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Cancer, Research, Science, Stanford News, Stem Cells

A stem cell “kill switch” may make therapies safer, say Stanford researchers

A stem cell "kill switch" may make therapies safer, say Stanford researchers

3225255407_596aa5bdff_zStem cell biologist Hiromitsu Nakauchi, MD, PhD, and his colleagues published an interesting article today about how to use stem cell technology to boost our body’s own immune cells to fight cancer or chronic viral infections like HIV or Epstein Barr virus. Because there’s a possible cancer risk with the use of induced pluripotent stem cells, or iPS cells, in humans, he and his colleagues have devised an innovative way to specifically eliminate these cells within the body if they start to cause problems. Their research appears today in Stem Cell Reports.

As Nakauchi explained to me in an email:

The discovery of induced pluripotent stem cells created promising new avenues for therapies. However, the tumorigenic potential of undifferentiated iPSCs is a major safety concern that must be addressed before iPS cell-based therapies can be routinely used in the clinic.

The researchers studied a type of immune cell called a cytotoxic T cell. These cells recognize specific sequences, or antigens, on the surface of other cells. Some antigens indicate that the cell is infected with a virus; others are found on cells that have become cancerous. When a cytotoxic T cells sees these antigens, it moves in to kill the cell and remove the threat.

In order to ensure that our immune systems recognize the widest variety of antigens, developing T cells randomly shuffle their genes to create unique antigen receptors. Researchers have found that it’s possible to identify, and isolate, T cell populations that specifically recognize cancer cells. By growing those cells in the laboratory, and then injecting them back into a patient, clinicians can give a boost to the immune response that can help kill tumor cells. The technique is known as adoptive immunotherapy, and it’s shown promise in treating melanoma. However, these cytotoxic T cells can become exhausted as they fight the cancer and become less effective over time.

Recently researchers in Nakauchi’s lab showed that it’s possible to create induced pluripotent stem cells from cytotoxic T cells. These iPS cells are then induced to again become cytotoxic T cells. These rejuvenated T cells, or rejT cells, recognize the same antigen they did before their brief dip in the pluripotency pool, but they are far more sprightly than the cells from which they were derived – they can divide many more times and have longer telomeres (an indicator of youthfulness).

So far, so good. But, as Nakauchi mentioned above, iPS cells carry their own set of risks. Because they are by definition pluripotent (they can become any cell in the body), they can easily grow out of control. In fact, one way of proving a cell’s pluripotency is to inject it into an animal and see if it forms a type of tumor called a teratoma, which is made up of multiple cell types.

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Cancer, Research, Science, Stanford News, Stem Cells

Liver stem cell identified in mice

Liver stem cell identified in mice

Image of liver stem cellsAn elusive quarry has finally been chased to ground. Or, more accurately, to the central vein of one of our most important organs: the liver. Developmental biologist Roel Nusse, PhD, and visiting scholar and gastroenterologist Bruce Wang, MD, announced the identification of the liver stem cell in mice today in Nature. The finding will help researchers better understand liver biology and disease. It may also aid in the decades-long quest to find a reliable and efficient way to grow liver cells, called hepatocytes, in the laboratory for study and to test the effect of drugs.

Until now, researchers had assumed that all hepatocytes were created equal. And none of them seemed to have stem-cell-like traits. As Nusse described in our release:

There’s always been a question as to how the liver replaces dying hepatocytes. Most other tissues have a dedicated population of cells that can divide to make a copy of themselves, which we call self-renewal, and can also give rise to the more-specialized cells that make up that tissue. But there never was any evidence for a stem cell in the liver.

Wang and Nusse took a different approach. They looked in the liver to see which cells, if any, were expressing a gene called Axin2. Axin2 is expressed when a cell encounters a member of the Wnt protein family. Years of previous work in the Nusse lab have shown that Wnt family members are critical regulators of embryonic development and stem cell maintenance.

