Understanding the basic biology of how a cell functions can be crucial to being able to better understand a disease and unlock a potential approach for a treatment. Stem cells are unique in that they give scientists the opportunity to create a controlled environment of cells that might be otherwise difficult to study. Dr. Eva Hedlund and a team of researchers at the Karolinska Institute in Sweden utilize a stem cell model approach to uncover findings related to Amyotrophic Lateral Sclerosis (ALS), also known as Lou Gehrig’s Disease.
ALS is a progressive neurodegenerative disease that destroys motor neurons, a type of nerve cell, that are important for voluntary muscle movement. When motor neurons can no longer send signals to the muscles, the muscles begin to deteriorate, a process formally known as atrophy. The progressive atrophy leads to muscle paralysis, including those in the legs and feet, arms and hands, and those that control swallowing and breathing. It affects about 30,000 people in the United States alone, with 5,000 new cases diagnosed each year. There is currently no cure.
In a previous study, researchers at the Karolinska Institute were able to successfully create oculomotor neurons from embryonic stem cells. For reasons not yet fully understood, oculomotor neurons are “ALS resilient” and can survive all stages of the disease.
In the current study, published in Stem Cell Reports, Dr. Hedlund and her team found that the oculomotor neurons they generated appeared more resilient to ALS-like degeneration when compared to spinal cord motor neurons, something commonly observed in humans. Furthermore, they discovered that their “ALS resilient” neurons generated from stem cells activate a survival-enhancing signal known as Akt, which is common in oculomotor neurons in humans and could explain their resilience. These results could potentially aid in identifying genetic targets for treatments protecting sensitive neurons from the disease.
From Day One CIRM’s goal has been to advance stem cell research in California. We don’t do that just by funding the most promising research -though the 51 clinical trials we have funded to date clearly shows we do that rather well – but also by trying to bring the best minds in the field together to overcome problems.
Over the years we
have held conferences, workshops and symposiums on everything from Parkinson’s
palsy and tissue
engineering. Each one attracted the key players and stakeholders in the
field, brainstorming ideas to get past obstacles and to explore new ways of
developing therapies. It’s an attempt to get scientists, who would normally be
rivals or competitors, to collaborate and partner together in finding the best
It’s not easy to do,
and the results are not always obvious right away, but it is essential if we
hope to live up to our mission of accelerating stem cell therapies to patients
with unmet medical needs.
For example. This
past week we helped organize two big events and were participants in another.
The first event we
pulled together, in partnership with Cedars-Sinai Medical Center, was a
workshop called “Brainstorm Neurodegeneration”. It brought together leaders in stem
cell research, genomics, big data, patient advocacy and the Food and Drug
Administration (FDA) to tackle some of the issues that have hampered progress
in finding treatments for things like Parkinson’s, Alzheimer’s, ALS and
ambitiously subtitled the workshop “a cutting-edge meeting to disrupt the field”
and while the two days of discussions didn’t resolve all the problems facing us
it did produce some fascinating ideas and some tantalizing glimpses at ways to
advance the field.
Two days later we partnered with UC San Francisco to host the Fourth Annual CIRM Alpha Stem Cell Clinics Network Symposium. This brought together the scientists who develop therapies, the doctors and nurses who deliver them, and the patients who are in need of them. The theme was “The Past, Present & Future of Regenerative Medicine” and included both a look at the initial discoveries in gene therapy that led us to where we are now as well as a look to the future when cellular therapies, we believe, will become a routine option for patients.
different groups together is important for us. We feel each has a key role to
play in moving these projects and out of the lab and into clinical trials and
that it is only by working together that they can succeed in producing the
treatments and cures patients so desperately need.
As always it was the patients who surprised us. One, Cierra Danielle Jackson, talked about what it was like to be cured of her sickle cell disease. I think it’s fair to say that most in the audience expected Cierra to talk about her delight at no longer having the crippling and life-threatening condition. And she did. But she also talked about how hard it was adjusting to this new reality.
Cierra said sickle
cell disease had been a part of her life for all her life, it shaped her daily
life and her relationships with her family and many others. So, to suddenly
have that no longer be a part of her caused a kind of identity crisis. Who was
she now that she was no longer someone with sickle cell disease?
She talked about how
people with most diseases were normal before they got sick, and will be normal
after they are cured. But for people with sickle cell, being sick is all they
have known. That was their normal. And now they have to adjust to a new normal.
It was a powerful
reminder to everyone that in developing new treatments we have to consider the
whole person, their psychological and emotional sides as well as the physical.
