“Junk” DNA is development gold for the dividing embryo

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Single two-cell mouse embryos with nuclear LINE1 RNA labeled magenta – Credit Ramalho-Santos lab

The DNA in our cells provide the instructions to make proteins, the workhorses of our body. Yet less than 2% of the 3 billion base pairs (the structural units of DNA) in each of our cells are actually involved in protein production. The rest, termed non-coding DNA for not being involved in protein production, has roles in regulating genetic activity, but, largely, these genetic regions have remained a mystery causing some to mis-characterize it as “junk” DNA.

One of the largest components of these “junk” DNA regions are transposons, which make up 50% of the genome. Transposons are variable length DNA segments that are able to duplicate and re-insert themselves into different locations of the genome which is why they’re often called “jumping genes”.

Transposons have been implicated in diseases like cancer because of their ability to disrupt normal gene function depending on where the transposon inserts itself. Now, a CIRM-funded study in Miguel Ramalho-Santos’ laboratory at UCSF has found a developmental function for transposons in the dividing embryo. The report was published today in the Journal Cell.

Of the transposons identified in humans, LINE1 is the most common, composing 24% of the entire human genome. Many investigators in the field had observed that LINE1 is highly expressed in embryonic stem cells, which seemed paradoxical given that these pieces of DNA were previously thought to be either inert or harmful. Because this DNA was present at such high levels, the investigators decided to eliminate it from fertilized mouse embryos at the two-cell stage and observe how this affected development.

To their surprise, they found that the embryo was not able to progress beyond this stage. Further investigation revealed that LINE1, along with other proteins, is responsible for turning off the genetic program that maintains the two-cell state, thus allowing the embryo to further divide and develop.

Dr. Ramalho-Santos believes that this is a fine-tuned mechanism to ensure that the early stages of develop progress successfully. Because there are so many copies of LINE1 in the genome, even if one is not functional, it is likely that there will be functional back up, an important factor in ensuring early mistakes in embryo development do not occur.

In a press release, Dr. Ramalho-Santos states:

“We now think these early embryos are playing with fire but in a very calculated way. This could be a very robust mechanism for regulating development…I’m personally excited to continue exploring novel functions of these elements in development and disease.”

Making stem cell-derived liver cells to study fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) affects approximately 30% of the population, with that number increasing to 75% in obese individuals. Shockingly, the number of cases is expected to increase 21% by the year 2030 in the United States alone.

liver_fattyliverNAFLD refers to a broad range of liver conditions, which are all characterized by abnormally high levels of fat deposits in the livers of people who do not drink excessive amounts of alcohol. While not always fatal, NAFLD can lead to liver cirrhosis, or extensive scaring of the liver tissue. Cirrhosis, in turn, can cause life-threatening conditions such as liver cancer or liver failure. Whether or not N

AFLD will lead to extensive liver damage is not well understood and the primary therapeutic option is weight loss with no FDA-approved drug options. The projected increase in NALD cases combined with the poor treatment options makes this disease a significant public health burden.

Studying NALD can be quite complicated because the liver is complex organ made up of multiple different cell types. Investigators at the University of Edinburgh have simplified some of this complexity by figuring out a way to generate liver cells in a dish.

In studies published in the Philosophical Transactions of the Royal Society B, these scientists used human embryonic stem cells to generate hepatocyte-like cells (HLCs), or cells that are highly similar to liver cells isolated from humans. When exposed to fatty acids, they saw that the HLCs exhibited hallmarks of NAFLD, such as fat accumulation in liver cells, and changes in gene expression that are indicative of NAFLD.

In a press release, Dr. David Hay, one of the two senior investigators of this study, states:

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Dr. David Hay

“Our ability to generate human hepatocytes from stem cells, using semi-automated procedures, allows us to study the mechanisms of human liver disease in a dish and at scale.”

 

This approach is particularly valuable because it would replace the need to use cancer cell lines for this type of work. While valuable for many reasons, research done in cancer cells lines can be difficult to draw therapeutic conclusions from, because cell lines have significant genetic alternations from normal cells. Generating liver cells from human stem cells provides an important tool for high throughput screening of medically relevant therapies for NALD.

