Stem Cell Tools: Helping Scientists Understand Complex Diseases

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:

Josh Stuart

“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:

Clay Fischer

“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.

What’s next?

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.


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Stem Cell Tools: Helping Scientists Model Complex Diseases

This blog is part of the Month of CIRM series and the first of two blogs focused on how CIRM-funded infrastructure initiatives are developing useful tools to advance stem cell research. 

Human stem cells are powerful tools for studying human disease.  Animal models like mice have been and continue to be important for studying physiological systems, but they are still different than human systems.  Other types of human cells studied in the lab often are isolated from cancers or modified to multiply indefinitely.  However, the genetic DNA blueprint of these modified cells are irreparably altered from the normal tissues that they came from.

Human pluripotent stem cells are unique in that they can be grown in the lab and turned into any type of normal cell in the body.  Many scientists now believe that creating such stem cell lines from patients and developing ‘disease-in-a-dish’ models will provide important insights that will lead to treatments for the disorders from which they came.  Challenges still remain to develop these models to their fullest potential.  Because the genetics underlying human disease is complex, detailed genetic information about each stem cell line, as well as a large number of lines  to represent the genetic variability between patients will be needed to make progress.

To address this need, CIRM funded the creation of the world’s largest induced pluripotent stem cell bank, which we call the CIRM iPSC Repository.  iPSCs are similar to embryonic stem cells in that they can develop into any cell type found in the body, but they differ in how they are derived. Scientists can take human skin or blood cells and genetically reprogram them into iPSCs that have the same genetic makeup, including any disease-causing mutations, as the person from which the original cells were taken. Embryonic stem cells, on the other hand, are derived from left over embryos donated by couples undergoing in vitro fertilization (IVF) treatments.

The CIRM iPSC Repository was established to harness the power of iPSCs as tools for disease modeling and drug discovery. The Repository currently offers scientists around the world access to over 1500 high-quality iPSC lines covering diseases of the brain, heart, liver, lung, and eye, and the collection will eventually hold over 3000 lines.  All iPSC lines are linked to publicly-accessible demographic and clinical information.

Making the Cell Lines

Making the iPSC Repository was no easy task – it took a village of doctors, scientists, patients and healthy volunteers. First, clinicians across California collected blood and skin samples from over 2800 people including individuals with common diseases, rare diseases and healthy controls. CIRM then awarded a grant to Cellular Dynamics International to create iPSC lines from these donors, and a second grant to the Coriell Institute to store and distribute the lines to interested labs around the world. Creating such a large number of lines in a single concerted effort has been a challenging logistical feat that has taken almost five years and is projected to finish in early 2018.

Joachim Hallmayer

We spoke with one of the tissue collectors, a scientist named Dr. Joachim Hallmayer at Stanford University, about the effort it took to obtain tissue samples for the Repository. Hallmayer is a Professor of Psychiatry and Behavioral Sciences at Stanford who studies Autism Spectrum Disorder (ASD) in children. With funding from a CIRM Tissue Collection for Disease Modeling award, Hallmayer collected tissue samples from children with ASD and children with normal development. His efforts resulted in the 164 ASD and 134 control samples for the Repository.

Hallmayer emphasized that each sample donation required significant attention and education from the clinical staff to the donor.  Communicating with patients and walking them through the consent process for donating their tissue for this purpose is an extremely important issue that is often overlooked. “Conveying information about the tissue collection process to patients takes a lot of time. However, deconstructing the consent process is essential for patients to understand what they are donating and why,” explained Hallmayer.

Now that the ASD lines are available, Hallmayer and his colleague Dr. Ruth O’Hara are formulating a plan to model ASD in a dish by differentiating the iPSC lines into neurons affected by this disorder. Says O’Hara:

Ruth O’Hara

“While the examination of live tissue from other organ systems has become increasingly viable, examining live neurons from patients with brain disorders has simply not been possible. Using iPSC-derived neurons, for the first time we can study live nerve cells from actual patients and compare these cells to those from humans without the disorder.”

Using iPSCs to Model Psychiatric Disorders

Ultimately, the goal of iPSCs for modeling disease is to identify mechanisms and therapeutic targets for the disorders that they represent.  Studying a disease through a single iPSC line may not shed enough light on that disorder.  Just as people have diverse traits, the way that a disease can affect individuals is also diverse.  Studying large numbers of lines in a time and cost-efficient manner that represent these diverse traits, and the genetic causes that underlie them, can be a powerful method to understand and address diseases.

