Stanford scientists are growing brain stem cells in bulk using 3D hydrogels

This blog is the final installment in our #MonthofCIRM series. Be sure to check out our other blogs highlighting important advances in CIRM-funded research and initiatives.

Neural stem cells from the brain have promising potential as cell-based therapies for treating neurological disorders such as Alzheimer’s disease, Parkinson’s, and spinal cord injury. A limiting factor preventing these brain stem cells from reaching the clinic is quantity. Scientists have a difficult time growing large populations of brain stem cells in an efficient, cost-effective manner while also maintaining the cells in a stem cell state (a condition referred to as “stemness”).

CIRM-funded scientists from Stanford University are working on a solution to this problem. Dr. Sarah Heilshorn, an associate professor of Materials Science and Engineering at Stanford, and her team are engineering 3D hydrogel technologies to make it easier and cheaper to expand high-quality neural stem cells (NSCs) for clinical applications. Their research was published yesterday in the journal Nature Materials.

Stem Cells in 3D

Similar to how moviegoers prefer to watch the latest Star Wars installment in 3D, compared to the regular screen, scientists are turning to 3D materials called hydrogels to grow large numbers of stem cells. Such an environment offers more space for the stem cells to proliferate and expand their numbers while keeping them happy in their stem cell state.

To find the ideal conditions to grow NSCs in 3D, Heilshorn’s team tested two important properties of hydrogels: stiffness and degradability (or how easy it is to remodel the structure of the hydrogel material). They designed a range of hydrogels, made from proteins with elastic qualities, that varied in these two properties. Interestingly, they found that the stiffness of the material did not have a profound effect on the “stemness” of NSCs. This result contrasts with other types of adult stem cells like muscle stem cells, which quickly differentiate into mature muscle cells when exposed to stiffer materials.

On the other hand, the researchers found that it was crucial for the NSCs to be able to remodel their 3D environment. NSCs maintained their stemness by secreting enzymes that broke down and rearranged the molecules in the hydrogels. If this enzymatic activity was blocked, or if the cells were grown in hydrogels that couldn’t be remodeled easily, NSCs lost their stemness and stopped proliferating. The team tested two other hydrogel materials and found the same results. As long as the NSCs were in a 3D environment they could remodel, they were able to maintain their stemness.

NSCs maintain their stemness in hydrogels that can be remodeled easily. Nestin (green) and Sox2 (red) are markers that indicate “high-quality” NSCs. (Image courtesy of Chris Madl, Stanford)

Caption: NSCs maintain their stemness in hydrogels that can be remodeled easily. Nestin (green) and Sox2 (red) are markers that indicate “high-quality” NSCs. (Images courtesy of Chris Madl)

Christopher Madl, a PhD student in the Heilshorn lab and the first author on the study, explained how remodeling their 3D environment allows NSCs to grow robustly in an interview with the Stem Cellar:

Chris Madl

“In this study, we identified that the ability of the neural stem cells to dynamically remodel the material was critical to maintaining the correct stem cell state. Being able to remodel (or rearrange) the material permitted the cells to contact each other.  This cell-cell contact is responsible for maintaining signals that allow the stem cells to stay in a stem-like state. Our findings allow expansion of neural stem cells from relatively low-density cultures (aiding scale-up) without the use of expensive chemicals that would otherwise be required to maintain the correct stem cell behavior (potentially decreasing cost).”

To 3D and Beyond

When asked what’s next on the research horizon, Heilshorn said two things:

Sarah Heilshorn

“First, we want to see if other stem cell types – for example, pluripotent stem cells – are also sensitive to the “remodel-ability” of materials. Second, we plan to use our discovery to create a low-cost, reproducible material for efficient expansion of stem cells for clinical applications. In particular, we’d like to explore the use of a single material platform that is injectable, so that the same material could be used to expand the stem cells and then transplant them.”

Heilshorn is planning to apply the latter idea to advance another study that her team is currently working on. The research, which is funded by a CIRM Tools and Technologies grant, aims to develop injectable hydrogels containing NSCs derived from human induced pluripotent stem cells to treat mice, and hopefully one day humans, with spinal cord injury. Heilshorn explained,

“In our CIRM-funded studies, we learned a lot about how neural stem cells interact with materials. This lead us to realize that there’s another critical bottleneck that occurs even before the stage of transplantation: being able to generate a large enough number of high-quality stem cells for transplantation. We are developing materials to improve the transplantation of stem cell-derived therapies to patients with spinal cord injuries. Unfortunately, during the transplantation process, a lot of cells can get damaged. We are now creating injectable materials that prevent this cell damage during transplantation and improve the survival and engraftment of NSCs.”