 

Stem Cell Roundup: Jake Javier’s amazing spirit; TV report highlights clinic offering unproven stem cell therapies

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Jake Javier: Photo Michael Clemens, Sees the Day

In the Roundup we usually focus on studies that highlight advances in stem cell research but today we’re going to do something a little different. Instead of relying on print for our stories, we’re turning to video.

We begin with a piece about Jake Javier. Regular readers of our blog will remember that Jake is the young man who broke his neck the day before he graduated high school, leaving him paralyzed from the upper chest down.

After enrolling in the CIRM-funded Asterias clinical trial, and receiving a transplant of 10 million stem cells, Jake regained enough use of his arms and hands to be able to go to Cal Poly and start his life over.

This video highlights the struggles and challenges he faced in his first year, and his extraordinary spirit in overcoming them.

(thanks to Matt Yoon and his Creative Services team at Cal Poly for this video)

Going Undercover

The second video is from the NBC7 TV station in San Diego and highlights one of the big problems in regenerative medicine today, clinics offering unproven therapies. The investigative team at NBC7 went undercover at a stem cell clinic seminar where presenters talked about “the most significant breakthrough in natural medicine” for improving mobility and reducing pain. As the reporter discovered, the reality didn’t live up to the promise.

NBC7 Investigative Report

 

New findings about muscle stem cells reveals the potential for growing replacement organs

Chrissa Kioussi’s group at Oregon State University has made exciting advances in further unraveling the scientific mysteries of stem cells. In work detailed in Scientific Reports, this group found that muscle-specific stem cells actually have the ability to make multiple different cell types.

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Pumping up our knowledge about muscle stem cells

Initially, this group was interested in understanding how gene expression changes during embryonic development of skeletal muscle. To understand this process, they labeled muscle stem cells with a kind of fluorescent dye, called GFP, which allowed them to isolate these cells at different stages of development.  Once isolated, they determined what genes were being expressed by RNA sequencing. Surprisingly, they found that in addition to genes involved in muscle formation, they also identified activation of genes involved in the blood, nervous, immune and skeletal systems.

This work is particularly exciting, because it suggests the existence of stem cell “pockets,” or stem cells that are capable of not only making a specific cell type, but an entire organ system.

In a press release, Dr. Kioussi said:

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Chrissa Kioussi, PhD

“That cell populations can give rise to so many different cell types, we can use it at the development stage and allow it to become something else over time… We can identify these cells and be able to generate not one but four different organs from them — this is a prelude to making body parts in a lab.” 

This study is particularly exciting because it gives more credence to the idea that entire limbs can be reconstructed from a small group of stem cells. Such advances could have enormous meaning for individuals who have lost body parts due to amputation or disease.

The moment of truth. A video about the stem cell therapy that could help millions of people going blind.

“No matter how much one prepares, the first patient is always something very special.” That’s how Dr. Mark Humayun describes his feelings as he prepared to deliver a CIRM-funded stem cell therapy to help someone going blind from dry age-related macular degeneration (AMD).

Humayun, an ophthalmologist and stem cell researcher at USC, spent years developing this therapy and so it’s understandable that he might be a little nervous finally getting a chance to see if it works in people.

It’s quite a complicated procedure, involving turning embryonic stem cells into the kind of cells that are destroyed by AMD, placing those cells onto a specially developed synthetic scaffold and then surgically implanting the cells and scaffold onto the back of the eye.

There’s a real need for a treatment for AMD, the leading cause of vision loss in the US. Right now, there is no effective therapy for AMD and some three million Americans are facing the prospect of losing their eyesight.

The first, preliminary, results of this trial were released last week and they were encouraging. You can read about them on our blog.

Thanks to USC you can also see the team that developed and executed this promising approach. They created a video capturing the moment the team were finally taking all that hard work and delivering it where it matters, to the patient.

Watching the video it’s hard not to think you are watching a piece of history, something that has the potential to do more than just offer hope to people losing their vision, it has the potential to stop and even reverse that process.