They found a small population of Axin2-expressing hepatocytes with just two copies of each chromosome surrounding the central vein of the liver. These cells can both self-renew and divide to create new hepatocytes that migrate outward from the vein. As they migrate, these cells become polyploid and begin to express hepatocyte-specific genes. Eventually much of the animals’ livers were made up of these stem-cell descendents. As Wang described:

People in the field have always thought of hepatocytes as a single cell type. And yet the cell we identified is clearly different from others in the liver. Maybe we should accept that there may be several subtypes of hepatocytes, potentially with different functions.

If this result in mice is also found to be true in humans, it’s possible that the liver stem cells may be easier to grow in the laboratory that normal hepatocytes. This would enable researchers to test the effect of drugs under development on human liver cells before they are tested in people (my colleague Bruce Goldman wrote about another potential solution to this problem last year). As Wang explained:

The most common reason that promising new drugs for any type of condition fail is that they are found to be toxic to liver. Researchers have been trying for decades to find a way to maintain hepatocytes in the laboratory on which to test the effects of potential medications before trying them in humans. Perhaps we haven’t been culturing the right subtype. These stem cells might be more likely to fare well in culture.

The finding opens the doors to answering other important questions as well, said Wang: “Does liver cancer arise from a specific subtype of cells? This model also gives us a way to understand how chromosome number is controlled. Does the presence of the Wnt proteins keep the stem cells in a diploid state? These are fundamental biological questions we can now begin to address.”

Previously: Which way is up? Stem cells take cues from localized signals, say Stanford scientists and The best toxicology lab: a mouse with a human liver
Photo of liver stem cells (red) and their progeny (green) by Bruce Wang

Genetics, In the News, Research, Science, Stanford News, Stem Cells, Technology

CRISPR marches forward: Stanford scientists optimize use in human blood cells

CRISPR marches forward: Stanford scientists optimize use in human blood cells

The CRISPR news just keeps coming. As we’ve described here before, CRISPR is a breakthrough way of editing the genome of many organisms, including humans — a kind of biological cut-and-paste function that is already transforming scientific and clinical research. However, there are still some significant scientific hurdles that exist when attempting to use the technique in cells directly isolated from human patients (these are called primary cells) rather than human cell lines grown for long periods of time in the laboratory setting.

Now pediatric stem cell biologist Matthew Porteus, MD, PhD, and postdoctoral scholars Ayal Hendel, PhD, and Rasmus Bak, PhD, have collaborated with researchers at Santa Clara-based Agilent Research Laboratories to show that chemically modifying the guide RNAs tasked with directing the site of genome snipping significantly enhances the efficiency of editing in human primary blood cells — an advance that brings therapies for human patients closer. The research was published yesterday in Nature Biotechnology.

As Porteus, who hopes to one day use the technique to help children with genetic blood diseases like sickle cell anemia, explained to me in an email:

We have now achieved the highest rates of editing in primary human blood cells. These frequencies are now high enough to compete with the other genome editing platforms for therapeutic editing in these cell types.

Porteus and Hendel previously developed a way to identify how frequently the CRISPR system does (or does not) modify the DNA where scientists tell it. Hendel characterizes the new research as something that will allow industrial-scale manufacturing of pharmaceutical-grade CRISPR reagents. As he told me:

Our research shows that scientists can now modify the CRISPR technology to improve its activity and specificity, as well as to open new doors for its use it for imaging, biochemistry, epigenetic, and gene activation or repression studies.

Rasmus agrees, saying, “Our findings will not only benefit researchers working with primary cells, but it will also accelerate the translation of CRISPR gene editing into new therapies for patients.”

Onward!

(Those of you wanting a thorough primer on CRISPR —how it works and what could be done with it — should check out Carl Zimmer’s comprehensive article in Quanta magazine. If you prefer to learn by listening (perhaps, as I sometimes do, while on the treadmill), I found this podcast from Radiolab light, but interesting.)

Previously: Policing the editor: Stanford scientists devise way to monitor CRISPR effectiveness and “It’s not just science fiction anymore”: Childx speakers talk stem cell and gene therapy

 

Applied Biotechnology, In the News, Research, Stem Cells, Transplants

“Supplying each cell with a scuba tank”: New advances in tissue engineering

"Supplying each cell with a scuba tank": New advances in tissue engineering

membrane-article.jpgResearchers in the U.K. have found a way to make growing synthetic tissue more sustainable. At present, the size of engineered tissues is limited because the cells die from lack of oxygen when the pieces get too big. By adding an oxygen-carrying protein to the stem cells prior to combining them with tissue scaffolding, the researchers overcame this problem.

