Multi-Talented Stem Cells: The Many Ways to Use Them in the Clinic

CIRM kicked off the 2016 International Society for Stem Cell Research (ISSCR) Conference in San Francisco with a public stem cell event yesterday that brought scientists, patients, patient advocates and members of the general public together to discuss the many ways stem cells are being used in the clinic to develop treatments for patients with unmet medical needs.

Bruce Conklin, Gladstone Institutes & UCSF

Bruce Conklin, Gladstone Institutes & UCSF

Bruce Conklin, an Investigator at the Gladstone Institutes and UCSF Professor, moderated the panel of four scientists and three patient advocates. He immediately captured the audience’s attention by showing a stunning video of human heart cells, beating in synchrony in a petri dish. Conklin explained that scientists now have the skills and technology to generate human stem cell models of cardiomyopathy (heart disease) and many other diseases in a dish.

Conklin went on to highlight four main ways that stem cells are contributing to human therapy. First is using stem cells to model diseases whose causes are still largely unknown (like with Parkinson’s disease). Second, genome editing of stem cells is a new technology that has the potential to offer cures to patients with genetic disorders like sickle cell anemia. Third, stem cells are known to secrete healing factors, and transplanting them into humans could be beneficial. Lastly, stem cells can be engineered to attack cancer cells and overcome cancer’s normal way of evading the immune system.

Before introducing the other panelists, Conklin made the final point that stem cell models are powerful because scientists can use them to screen and develop new drugs for diseases that have no treatments or cures. His lab is already working on identifying new drugs for heart disease using human induced pluripotent stem cells derived from patients with cardiomyopathy.

Scientists and Patient Advocates Speak Out

Malin Parmar, Lund University

Malin Parmar, Lund University

The first scientist to speak was Malin Parmar, a Professor at Lund University. She discussed the history of stem cell development for clinical trials in Parkinson’s disease (PD). Her team is launching the first in-human trial for Parkinson’s using cells derived from human pluripotent stem cells in 2016. After Parmar’s talk, John Lipp, a PD patient advocate. He explained that while he might look normal standing in front of the crowd, his PD symptoms vary wildly throughout the day and make it hard for him to live a normal life. He believes in the work that scientists like Parmar are doing and confidently said, “In my lifetime, we will find a stem cell cure for Parkinson’s disease.”

Adrienne Shapiro, Patient Advocate

Adrienne Shapiro, Patient Advocate

The next scientist to speak was UCLA Professor Donald Kohn. He discussed his lab’s latest efforts to develop stem cell treatments for different blood disorder diseases. His team is using gene therapy to modify blood stem cells in bone marrow to treat and cure babies with SCID, also known as “bubble-boy disease”. Kohn also mentioned their work in sickle cell disease (SCD) and in chronic granulomatous disease, both of which are now in CIRM-funded clinical trials. He was followed by Adrienne Shapiro, a patient advocate and mother of a child with SCD. Adrienne gave a passionate and moving speech about her family history of SCD and her battle to help find a cure for her daughter. She said “nobody plans to be a patient advocate. It is a calling born of necessity and pain. I just wanted my daughter to outlive me.”

Henry Klassen (UC Irvine)

Henry Klassen, UC Irvine

Henry Klassen, a professor at UC Irvine, next spoke about blinding eye diseases, specifically retinitis pigmentosa (RP). This disease damages the photo receptors in the back of the eye and eventually causes blindness. There is no cure for RP, but Klassen and his team are testing the safety of transplanting human retinal progenitor cells in to the eyes of RP patients in a CIRM-funded Phase 1/2 clinical trial.

Kristen MacDonald, RP patient

Kristen MacDonald, RP patient

RP patient, Kristen MacDonald, was the trial’s first patient to be treated. She bravely spoke about her experience with losing her vision. She didn’t realize she was going blind until she had a series of accidents that left her with two broken arms. She had to reinvent herself both physically and emotionally, but now has hope that she might see again after participating in this clinical trial. She said that after the transplant she can now finally see light in her bad eye and her hope is that in her lifetime she can say, “One day, people used to go blind.”

Lastly, Catriona Jamieson, a professor and Alpha Stem Cell Clinic director at UCSD, discussed how she is trying to develop new treatments for blood cancers by eradicating cancer stem cells. Her team is conducting a Phase 1 CIRM-funded clinical trial that’s testing the safety of an antibody drug called Cirmtuzumab in patients with chronic lymphocytic leukemia (CLL).

Scientists and Patients need to work together

Don Kohn, Catriona Jamieson, Malin Parmar

Don Kohn, Catriona Jamieson, Malin Parmar

At the end of the night, the scientists and patient advocates took the stage to answer questions from the audience. A patient advocate in the audience asked, “How can we help scientists develop treatments for patients more quickly?”

The scientists responded that stem cell research needs more funding and that agencies like CIRM are making this possible. However, we need to keep the momentum going and to do that both the physicians, scientists and patient advocates need to work together to advocate for more support. The patient advocates in the panel couldn’t have agreed more and voiced their enthusiasm for working together with scientists and clinicians to make their hopes for cures a reality.

The CIRM public event was a huge success and brought in more than 150 people, many of whom stayed after the event to ask the panelists more questions. It was a great kick off for the ISSCR conference, which starts today. For coverage, you can follow the Stem Cellar Blog for updates on interesting stem cell stories that catch our eye.

CIRM Public Stem Cell Event

CIRM Public Stem Cell Event