And so on to the third event we were part of, the Stanford Drug Discovery Symposium. This was a high level, invitation-only scientific meeting that included some heavy hitters – such as Nobel Prize winners Paul Berg and Randy Schekman, former FDA Commissioner Robert Califf. Over the course of two days they examined the role that philanthropy plays in advancing research, the increasingly important role of immunotherapy in battling diseases like cancer and how tools such as artificial intelligence and big data are shaping the future.
CIRM’s President and CEO, Dr. Maria Millan, was one of those invited to speak and she talked about how California’s investment in stem cell research is delivering Something Better than Hope – which by a happy coincidence is the title of our 2018 Annual Report. She highlighted some of the 51 clinical trials we have funded, and the lives that have been changed and saved by this research.
The presentations at
these conferences and workshops are important, but so too are the conversations
that happen outside the auditorium, over lunch or at coffee. Many great
collaborations have happened when scientists get a chance to share ideas, or
when researchers talk to patients about their ideas for a successful clinical
It’s amazing what happens when you bring people together who might otherwise never have met. The ideas they come up with can change the world.
There has been a lot of conversation surrounding CRISPR-Cas9 in these recent months as well as many sensational news stories. Some of these stories highlight the promise this technology holds, while others emphasize a word of caution. But what exactly does this technology do and how does it work? Here is a breakdown that will help you better understand.
To start off, CRISPR is a naturally occurring process found in bacteria used as an immune system to defend against viruses. CRISPR simply put, are strands of DNA segments that contain repeating patterns. There are “scissor like” CRISPR proteins that have the ability to cut DNA segments. When a copy of a virus enters the bacteria, these “scissor like” proteins cut a segment of DNA from the virus and insert it into CRISPR. A copy of the viral DNA is made and another “attack” protein known as Cas9 attaches to it. By binding to the viral copy, Cas9 is able to sense that virus. When the same virus tries to enter the bacteria, Cas9 is able to seek and destroy it.
You can view a more detailed video explaining this concept below.
Many scientists analyzed this process in detail and it was eventually discovered that this CRISPR-Cas9 complex could be used to removed unwanted genes and insert a corrected copy, revolutionizing the way that we view the approach towards treating a wide variety of genetic diseases.
In fact, researchers at the Dana-Farber/Boston Children’s Cancer and Blood Disorders Center and the University of Massachusetts Medical School have developed a strategy using this complex to treat two inherited, lethal blood disorders, sickle cell disease (SCD) and beta thalassemia. Both of these diseases involve a mutation that effects production of red blood cells, which are produced by blood stem cells. In beta-thalassemia, the mutation prevent red blood cells from being able to carry enough oxygen, leading to anemia. In SCD, the mutations cause red blood cells to take on a “sickle” shape which can block blood vessels.
By using CRISPR-Cas9 to insert a corrected copy of the gene into a patient’s own blood stem cells, this team demonstrated that functional red blood cells can then be produced. These results pay the way for other blood disorders as well.
In a press release , Dr. Daniel Bauer, an attending physician with Dana-Farber and a senior author on both of these studies stated that,
“Combining gene editing with an autologous stem-cell transplant could be a therapy for sickle-cell disease, beta-thalassemia and other blood disorders.”
In a separate study, scientists at University of Massachusetts Medical School have developed a strategy that could be used to treat genetic disorders associated with unintentional repeats or copies of small DNA segments. These problematic small segments of DNA are called microduplications and cause as many as 143 different diseases, including limb-girdle muscular dystrophy, Hermansky-Pudlak syndrome, and Tay-Sachs.
Because these are issues caused by repeats or copies of small DNA segments, the CRISPR-Cas9 complex can be used to remove microduplications without having to insert any additional genetic material.
Dr. Scot A. Wolfe, a co-investigator of this study, stated that,
“It’s like hitting the reset button. We don’t have to add any corrective genetic material, instead the cell stitches the DNA back together minus the duplication. It’s a shortcut for gene correction with potential therapeutic appeal.”
Although there has been a lot progress made with this technology, there are still concerns that need to be addressed. An article in Science mentions how two studies have shown that CRISPR can still make unintended changes to DNA, which can be potentially dangerous. In the article, Dr. Jin-Soo Kim, a CRISPR researcher at Seoul National University is quoted as saying,
“It is now important to determine which component is responsible for the collateral mutations and how to reduce or avoid them.”
Overall, CRISPR-Cas9 has revolutionized the approach of precision medicine. A wide variety of diseases are caused by small, unexpected segments of DNA. By applying this approach found in bacteria to humans, we have uncovered a way to correct these segments at the microscopic level. However, there is still much that needs to be learned and perfected before it can be utilized in patients.