The study, led by Adam Perriman, PhD, research fellow at the University of Bristol’s Synthetic Biology Research Centre, and Anthony Hollander, PhD, professor of integrative biology at the University of Liverpool, was published yesterday in Nature Communications. The tissue they were fabricating was cartilage, but the process could potentially be applied to other tissues, as well.

Perriman describes the findings in a press release:

We were surprised and delighted to discover that we could deliver the necessary quantity [of oxygen] to the cells to supplement their oxygen requirements. It’s like supplying each cell with its own scuba tank, which it can use to breathe from when there is not enough oxygen in the local environment.

Hollander also comments on the significance of the research:

We have already shown that stem cells can help create parts of the body that can be successfully transplanted into patients, but we have now found a way of making their success even better. Growing large organs remains a huge challenge but with this technology we have overcome one of the major hurdles.

Creating larger pieces of cartilage gives us a possible way of repairing some of the worst damage to human joint tissue, such as the debilitating changes seen in hip or knee osteoarthritis or the severe injuries caused by major trauma, for example in road traffic accidents or war injuries.

Previously: Building bodies, one organ at a time, How Stanford researchers are engineering materials that mimic those found in our own bodies and A brief look at “caring” for engineered tissue
Photo by Warwick Bromley

Autism, Mental Health, Neuroscience, Research, Science, Stanford News, Stem Cells

Brain cell spheres in a lab dish mimic human cortex, Stanford study says

Brain cell spheres in a lab dish mimic human cortex, Stanford study says

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Mental disorders like autism and schizophrenia are notoriously difficult to study at the molecular level. Understandably, people are reluctant to donate pieces of living brain for study, and postmortem tissue lets researchers see the structure, but not the function, of the cells.

Now researchers in the laboratories of psychiatrist Sergiu Pasca, MD, and neurobiologist Ben Barres, MD, PhD, have found a way to make balls of cells that mimic the activity of the human cortex. They use a person’s skin cells, so the resulting “human cortical spheroid” has the same genetic composition as the donor. The research was published in Nature Methods yesterday.

According to our release:

Previous attempts to create patient-specific neural tissue for study have either generated two-dimensional colonies of immature neurons that do not create functional synapses, or required an external matrix on which to grow the cells in a series of laborious and technically difficult steps.

In contrast, the researchers found they were able to easily make hundreds of what they’ve termed “human cortical spheroids” using a single human skin sample. These spheroids grow to be as large as 5 millimeters in diameter and can be maintained in the laboratory for nine months or more. They exhibit complex neural network activity and can be studied with techniques well-honed in animal models.

The researchers, which include neonatology fellow Anca Pasca, MD, and graduate student Steven Sloan, hope to use the technique to help understand how the human brain develops, and what sometimes goes wrong. As described by Barres:

The power and promise of this new method is extraordinary. For instance, for developmental brain disorders, one could take skin cells from any patient and literally replay the development of their brain in a culture dish to figure out exactly what step of development went awry — and how it might be corrected.

The research is starting to garner attention, including this nice article from Wired yesterday. Pasca’s eager to note, however, that he’s not working to create entire brains, which would be ethically and technically challenging, to say the least. But simply generating even a few of the cell types in the cortex will give researchers a much larger canvas with which to study some devastating conditions. As Pasca notes in our release:

I am a physician by training. We are often very limited in the therapeutic options we can offer patients with mental disorders. The ability to investigate in a dish neuronal and glial function, as well as network activity, starting from patient’s own cells, has the potential to bring novel insights into psychiatric disorders and their treatment.

