A model for success

Dr. Maria Millan, CIRM’s President & CEO

Funding models are rarely talked about in excited tones.  It’s normally relegated to the dry tomes of academia. But in CIRM’s case, the funding model we have created is not just fundamental to our success in advancing regenerative medicine in California, it’s also proving to be a model that many other agencies are looking at to see if they can replicate it.

A recent article in the journal Cell & Gene Therapy Insights looks at what the CIRM model does and how it has achieved something rather extraordinary.

Full disclosure. I might be a tad biased here as the article was written by my boss, Dr. Maria Millan, and two of my colleagues, Dr. Sohel Talib and Dr. Shyam Patel.

I won’t go into huge detail here (you can get that by reading the article itself) But the article “highlights 3 elements of CIRM’s funding model that have enabled California academic researchers and companies to de-risk development of novel regenerative medicine therapies and attract biopharma industry support.”

Those three elements are:

1. Ensuring that funding mechanisms bridge the entire translational “Valley of Death”

2. Constantly optimizing funding models to meet the needs of a rapidly evolving industry

3. Championing the portfolio and proactively engaging potential industry partners

As an example of the first, they point to our Disease Team awards. These were four-year investments that gave researchers with promising projects the time, support and funds they needed to not only develop a therapy, but also move it out of academia into a company and into patients.  Many of these projects had struggled to get outside investment until CIRM stepped forward. One example they offer is this one.

“CIRM Disease Team award funding also enabled Dr. Irving Weissman and the Stanford University team to discover, develop and obtain first-in-human clinical data for the innovative anti-CD47 antibody immunotherapy approach to cancer. The spin-out, Forty Seven, Inc., then leveraged CIRM funding as well as venture and public market financing to progress clinical development of the lead candidate until its acquisition by Gilead Sciences in April 2020 for $4.9B.”

But as the field evolved it became clear CIRM’s funding model had to evolve too, to better meet the needs of a rapidly advancing industry. So, in 2015 we changed the way we worked. For example, with clinical trial stage projects we reduced the average time from application to funding from 22 months to 120 days. In addition to that applications for new clinical stage projects were able to be submitted year-round instead of only once or twice a year as in the past.

We also created hard and fast milestones for all programs to reach. If they met their milestone funding continued. If they didn’t, funding stopped. And we required clinical trial stage projects, and those for earlier stage for-profit companies, to put up money of their own. We wanted to ensure they had “skin in the game” and were as committed to the success of their project as we were.

Finally, to champion the portfolio we created our Industry Alliance Program. It’s a kind of dating program for the researchers CIRM funds and companies looking to invest in promising projects. Industry partners get a chance to look at our portfolio and pick out projects they think are interesting. We then make the introductions and see if we can make a match.

And we have.

“To date, the IAP has also formally enrolled 8 partners with demonstrated commitment to cell and gene therapy development. The enrolled IAP partners represent companies both small and large, multi-national venture firms and innovative accelerators.

Over the past 18 months, the IAP program has enabled over 50 one-on-one partnership interactions across CIRM’s portfolio from discovery stage pluripotent stem cell therapies to clinical stage engineered HSC therapies.”

As the field continues to mature there are new problems emerging, such as the need to create greater manufacturing capacity to meet the growth in demand for high quality stem cell products. CIRM, like all other agencies, will also have to evolve and adapt to these new demands. But we feel with the model we have created, and the flexibility we have to pivot when needed, we are perfectly situated to do just that.

Partners in health

From left to right: Heather Dahlenburg, Jan Nolta, Jeannine Logan White, Sheng Yang
From left to right: Heather Dahlenburg, staff research associate; Jan Nolta, director of the Stem Cell Program; Jeannine Logan White, advanced cell therapy project manager; Sheng Yang, graduate student, Bridges Program, Humboldt State University, October 18, 2019. (AJ Cheline/UC Davis)

At CIRM we are modest enough to know that we can’t do everything by ourselves. To succeed we need partners. And in UC Davis we have a terrific partner. The work they do in advancing stem cell research is exciting and really promising. But it’s not just the science that makes them so special. It’s also their compassion and commitment to caring for patients.