Stem cell photo of the week: high schooler becoming a stem cell pro this summer
High school student Anna Guzman learning important lab skills at UC Davis
This summer’s CIRM SPARK Programs, stem cell research internships for high school students, are in full swing. Along with research assignments in top-notch stem cell labs, we’ve asked the students to chronicle their internship experiences through Instagram. And today’s stem cell photo of the week is one of those student-submitted posts. The smiling intern in this photo set is Anna Guzman, a rising junior from Sheldon High School who is in the UC Davis SPARK Program. In her post, she describes the lab procedure she is doing:
“The last step in our process to harvest stem cells from a sample of umbilical cord blood! We used a magnet to isolate the CD34 marked stem cells [blood stem cells] from the rest of the solution.”
Only a few days in and Anna already looks like a pro! It’s important lab skills like this one that could land Anna a future job in the stem cell field. Check out #cirmsparklab on Instagram to view the ever-growing number of posts.
Swiss team identifies a cell type that block formation of fat cells
(Left) Mature human fat cells grown in a Petri dish (green, lipid droplets). (Right) A section of mouse fat tissue showing, in the middle, a blood vessel (red circle) surrounded by fat cell blocking cells called Aregs (arrows). [Bart Deplancke/EPFL]
Liposuction surgery helps slim and reshape areas of a person’s body through the removal of excess fat tissue. While the patient is certainly happy to get rid of those extra pounds, that waste product is sought after by researchers because it’s a rich source of regenerative cells including fat stem cells.
The exact populations of cells in this liposuction tissue has been unclear, so a collaboration of Swiss researchers – at Ecole Polytechnique Fédérale de Lausanne (EPFL) and Eidgenössische Technische Hochschule Zürich (ETHZ) – used a cutting-edge technique allowing them to examine the gene activity within single cells.
The analysis was successful in identifying several newly defined subpopulations of cells in the fat tissue. To their surprise, one of those cell types did not specialize into fat cells but instead did the opposite: they inhibited other fat stem cells from giving rise to fat cells. The initial experiments were carried out in mice, but the team went on to show similar fat-blocking cells in human tissue. Further experiments will explore the tantalizing prospect of applying these cells to control obesity and the many diseases, like diabetes, that result from it.
Connection identified between recent human evolution & risk for premature birth Evidence of recent evolution in a human gene that’s critical for maintaining pregnancy may help explain why some populations have a higher risk for giving birth prematurely than others. That’s according to a recent report by researchers at the University of Stanford School of Medicine.
The study, funded in part by CIRM’s Genomics Initiative, compared DNA from people with East Asian, European and African ancestry. They specifically examined the gene encoding the progesterone hormone receptor which helps keep a pregnant woman from going into labor too soon. The gene is also associated with preterm births, the leading cause of infant death in the U.S.
The team was very surprise to find that people with East Asian ancestry had an evolutionarily new version of the gene while the European and African populations had mixtures of new and ancient versions. These differences may explain why the risk for premature birth among East Asian populations is lower than among pregnant women of European and African descent, though environment clearly plays a role as well.
Pediatrics professor Gary Shaw, PhD, one of the team leaders, put the results in perspective:
“Preterm birth has probably been with us since the origin of the human species,” said Shaw in a press release, “and being able to track its evolutionary history in a way that sheds new light on current discoveries about prematurity is really exciting.”
Yesterday, we discussed a useful stem cell tool called the CIRM iPSC Repository, which will contain over 3000 human induced pluripotent stem cell (iPSC) lines – from patients and healthy individuals – that contain a wealth of information about human diseases. Now that scientists have access to these lines, they need the proper tools to study them. This is where CIRM’s Genomics Initiative comes into play.
Crunching stem cell data
In 2014, CIRM funded the Genomics Initiative, which created the Center of Excellence in Stem Cell Genomics (CESCG). The goal of the CESCG is to develop novel genomics and bioinformatics tools specifically for stem cell research. These technologies aim to advance our fundamental understanding of human development and disease mechanisms, improve current cell and tissue production methods, and accelerate personalized stem cell-based therapies.
The CESCG is a consortium between Stanford University, the Salk Institute and UC Santa Cruz. Together, the groups oversee or support more than 20 different research projects throughout California focused on generating and analyzing sequencing data from stem or progenitor cells. Sequencing technology today is not only used to decode DNA, but also used to study other genomic data like that provides information about how gene activity is regulated.