Previously: More than just glue, glial cells challenge neuron’s top slot and Star-shaped cells nab new starring role in sculpting brain circuits
Photo of spheroid cross-section by Anca Pasca

Pediatrics, Research, Stanford News, Stem Cells

Near approval: A stem cell gene therapy developed by Stanford researcher

Near approval: A stem cell gene therapy developed by Stanford researcher

It has been a momentous month for Stanford researcher Maria Grazia Roncarolo, MD. Following decades of research in Roncarolo’s lab and the clinic, pharmaceutical company Glaxo SmithKline has applied for final approval by European Medicines Agency (EMA) of a treatment she developed to cure a deadly childhood immune disorder. If approved by the EMA, which is Europe’s equivalent of the U.S. Food and Drug Administration (FDA), the treatment would be the first gene stem cell therapy to be granted approval by a major medical regulatory agency.

The therapy cures a disease called severe combined immune deficiency (SCID), sometimes called the “bubble boy disease,” by inserting a gene into blood stem cells and transplanting the stem cells into the patient’s body. The treatment is still being evaluated by the FDA.

My greatest satisfaction is that kids who were once incurable now have options

If approved, the treatment will no longer be considered an experimental therapy in Europe, and “people will be able to get this treatment as they would any other, and will be able to get their insurance company to pay for it,” Roncarolo told me. The final regulatory review marks the beginning of a new era in which genetically modified stem cells might be used to treat or cure a wide variety of human diseases, she also noted.

Roncarolo developed the treatment while she was scientific director at the San Raffaele Scientific Institute in Milan, Italy. There, she treated kids who were born with an inability to make the enzyme adenosine deaminase (ADA), which leaves them unable to make certain immune cells that protect them from infection. For that reason, children with ADA-SCID are forced to spend their lives in a sterile environment that protects them from infections that most people would easily fight off but are deadly for them.

Roncarolo and her team inserted the gene for ADA into blood stem cells which were transplanted into 18 children with the disease. Once the modified blood stem cells could produce the enzyme, they were able to form the necessary immune cells and the children were able to leave their sterile environment. “Those children have been effectively cured,” Roncarolo said.

Other gene therapies have been developed before, but those therapies modified more mature cells that cannot reproduce themselves. Only stem cells can both make more copies of themselves and also produce more specialized cells. If gene therapy is used to modify cells that are not stem cells, the treatment will only last as long as the cells last. Eventually, mature cells age and die, and the disorder returns.

Last year, Roncarolo was recruited to Stanford to continue her work while serving as co-director of the Institute for Stem Cell Biology and Regenerative Medicine. She is busy researching cures for other congenital immune disorders and developing methods that could lead to stem cell treatments for a wide variety of other diseases.

“My greatest satisfaction is that kids who were once incurable now have options,” Roncarolo said.

Previously: Countdown to Childx: Stanford expert highlights future of stem cell and gene therapies

Bioengineering, Imaging, Neuroscience, Research, Stanford News, Stem Cells

New way to watch what stem cells transplanted into the brain do once they get there

New way to watch what stem cells transplanted into the brain do once they get there

binocularsStem cell replacement therapy is a promising but problem-plagued medical intervention.

In a recent news release detailing a possible way forward, I wrote:

Many brain disorders, such as Parkinson’s disease, are characterized by defective nerve cells in specific brain regions. This makes disorders such as Parkinson’s excellent candidates for stem cell therapies, in which the defective nerve cells are replaced. But the experiments in which such procedures have been attempted have met with mixed results, and those conducting the experiments are hard put to explain them.

That’s because there’s been no good way to evaluate what those transplanted stems cells are doing once you’ve put them inside a living individual. I mean, you’re not gonna break into someone’s brain every couple of days to take a peek, right? Instead, you have to look for behavioral changes. Is the patient or experimental animal walking better (if you’re trying to treat Parkinson’s), or (if it’s Alzheimer’s) remembering better ? Then, even when you see those changes, you still don’t know whether new nerve cells derived from the newly transplanted cells integrated into the proper brain circuits and are now functioning correctly there, or whether the originally transplanted cells are just sitting around secreting some kind of feel-good factor to pep up ailing cells in the vicinity, juicing their  performance. Or maybe it was a placebo effect.

It’s hard to improve on a procedure when you don’t really know what went wrong – or even what went right – on the last attempt. Optimizing the regimen becomes a matter of guesswork and luck.