What follows is an excerpt from an article by Lisa Howard on the work they do at UC Davis. When you read it you’ll see why we are honored to be a part of this research.

Gene therapy research at UC Davis

UC Davis’ commitment to stem cell and gene therapy research dates back more than a decade.

In 2010, with major support from the California Institute for Regenerative Medicine (CIRM), UC Davis launched the UC Davis Institute for Regenerative Cures, which includes research facilities as well as a Good Manufacturing Practice (GMP) facility.

In 2016, led by Fred Meyers, a professor in the School of Medicine, UC Davis launched the Center for Precision Medicine and Data Sciences, bringing together innovations such as genomics and biomedical data sciences to create individualized treatments for patients.

Last year, the university launched the Gene Therapy Center, part of the IMPACT Center program.

Led by Jan Nolta, a professor of cell biology and human anatomy and the director of the UC Davis Institute for Regenerative Cures, the new center leverages UC Davis’ network of expert researchers, facilities and equipment to establish a center of excellence aimed at developing lifelong cures for diseases.

Nolta began her career at the University of Southern California working with Donald B. Kohn on a cure for bubble baby disease, a condition in which babies are born without an immune system. The blood stem cell gene therapy has cured more than 50 babies to date.

Work at the UC Davis Gene Therapy Center targets disorders that potentially can be treated through gene replacement, editing or augmentation.

“The sectors that make up the core of our center stretch out across campus,” said Nolta. “We work with the MIND Institute a lot. We work with the bioengineering and genetics departments, and with the Cancer Center and the Center for Precision Medicine and Data Sciences.”

A recent UC Davis stem cell study shows a potential breakthrough for healing diabetic foot ulcers with a bioengineered scaffold made up of human mesenchymal stem cells (MSCs). Another recent study revealed that blocking an enzyme linked with inflammation enables stem cells to repair damaged heart tissue. A cell gene therapy study demonstrated restored enzyme activity in Tay-Sachs disease affected cells in humanized mouse models.

Several cell and gene therapies have progressed to the point that ongoing clinical trials are being conducted at UC Davis for diseases, including sickle-cell anemia, retinopathy, muscle injury, dysphasia, advanced cancer, and Duchenne muscular dystrophy, among others.

“Some promising and exciting research right now at the Gene Therapy Center comes from work with hematopoietic stem cells and with viral vector delivery,” said Nolta.

Hematopoietic stem cells give rise to other blood cells. A multi-institutional Phase I clinical trial using hematopoietic stem cells to treat HIV-lymphoma patients is currently underway at UC Davis.

.Joseph Anderson

Joseph Anderson

“We are genetically engineering a patient’s own blood stem cells with genes that block HIV infection,” said Joseph Anderson, an associate professor in the UC Davis Department of Internal Medicine. The clinical trial is a collaboration with Mehrdad Abedi, the lead principal investigator.

“When the patients receive the modified stem cells, any new immune system cell, like T-cell or macrophage, that is derived from one of these stem cells, will contain the HIV-resistant genes and block further infection,” said Anderson.

He explained that an added benefit with the unique therapy is that it contains an additional gene that “tags” the stem cells. “We are able to purify the HIV-resistant cells prior to transplantation, thus enriching for a more protective cell population.

Kyle David Fink

Kyle David Fink

Kyle David Fink, an assistant professor of neurology at UC Davis, is affiliated with the Stem Cell Program and Institute for Regenerative Cures. His lab is focused on leveraging institutional expertise to bring curative therapies to rare, genetically linked neurological disorders.

“We are developing novel therapeutics targeted to the underlying genetic condition for diseases such as CDKL5 deficiency disorder, Angelman, Jordan and Rett syndromes, and Juvenile Huntington’s disease,” said Fink.

The lab is developing therapies to target the underlying genetic condition using DNA-binding domains to modify gene expression in therapeutically relevant ways. They are also creating novel delivery platforms to allow these therapeutics to reach their intended target: the brain.

“The hope is that these highly innovative methods will speed up the progress of bringing therapies to these rare neurodegenerative disease communities,” said Fink.Jasmine Carter, a graduate research assistant at the UC Davis Stem Cell Program.