An injectable material that promotes the expansion of large populations of clinical grade stem cells that can also differentiate into mature cells is highly desired by scientists pursuing the development of cell replacement therapies. Heilshorn and her team at Stanford have made significant progress on this front and are hoping that in time, this technology will prove effective enough to reach the clinic.

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CIRM stories that caught our eye: UCSD team stops neuromuscular disease in mice, ALS trial enrolls 1st patients and Q&A with CIRM Prez

Ordinarily, we end each week at the Stem Cellar with a few stem cell stories that caught our eye. But, for the past couple of weeks we’ve been busy churning out stories related to our Month of CIRM blog series, which we hope you’ve found enlightening. To round out the series, we present this “caught our eye” blog of CIRM-specific stories from the last half of October.

Stopping neurodegenerative disorder with blood stem cells. (Karen Ring)

CIRM-funded scientists at the UC San Diego School of Medicine may have found a way to treat a progressive neuromuscular disorder called Fredreich’s ataxia (FA). Their research was published last week in the journal Science Translational Medicine.

FA is a genetic disease that attacks the nervous tissue in the spinal cord leading to the loss of sensory nerve cells that control muscle movement. Early on, patients with FA experience muscle weakness and loss of coordination. As the disease progresses, FA can cause scoliosis (curved spine), heart disease and diabetes. 1 in 50,000 Americans are afflicted with FA, and there is currently no effective treatment or cure for this disease.

cherqui

In this reconstituted schematic, blood stem cells transplanted in a mouse model of Friedreich’s ataxia differentiate into microglial cells (red) and transfer mitochondrial protein (green) to neurons (blue), preventing neurodegeneration. Image courtesy of Stephanie Cherqui, UC San Diego School of Medicine.

UCSD scientists, led by CIRM grantee Dr. Stephanie Cherqui, found in a previous study that transplanting blood stem and progenitor cells was an effective treatment for preventing another genetic disease called cystinosis in mice. Cherqui’s cystinosis research is currently being funded by a CIRM late stage preclinical grant.

In this new study, the UCSD team was curious to find out whether a similar stem cell approach could also be an effective treatment for FA. The researchers used an FA transgenic mouse model that was engineered to harbor two different human mutations in a gene called FXN, which produces a mitochondrial protein called frataxin. Mutations in FXN result in reduced expression of frataxin, which eventually leads to the symptoms experienced by FA patients.

When they transplanted healthy blood stem and progenitor cells (HSPCs) from normal mice into FA mice, the cells developed into immune cells called microglia and macrophages. They found the microglia in the brain and spinal cord and the macrophages in the spinal cord, heart and muscle tissue of FA mice that received the transplant. These normal immune cells produced healthy frataxin protein, which was transferred to disease-affected nerve and muscle cells in FA mice.

Cherqui explained their study’s findings in a UC San Diego Health news release:

“Transplantation of wildtype mouse HSPCs essentially rescued FA-impacted cells. Frataxin expression was restored. Mitochondrial function in the brains of the transgenic mice normalized, as did in the heart. There was also decreased skeletal muscle atrophy.”

In the news release, Cherqui’s team acknowledged that the FA mouse model they used does not perfectly mimic disease progression in humans. In future studies, the team will test their method on other mouse models of FA to ultimately determine whether blood stem cell transplants will be an effective treatment option for FA patients.

Brainstorm’s CIRM funded clinical trial for ALS enrolls its first patients
“We have been conducting ALS clinical trials for more than two decades at California Pacific Medical Center (CPMC) and this is, by far, the most exciting trial in which we have been involved to date.”

Those encouraging words were spoken by Dr. Robert Miller, director of CPMC’s Forbes Norris ALS Research Center in an October 16th news release posted by Brainstorm Cell Therapeutics. The company announced in the release that they had enrolled the first patients in their CIRM-funded, stem cell-based clinical trial for the treatment of amyotrophic lateral sclerosis (ALS).