But in a new study in NeuroImage, neuroscientist/bioengineer Jin Hyung Lee, PhD, and her colleagues came up with a way to peer deep into the living brain and view the results of a stem-cell transplant procedure. They combined an established brain-imaging technique with a newer but increasingly widespread one, called optogenetics, that lets researchers stimulate specific cells.

The first step in optogenetics is to genetically modify the cells you want to stimulate, so that their surfaces become coated by a photosensitive protein that generates electric current in response to laser light. Lee’s team performed this operation on the stem cells before transplanting them into rats’ brains. This way, they could selectively stimulate nerve cells derived from those stem cells and,  using the brain-imaging technique, see if doing so triggered nerve-cell activity at the site of the transplant as well as other places in the brain with which the new cells had established connections.

In these experiments, the stem-cell-derived nerve cells survived, matured into nerve cells, integrated into targeted brain circuits and, most important, fired on cue and ignited activity in downstream nerve circuits. But had all that not happened, at least the researchers would have been able to pinpoint the weak link in the chain.

In principle, the new approach should be possible to use for all kinds of stem-cell therapies, and in humans as well as animals. As Lee told me when I interviewed her for my release on her new study, “If we can watch the new cells’ behaviors for weeks and months after we’ve transplanted them, we can learn – much more quickly and in a guided way rather than a trial-and-error fashion – what kind of cells to put in, exactly where to put them, and how.”

If this light-driven stem-cell-monitoring technique or some others I’ve reported on hold up, brave explorers may no longer have to poke around in the dark.

Previously: Alchemy: From liposuction fluid to new liver cells, Iron-supplement-slurping stem cells can be transplanted, then tracked to make sure they’re making new knees, You’ve got a lot of nerve! Industrial-scale procedure for generating plenty of personalized nerve cells and Nano-hitchhikers ride stem cells into heart, let researchers watch in real time and weeks later
Photo by Nicki Dugan Pogue

AHCJ15, Science, Science Policy, Stem Cells

Stanford stem cell experts highlight “inherent flaw” in drug development system

Stanford stem cell experts highlight "inherent flaw" in drug development system

Academic institutions are in a much better position than pharmaceutical companies to make the best decisions about which therapies deserve further development. That was the underlying message from a pair of Stanford researchers at a panel on stem cell science at last weekend’s Association of Health Care Journalism 2015 conference.

“There’s an inherent flaw in our system,” said Irving Weissman, MD, director of the Stanford Institute for Stem Cell Biology and Regenerative Medicine. “Companies are driven by the desire for profits rather than the desire to find the best therapy, and they often give up on discoveries too early.”

Weissman cited studies that were done long ago at Stanford and proven in mouse models or human clinical trials that pharmaceutical companies have failed to develop. “In mice, transplantation of purified blood stem cell and insulin producing cells from closely related mice leads to a permanent cure,” Weissman says. “We discovered that 16 years ago, and a therapy is still not available.”

A therapy involving high-dose chemotherapy followed by purified stem cell transplant for stage 4 breast cancer cured a relatively high number of women in a small trial almost 20 years ago but the pharmaceutical company with the rights to the technology decided not to develop the treatment, Weissman says. A larger trial of this therapy is currently being planned at Stanford.

Maria Grazia Roncarolo, MD, co-director of the institute, spoke about her own experience in an academic environment developing therapies for diseases that pharmaceutical companies deem to rare to merit their attention. Only after she showed that a therapy for severe combined immune deficiency could work did pharmaceutical companies get interested.

“Academic researchers should have the ability to test a therapy, to have control of the design and execution of the clinical trials, and pharmaceutical companies should do the production and marketing,” Roncarolo told the journalists attending the session.

Allowing academic institutions to run clinical trials is “a big effort that will require a team, institutional commitment and robust funding,” Roncarolo said. Comparing the situation in the United States to that in Europe, where she has done much of her research, she notes that “in this country there is little funding for proof of concept trials to bring therapies from the lab bench to the bedside.”

Previously: An inside look at drug development, Stanford’s Irving Weissman on the (lost?) promise of stem cells and The largest stem cell research building in the U.S.