 To leverage the iPSC collection for this purpose, CIRM and a group of scientists at the Broad Institute’s Stanley Center for Psychiatric Research and Harvard University have entered into a collaboration to study psychiatric disorders such as ASD.  Because the donor samples were collected on the basis of clinical information, the genetic information about what caused their disease remains unknown.  Therefore, the Stanley Center will embark on whole genome sequencing (WGS) of hundreds of lines from the CIRM iPSC repository. Adding donor WGS sequence information to the CIRM repository will significantly increase its value, as scientists will be able to use DNA sequence information to select the ideal lines for disease modeling and therapeutic discovery efforts. The collaboration aims to identify the genes that shape neuronal phenotypes in iPSC-derived neurons from patients with psychiatric disorders.

“A central challenge today is to discover how inherited genetic variation gives rise to functional variation in the properties of neurons and other cells,” said Steven McCarroll, Director of Genetics at the Broad Institute’s Stanley Center for Psychiatric Research, and associate professor at Harvard Medical School’s Department of Genetics. “We hope with the analysis of cells from very large numbers of genetically diverse individuals will begin to address longstanding problems at the interface of human genetics and biology.”

iPSC derived neurons growing in a dish. (Image courtesy of Ralda Nehme, Research Scientist at the Broad Institute).

Such efforts require technologies such as Drop-seq, developed in the McCarroll lab, where genome-wide expression of thousands of separate cells can be analyzed in one experiment. These efforts also rely on scaling functional analysis of stem cell-based disease models, a vexing bottleneck for the field. “The CIRM iPSC Repository is the largest and most ambitious of its kind”, said Kevin Eggan, Professor of Stem Cell and Regenerative Biology at Harvard University, and Director of Stem Cell Biology at the Broad Institute’s Stanley Center for Psychiatric Research. Efforts underway in Dr. Eggan’s lab are directed at developing approaches to analyze large numbers of stem cell lines in parallel.

“The scale of the CIRM iPSC collection will allow us to investigate how variation that is common among many of us predisposes certain individuals to major mental illnesses such as autism and other neurodevelopmental disorders. We are incredibly excited about entering this long-term collaboration.”

Members of the Eggan and McCarroll labs at the Broad Institute’s Stanley Center for Psychiatric Research. (Image courtesy of Kiki Lilliehook)

From Cell Lines to Data

It’s clear from these stories, that the iPSC Repository is a unique and powerful tool for the stem cell research community. But for the rewards to be truly reaped, more tools are needed that will help scientists study these cell lines. This is where the CIRM Genomics Initiative comes into play.

Be sure to read Part 2 of our Stem Cell Tools series tomorrow to find out how our Genomics Initiative is funding the development of genomic and bioinformatics tools that will allow scientists to decipher complex stem cell data all the way from mapping the developmental states of cells to predicting the accuracy of stem cell-based models.

This blog was written in collaboration with Dr. Kiki Lilliehook, the Manager of the Stem Cell Program at the Stanley Center for Psychiatric Research at the Broad Institute in Cambridge, Massachusetts.

Streamlining Stem Cell Therapy Development for Impatient Patients

During this third week of the Month of CIRM, we are focusing on CIRM’s Infrastructure programs which are all focused on helping to accelerate stem cell treatments to patients with unmet medical needs.

Time is money. It’s a cliché but still very true, especially in running a business. The longer it takes to get things done, the more costs you’ll most likely face. But in the business of developing new medical therapies, time is also people’s lives.

Currently, it takes about eight years to move a promising stem cell treatment from the lab into clinical trials. For patients with fatal, incurable diseases, that is eight years too long. And even when promising therapies reach clinical trials, only about 1 out of 10 get approved, according to a comprehensive 2014 study in Nature Biotechnology. These sobering stats slow the process of getting treatments to patients with unmet medical needs.