BrainStorm

Also known as Lou Gehrig’s disease, ALS is a cruel, devastating disease that gradually destroys motor neurons, the cells in the brain or spinal cord that instruct muscles to move. People with the disease lose the ability to move their muscles and, over time, the muscles atrophy leading to paralysis. Most people with ALS die within 3 to 5 years from the onset of symptoms and there is no effective therapy for the disease.

Brainstorm’s therapy product, called NurOwn®, is made from mesenchymal stem cells that are taken from the patient’s own bone marrow. These stem cells are then modified to boost their production and release of factors, which are known to help support and protect the motor neurons destroyed by the disease. Because the cells are derived directly from the patient, no immunosuppressive drugs are necessary, which avoids potentially dangerous side effects. The trial aims to enroll 200 patients and is a follow up of a very promising phase 2 trial. CIRM’s $16 million grant to the Israeli company which also has headquarters in the United States will support clinical studies at multiple centers in California. And Abla Creasey, CIRM’s Senior Director of Strategic Infrastructure points out in the press release, the Agency support of this trial goes beyond this single grant:

“Brainstorm will conduct this trial at multiple sites in California, including our Alpha Clinics Network and will also manufacture its product in California using CIRM-funded infrastructure.”

An initial analysis of the effectiveness of NurOwn® in this phase 3 trial is expected in 2019.

CIRM President Maria Millan reflects on her career, CIRM’s successes and the outlook for stem cell biology 

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Maria T. Millan, M.D., CIRM President and CEO

RegMedNet a networking website that provides content related to the regenerative medicine community, published an interview this morning with Maria Millan, M.D., CIRM’s new President and CEO. The interview covers the impressive accomplishments that Dr. Millan had achieved before coming to CIRM, with details that even some of us CIRM team members may not have been aware of. In addition to describing her pre-CIRM career, Dr. Millan also describes the Agency’s successes during her term as Vice President of CIRM’s Therapeutics group and she gives her take on future of Agency and the stem cell biology field in general over the next five years and beyond. File this article under “must read”.

Turning the corner with the FDA and NIH; CIRM creates new collaborations to advance stem cell research

FDAThis blog is part of the Month of CIRM series on the Stem Cellar

A lot can change in a couple of years. Just take our relationship with the US Food and Drug Administration (FDA).

When we were putting together our Strategic Plan in 2015 we did a survey of key players and stakeholders at CIRM – Board members, researchers, patient advocates etc. – and a whopping 70 percent of them listed the FDA as the biggest impediment for the development of stem cell treatments.

As one stakeholder told us at the time:

“Is perfect becoming the enemy of better? One recent treatment touted by the FDA as a regulatory success had such a high clinical development hurdle placed on it that by the time it was finally approved the standard of care had evolved. When it was finally approved, five years later, its market potential had significantly eroded and the product failed commercially.”

Changing the conversation

To overcome these hurdles we set a goal of changing the regulatory landscape, finding a way to make the system faster and more efficient, but without reducing the emphasis on the safety of patients. One of the ways we did this was by launching our “Stem Cell Champions” campaign to engage patients, patient advocates, the public and everyone else who supports stem cell research to press for change at the FDA. We also worked with other organizations to help get the 21st Century Cures Act passed.

21 century cures

Today the regulatory landscape looks quite different than it did just a few years ago. Thanks to the 21st Century Cures Act the FDA has created expedited pathways for stem cell therapies that show promise. One of those is called the Regenerative Medicine Advanced Therapy (RMAT) designation, which gives projects that show they are both safe and effective in early-stage clinical trials the possibility of an accelerated review by the FDA. Of the first projects given RMAT designation, three were CIRM-funded projects (Humacyte, jCyte and Asterias)

Partnering with the NIH

Our work has also paved the way for a closer relationship with the National Institutes of Health (NIH), which is looking at CIRM as a model for advancing the field of regenerative medicine.

In recent years we have created a number of innovations including introducing CIRM 2.0, which dramatically improved our ability to fund the most promising research, making it faster, easier and more predictable for researchers to apply. We also created the Stem Cell Center  to make it easier to move the most promising research out of the lab and into clinical trials, and to give researchers the support they need to help make those trials successful. To address the need for high-quality stem cell clinical trials we created the CIRM Alpha Stem Cell Clinic Network. This is a network of leading medical centers around the state that specialize in delivering stem cell therapies, sharing best practices and creating new ways of making it as easy as possible for patients to get the care they need.

