Next generation of stem cell scientists leave their mark

One of the favorite events of the year for the team here at CIRM is our annual SPARK (Summer Program to Accelerate Regenerative Medicine Knowledge) conference. This is where high school students, who spent the summer interning at world class stem cell research facilities around California, get to show what they learned. It’s always an engaging, enlightening, and even rather humbling experience.

The students, many of whom are first generation Californians, start out knowing next to nothing about stem cells and end up talking as if they were getting ready for a PhD. Most say they went to their labs nervous about what lay ahead and half expecting to do menial tasks such as rinsing out beakers. Instead they were given a lab coat, safety glasses, stem cells and a specific project to work on. They learned how to handle complicated machinery and do complex scientific experiments.

But most importantly they learned that science is fun, fascinating, frustrating sometimes, but also fulfilling. And they learned that this could be a future career for them.

We asked all the students to blog about their experiences and the results were extraordinary. All talked about their experiences in the lab, but some went beyond and tied their internship to their own lives, their past and their hopes for the future.

Judging the blogs was a tough assignment, deciding who is the best of a great bunch wasn’t easy. But in the end, we picked three students who we thought captured the essence of the SPARK program. This week we’ll run all those blogs.

We begin with our third place blog by Dayita Biswas from UC Davis.

Personal Renaissance: A Journey from Scientific Curiosity to Confirmed Passions

By Dayita Biswas

As I poured over the pages of my battered Campbell textbook, the veritable bible for any biology student, I saw unbelievable numbers like how the human body is comprised of over 30 trillion cells! Or how we have over 220 different types of cells— contrary to my mental picture of a cell as a circle. Science, and biology in particular, has no shortage of these seemingly impossible Fermi-esque statistics that make one do a double-take. 

My experience in science had always been studying from numerous textbooks in preparation for a test or competitions, but textbooks only teach so much. The countless hours I spent reading actually demotivated me and I constantly asked myself what was the point of learning about this cycle or that process — the overwhelming “so what?” question. Those intriguing numbers that piqued my interest were quickly buried under a load of other information that made science a static stream of words across a page. 

That all changed this summer when I had the incredible opportunity to work in the Nolta lab under my mentor, Whitney Cary. This internship made science so much more tangible and fun to be a part of.  It was such an amazing environment, being in the same space with people who all have the same goals and passion for science that many high school students are not able to truly experience. Everyone was so willing to explain what they were doing, and even went out of their way to help if I needed papers or had dumb questions.

This summer, my project was to create embryoid bodies and characterize induced pluripotent stem cells (iPSCs) from children who had Jordan’s Syndrome, an extremely rare neurodevelopmental disease whose research has applications in Alzheimer’s and autism.

 I had many highs and lows during this research experience. My highs were seeing that my iPSCs were happy and healthy. I enjoyed learning lab techniques like micro-pipetting, working in a biological safety hood, feeding, freezing, and passaging cells. My lows were having to bleach my beloved iPSCs days after they failed to survive, and having unsuccessful protocols. However, while my project consistently failed, these failures taught me more than my successes.

I learned that there is a large gap between being able to read about techniques and being “book smart” and actually being able to think critically about science and perform research. Science, true science, is more than words on a page or fun facts to spout at a party. Science is never a straight or easy answer, but the mystery and difficulty is part of the reason it is so interesting. Long story short: research is hard and it takes time and patience, it involves coming in on weekends to feed cells, and staying up late at night reading papers.         

The most lasting impact that this summer research experience had was that everything we learn in school and the lab are all moving us towards the goal of helping real people. This internship renewed my passion for biology and cemented my dream of working in this field. It showed me that I don’t have to wait to be a part of dynamic science and that I can be a small part of something that will change, benefit, and save lives.

This internship meant being a part of something bigger than myself, something meaningful. We must always think critically about what consequences our actions will have because what we do as scientists and researchers— and human beings will affect the lives of real people. And that is the most important lesson anyone can hope to learn.

                                                                                                   

And here’s a bonus, a video put together by the SPARK students at Cedars-Sinai Medical Center.

Stem cell stories that caught our eye: update on Capricor’s heart attack trial; lithium on the brain; and how stem cells do math

Capricor ALLSTARToday our partners Capricor Therapeutics announced that its stem cell therapy for patients who have experienced a large heart attack is unlikely to meet one of its key goals, namely reducing the scar size in the heart 12 months after treatment.