While a lack of therapy effectiveness or safety play into the low success rate, other factors can have a significant impact on the delay or suspension of a trial. An article, “Why Do Clinical Trials Fail?” in Clinical Trials Arena from a couple years back outlined a few. Here’s a snippet from that article:

  • “Poor study design: Selecting the wrong patients, the wrong dosing and the wrong endpoint, as well as bad data and bad site management cause severe problems.”
  • “Complex protocol: Simple is better. A complex protocol, which refers to trying to answer too many questions in one single trial, can produce faulty data and contradictory results.”
  • “Poor management: A project manager who does not have enough experience in costing and conducting clinical trials will lead to weak planning, with no clear and real timelines, and to ultimate failure.”

CIRM recognized that these clinical trial planning and execution setbacks can stem from the fact that, although lab researchers are experts at transforming an idea into a candidate therapy, they may not be masters in navigating the complex regulatory requirements of the Food and Drug Administration (FDA). Many simply don’t have the experience to get those therapies off the ground by themselves.

Lab researchers are experts at transforming an idea into a candidate therapy but most are inexperienced at navigating the complex regulatory requirements of the Food and Drug Administration (FDA).

So, to help make this piece of the therapy development process more efficient and faster, the CIRM governing Board last year approved the launch of the Translating Center and Accelerating Center: two novel infrastructure programs which CIRM grantees can tap into as they carry their promising candidate therapies from lab experiments in cells to preclinical studies in animals to clinical trials in people. Both centers were awarded to QuintilesIMS which collectively dubbed them The Stem Cell Center.

The Stem Cell Center acts as a one-stop-shop, stem cell therapy development support system for current and prospective CIRM grantees, giving them advanced priority for QuintilesIMS services. So how does it work? When a scientist’s initial idea for a cell therapy gains traction and, through a lot of effort in the lab, matures into a bona fide therapy candidate to treat a particular disease, the next big step is to prepare the therapy for testing in people. But that’s easier said than done. To ensure safety, the Food and Drug Administration requires a rigorous set of tests and documentation that make up an Investigational New Drug (IND) application, which must be submitted before any testing in people take can place in the U.S.

That’s where the Translation Center comes into the picture. It carries out the necessary research activities to show, as much as is possible in animals, that the therapy is safe. The Translating Center also helps at this stage with manufacturing the cell therapy product so that it’s of a consistent quality for both the preclinical and future clinical trial studies. If all goes as planned, the grantee will have the necessary pieces to file an IND. At this stage, the Translating Center coordinates with the Accelerating Center which focuses on supporting the many facets of a clinical study including the IND filing, clinical trial design, monitoring of patient safety, and project management.

Because the work of Translating and Accelerating Centers is focused on these regulatory activities day in and day out, they have the know-how to pave a clearer path, with fewer pitfalls, for the grantee to navigate the complex maze we call cell therapy development. It’s not just helpful for the researchers seeking approval from the FDA, but it helps the FDA too. Because cell therapies are still so new, creating a standardized, uniform approach to stem cell-based clinical trial projects will help the FDA streamline their evaluation of the projects.

Ultimately, and most importantly, all of those gears running smoothly in sync will help leave a lasting legacy for California and the world: an acceleration in the development of stem cell treatment for patients with unmet medical needs.

The Alpha Stem Cell Clinics: Innovation for Breakthrough Stem Cell Treatments

During this third week of the Month of CIRM, we are focusing on CIRM’s Infrastructure programs which are all focused on helping to accelerate stem cell treatments to patients with unmet medical needs.

So here is the question of the day: What is the world’s largest network of medical centers dedicated to providing stem cell treatments to patients?

The answer is the CIRM Alpha Stem Cell Clinics Network.

The CIRM Alpha Stem Cell Clinics Network consists of leading medical institutions throughout California.

The ASCC Network consists of six leading medical centers throughout California. In 2015, the Network was launched in southern California at the City of Hope, UC Irvine, UC Los Angeles, and UC San Diego. In September 2017, CIRM awarded funding to UC Davis and UC San Francisco to enable the Network to better serve patients throughout the state. Forty stem cell clinical trials have been conducted within the Network with hundreds of patients being treat for a variety of conditions, including:

  • Cancers of the blood, brain, lung and other sites
  • Organ diseases of the heart and kidney
  • Pediatric diseases
  • Traumatic injury to the brain and spine

A complete list of clinical trials may be found on our website.