Jasmine Carter, a graduate research assistant at the UC Davis Stem Cell Program, October 18, 2019. (AJ Cheline/UC Davis)

Developing potential lifetime cures

Among Nolta’s concerns is how expensive gene therapy treatments can be.

“Some of the therapies cost half a million dollars and that’s simply not available to everyone. If you are someone with no insurance or someone on Medicare, which reimburses about 65 percent, it’s harder for you to get these life-saving therapies,” said Nolta.

To help address that for cancer patients at UC Davis, Nolta has set up a team known as the “CAR T Team.”

Chimeric antigen receptor (CAR) T-cell therapy is a type of immunotherapy in which a patient’s own immune cells are reprogrammed to attack a specific protein found in cancer cells.

“We can develop our own homegrown CAR T-cells,” said Nolta. “We can use our own good manufacturing facility to genetically engineer treatments specifically for our UC Davis patients.”

Although safely developing stem cell treatments can be painfully slow for patients and their families hoping for cures, Nolta sees progress every day. She envisions a time when gene therapy treatments are no longer considered experimental and doctors will simply be able to prescribe them to their patients.

“And the beauty of the therapy is that it can work for the lifetime of a patient,” said Nolta.

Battling COVID and turning back the clock on stem cell funding

Coronavirus

Battling the virus that causes COVID-19 is something that is top of everyone’s mind right now. That’s why CIRM is funding 17 different projects targeting the virus. But one of the most valuable tools in helping develop vaccines against a wide variety of diseases in the past is now coming under threat. We’ll talk about both issues in a live broadcast we’re holding on Wednesday, October 14th at noon (PDT).

That date is significant because it’s Stem Cell Awareness Day and we thought it appropriate to host a meeting looking at two of the most important issues facing the field.

The first part of the event will focus on the 17 projects that CIRM is funding that target COVID-19. This includes three clinical trials aiming to treat people who have been infected with the virus and are experiencing some of the more severe effects, such as damaged lungs.

We’ll also look at some of the earlier stage research that includes:

  • Work to help develop a vaccine
  • Using muscle stem cells to help repair damage to the diaphragm in patients who have spent an extended period on a ventilator
  • Boosting immune system cells to help fight the virus

The second part of the event will look at ways that funding for stem cell research at the federal level is once again coming into question. The federal government has already imposed new restrictions on funding for fetal tissue research, and now there are efforts in Congress to restrict funding for embryonic stem cell research.

The impacts could be significant. Fetal tissue has been used for decades to help develop some of the most important vaccines used today including rubella, chickenpox, hepatitis A, and shingles. They have also been used to make approved drugs against diseases including hemophilia, rheumatoid arthritis, and cystic fibrosis.

We’ll look at some of the reasons why we are seeing these potential restrictions on the medical research and what impact they could have on the ability to develop new treatments for the coronavirus and other deadly diseases.

You can watch the CIRM Stem Cell Awareness Day live event by going here: https://www.youtube.com/c/CIRMTV/videos at noon on Wednesday, October 14th.

Feel free to share news about this event with anyone you think might be interested.

We look forward to seeing you there.

Byron’s story

Bryon Jenkin’s is one of the people we profiled in our recent 18 Month Report. The theme of the report is “Perseverance” and Byron certainly epitomizes that. This is his story.

Photo of Byron Jenkins – hand on the plane – in his Navy fighter pilot days

A former Navy flight officer and accomplished athlete Byron Jenkins learned in June 2013 that he had multiple myeloma, an incurable blood cancer, and that it was eating through his bones. After five years of, chemotherapy, radiation, immunotherapy, and experimental procedures, he found himself bed ridden, exhausted, barely able to move. Byron says: “I was alive, but I wasn’t living.” 

Byron in the hospital

As the treatments lost their ability to hold the cancer at bay, Byron’s wife, family and close friends had made preparations for his seemingly inevitable demise. 

Then Byron took part in a CIRM-funded CAR-T clinical trial for a treatment developed by Poseida Therapeutics. The team used Byron’s own immune system cells, re-engineered in the lab, to recognize the cancer and to fight back. Within two weeks Byron was feeling so much better he was able to stop taking all of his medications. “I haven’t taken so much as an aspirin since then.”  