The news came after analyzing results from patients at the halfway point of the trial, six months after their treatment in the Phase 2 ALLSTAR clinical trial which CIRM was funding. They found that there was no significant difference in the reduction in scarring on the heart for patients treated with donor heart-derived stem cells, compared to patients given a placebo.

Obviously this is disappointing news for everyone involved, but we know that not all clinical trials are going to be successful. CIRM supported this research because it clearly addressed an unmet medical need and because an earlier Phase 1 study had showed promise in helping prevent decline in heart function after a heart attack.

Yet even with this failure to repeat that promise in this trial,  we learned valuable lessons.

In a news release, Dr. Tim Henry, Director of the Division of Interventional Technologies in the Heart Institute at Cedars-Sinai Medical Center and a Co-Principal Investigator on the trial said:

“We are encouraged to see reductions in left ventricular volume measures in the CAP-1002 treated patients, an important indicator of reverse remodeling of the heart. These findings support the biological activity of CAP-1002.”

Capricor still has a clinical trial using CAP-1002 to treat boys and young men developing heart failure due to Duchenne Muscular Dystrophy (DMD).

Lithium gives up its mood stabilizing secrets

As far back as the late 1800s, doctors have recognized that lithium can help people with mood disorders. For decades, this inexpensive drug has been an effective first line of treatment for bipolar disorder, a condition that causes extreme mood swings. And yet, scientists have never had a good handle on how it works. That is, until this week.

evan snyder

Evan Snyder

Reporting in the Proceedings of the National Academy of Sciences (PNAS), a research team at Sanford Burnham Prebys Medical Discovery Institute have identified the molecular basis of the lithium’s benefit to bipolar patients.  Team lead Dr. Evan Snyder explained in a press release why his group’s discovery is so important for patients:

“Lithium has been used to treat bipolar disorder for generations, but up until now our lack of knowledge about why the therapy does or does not work for a particular patient led to unnecessary dosing and delayed finding an effective treatment. Further, its side effects are intolerable for many patients, limiting its use and creating an urgent need for more targeted drugs with minimal risks.”

The study, funded in part by CIRM, attempted to understand lithium’s beneficial effects by comparing cells from patient who respond to those who don’t (only about a third of patients are responders). Induced pluripotent stem cells (iPSCs) were generated from both groups of patients and then the cells were specialized into nerve cells that play a role in bipolar disorder. The team took an unbiased approach by looking for differences in proteins between the two sets of cells.

The team zeroed in on a protein called CRMP2 that was much less functional in the cells from the lithium-responsive patients. When lithium was added to these cells the disruption in CRMP2’s activity was fixed. Now that the team has identified the molecular location of lithium’s effects, they can now search for new drugs that do the same thing more effectively and with fewer side effects.

The stem cell: a biological calculator?

math

Can stem cells do math?

Stem cells are pretty amazing critters but can they do math? The answer appears to be yes according to a fascinating study published this week in PNAS Proceedings of the National Academy of Sciences.

Stem cells, like all cells, process information from the outside through different receptors that stick out from the cells’ outer membranes like a satellite TV dish. Protein growth factors bind those receptors which trigger a domino effect of protein activity inside the cell, called cell signaling, that transfers the initial receptor signal from one protein to another. Ultimately that cascade leads to the accumulation of specific proteins in the nucleus where they either turn on or off specific genes.

Intuition would tell you that the amount of gene activity in response to the cell signaling should correspond to the amount of protein that gets into the nucleus. And that’s been the prevailing view of scientists. But the current study by a Caltech research team debunks this idea. Using real-time video microscopy filming, the team captured cell signaling in individual cells; in this case they used an immature muscle cell called a myoblast.

goentoro20170508

Behavior of cells over time after they have received a Tgf-beta signal. The brightness of the nuclei (circled in red) indicates how much Smad protein is present. This brightness varies from cell to cell, but the ratio of brightness after the signal to before the signal is about the same. Image: Goentoro lab, CalTech.

To their surprise the same amount of growth factor given to different myoblasts cells led to the accumulation of very different amounts of a protein called Smad3 in the cells’ nuclei, as much as a 40-fold difference across the cells. But after some number crunching, they discovered that dividing the amount of Smad3 after growth factor stimulation by the Smad3 amount before growth stimulation was similar in all the cells.