The NIH looked at these innovations and liked them. So much so they invited CIRM to come to Washington DC and talk about them. It was a great opportunity so, of course, we said yes. We expected them to carve out a few hours for us to chat. Instead they blocked out a day and a half and brought in the heads of their different divisions to hear what we had to say.

A model for the future

We hope the meeting is, to paraphrase Humphrey Bogart at the end of Casablanca, “the start of a beautiful friendship.” We are already seeing signs that it’s not just a passing whim. In July the NIH held a workshop that focused on what will it take to make genome editing technologies, like CRISPR, a clinical reality. Francis Collins, NIH Director, invited CIRM to be part of the workshop that included thought leaders from academia, industry and patients advocates. The workshop ended with a recommendation that the NIH should consider building a center of excellence in gene editing and transplantation, based on the CIRM model (my emphasis).  This would bring together a multidisciplinary disease team including, process development, cGMP manufacturing, regulatory and clinical development for Investigational New Drug (IND) filing and conducting clinical trials, all under one roof.

dr_collins

Dr. Francis Collins, Director of the NIH

In preparation, the NIH visited the CIRM-funded Stem Cell Center at the City of Hope to explore ways to develop this collaboration. And the NIH has already begun implementing these suggestions starting with a treatment targeting sickle cell disease.

There are no guarantees in science. But we know that if you spend all your time banging your head against a door all you get is a headache. Today it feels like the FDA has opened the door and that, together with the NIH, they are more open to collaborating with organizations like CIRM. We have removed the headache, and created the possibility that by working together we truly can accelerate stem cell research and deliver the therapies that so many patients desperately need.

 

 

 

 

 

 

Meet Team CIRM: the People Behind the Mission to Save Lives

During our Month of CIRM blog series, we’ve been featuring the researchers, clinicians, patients, patient advocates, institutions and companies that are striving to accelerate stem cell treatments to patients with unmet medical needs.

GameBallWinners

But there’s one group that we haven’t discussed yet: the dedicated members of the CIRM team.  They don’t get a lot of attention in our blog but they are critical to the day to day operations of the Agency. I don’t have the word space in this blog to introduce you to them all so, for today, say hello to a few of our 2017 CIRM Game Ball winners.  At our quarterly Team meetings, we honor and celebrate members whose efforts reflect our “All In” culture with this award.




CIRM’s Clinical Dashboard: An Interactive Guide Makes Learning About Stem Cell Trials Easier

This blog is part of the Month of CIRM series on the Stem Cellar.

The questions we get most frequently from members of the public are about our clinical trials. Typically, people want to know what stem cell-based trials our Agency is funding or whether we’re funding trials for specific diseases or disorders that either they or their loved one are afflicted with.

During these conversations, we refer people to our website’s clinical trials page, which lists all of the trials CIRM has funded since our Agency was established in 2004. This page previously featured a simple table (see image below) that listed basic information about CIRM-funded trials including links to CIRM grants and to trial details on clinicaltrials.gov. This table was not the most exciting way to feature our clinical portfolio, but it did what it needed to do at the time.

CIRM’s former clinical trials table.

Here’s where I reference Bob Dylan’s famous lyric, “the times, they are a-changing”. CIRM’s clinical portfolio has rapidly expanded from 17 funded trials to 40 since the launch of our Strategic Plan in 2016. That’s 23 new trials in less than two years. The number of CIRM-funded trials will continue to climb steadily each year as we strive to reach our Strategic Plan’s goal of funding an additional 27 new trials by 2020.

This rapid expansion in our clinical portfolio is very exciting because it brings us closer to achieving our mission of accelerating stem cell treatments to patients with unmet medical needs. It also means that it’s finally time to retire our old clinical trials table and replace it with something that does our expanding portfolio justice, and makes it easier for anyone who is interested to learn about the trials we’re funding.

That something is already here and it’s called the Clinical Dashboard. It’s an interactive Dashboard that allows users to filter through CIRM’s clinical portfolio by clicking on tabs for major disease indications. Users can also sort trials by disease area, investigator, organization, and the phase or status of the trial.

The CIRM Clinical Dashboard was launched in September, 2017.