Two years later he is once again able to enjoy a full, active life with his family; biking, hiking and skiing with his wife and kids. He is back working full-time and only checks in with his oncologist once in a while.

Byron taking a selfie with his family

Byron says despite his ordeal he never lost faith, that the love of his family helped give him the strength to continue to fight. “Hope kept me going through this long arduous process. This is the first treatment to give me a continued normal life. CAR-T was the answer to my prayers.”

Byron: Photo courtesy Miranda Drummond of Catherine Rae Photography

Creating an on-off switch to test stem cell therapy for Parkinson’s Disease

Sometimes you read about a new study where the researchers did something that just leaves you gob smacked. That’s how I felt when I read a study in the journal Cell Stem Cell about a possible new approach to helping people with Parkinson’s Disease (PD).

More on the gob smacking later. But first the reason for the study.

We know that one of the causes of Parkinson’s disease is the death of dopamine-producing neurons, brain cells that help plan and control body movement. Over the years, researchers have tried different ways to try and replace those cells but getting the cells where they need to be and getting them to integrate into the brain has proved challenging.

A team at the University of Wisconsin-Madison think they may have found a way to fix that. In an article in Drug Target Review  lead researcher Dr. Su-Chun Zhang, explained their approach:

“Our brain is wired in such an accurate way by very specialized nerve cells in particular locations so we can engage in all our complex behaviors. This all depends on circuits that are wired by specific cell types. Neurological injuries usually affect specific brain regions or specific cell types, disrupting circuits. In order to treat those diseases, we have to restore these circuits.”

The researchers took human embryonic stem cells and transformed them into dopamine-producing neurons, then they transplanted those cells into mice specially bred to display PD symptoms. After several months the team were able to show that not only had the mice improved motor skills but that the transplanted neurons were able to connect to the motor-control regions of the brain and also establish connections with regulatory regions of the brain, which prevented over stimulation. In other words, the transplanted cells looked and behaved the way they would in a healthy human brain.

Now here comes the gob smack part. The team wanted to make sure the cells they transplanted were the reason for the improved motor control in the mice. So, they had inserted a genetic on-and-off switch into the stem cells. By using specially designed drugs the researchers were able to switch the cells on or off.

When the cells were switched off the mice’s motor improvements stopped. When they were switched back on, they were restored.

Brilliant right! Well, I thought it was.

Next step is to test this approach in larger animals and, if all continues to look promising, to move into human clinical trials.

CIRM is already funding one clinical trial in Parkinson’s disease. You can read about it here.

Exploring tough questions, looking for answers

COVID-19 and social and racial injustice are two of the biggest challenges facing the US right now. This Thursday, October 8th, we are holding a conversation that explores finding answers to both.

The CIRM Alpha Stem Cell Clinic Network Symposium is going to feature presentations about advances in stem cell and regenerative research, highlighting treatments that are already in the clinic and being offered to patients.

But we’re also going to dive a little deeper into the work we support, and use it to discuss two of the most pressing issues of the day.

One of the topics being featured is research into COVID-19. To date CIRM has funded 17 different projects, including three clinical trials. We’ll talk about how these are trying to find ways to help people infected with the virus, seeing if stem cells can help restore function to organs and tissues damaged by the virus, and if we can use stem cells to help develop safe and effective vaccines.

Immediately after that we are going to use COVID-19 as a way of exploring how the people most at risk of being infected and suffering serious consequences, are also the ones most likely to be left out of the research and have most trouble accessing treatments and vaccines.

Study after study highlights how racial and ethnic minorities are underrepresented in clinical trials and disproportionately affected by debilitating diseases. We have a responsibility to change that, to ensure that the underserved are given the same opportunity to take part in clinical trials as other communities.

How do we do that, how do we change a system that has resisted change for so long, how do we overcome the mistrust that has built up in underserved communities following decades of abuse? We’ll be talking about with experts who are on the front lines of this movement.

It promises to be a lively meeting. We’d love to see you there. It’s virtual – of course – it’s open to everyone, and it’s free.