The Alpha Clinics at UC Los Angeles and San Francisco are working collaboratively on breakthrough treatments for serious childhood diseases. This video highlights a CIRM-funded clinical trial at the UCLA Alpha Clinic that is designed to restore the immune system of patients with life-threatening immune deficiencies. A similar breakthrough treatment is also being used at the UCLA Alpha Clinic to treat sickle cell disease. A video describing this treatment is below.

Why do we need a specialized Network for stem cell clinical trials?

Stem cell treatments are unique in many ways. First, they consist of cells or cell products that frequently require specialized processing. For example, the breakthrough treatments for children, described above, requires the bone marrow to be genetically modified to correct defects. This “gene therapy” is performed in the Alpha Clinic laboratories, which are specifically designed to implement cutting edge gene therapy techniques on the patient’s stem cells.

Many of the cancer clinical trials also take the patient’s own cells and then process them in a laboratory. This processing is designed to enhance the patient’s ability to fight cancer using their own immune cells. Each Alpha Clinic has specialized laboratories to process cells, and the sites at City of Hope and UC Davis have world-class facilities for stem cell manufacturing. The City of Hope and Davis facilities produce high quality therapeutic products for commercial and academic clinical trial sponsors. Because of this ability, the Network has become a prime location internationally for clinical trials requiring processing and manufacturing services.

Another unique feature of the Network is its partnership with CIRM, whose mission is to accelerate stem cell treatments for patients with unmet medical needs. Often, this means developing treatments for rare diseases in which the patient population is comparatively small. For example, there about 40-100 immune deficient children born each year in the United States. We are funding clinical trials to help treat those children. The Network is also treating rare brain and blood cancers.

To find patients that may benefit from these treatments, the Network has developed the capacity to confidentially query over 20 million California patient records. If a good match is found, there is a procedure in place, that is reviewed by an ethics committee, where the patient’s doctor can be notified of the trial and pass that information to the patient. For patients that are interested in learning more, each Alpha Clinic has a Patient Care Coordinator with the job of coordinating the process of educating patients about the trial and assisting them if they choose to participate.

How Can I Learn More?

If you are a patient or a family member and would like to learn more about the CIRM Alpha Clinics, click here. There is contact information for each clinic so you can learn more about specific trials, or you can visit our Alpha Clinics Trials page for a complete list of trials ongoing in the Network.

If you are a patient or a trial sponsor interested in learning more about the services offered through our Alpha Clinics Network, visit our website.

Building California’s stem cell research community, from the ground up

For week three of the Month of CIRM, our topic is infrastructure. What is infrastructure? Read on for a big picture overview and then we’ll fill in the details over the course of the week.

When CIRM was created in 2001, our goal was to grow the stem cell research field in California. But to do that, we first had to build some actual buildings. Since then, our infrastructure programs have taken on many different forms, but all have been focused on a single mission – helping accelerate stem cell research to patients with unmet medical needs.
CIRM_Infrastucture-program-iconScreen Shot 2017-10-16 at 10.58.38 AM

In the early 2000’s, stem cell scientists faced a quandary. President George W. Bush had placed limits on how federal funds could be used for embryonic stem cell research. His policy allowed funding of research involving some existing embryonic stem cell lines, but banned research that developed or conducted research on new stem lines.

Many researchers felt the existing lines were not the best quality and could only use them in a limited capacity. But because they were dependent on the government to fund their work, had no alternative but to comply. Scientists who chose to use non-approved lines were unable to use their federally funded labs for stem cell work.

The creation of CIRM changed that. In 2008, CIRM launched its Major Facilities Grant Program. The program had two major goals:

1) To accommodate the growing numbers of stem cell researchers coming in California as a result of CIRM’s grants and funding.

2) To provide new research space that didn’t have to comply with the federal restrictions on stem cell research.

Over the next few years, the program invested $271million to help build 12 new research facilities around California from Sacramento to San Diego. The institutions used CIRM’s funding to leverage and attract an additional $543 million in funds from private donors and institutions to construct and furnish the buildings.

These world-class laboratories gave scientists the research space they needed to work with any kind of stem cell they wanted and develop new potential therapies. It also enabled the institutions to bring together under one roof, all the stem cell researchers, who previously had been scattered across each campus.

One other important benefit was the work these buildings provided for thousands of construction workers at a time of record unemployment in the industry. Here’s a video about the 12 facilities we helped build:

But building physical facilities was just our first foray into developing infrastructure. We were far from finished.