Many of the projects within the CESCG are using these sequencing techniques to define the basic genetic properties of specific cell types, and will use this information to create better iPSC-based tissue models. For example, scientists can determine what genes are turned on or off in cells by analyzing raw data from RNA sequencing experiments (RNA is like a photocopy of DNA sequences and is the cell’s way of carrying out the instructions contained in the DNA. This technology sequences and identifies all the RNA that is generated in a tissue or cell at a specific moment). Single cell RNA sequencing, made possible by techniques such as Drop-seq mentioned in yesterday’s blog, are now further revealing the diversity of cell types within tissues and creating more exact reference RNA sequences to identify a specific cell type. By comparing RNA sequencing data from single cells of stem cell-based models to previously referenced cell types, researchers can estimate how accurate, or physiologically relevant, those stem cell models are.
Such comparative analyses can only be done using powerful software that can compare millions of sequence data at the same time. Part of a field termed bioinformatics, these activities are a significant portion of the CESCG and several software tools are being created within the Initiative. Josh Stuart, a faculty member at UC Santa Cruz School of Engineering and a primary investigator in the CESCG, explained their team’s vision:
“A major challenge in the field is recognizing cell types or different states of the same cell type from raw data. Another challenge is integrating multiple data sets from different labs and figuring out how to combine measurements from different technologies. At the CESCG, we’re developing bioinformatics models that trace through all this data. Our goal is to create a database of these traces where each dot is a cell and the curves through these dots explain how the cells are related to one another.”
Stuart’s hope is that scientists will input their stem cell data into the CESCG database and receive a scorecard that explains how accurate their cell model is based on a specific genetic profile. The scorecard will help will not only provide details on the identity of their cells, but will also show how they relate to other cell types found in their database.
The Brain of Cells
An image of a 3D brain organoid grown from stem cells in the Kriegstein Lab at UCSF. (Photo by Elizabeth DiLullo)
A good example of how this database will work is a project called the Brain of Cells (BOC). It’s a collection of single cell RNA sequencing data from thousands of fetal-derived brain cells provided by multiple labs. The idea is that researchers will input RNA sequencing data from the stem cell-derived brain cells they make in their labs and the BOC will give them back a scorecard that describes what types of cells they are and their developmental state by comparing them to the referenced brain cells.
One of the labs that is actively involved in this project and is providing the bulk of the BOC datasets is Arnold Kriegstein’s lab at UC San Francisco. Aparna Bhaduri, a postdoctoral fellow in the Kriegstein lab working on the BOC project, outlined the goal of the BOC and how it will benefit researchers:
“The goal of the Brain of Cells project is to find ways to leverage existing datasets to better understand the cells in the developing human brain. This tool will allow researchers to compare cell-based models (such as stem cell-derived 3D organoids) to the actual developing brain, and will create a query-able resource for researchers in the stem cell community.”
Pablo Cordero, a former postdoc in Josh Stuart’s lab who designed a bioinformatics tool used in BOC called SCIMITAR, explained how the BOC project is a useful exercise in combining single cell data from different external researchers into one map that can predict cell type or cell fate.
“There is no ‘industry standard’ at the moment,” said Cordero. “We have to find various ways to perform these analyses. Approximating the entire human cell lineage is the holy grail of regenerative medicine since in theory, we would have maps of gene circuits that guide cell fate decisions.”
Once the reference data from BOC is ready, the group will use a bioinformatics program called Sample Psychic to create the scorecards for outside researchers. Clay Fischer, project manager of the CESCG at UC Santa Cruz, described how Sample Psychic works:
“Sample Psychic can look at how often genes are being turned off and on in cells. It uses this information to produce a scorecard, which shows how closely the data from your cells maps up to the curated cell types and can be used to infer the probability of the cell type.”
The BOC group believes that the analyses and data produced in this effort will be of great value to the research community and scientists interested in studying developmental neuroscience or neurodegeneration.
The Brain of Cells project is still in its early stages, but soon scientists will be able to use this nifty tool to help them build better and more accurate models of human brain development and brain-related diseases.
CESCG is also pursuing stem cell data driven projects focused on developing similar databases and scorecards for heart cells and pancreatic cells. These genomics and bioinformatics tools are pushing the envelope to a day when scientists can connect the dots between how different cell states and cell fates are determined by computational analysis and leverage this information to generate better iPSC-based systems for disease modeling in the lab or therapeutics in the clinic.
The Bee Gees, pioneers in trying to find ways to mend a broken heart. Photograph: Michael Ochs Archives
This may be the first time that the Australian pop group the Bee Gees have ever been featured in a blog about stem cell research, but in this case I think it’s appropriate. One of the Bee Gees biggest hits was “How can you mend a broken heart” and while it was a fine song, Barry and Robin Gibb (who wrote the song) never really came up with a viable answer.