Evolution, Genetics, Microbiology, Pregnancy, Research, Science, Stanford News, Stem Cells

My baby, my… virus? Stanford researchers find viral proteins in human embryonic cells

My baby, my... virus? Stanford researchers find viral proteins in human embryonic cells

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One thing I really enjoy about my job is the opportunity to constantly be learning something new. For example, I hadn’t realized that about eight percent of human DNA is actually left-behind detritus from ancient viral infections. I knew they were there, but eight percent? That’s a lot of genetic baggage.

These sequences are often inactive in mature cells, but recent research has shown they can become activated in some tumor cells or in human embryonic stem cells. Now developmental biologist Joanna Wysocka, PhD, and graduate student Edward Grow, have shown that some of these viral bits and pieces spring back to life in early human embryos and may even affect their development.

Their research was published today in Nature. As I describe in our press release:

Retroviruses are a class of virus that insert their DNA into the genome of the host cell for later reactivation. In this stealth mode, the virus bides its time, taking advantage of cellular DNA replication to spread to each of an infected cell’s progeny every time the cell divides. HIV is one well-known example of a retrovirus that infects humans.

When a retrovirus infects a germ cell, which makes sperm and eggs, or infects a very early-stage embryo before the germ cells have arisen, the viral DNA is passed along to future generations. Over evolutionary time, however, these viral genomes often become mutated and inactivated. About 8 percent of the human genome is made up of viral sequences left behind during past infections. One retrovirus, HERVK, however, infected humans repeatedly relatively recently — within about 200,000 years. Much of HERVK’s genome is still snuggled, intact, in each of our cells.

Wysocka and Grow found that human embryonic cells begin making viral proteins from these HERVK sequences within just a few days after conception. What’s more, the non-human proteins have a noticeable effect on the cells, increasing the expression of a cell surface protein that makes them less susceptible to subsequent viral infection and also modulating human gene expression.

More from our release:

But it’s not clear whether this sequence of events is the result of thousands of years of co-existence, a kind of evolutionary symbiosis, or if it represents an ongoing battle between humans and viruses.

“Does the virus selfishly benefit by switching itself on in these early embryonic cells?” said Grow. “Or is the embryo instead commandeering the viral proteins to protect itself? Can they both benefit? That’s possible, but we don’t really know.”

Wysocka describes the findings as “fascinating, but a little creepy.” I agree. But I can’t wait to hear what they discover next.

Previously: Viruses can cause warts on your DNA, Stanford researcher wins Vilcek Prize for Creative Promise in Biomedical Science and Species-specific differences among placentas due to long-ago viral infection, say Stanford researchers
Photo of Joanna Wysocka by Steve Fisch

otolaryngology, Research, Science, Stanford News, Stem Cells

Molecular sleuthing uncovers new clue toward deafness cure

Molecular sleuthing uncovers new clue toward deafness cure

In another step along the path toward finding cures for deafness, Stanford scientists report they have discovered a subset of cells in the mammalian utricle, the inner ear structure that controls balance, that can regenerate into hair cells when damaged.

The study was published today in Nature Communications, and senior author Alan Cheng, MD, explained the significance of the findings to me this way:

We rely on our inner ear sensory organs to hear and sense motion. Such functions require specialized hair cells to detect the vibrations of sound or motion. Once lost, hair cells needed for hearing do not regenerate and thus hearing loss is permanent, while those to sense motion can regenerate to a limited degree. Until now, the origin of these regenerated hair cells and the mechanisms that limit this process of regeneration in the utricle have not been clear. Here, we found two distinct populations of such hair cell progenitors in the neonatal mouse utricle, where they can regenerate lost hair cells. Unlike the utricle from older mice, the degree of regeneration and also cell division at this age are a lot more robust.

The study also provides an improved understanding of the molecular pathway that leads to this transformation, knowledge that could maybe one day be used to help researchers figure out how to artificially encourage hair cell renewal in humans.

Previously: Understanding hearing loss at the molecular level, New version of popular antibiotic eliminates side effect of deafness and Stanford chair of otolarnygology discusses future regenerative therapies for hearing loss

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