In the early days of stem cell research, many scientists used cells from different sources, created using different methods. This meant it was often hard to compare results from one study to another. So, in 2013 CIRM created an iPSC Repository, a kind of high tech stem cell bank. The repository collected tissue samples from people who have different diseases, turned those samples into high quality stem cell lines – the kind known as induced pluripotent stem cells (iPSC) – and then made those samples available to researchers around the world. This not only gave researchers a powerful resource to use in developing a deeper understanding of different diseases, but because the scientists were all using the same cell lines that meant their findings could be compared to each other.

That same year we also launched a plan to create a new, statewide network of clinics that specialize in using stem cells to treat patients. The goal of the Alpha Stem Cell Clinics Network is to support and accelerate clinical trials for programs funded by the agency, academic researchers or industry. We felt that because stem cell therapies are a completely new way of treating diseases and disorders, we needed a completely new way of delivering treatments in a safe and effective manner.

The network began with three clinics – UC San Diego, UCLA/UC Irvine, and City of Hope – but at our last Board meeting was expanded to five with the addition of UC Davis and UCSF Benioff Children’s Hospital Oakland. This network will help the clinics streamline challenging processes such as enrolling patients, managing regulatory procedures and sharing data and will speed the testing and distribution of experimental stem cell therapies. We will be posting a more detailed blog about how our Alpha Clinics are pushing innovative stem cell treatments tomorrow.

As the field advanced we knew that we had to find a new way to help researchers move their research out of the lab and into clinical trials where they could be tested in people. Many researchers were really good at the science, but had little experience in navigating the complex procedures needed to get the green light from the US Food and Drug Administration (FDA) to test their work in a clinical trial.

So, our Agency created the Translating (TC) and Accelerating Centers (AC). The idea was that the TC would help researchers do all the preclinical testing necessary to apply for permission from the FDA to start a clinical trial. Then the AC would help the researchers set up the trial and actually run it.

In the end, one company, Quintiles IMS, won both awards so we combined the two entities into one, The Stem Cell Center, a kind of one-stop-shopping home to help researchers move the most promising treatments into people.

That’s not the whole story of course – I didn’t even mention the Genomics Initiative – but it’s hard to cram 13 years of history into a short blog. And we’re not done yet. We are always looking for new ways to improve what we do and how we do it. We are a work in progress, and we are determined to make as much progress as possible in the years to come.

Saving Ronnie: Stem Cell & Gene Therapy for Fatal Bubble Baby Disease [Video]

During this second week of the Month of CIRM, we’ve been focusing on the people who are critical to accomplishing our mission to accelerate stem cell treatments to patients with unmet medical needs.

These folks include researchers, like Clive Svendsen and his team at Cedars-Sinai Medical Center who are working tirelessly to develop a stem cell therapy for ALS. My colleague Karen Ring, CIRM’s Social Media and Website Manager, featured Dr. Svendsen and his CIRM-funded clinical trial in Monday’s blog. And yesterday, in recognition of Stem Cell Awareness Day, Kevin McCormack, our Senior Director of Public Communications, blogged about the people within the stem cell community who have made, and continue to make, the day so special.

Today, in a new video, I highlight a brave young patient, Ronnie, and his parents who decided to participate in a CIRM-funded clinical trial run by St. Jude Children’s Research Hospital and UC San Francisco in an attempt to save Ronnie’s life from an often-fatal disease called severe combined immunodeficiency (SCID). This disorder, also known as bubble baby disease, leaves newborns without a functioning immune system which can turn a simple cold into a potentially deadly infection.

Watch this story’s happy ending in the video above.

For more details about all CIRM-funded clinical trials, visit our clinical trials page and read our clinical trials brochure which provides brief overviews of each trial.

Can Stem Cell Therapies Help ALS Patients?

A scientist’s fifteen-year journey to develop a stem cell-based therapy that could one day help ALS patients.

Jan Kaufman

Photo of Clive Svendsen (top left) and Jan & Jeff Kaufman

“Can stem cells help me Clive?”

The sentence appeared slowly on a computer screen, each character separated by a pause while its author searched for the next character using a device controlled by his eye muscle.

The person asking the question was Jeff Kaufman, a Wisconsin man in his 40s completely paralyzed by amyotrophic lateral sclerosis (ALS). On the receiving end was Clive Svendsen, PhD, then a scientist at the University of Wisconsin-Madison, determined to understand how stem cells could help patients like Jeff.