Happily some researchers at the University of Southern California may succeed where Barry and Robin failed. In a study, published in the journal Nature Genetics, the USC team identify a gene that may help regenerate damaged heart tissue after a heart attack.
When babies are born they have a lot of a heart muscle cell called a mononuclear diploid cardiomyocyte or MNDCM for short. This cell type has powerful regenerative properties and so is able to rebuild heart muscle. However, as we get older we have less and less MNDCMs. By the time most of us are at an age where we are most likely to have a heart attack we are also most likely to have very few of these cells, and so have a limited ability to repair the damage.
Michaela Patterson, and her colleagues at USC, set out to find ways to change that. They found that in some adult mice less than 2 percent of their heart cells were MNDCMs, while other mice had a much higher percentage, around 10 percent. Not surprisingly the mice with the higher percentage of MNDCMs were better able to regenerate heart muscle after a heart attack or other injury.
So the USC team – with a little help from CIRM funding – dug a little deeper and did a genome-wide association study of these mice, that’s where they look at all the genetic variants in different individuals to see if they can spot common traits. They found one gene, Tnni3k, that seems to play a key role in generating MNDCMs.
Turning Tnni3K off in mice resulted in higher numbers of MNDCMs, increasing their ability to regenerate heart muscle. But when they activated Tnni3k in zebrafish it reduced the number of MNDCMs and impaired the fish’s ability to repair heart damage.
While it’s a long way from identifying something interesting in mice and zebrafish to seeing if it can be used to help people, Henry Sucov, the senior author on the study, says these findings represent an important first step in that direction:
“The activity of this gene, Tnni3k, can be modulated by small molecules, which could be developed into prescription drugs in the future. These small molecules could change the composition of the heart over time to contain more of these regenerative cells. This could improve the potential for regeneration in adult hearts, as a preventative strategy for those who may be at risk for heart failure.”
Nanomagnets: the future of targeted stem cell therapies? Your blood vessels are made up of tightly-packed endothelial cells. This barrier poses some big challenges for the delivery of drugs via the blood. While small molecules are able make their way through the small gaps in the blood vessel walls, larger drug molecules, including proteins and cells, are not able to penetrate the vessel to get therapies to diseased areas.
This week, researchers at Rice University report in Nature Communications on an ingenious technique using tiny magnets that may overcome this drug delivery problem.
At left, the nanoparticles are evenly distributed among the microtubules that help give the cells their shape. At right, after a magnetic field is applied, the nanoparticles are pulled toward one end of the cells and change their shapes. Credit: Laboratory of Biomolecular Engineering and Nanomedicine/Rice University
Initial studies showed that adding magnetic nanoparticles to the endothelial cells and then applying a magnetic field affected the cells’ internal scaffolding, called microtubules. These structures are responsible for maintaining the tight cell to cell connections. The team took the studies a step further by growing the cells in specialized petri dishes containing tiny, tube-shaped channels. Applying a magnetic field to the cells caused the cell-cell junctions to form gaps, making the blood vessel structures leaky. Simply turning off the magnetic field closed up the gaps within a few hours.
Though a lot of research remains, the team aims to apply this on-demand induction of cell leakiness along with adding the magnetic nanoparticles to stem cell therapy products to help target the treatment to specific area. In a press release, team leader Dr. Gang Bao spoke about possible applications to arthritis therapy:
“The problem is how to accumulate therapeutic stem cells around the knee and keep them there. After injecting the nanoparticle-infused cells, we want to put an array of magnets around the knee to attract them.”
To differentiate or not differentiate: new insights During the body’s development, stem cells must differentiate, or specialize, into functional cells – like liver, heart, brain. But once that specialization occurs, the cells lose their pluripotency, or the ability to become any type of cell. So, stem cells must balance the need to differentiate with the need to make copies of itself to maintain an adequate supply of stem cells to complete the development process. And even after a fully formed baby is born, it’s still critical for adult stem cells to balance the need to regenerate damaged tissue versus stashing away a pool of stem cells in various organs for future regeneration and replacement of damaged or diseased tissues.
Visualizing activation of Nanog gene activity (bright green spot) within cell nucleus. Image: Courtesy of Bony De Kumar, Ph.D., and Robb Krumlauf, Ph.D., Stowers Institute for Medical Research
A report this week in the Proceedings of the National Academy of Sciences finds evidence that the two separate processes – differentiation and pluripotency – directly communicate with each other as way to ensure a proper balance between the two states.