Here’s where you can register and find out more about the Symposium

Remembering a stem cell pioneer in the fight against HIV/AIDS

Timothy Ray Brown. Photo courtesy Seattle Times

Timothy Ray Brown, a man who was the first person to be cured of HIV, giving hope to millions of people around the world, died at his home in Palm Springs this week. He was just 54 years old.

For years Brown was known simply as “the Berlin patient” because that was where he was living when he made medical history. He was diagnosed with HIV in 1995 and began taking medications to keep the virus under control. He was later also diagnosed with leukemia. He underwent several rounds of treatment for the leukemia, but it kept recurring.

By 2007 Brown’s physician decided the best way to treat the leukemia was with a blood stem cell transplant. But the doctor also wanted to see if using the stem cells from a donor who had a natural immunity to the AIDS virus could help treat Brown’s HIV. While such donors are very rare, the doctor succeeded in finding one whose bone marrow carried the CCR5 gene, a mutation that is believed to provide resistance to HIV. The transplant was a success, putting Brown’s leukemia into remission and eliminating detectable traces of HIV. For the first time in years he was able to stop taking the medications that had helped keep the virus under control.

The procedure quickly garnered world-wide attention. But not everyone was convinced it was real. Some questioned if Brown’s HIV had really been eradicated and speculated that the virus was merely suppressed. But with each passing year, and no signs of the virus recurring, more and more people came to believe it was a cure.

Initially Brown remained in the background, preferring not to be identified. But three years after his transplant he decided he had to come forward and put a face on “the Berlin patient”. In an interview with the website ContagionLive he explained why:

“At some point, I decided I didn’t want to be the only person in the world cured of H.I.V.,” I wanted there to be more. And the way to do that was to show the world who I am and be an advocate for H.I.V.”

He proved to be a powerful advocate, talking at international conferences and serving as living-proof that stem cells could help lead to a cure for HIV.

But while he managed to beat HIV, he could not beat leukemia. He suffered relapses that required another transplant and a difficult recovery. When it returned again this time, there was little physicians could do.

But Timothy Ray Brown did get to see his hope of not being the only patient cured seemingly come true. In September of last year researchers announced they had successfully treated a second person, known as “the London patient” using the same technique that cured Brown.

While it wasn’t the role he would have chosen Brown was a pioneer. His experience showed that a deadly virus could be cured. His courage in not just overcoming the virus but in overcoming his own reluctance to take center stage and becoming a symbol of hope for millions remain and will never die.  

Since Brown’s transplant many other scientists have attempted to replicate the procedure that cured Brown, in the hopes of making it available to many more people.

CIRM has funded three clinical trials targeting HIV, two of which are still active. Dr. Mehrdad Abedi at UC Davis and Dr. John Zaia at City of Hope are both using the patient’s own blood forming stem cells to try and defeat the virus.

If they succeed, some of the credit should go to Timothy Ray Brown, the man who led the way.

It’s all about the patients

Ronnie, born with a fatal immune disorder now leading a normal life thanks to a CIRM-funded stem cell/gene therapy: Photo courtesy of his mum Upasana

Whenever you are designing something new you always have to keep in mind who the end user is. You can make something that works perfectly fine for you, but if it doesn’t work for the end user, the people who are going to work with it day in and day out, you have been wasting your time. And their time too.

At CIRM our end users are the patients. Everything we do is about them. Starting with our mission statement: to accelerate stem cell treatments to patients with unmet medical needs. Everything we do, every decision we make, has to keep the needs of the patient in mind.

So, when we were planning our recent 2020 Grantee Meeting (with our great friends and co-hosts UC Irvine and UC San Diego) one of the things we wanted to make sure didn’t get lost in the mix was the face and the voice of the patients. Often big conferences like this are heavy on science with presentations from some of the leading researchers in the field. And we obviously wanted to make sure we had that element at the Grantee meeting. But we also wanted to make sure that the patient experience was front and center.

And we did just that. But more on that in a minute. First, let’s talk about why the voice of the patient is important.