The video is a salute to the researchers who developed the therapy, and the doctors, nurses and Operating Room team who delivered it. It’s also a salute to the person lying down, the patient who volunteered to be the first to try this. Everyone in that room is a pioneer.

Encouraging news about CIRM-funded clinical trial targeting vision loss

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An eye affected by dry age-related macular degeneration

Dry age-related macular degeneration (AMD) is the leading cause of vision loss in the U.S. By 2020 it’s estimated that as many as three million Americans will be affected by the disease. Right now, there is no effective therapy. But that could change. A new CIRM-funded clinical trial is showing promise in helping people battling the disease not just in stabilizing their vision loss, but even reversing it.

In AMD, cells in the retina, the light-sensitive tissue at the back of the eye, are slowly destroyed affecting a person’s central vision. It can make it difficult to do everyday activities such as reading or watching TV and make it impossible for a person to drive.

Researchers at the University of Southern California (USC) Roski Eye Institute at the Keck School of Medicine, and Regenerative Patch Technologies, have developed a therapy using embryonic stem cells that they turned into retinal pigment epithelium (RPE) cells – the kind of cell destroyed by AMD. These cells were then placed on a synthetic scaffold which was surgically implanted in the back of the eye.

Imaging studies showed that the RPE cells appeared to integrate well into the eye and remained in place during follow-up tests 120 to 365 days after implantation.

Encouraging results

Of the five patients enrolled in the Phase 1/2a trial, four maintained their vision in the treated eye, two showed improvement in the stability of their vision, and one patient had a 17-letter improvement in their vision on a reading chart. In addition, there were no serious side effects or unanticipated problems.

There were other indications the implants were proving beneficial.  People with normal vision have the ability to focus their gaze on a single location. People with advanced AMD lose that ability. In this trial, two of the patients recovered stable fixation. These improvements were maintained in follow-up tests.

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Abla Creasey, Ph.D., CIRM’S Vice President of Therapeutics and Strategic Infrastructure says even these small benefits are important:

“Having a therapy with a favorable safety profile, that could slow down the progression, or even reverse the vision loss would benefit millions of Americans. That’s why these results, while still in an early stage are encouraging, because the people treated in the trial are ones most severely affected by the disease who have the least potential for visual recovery.”

This study reflects CIRM’s long-term commitment to supporting the most promising stem cell research. The Stem Cell Agency began supporting USC’s Dr. Mark Humayun, the lead inventor of the implant, in 2010 and has been a partner with him and his team since then.

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In a news release Dr. Humayun said they plan to recruit another 15 patients to see if these results hold up:

“Our study shows that this unique stem cell–based retinal implant thus far is well-tolerated, and preliminary results suggest it may help people with advanced dry age-related macular degeneration.”

While the results, published in the journal Science Translational Medicine, are encouraging the researchers caution that this was a very early stage clinical trial, with a small number of patients. They say the next step is to continue to follow the four patients treated in this trial to see if there are any further changes to their vision, and to conduct a larger trial.

 

 

Stem Cell Roundup: hESCs turn 20, tracking cancer stem cells, new ALS gene ID’d

Stem Cell Image of the Week

Picture1This week’s stunning stem cell image is brought to you by researchers in the Brivanlou Lab at Rockefeller University. What looks like the center of a sunflower is actual a ball of neural rosettes derived from human embryonic stem cells (ESCs). Neural rosettes are structures that contain neural stem and progenitor cells that can further specialize into mature brain cells like the stringy, blue-colored neurons in this photo.

This photo was part of a Nature News Feature highlighting how 20 years ago, human ESCs sparked a revolution in research that’s led to the development of ESC-based therapies that are now entering the clinic. It’s a great read, especially for those of you who aren’t familiar with the history of ESC research.

Increase in cancer stem cells tracked during one patient’s treatment
Cancer stem cells are nasty little things. They have the ability to evade surgery, chemotherapy and radiation and cause a cancer to return and spread through the body. Now a new study says they are also clever little things, learning how to mutate and evolve to be even better at evading treatment.