Also known as Lou Gehrig’s disease, ALS is a rapid, aggressive neurodegenerative disease with a two to four-year life expectancy. ALS destroys the nerve cells that send signals from the brain and spinal cord to the muscles that control movement. Denervation, or loss of nerves, causes muscle weakness and atrophy, leaving patients unable to control their own bodies. Currently there are two FDA-approved ALS drugs in the US – riluzole and a new drug called edaravone (Radicava). However, they only slow disease progression in some ALS patients by a few months and there are no effective treatments that stop or cure the disease.

Given this poor prognosis, making ALS the focus of his research career was an easy decision. However, developing a therapeutic strategy was challenging to Svendsen. “The problem with ALS is we don’t know the cause,” he said. “Around 10% of ALS cases are genetic, and we know some of the genes involved, but 90% of cases are sporadic.” He explained that this black box makes it difficult for scientists to know where to start when trying to develop treatments for sporadic ALS cases that have no drug targets.

From Parkinson’s disease to ALS

Svendsen, who moved to Cedars-Sinai in Los Angeles to head the Cedars-Sinai Board of Governors Regenerative Medicine Institute in 2010, has worked on ALS for the past 15 years. Before that, he studied Parkinson’s disease, a long-term neurodegenerative disorder that affects movement, balance and speech. Unlike ALS, Parkinson’s patients have a longer life expectancy and more treatment options that alleviate symptoms of the disease, making their quality of life far better than ALS patients.

Clive Svendsen, PhD, Director, Regenerative Medicine Institute. (Image courtesy of Cedars-Sinai)

“I chose to work on ALS mainly because of the effects it has on ALS families,” explained Svendsen. “Being normal one day, and then becoming rapidly paralyzed was hard to see.”

The transition from Parkinson’s to ALS was not without a scientific reason however. Svendsen was studying how an important growth factor in the brain called Glial Cell Line-Derived Neurotrophic Factor or GDNF could be used to protect dopamine neurons in order to treat Parkinson’s patients. However other research suggested that GDNF was even more effective at protecting motor neurons, the nerve cells destroyed by ALS.

Armed with the knowledge of GDNF’s ability to protect motor neurons, Svendsen and his team developed an experimental stem cell-based therapy that they hoped would treat patients with the sporadic form of ALS. Instead of using stem cells to replace the motor neurons lost to ALS, Svendsen placed his bets on making another cell type in the brain, the astrocyte.

Rooting for the underdog

Astrocytes are the underdog cells of the brain, often overshadowed by neurons that send and receive information from the central nervous system to our bodies. Astrocytes have many important roles, one of the most critical being to support the functions of neurons. In ALS, astrocytes are also affected but in a different way than motor neurons. Instead of dying, ALS astrocytes become dysfunctional and thereby create a toxic environment inhospitable to the motors neurons they are supposed to assist.

Fluorescent microscopy of astrocytes (red) and cell nuclei (blue). Image: Wikipedia.

“While the motor neurons clearly die in ALS, the astrocytes surrounding the motor neurons are also sick,” said Svendsen. “It’s a huge challenge to replace a motor neuron and make it grow a cable all the way to the muscle in an adult human. We couldn’t even get this to work in mice. So, I knew a more realistic strategy would be to replace the sick astrocytes in an ALS patients with fresh, healthy astrocytes. This potentially would have a regenerative effect on the environment around the existing motor neurons.”

The big idea was to combine both GDNF and astrocyte replacement. Svendsen set out to make healthy astrocytes from human brain stem cells that also produce therapeutic doses of GDNF and transplant these cells into the ALS patient spinal cord. Simply giving patients GDNF via pill wouldn’t work because the growth factor is unable to enter the brain or spinal cord tissue where it is needed. The hope, instead, was that the astrocytes would secrete the protective factor that would keep the patients’ motor neurons healthy and alive.

With critical funding from a CIRM Disease Team grant, Svendsen and his colleagues at Cedars-Sinai tested the feasibility of transplanting human brain stem cells (also referred to as neural progenitor cells) that secreted GDNF into a rat model of ALS. Their results were encouraging – the neural progenitor cells successfully developed into astrocytes and secreted GDNF, which collectively protected the rat motor neurons.