Some years ago, Dr. David Higgins, a CIRM Board member and patient advocate for Parkinson’s Disease (PD), said that when researchers are talking about finding treatments for PD they often focus on the dyskinesia, the trembling and shaking and muscle problems. However, he said if you actually asked people with PD you’d find they were more concerned with other aspects of the disease, the insomnia, anxiety and depression among other things. The key is you have to ask.

Frances Saldana, a patient advocate for research into Huntington’s disease

So, we asked some of our patient advocates if they would be willing to be part of the Grantee Meeting. All of them, without hesitation, said yes. They included Frances Saldana, a mother who lost three of her children to Huntington’s disease; Kristin MacDonald, who lost her sight to a rare disorder but regained some vision thanks to a stem cell therapy and is hoping the same therapy will help restore some more; Pawash Priyank, whose son Ronnie was born with a fatal immune disorder but who, thanks to a stem cell/gene therapy treatment, is now healthy and leading a normal life.

Because of the pandemic everything was virtual, but it was no less compelling for that. We interviewed each of the patients or patient advocates beforehand and those videos kicked off each session. Hearing, and seeing, the patients and patient advocates tell their stories set the scene for what followed. It meant that the research the scientists talked about took on added significance. We now had faces and names to highlight the importance of the work the scientists were doing. We had human stories. And that gave a sense of urgency to the work the researchers were doing.

But that wasn’t all. After all the video presentations each session ended with a “live” panel discussion. And again, the patients and patient advocates were a key part of that. Because when scientists talk about taking their work into a clinical trial they need to know if the way they are setting up the trial is going to work for the patients they’re hoping to recruit. You can have the best scientists, the most promising therapy, but if you don’t design a clinical trial in a way that makes it easy for patients to be part of it you won’t be able to recruit or retain the people you need to test the therapy.

Patient voices count. Patient stories count.

But more than anything, hearing and seeing the people we are trying to help reminds us why we do this work. It’s so easy to get caught up in the day to day business of our jobs, struggling to get an experiment to work, racing to get a grant application in before the deadline. Sometimes we get so caught up in the minutiae of work we lose sight of why we are doing it. Or who we are doing it for.

At CIRM we have a saying; come to work every day as if lives depend on you, because lives depend on you. Listening to the voices of patients, seeing their faces, hearing their stories, reminds us not to waste a moment. Because lives depend on all of us.

Here’s one of the interviews that was featured at the event. I do apologize in advance for the interviewer, he’s rubbish at his job.

CIRM-funded kidney transplant procedure eyeing faster approval

Kidney transplant surgery.

Medeor Therapeutics, which is running a CIRM-funded clinical trial to help people getting kidney transplants, just got some really good news. The US Food and Drug Administration (FDA) has just granted their product Regenerative Medicine Advanced Therapy (RMAT) designation. That’s a big deal because it means they may be able to apply for faster review and approval and get their therapy to more patients faster.

Here’s why that RMAT designation matters.

Over 650,000 Americans suffer from end-stage kidney disease – a life-threatening condition caused by the loss of kidney function. The best available treatment for these patients is a kidney transplant from a genetically matched living donor. However, patients who receive a transplant must take life-long immunosuppressive drugs to prevent their immune system from rejecting the transplanted organ. Over time, these drugs are toxic and can increase a patient’s risk of infection, heart disease, cancer and diabetes.  Despite these drugs, many patients still lose transplanted organs due to rejection.

To tackle this problem Medeor is developing a stem cell-based therapy called MDR-101. This is being tested in a Phase 3 clinical trial and it’s hoped it will eliminate the need for immunosuppressive drugs in genetically matched kidney transplant patients.

The company takes blood-forming stem cells and immune cells from the organ donor and infuses them into the patient receiving the donor’s kidney. Introducing the donor’s immune cells into the patient creates a condition called “mixed chimerism” where immune cells from the patient and the donor are able to co-exist. In this way, the patient’s immune system is able to adapt to and tolerate the donor’s kidney, potentially eliminating the need for the immunosuppressive drugs that are normally necessary to prevent transplant rejection.

So how does getting RMAT designation help that? Well, the FDA created the RMAT program to help speed up the development and review of regenerative medicine therapies that can treat, modify, reverse, or cure a serious condition. If MDR-101shows it is both safe and effective RMAT could help it get faster approval for wider use.