The Dashboard is a snapshot of the essential information a scientist, patient, or member of the public needs to know about our trials. Users who want to learn more about a given trial, beyond what’s listed in the Dashboard, can click on the arrow in the “Detail” column. This takes users to a detailed trials page featuring information about the treatment being tested, the CIRM clinical award that funded the trial, information about trial’s design, goals and patient enrollment status, and any recently published news about the trial.

The details page also has resources specifically for patients including a link for patients to contact the trial sponsor to ask about trial eligibility and enrollment and links to general information about stem cell trials on the CIRM website and from other organizations.

You can learn more about specific CIRM-funded trials by clicking the “Detail” icon on the Dashboard.

With our new Clinical Dashboard, we hope to raise the visibility of CIRM’s expanding clinical trial portfolio and to provide an all-in-one resource that is useful for multiple audiences.

Dr. Maria Millan, President and CEO of CIRM, concluded:

“CIRM is a global leader in funding high-quality stem cell trials for patients. We created the Clinical Dashboard for our website so that people can easily access important information about CIRM-funded trials and the promising treatments they are testing. As our Agency continues to fund new trials, we hope the Clinical Dashboard will prove to be an invaluable resource for patients, the public, and the stem cell research community.”

Getting faster, working smarter: how changing the way we work is paying big dividends

This blog is part of the Month of CIRM series

Speeding up the way you do things isn’t always a good idea. Just ask someone who got a ticket for going 65mph in a 30mph zone. But at CIRM we have found that doing things at an accelerated pace is paying off in a big way.

When CIRM started back in 2004 we were, in many ways, a unique organization. That meant we pretty much had to build everything from scratch, creating our own ways of asking for applications, reviewing those applications, funding them etc. Fast forward ten years and it was clear that, as good a job as we did in those early days, there was room for improvement in the way we operated.

So we made some changes. Big changes.

We adopted as our mantra the phrase “operational excellence.” It doesn’t exactly trip off the tongue but it does reflect what we were aiming for. The Business Dictionary defines operational excellence as:

 “A philosophy of the workplace where problem-solving, teamwork, and leadership results in the ongoing improvement in an organization.”

We didn’t want to just tinker with the way we worked, we wanted to reinvent every aspect of our operation. To do that we involved everyone in the operation. We held a series of meetings where everyone at CIRM, and I do mean everyone, was invited to join in and offer their ideas on how to improve our operation.

CIRM2.0_Logo

The end result was CIRM 2.0. At the time we described it as “a radical overhaul” of the way we worked. That might have been an understatement. We increased the speed, frequency and volume of the programs we offered, making it easier and more predictable for researchers to apply to us for funding, and faster for them to get that funding if they were approved.

For example, before 2.0 it took almost two years to go from applying for funding for a clinical trial to actually getting that funding. Today it takes around 120 days.

But it’s not just about speed. It’s also about working smarter. In the past if a researcher’s application for funding for a clinical trial failed it could be another 12 months before they got a chance to apply again. With many diseases 12 months could be a death sentence. So we changed the rules. Now if you have a project ready for a clinical trial you can apply any time. And instead of recommending or not recommending a project, basically voting it up or down, our independent panel of expert reviewers now give researchers with good but not great applications constructive feedback, enabling the researchers to make the changes needed to improve their project, and reapply for funding within 30 days.

This has not only increased the number of applications for clinical trials, it has also increased the quality of those applications.

We made similar changes in our Discovery and Translation programs. Increasing the frequency of each award, making it easier for researchers to know when the next round of funding was coming up. And we added incentives to encourage researchers to move successful projects on to the next level. We wanted to create a pipeline of the most promising projects steadily moving towards the clinic.

The motivation to do this comes from our patients. At CIRM we are in the time business. Many of the patients who are looking to stem cells to help them don’t have the luxury of time; they are rapidly running out of it. So we have a responsibility to do all we can to reduce the amount of time it takes to get the most promising therapies to them, without in any way compromising safety and jeopardizing their health.

By the end of 2016 those changes were very clearly paying dividends as we increased the frequency of reviews and the number of projects we reviewed but at the same time decreased the amount of time it took us to do all that.

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But we are not done yet. We have done a good job of improving the way we work. But there is always room to be even better, to go even faster and be more efficient.

We are not done accelerating. Not by a long shot.

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.


Related Links:

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.