Researchers at the Colorado Cancer Center did three biopsies of tumors taken from a patient who underwent three surgeries for salivary gland cancer. They found that the number of cancer stem cells increased with each surgery. For example, in the first surgery the tumor contained 0.2 percent cancer stem cells. By the third surgery the number of cancer stem cells had risen to 4.5 percent.

Even scarier, the tumor in the third surgery had 50 percent more cancer-driving mutations meaning it was better able to resist attempts to kill it.

In a news release, Dr. Daniel Bowles, the lead investigator, said the tumor seemed to learn and become ever more aggressive:

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Daniel Bowles

“People talk about molecular evolution of cancer and we were able to show it in this patient. With these three samples, we could see across time how the tumor developed resistance to treatment.”

 

The study is published in the journal Clinical Cancer Research.

New gene associated with ALS identified.
This week, researchers at UMass Medical School and the National Institute on Aging reported the identification of a new gene implicated in the development of amyotrophic lateral sclerosis (ALS). Also known as Lou Gehrig’s disease, ALS is a horrific neurodegenerative disorder that degrades the connection between nerve signals and the muscles. Sufferers are robbed of their ability to move and, ultimately, even to breathe. Life expectancy is just 3 to 5 years after diagnosis.

To identify the gene, called KIF5A, the team carried out the largest genetics effort in ALS research with support from the ALS Association, creators of the Ice Bucket Challenge that raised a $115 million for research. The study compared the genomes between a group of nearly 22,000 people with ALS versus a group of over 80,000 healthy controls. Two independent genetic analyses identified differences in the expression of the KIF5A gene between the two groups.

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Cartoon representing the role that KIF5A plays in neurons. (Image: UMass Medical School)

KIF5A is active in neurons where it plays a key role in transporting cell components across the cell’s axon, the long, narrow portion of the cell that allows neurons to send long-range signals to other cells. It carries out this transport by tethering cell components on the axon’s cytoskeleton, a structural protein matrix within the cells. Several mutations in KIF5A were found in the ALS group which corroborates previous studies showing that mutations in other cytoskeleton genes are associated with ALS.

One next step for the researchers is to further examine the KIF5A mutations using patient-derived induced pluripotent stem cells.

The study was published in Neuron and picked up by Eureka Alert!

Stem Cell Patch Restores Vision in Patients with Age-Related Macular Degeneration

Stem cell-derived retinal pigmented epithelial cells. Cell borders are green and nuclei are red. (Photo Credit: Dennis Clegg, UCSB Center for Stem Cell Biology and Engineering)

Two UK patients suffering from vision loss caused by age-related macular degeneration (AMD) have regained their sight thanks to a stem cell-based retinal patch developed by researchers from UC Santa Barbara (UCSB). The preliminary results of this promising Phase 1 clinical study were published yesterday in the journal Nature Biotechnology.

AMD is one of the leading causes of blindness and affects over six million people around the world. The disease causes the blurring or complete loss of central vision because of damage to an area of the retina called the macula. There are different stages (early, intermediate, late) and forms of AMD (wet and dry). The most common form is dry AMD which occurs in 90% of patients and is characterized by a slow progression of the disease.

Patching Up Vision Loss

In the current study, UCSB researchers engineered a retinal patch from human embryonic stem cells. These stem cells were matured into a layer of cells at the back of the eye, called the retinal pigment epithelium (RPE), that are damaged in AMD patients. The RPE layer was placed on a synthetic patch that is implanted under the patient’s retina to replace the damaged cells and hopefully improve the patient’s vision.

The stem cell-based eyepatches are being implanted in patients with severe vision loss caused by the wet form of AMD in a Phase 1 clinical trial at the Moorfields Eye Hospital NHS Foundation Trust in London, England. The trial was initiated by the London Project to Cure Blindness, which was born from a collaboration between UCSB Professor Peter Coffey and Moorsfields retinal surgeon Lyndon da Cruz. Coffey is a CIRM grantee and credited a CIRM Research Leadership award as one of the grants that supported this current study.