The study, carried out by researchers at Stowers Institute for Medical Research in Kansas City, Missouri, focused on the regulation of two genes: Nanog and Hox. Nanog is critical for maintaining a stem cell’s ability to become a specialized cell type. In fact, it’s one of the four genes initially used to reprogram adult cells back into induced pluripotent stem cells. The Hox gene family is responsible for generating a blueprint of the body plan in a developing embryo. Basically, the pattern of Hox gene activity helps generate the body plan, basically predetermining where the various body parts and organs will form.
Now, both Nanog and Hox proteins act by binding to DNA and turning on a cascade of other genes that ultimately maintain pluripotency or promote differentiation. By examining these other genes, the researchers were surprised to find that both Nanog and Hox were bound to both the pluripotency and differentiation genes. They also found that Nanog and Hox can directly inhibit each other. Taken together, these results suggest that exquisite control of both processes occurs cross regulation of gene activity.
Dr. Robb Krumlauf one of authors on the paper talked about the significance of the result in a press release:
“Over the past 10 to 20 years, biologists have shown that cells are actively assessing their environment, and that they have many fates they can choose. The regulatory loops we’ve found show how the dynamic nature of cells is being maintained.”
Color me stem cells Looking to improve your life and the life of those around you? Then we highly recommend you pay a visit to today’s issue of Right Turn, a regular Friday feature of Signals, the official blog of CCRM, Canada’s public-private consortium supporting the development of regenerative medicine technologies.
Collage sample of CCRM’s new coloring sheets. Image: copyright CCRM 2017
As part of an public outreach effort they have created four new coloring sheets that depict stem cells among other sciency topics. They’ve set up a DropBox link to download the pictures so you can get started right away.
Adult coloring has swept the nation as the hippest new pastime. And it’s not just a frivolous activity, as coloring has been shown to have many healthy benefits like reducing stressed and increasing creativity. Just watch any kid who colors. In fact, share these sheet with them, it’s intended for children too.
It’s full steam ahead for the development of induced pluripotent stem cell (iPSC)-derived clinical trials. That’s according to a group at the National Human Genome Research Institute in Bethesda, Maryland who report this week in PNAS that the process of reprogramming a skin cell into the embryonic stem cell-like state of an iPSC does not itself cause an increased number of genetic mutations.
Ever since the technique was first devised ten years ago, there has been a lot of excitement about applying IPSCs to cell therapies for patients with unmet medical needs. Unlike human embryonic stem cells (hESCs) which are generated through the destruction of a fertilized embryo, iPSCs avoid ethical concerns because they’re obtained using adult cells like blood or skin. And the fact they’re patient specific carries the additional advantage of delivering iPSC-derived therapies back to the same patient with less concerns of rejection by the immune system.
Still, the use of iPSC-derived therapies has certainly not been worry-free and their translation into human clinical trials has been slow. One big concern is that the process of reprogramming inherently causes cell stress leading to an increased rate of genetic mutations in the cells. An abnormal number of mutations is bad news for cell therapies because they could carry an increased risk of becoming cancerous after being injected into a patient – an event that would end up causing more harm than good. Previous DNA sequencing studies comparing iPSCs with their cell source (skin, blood, etc.) identified many new sequence mutations in the iPSCs. But other studies suggested that many of those mutations already existed in the source cells and so they were essentially inherited during the iPSC process.
The team in this study sought out a definitive answer by tackling this mutation question using an “apples to apples” approach. To explain their approach, let’s first understand a technical detail about the iPSC method. When the iPSC reprogramming factors are added to the adult skin cells, the process is not efficient and only a few become iPSCs. Single iPSCs are then isolated and allowed to divide and make clones of themselves. This population of cells is called a cell “line” and takes several rounds of cell division to multiply into enough numbers to analyze their DNA sequence.
Credit: Darryl Leja and Ernesto Del Aguila III, NHGRI
So the researchers decided to also go through the process of making cell lines from the original skin cells but in this set they did not add the iPSC reprogramming factors. Now, they could compare the fate of DNA sequences in skin cell lines with and without the iPSC reprogramming method. The sequencing results showed that mutations occurred at the same rate in both the skin cell lines and the iPSC cell lines. This direct comparison suggests that iPSCs aren’t any less stable than non-reprogrammed cells. This finding bodes well for moving ahead with iPS-derived clinical trials. That’s certainly the perspective Erika Mijin Kwon, a co-author on the publication:
“Based on this data, we plan to start using iPSCs to gain a deeper understanding of how diseases start and progress,” said Kwon, in a press release. “We eventually hope to develop new therapies to treat patients with leukemia using their own iPSCs. We encourage other researchers to embrace the use of iPSCs.”