In a news release Giovanni Ferrara, President and CEO of Medeor, welcomed the news.

“This important designation underscores the tremendous unmet medical need for alternatives to today’s immunosuppressive therapies for transplantation. We have the potential to help people live longer, healthier lives without the need for high dose and chronic immunosuppression and we thank the FDA for this designation that will assist us progressing as efficiently as possible toward a commercially available product.”

This is the seventh CIRM-supported project that has been granted RMAT designation. The others are jCyte, Lineage, Humacyte, St. Jude’s/UCSF X-linked SCID, Poseida, Capricor

Scientists develop faster, smarter way to classify tumors using single-cell technology

Dr. Stephen Lin, CIRM Senior Science Officer

By Dr. Stephen Lin

Single-cell.  It is the new buzzword in biology.  Single-cell biology refers to the in-depth characterization of individual cells in an organ or similar microenvironment.  Every organ, like the brain or heart, is composed of thousands to millions of cells.  Single-cell biology breaks those organs down into their individual cell components to study the diversity within those cells.  For example, the heart is composed of cardiomyocytes, but within that bulk population of cardiomyocytes there are specialized cardiomyocytes for the different chambers of the heart and others that control beating, plus others not even known yet.  Single-cell studies characterize cell-to-cell variability in the body down to this level of detail to gain knowledge of tissues in a way that was not possible before.   

The majority of single-cell studies are based on next generation sequencing technologies of genetic material such as DNA or RNA.  The cost of sequencing each base of DNA or RNA has dropped precipitously since the first human genome was published in 2000, often compared to the trend seen with Moore’s Law in computing.  As a result it is now possible to sequence every gene that is expressed in an individual cell, called the transcriptome, for thousands and thousands of cells.   

The explosion of data coming from these technologies requires new approaches to study and analyze the information.  The scale of the genetic sequences that can be generated is so big that it is often not possible anymore for scientists to interpret the data manually as had been traditionally done.  To apply this exciting field to stem cell research and therapies, CIRM funded the Genomics Initiative which created the Centers of Excellence in Stem Cell Genomics (CESCG).  The goal of the CESCG is to create novel genomic information and create new bioinformatics tools (i.e. computer software) specifically for stem cell research, some of which was highlighted in past blogs.  Some of the earliest single-cell gene expression atlases of the human body were created under the CESCG. 

The latest study from CESCG investigators creates both new information and new tools for single-cell genomics.  In work funded by the Genomics Initiative, Stephen Quake and colleagues at Stanford University and the Chan-Zuckerberg Biohub studied tumor formation using single-cell approaches.  Drawing from one of the earliest published single-cell studies, the team had surveyed human brain transcriptome diversity that included samples from the brain cancer, glioblastoma. 

Recognizing that the data coming from these studies would eventually become too large and numerous to classify all of the cell types by hand, they created a new bioinformatics tool called Northstar to apply artificial intelligence to automatically classify cell types generated by single-cell studies.  The cell classifications generated by Northstar were similar to the original classifications created manually several years ago including the identification of specific cancerous cells. 

Some of the features that make Northstar a powerful bioinformatics tool for these studies are that the software is scalable for large numbers of cells, it performs the computations to classify cells very fast, and it requires relatively low computer processing power to go through literally millions of data points. 

The scalability of the tool was demonstrated on the Tabula Muris data collection, a single-cell compendium of 20 mouse organs with over 200,000 cells of data.  Finally, Northstar was used to classify the tumors from new single-cell data generated by the CESCG via samples of 11 patient pancreatic cancer patients obtained from Stanford Hospital.  Northstar correctly found the origins of cancerous cells from the specific diagnoses of pancreatic cancer that the patients had, for example cancerous cells in the endocrine cell lineage from a patient diagnosed with neuroendocrine pancreas cancer.  Furthermore, Northstar identified previously unknown origins of cancerous cell clusters from other patients with pancreatic cancer.  These new computational tools demonstrate how big data from genomic studies can become important contributors to personalized medicine.

The full study was published in Nature.