Svendsen describes the strategy as “a double whammy”: adding both healthy astrocytes and GDNF secretion to protect the motor neurons. “Replacing astrocytes has the potential to rejuvenate the niche where the motor neurons are. I think that’s a very powerful experimental approach to ALS.”

A fifteen year journey from bench to bedside

With promising preclinical data under his belt, Svendsen and his colleagues, including Robert Baloh, MD, PhD, director of neuromuscular medicine at the Cedars-Sinai Department of Neurology, and neurosurgeon J. Patrick Johnson, MD, designed a clinical trial that would test this experimental therapy in ALS patients. In October 2016, CIRM approved funding for a Phase I/IIa clinical trial assessing the safety of this novel human neural progenitor cell and gene therapy.

Clive Svendsen, PhD, director of the Cedars-Sinai Board of Governors Regenerative Medicine Institute, and Robert Baloh, MD, PhD, director of neuromuscular medicine in the Cedars-Sinai Department of Neurology, in the lab. Svendsen is the sponsor of a current ALS clinical trial at Cedars-Sinai and the overall director of the program. Baloh is the principal investigator for the clinical trial. (Image courtesy of Cedars-Sinai)

This is a first-in-human study, and as such, the U.S. Food and Drug Administration (FDA) required the team to transplant the cells into only one side of the lumbar spinal cord, which effectively means that only one of the patient’s legs will get the treatment. This will allow for a comparison of the function and progression of ALS in the leg on the treated side of the spinal cord compared with the leg on the untreated side.

The trial was approved to treat a total of 18 patients and started in May 2017.

 Svendsen, who first started working on ALS back in 2002, describes his path to the clinic as a “very long and windy road.” He emphasized that this journey wouldn’t be possible without the hard work of his team, Cedars-Sinai and financial support from CIRM.

“It took ten years of preclinical studies and an enormous amount of work from many different people. Just producing the cells that we’re going to use took three years and a lot of trials and tribulations to make it a clinically viable product. It was really thanks to CIRM’s funding and the support of Cedars-Sinai that we got through it all. Without that kind of infrastructure, I can safely say we wouldn’t be here today.”

This “behind-the-scenes” view of how much time and effort it takes to translate a stem cell therapy from basic research into the clinic isn’t something that the public is often exposed to or aware of. Just as “Rome wasn’t built in a day,” Svendsen stressed that good quality stem cell trials take time, and that it’s important for people know how complicated these trials are.

It’s all about the patients

So, what motivates Svendsen to continue this long and harrowing journey to develop a treatment for ALS? He said the answer is easy. “I’m doing it for the patients,” he explained. “I’m not doing this for the money or glory. I just want to develop something that works for ALS, so we can help these patients.”

Svendsen revisited his story about Jeff Kaufman, a man he befriended at the Wisconsin ALS Chapter in 2003. Jeff had three daughters and a son, a wonderful wife, and was a successful lawyer when he was diagnosed with ALS.

“Jeff had basically everything, and then he was stricken with ALS. I still remember going to his house and he could only move his eyes at that point. He tapped out the words ‘Can stem cells help me Clive?’ on his computer screen. And my heart sank because I knew how much and how long it was going to take. I was very realistic so I said, ‘Yes Jeff, but it’s going to take time and money. And even then, it’s a long shot.’ And he told me to go for it, and that stuck in my brain.”

It’s people like Jeff that make Svendsen get out of bed every morning and doggedly pursue a treatment for ALS. Sadly, Jeff passed away due to complications from ALS in 2010. Svendsen says what Jeff and other patients go through is tragic and unfair.

“There’s a gene that goes along with ALS and it’s called the ‘nice person gene,’” he said. “People with ALS are nice. I can’t explain it, but neurologists would say the same thing. You feel like it’s just not fair that it happens to those people.”

The future of stem cell therapies for ALS

It’s clear from speaking with Svendsen, that he is optimistic about the future of stem cell-based therapies for ALS. Scientists still need to unravel the actual causes of ALS. But the experimental stem cell treatments currently in development, including Svendsen’s, will hopefully prove effective at delaying disease progression and give ALS patients more quality years to live.