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.
Directing the creation of T cells. To paraphrase the GOP Presidential nominee, any sane person LOVES, LOVES LOVES their T cells, in a HUGE way, so HUGE. They scamper around the body getting rid of viruses and the tiny cancers we all have in us all the time. A CIRM-funded team at CalTech has worked out the steps our genetic machinery must take to make more of them, a first step in letting physicians turn up the action of our immune systems.
We have known for some time the identity of the genetic switch that is the last, critical step in turning blood stem cells into T cells, but nothing in our body is as simple as a single on-off event. The Caltech team isolated four genetic factors in the path leading to that main switch and, somewhat unsuspected, they found out those four steps had to be activated sequentially, not all at the same time. They discovered the path by engineering mouse cells so that the main T cell switch, Bcl11b, glows under a microscope when it is turned on.
“We identify the contributions of four regulators of Bcl11b, which are all needed for its activation but carry out surprisingly different functions in enabling the gene to be turned on,” said Ellen Rothenberg, the senior author in a university press release picked up by Innovations Report. “It’s interesting–the gene still needs the full quorum of transcription factors, but we now find that it also needs them to work in the right order.”
Video primer on stem cells in the brain. In conjunction with an article in its August issue, Scientific Americanposted a video from the Brain Forum in Switzerland of Elena Cattaneo of the University of Milan explaining the basics of adult versus pluripotent stem cells, and in particular how we are thinking about using them to repair diseases in the brain.
The 20-minute talk gives a brief review of pioneers who “stood alone in unmarked territory.” She asks how can stem cells be so powerful; and answers by saying they have lots of secrets and those secrets are what stem cell scientist like her are working to unravel. She notes stem cells have never seen a brain, but if you show them a few factors they can become specialized nerves. After discussing collaborations in Europe to grow replacement dopamine neurons for Parkinson’s disease, she went on to describe her own effort to do the same thing in Huntington’s disease, but in this case create the striatal nerves lost in that disease.
The video closes with a discussion of how basic stem cell research can answer evolutionary questions, in particular how genetic changes allowed higher organisms to develop more complex nervous systems.
CIRM Science Officers Kelly Shepard and Kent Fitzgerald
A stem cell review that hits close to home. IEEE Pulse, a publication for scientists who mix engineering and medicine and biology, had one of their reporters interview two of our colleagues on CIRM’s science team. They asked senior science officers Kelly Shepard and Kent Fitzgerald to reflect on how the stem cell field has progressed based on their experience working to attract top researchers to apply for our grants and watching our panel of outside reviewers select the top 20 to 30 percent of each set of applicants.
One of the biggest changes has been a move from animal stem cell models to work with human stem cells, and because of CIRM’s dedicated and sustained funding through the voter initiative Proposition 71, California scientists have led the way in this change. Kelly described examples of how mouse and human systems are different and having data on human cells has been critical to moving toward therapies.
Kelly and Kent address several technology trends. They note how quickly stem cell scientists have wrapped their arms around the new trendy gene editing technology CRISPR and discuss ways it is being used in the field. They also discuss the important role of our recently developed ability to perform single cell analysis and other technologies like using vessels called exosomes that carry some of the same factors as stem cells without having to go through all the issues around transplanting whole cells.
“We’re really looking to move things from discovery to the clinic. CIRM has laid the foundation by establishing a good understanding of mechanistic biology and how stem cells work and is now taking the knowledge and applying it for the benefit of patients,” Kent said toward the end of the interview.
Jake Javier and his family
Jake’s story: one young man’s journey to and through a stem cell transplant; As a former TV writer and producer I tend to be quite critical about the way TV news typically covers medical stories. But a recent story on KTVU, the Fox News affiliate here in the San Francisco Bay Area, showed how these stories can be done in a way that balances hope, and accuracy.
Reporter Julie Haener followed the story of Jake Javier – we have blogged about Jake before – a young man who broke his spine and was then given a stem cell transplant as part of the Asterias Biotherapeutics clinical trial that CIRM is funding.
It’s a touching story that highlights the difficulty treating these injuries, but also the hope that stem cell therapies holds out for people like Jake, and of course for his family too.
If you want to see how a TV story can be done well, this is a great example.
Understanding a complicated neurodegenerative disorder like Parkinson’s disease (PD) is no easy task. While there are known genetic risk factors that cause PD, only about 10 percent of cases are linked to a genetic cause. The majority of patients suffer from the sporadic form of PD, where the causes are unknown but thought to be a combination of environmental, lifestyle and genetic factors.