The trial treated a total of 10 patients with the engineered patches and reported 12-month data for two of these patients (a woman in her 60s and a man in his 80s) in the Nature Biotech study. All patients were given local immunosuppression to prevent the rejection of the implanted retinal patches. The study reported “three serious adverse events” that required patients to be readmitted to the hospital, but all were successfully treated. 12-months after treatment, the two patients experienced a significant improvement in their vision and went from not being able to read at all to reading 60-80 words per minute using normal reading glasses.

Successfully Restoring Sight

Douglas Waters, the male patient reported on, was diagnosed with wet AMD in July 2015 and received the treatment in his right eye a few months later. He spoke about the remarkable improvement in his vision following the trial in a news release:

“In the months before the operation my sight was really poor, and I couldn’t see anything out of my right eye. I was struggling to see things clearly, even when up-close. After the surgery my eyesight improved to the point where I can now read the newspaper and help my wife out with the gardening. It’s brilliant what the team have done, and I feel so lucky to have been given my sight back.”

This treatment is “the first description of a complete engineered tissue that has been successfully used in this way.” It’s exciting not only that both patients had a dramatic improvement in their vision, but also that the engineered patches were successful at treating an advanced stage of AMD.

The team will continue to monitor the patients in this trial for the next five years to make sure that the treatment is safe and doesn’t cause tumors or other adverse effects. Peter Coffey highlighted the significance of this study and what it means for patients suffering from AMD in a UCSB news release:

Peter Coffey

“This study represents real progress in regenerative medicine and opens the door to new treatment options for people with age-related macular degeneration. We hope this will lead to an affordable ‘off-the-shelf’ therapy that could be made available to NHS patients within the next five years.”

Stem Cell Roundup: No nerve cells for you, old man; stem cells take out the trash; clues to better tattoo removal

Stem cell image of the week: Do they or don’t they? The debate on new nerve cell growth in adult brain rages on.

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Young neurons (green) are shown in the human hippocampus at the ages of (from left) birth, 13 years old and 35 years old. Images by Arturo Alvarez-Buylla lab

For the longest time, it was simply a given among scientists that once you reach adulthood, your brain’s neuron-making days were over. Then, over the past several decades, evidence emerged that the adult brain can indeed make new neurons, in a process called neurogenesis. Now the pendulum of understanding may be swinging back based on research reported this week out of Arturo Alvarez-Buylla’s lab at UCSF.

Through the careful examination of 59 human brain samples (from post mortem tissue and those collected during epilepsy surgery), Alvarez-Buylla’s team in collaboration with many other labs around the world, found lots of neurogenesis in neonatal and newborn brains. But after 1 year of age, a steep drop in the number of new neurons was observed. Those numbers continued to plummet through childhood and were barely detectable in samples from teens. New neurons were undetectable in adult brain samples.

This week’s stem cell image shows this dramatic decline of new neurons when comparing brain samples from a newborn, a 13 year-old and a 35 year-old.

It was no surprise that these surprising results, published in Nature, got quite a bit of attention by a wide range of news outlets including the LA Times, CNN, The Scientist and NPR to name just a few.

Limitless life of stem cells requires taking out the trash

It’s minding blowing to me that, given the proper nutrients, an embryonic stem cell in a lab dish can exist indefinitely. The legendary fountain of youth that Ponce de León searched in vain for is actually hidden inside these remarkable cells. So how do they do it? It’s a tantalizing question for researchers because the answers could lead to a better understanding of and eventually novel therapies for age-related diseases.

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Cartoon of a proteosome, the cell’s garbage disposal. Image: Wikipedia

A team from the University of Cologne reports this week on a connection between the removal of degraded proteins and the longevity of stem cells. Cells in general use special enzymes to tag wonky proteins for the cellular trash heap, called a proteasome. Without this ability to clean up, unwanted proteins can accumulate and make cells unhealthy, a scenario that is seen in age-related diseases like Alzheimer’s. The research team found that reducing the protein disposal activity in embryonic stem cells disrupted characteristics that are specific to these cells. So, one way stem cells may keep their youthful appearance is by being good about taking out their trash.