In the meantime, what concerns Svendsen is how vulnerable ALS patients are to being misled by unapproved stem cell clinics that claim to have cures. “Unfortunately, there are a lot of charlatans out there, and there are a lot of false claims being made. People feed off the desperation that you have in ALS. It’s not fair, and it’s completely wrong. They’ll mislead patients by saying ‘For $40,000 you can get a cure!’”

Compelling stories of patients cured of knee pain or diseases like ALS with injections of their own adult stem cells pop up in the news daily. Many of these stories refer to unapproved treatments from clinics that don’t provide scientific evidence that these treatments are safe and effective. Svendsen said there are reasonable, research-backed trials that are attempting to use adult stem cells to treat ALS. He commented, “I think it’s hard for the public to wade through all of these options and understand what’s real and what’s not real.”

Svendsen’s advice for ALS patients interested in enrolling in a stem cell trial or trying a new stem cell treatment is to be cautious. If a therapy sounds too good to be true, it probably is, and if it costs a lot of money, it probably isn’t legitimate, he explained.

He also wants patients to understand the reality of the current state of ALS stem cell trials. The approved stem cell trials he is aware of are not at the treatment stage yet.

“If you’re enrolled in a stem cell trial that is funded and reputable, then they will tell you honestly that it’s not a treatment. There is currently no approved treatment using stem cells for ALS,” Svendsen said.

This might seem like discouraging news to patients who don’t have time to wait for these trials to develop into treatments, but Svendsen pointed out that the when he started his research 15 years ago, the field of stem cell research was still in its infancy. A lot has been accomplished in the past decade-and-a-half and with talented scientists dedicated to ALS research like Svendsen, the next 15 years will likely offer new insights into ALS and hopefully stem cell-based treatments for a devastating disease that has no cure.

Svendsen hopes that one day, when someone like Jeff Kaufman asks him “Can stem cells help me Clive?” He’ll be able to say, yes they can, yes they can.

CIRM-Funded Clinical Trials Targeting Blood and Immune Disorders

This blog is part of our Month of CIRM series, which features our Agency’s progress towards achieving our mission to accelerate stem cell treatments to patients with unmet medical needs.

This week, we’re highlighting CIRM-funded clinical trials to address the growing interest in our rapidly expanding clinical portfolio. Today we are featuring trials in our blood and immune disorders portfolio, specifically focusing on sickle cell disease, HIV/AIDS, severe combined immunodeficiency (SCID, also known as bubble baby disease) and rare disease called chronic granulomatous disease (CGD).

CIRM has funded a total of eight trials targeting these disease areas, all of which are currently active. Check out the infographic below for a list of those trials.

For more details about all CIRM-funded clinical trials, visit our clinical trials page and read our clinical trials brochure which provides brief overviews of each trial.

CIRM-Funded Clinical Trials Targeting the Heart, Pancreas, and Kidneys

This blog is part of our Month of CIRM series, which features our Agency’s progress towards achieving our mission to accelerate stem cell treatments to patients with unmet medical needs.

This week, we’re highlighting CIRM-funded clinical trials to address the growing interest in our rapidly expanding clinical portfolio. Today we are featuring trials in our organ systems portfolio, specifically focusing on diseases of the heart/vasculature system, the pancreas and the kidneys.

CIRM has funded a total of nine trials targeting these disease areas, and eight of these trials are currently active. Check out the infographic below for a list of our currently active trials.

For more details about all CIRM-funded clinical trials, visit our clinical trials page and read our clinical trials brochure which provides brief overviews of each trial.

CIRM-Funded Clinical Trials Targeting Brain and Eye Disorders

This blog is part of our Month of CIRM series, which features our Agency’s progress towards achieving our mission to accelerate stem cell treatments to patients with unmet medical needs.

 This week, we’re highlighting CIRM-funded clinical trials to address the growing interest in our rapidly expanding clinical portfolio. Our Agency has funded a total of 40 trials since its inception. 23 of these trials were funded after the launch of our Strategic Plan in 2016, bringing us close to the half way point of our goal to fund 50 new clinical trials by 2020.

Today we are featuring CIRM-funded trials in our neurological and eye disorders portfolio.  CIRM has funded a total of nine trials targeting these disease areas, and seven of these trials are currently active. Check out the infographic below for a list of our currently active trials.

For more details about all CIRM-funded clinical trials, visit our clinical trials page and read our clinical trials brochure which provides brief overviews of each trial.