Unfortunately, there is no cure for PD, and current treatments only help PD patients manage the symptoms of their disease and inevitably lose their effectiveness over time. Another troubling issue is that doctors and scientists don’t have good ways to predict who is at risk for PD, which closes an important window of opportunity for delaying the onset of this devastating disease.
Scientists have long sought relevant disease models that mimic the complicated pathological processes that occur in PD. Current animal models have failed to truly represent what is going on in PD patients. But the field of Parkinson’s research is not giving up, and scientists continue to develop new and improved tools, many of them based on human stem cells, to study how and why this disease happens.
New Stem Cell Tools for Parkinson’s
Speaking of new tools, scientists from the Buck Institute for Research on Aging published a study that generated 10 induced pluripotent stem cell (iPS cell) lines derived from PD patients carrying well known genetic mutations linked to PD. These patient cell lines will be a useful resource for studying the underlying causes of PD and for potentially identifying therapeutics that prevent or treat this disorder. The study was partly funded by CIRM and was published today in the journal PLOS ONE.
Dr. Xianmin Zeng, the senior author on the study and Associate Professor at Buck Institute, developed these disease cell lines as tools for the larger research community to use. She explained in a news release:
Xianmin Zeng, Buck Institute
“We think this is the largest collection of patient-derived lines generated at an academic institute. We believe the [iPS cell] lines and the datasets we have generated from them will be a valuable resource for use in modeling PD and for the development of new therapeutics.”
The datasets she mentions are part of a large genomic analysis that was conducted on the 10 patient stem cell lines carrying common PD mutations in the SNCA, PARK2, LRRK2, or GBA genes as well as control stem cell lines derived from healthy patients of the same age. Their goal was to identify changes in gene expression in the Parkinson’s stem cell lines as they matured into the disease-affected nerve cells of the brain that could yield clues into how PD develops at the molecular level.
Using previous methods developed in her lab, Dr. Zeng coaxed the iPS cell lines into neural stem cells (brain stem cells) and then further into dopaminergic neurons – the nerve cells that are specifically affected and die off in Parkinson’s patients. Eight of the ten patient lines were able to generate neural stem cells, and all of the neural stem cell lines could be coaxed into dopaminergic neurons – however, some lines were better at making dopaminergic neurons than others.
When they analyzed these lines, surprisingly they found that the overall gene expression patterns were similar between diseased and healthy cell lines no matter what cell stage they were at (iPS cells, neural stem cells, and neurons). They next stressed the cells by treating them with a drug called MPTP that is known to cause Parkinson’s like symptoms in humans. MPTP treatment of dopaminergic neurons derived from PD patient iPS cell lines did cause changes in gene expression specifically related to mitochondrial function and death, but these changes were also seen in the healthy dopaminergic neurons.
Parkinson’s, It’s complicated…
These interesting findings led the authors to conclude that while their new stem cell tools certainly display some features of PD, individually they are not sufficient to truly model all aspects of PD because they represent a monogenic (caused by a single mutation) form of the disease.
They explain in their conclusion that the power of their PD patient iPS cell lines will be achieved when combined with additional patient lines, better controls, and more focused data analysis:
“Our studies suggest that using single iPSC lines for drug screens in a monogenic disorder with a well-characterized phenotype may not be sufficient to determine causality and mechanism of action due to the inherent variability of biological systems. Developing a database to increase the number of [iPS cell] lines, stressing the system, using isogenic controls [meaning the lines have identical genes], and using more focused strategies for analyzing large scale data sets would reduce the impact of line-to-line variations and may provide important clues to the etiology of PD.”
Brian Kennedy, Buck Institute President and CEO, also pointed out the larger implications of this study by commenting on how these stem cell tools could be used to identify potential drugs that specifically target certain Parkinson’s mutations:
Brian Kennedy, Buck Institute
“This work combined with dozens of other control, isogenic and reporter iPSC lines developed by Dr. Zeng will enable researchers to model PD in a dish. Her work, which we are extremely proud of, will help researchers dissect how genes interact with each other to cause PD, and assist scientists to better understand what experimental drugs are doing at the molecular level to decide what drugs to use based on mutations.”
Overall, what inspires me about this study is the author’s mission to provide a substantial number of PD patient stem cell lines and genomic analysis data to the research community. Hopefully their efforts will inspire other scientists to add more stem cell tools to the Parkinson’s tool box. As the saying goes, “it takes an army to move a mountain”, in the case of curing PD, the mountain seems more like Everest, and we need all the tools we can get.