The study was published in Scientific Reports and picked up by Science Daily.

Why tattoos stay when your skin cells don’t ( by Kevin McCormack)

We replace our skin cells every two or three weeks. As each layer dies, the stem cells in the skin replace them with a new batch. With that in mind you’d think that a tattoo, which is just ink injected into the skin with a needle, would disappear as each layer of skin is replaced. But obviously it doesn’t. Now some French researchers think they have figured out why.

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Thank your macrophages for keeping your tattoo intact. Tattoo by: Sansanana

It’s not just fun science, published in the Journal of Experimental Medicine, it could also mean that that embarrassing tattoo you got saying you would love Fred or Freda forever, can one day be easily removed.

The researchers found that when the tattoo needle inflicts a wound on the skin, specialized cells called macrophages flock to the site and take up the ink. As those macrophages die, instead of the ink disappearing with them, new macrophages come along, gobble up the ink and so the tattoo lives on.

In an interview with Health News Digest, Bernard Malissen, one of the lead investigators, says the discovery, could help erase a decision made in a moment of madness:

“Tattoo removal can be likely improved by combining laser surgery with the transient ablation of the macrophages present in the tattoo area. As a result, the fragmented pigment particles generated using laser pulses will not be immediately recaptured, a condition increasing the probability of having them drained away via the lymphatic vessels.”

Breaking the isolation of rare diseases

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Rare Disease Day in Sacramento, California

How can something that affects 30 million Americans, one in ten people in the US, be called rare? But that’s the case with people who have a rare disease. There are around 7,000 different diseases that are categorized as rare because they affect fewer than 200,000 people. Less than five percent of these diseases have a treatment.

That’s why last Wednesday, in cities across the US, members of the rare disease community gathered to call for more support, more research, and more help for families battling these diseases. Their slogan tells their story, ‘Alone we are rare; Together we are strong.’

At the Rare Disease Day rally in Sacramento, California, I met Kerry Rivas. Kerry’s son Donovan has a life-threatening condition called Shprintzen-Goldberg Syndrome. Talk about rare. There are only 70 documented cases of the syndrome worldwide. Just getting a diagnosis for Donovan took years.

DonovanDonovan suffers from a lot of problems but the most serious affect his heart, lungs and spinal cord. Getting him the care he needs is time consuming and expensive and has forced Kerry and her family to make some big sacrifices. Even so they work hard to try and see that Donovan is able to lead as normal a life as is possible.

While the disease Kerry’s son has is rarer than most, everyone at Rare Disease Day had a similar story, and an equal commitment to doing all they can to be an effective advocate. And their voices are being heard.

To honor the occasion the US Food and Drug Administration (FDA) announced it was partnering with the National Organization of Rare Diseases (NORD) to hold listening sessions involving patients and FDA medical reviewers.

In a news release Peter L. Saltonstall, President and CEO of NORD, said:

“These listening sessions will provide FDA review division staff with better insight into what is important to patients in managing their diseases and improving their quality of life. It is important for FDA to understand, from the patient perspective, disease burden, management of symptoms, daily impact on quality of life, and patients’ risk tolerance. Patients and caregivers bring a pragmatic, realistic perspective about what they are willing to deal with in terms of potential risks and benefits for new therapies.”

FDA Commissioner Dr. Scott Gottlieb said his agency is committed to doing everything possible to help the rare disease community:

“Despite our successes, there are still no treatments for the vast proportion of rare diseases or conditions. FDA is committed to do what we can to stimulate the development of more products by improving the consistency and efficiency of our reviews, streamlining our processes and supporting rare disease research.”

At CIRM we are also committed to doing all we can to help the cause. Many of the diseases we are currently funding in clinical trials are rare diseases like ALS or Lou Gehrig’s disease, SCID, spinal cord injury and sickle cell disease.

Many pharmaceutical companies are shy about funding research targeting these diseases because the number of patients involved is small, so the chances of recouping their investment or even making a profit is small.

At CIRM we don’t have to worry about those considerations. Our focus is solely on helping those in need. People like Donovan Rivas.