As team lead Dr. Lea Goentoro mentions in a press release, this result has some very important implications for studying human disease:

“Prior to this work, researchers trying to characterize the properties of a tumor might take a slice from it and measure the total amount of Smad in cells. Our results show that to understand these cells one must instead measure the change in Smad over time.”

Stem cell stories that caught our eye: turning on T cells; fixing our brains; progress and trends in stem cells; and one young man’s journey to recover from a devastating injury

Healthy_Human_T_Cell

A healthy T cell

Here are some stem cell stories that caught our eye this past week. Some are groundbreaking science, others are of personal interest to us, and still others are just fun.

Directing the creation of T cells. To paraphrase the GOP Presidential nominee, any sane person LOVES, LOVES LOVES their T cells, in a HUGE way, so HUGE. They scamper around the body getting rid of viruses and the tiny cancers we all have in us all the time. A CIRM-funded team at CalTech has worked out the steps our genetic machinery must take to make more of them, a first step in letting physicians turn up the action of our immune systems.

We have known for some time the identity of the genetic switch that is the last, critical step in turning blood stem cells into T cells, but nothing in our body is as simple as a single on-off event. The Caltech team isolated four genetic factors in the path leading to that main switch and, somewhat unsuspected, they found out those four steps had to be activated sequentially, not all at the same time. They discovered the path by engineering mouse cells so that the main T cell switch, Bcl11b, glows under a microscope when it is turned on.

“We identify the contributions of four regulators of Bcl11b, which are all needed for its activation but carry out surprisingly different functions in enabling the gene to be turned on,” said Ellen Rothenberg, the senior author in a university press release picked up by Innovations Report. “It’s interesting–the gene still needs the full quorum of transcription factors, but we now find that it also needs them to work in the right order.”

Video primer on stem cells in the brain.  In conjunction with an article in its August issue, Scientific American posted a video from the Brain Forum in Switzerland of Elena Cattaneo of the University of Milan explaining the basics of adult versus pluripotent stem cells, and in particular how we are thinking about using them to repair diseases in the brain.

The 20-minute talk gives a brief review of pioneers who “stood alone in unmarked territory.” She asks how can stem cells be so powerful; and answers by saying they have lots of secrets and those secrets are what stem cell scientist like her are working to unravel.  She notes stem cells have never seen a brain, but if you show them a few factors they can become specialized nerves. After discussing collaborations in Europe to grow replacement dopamine neurons for Parkinson’s disease, she went on to describe her own effort to do the same thing in Huntington’s disease, but in this case create the striatal nerves lost in that disease.

The video closes with a discussion of how basic stem cell research can answer evolutionary questions, in particular how genetic changes allowed higher organisms to develop more complex nervous systems.

kelley and kent

CIRM Science Officers Kelly Shepard and Kent Fitzgerald

A stem cell review that hits close to home.  IEEE Pulse, a publication for scientists who mix engineering and medicine and biology, had one of their reporters interview two of our colleagues on CIRM’s science team. They asked senior science officers Kelly Shepard and Kent Fitzgerald to reflect on how the stem cell field has progressed based on their experience working to attract top researchers to apply for our grants and watching our panel of outside reviewers select the top 20 to 30 percent of each set of applicants.

One of the biggest changes has been a move from animal stem cell models to work with human stem cells, and because of CIRM’s dedicated and sustained funding through the voter initiative Proposition 71, California scientists have led the way in this change. Kelly described examples of how mouse and human systems are different and having data on human cells has been critical to moving toward therapies.

Kelly and Kent address several technology trends. They note how quickly stem cell scientists have wrapped their arms around the new trendy gene editing technology CRISPR and discuss ways it is being used in the field. They also discuss the important role of our recently developed ability to perform single cell analysis and other technologies like using vessels called exosomes that carry some of the same factors as stem cells without having to go through all the issues around transplanting whole cells.

“We’re really looking to move things from discovery to the clinic. CIRM has laid the foundation by establishing a good understanding of mechanistic biology and how stem cells work and is now taking the knowledge and applying it for the benefit of patients,” Kent said toward the end of the interview.

jake and family

Jake Javier and his family

Jake’s story: one young man’s journey to and through a stem cell transplant; As a former TV writer and producer I tend to be quite critical about the way TV news typically covers medical stories. But a recent story on KTVU, the Fox News affiliate here in the San Francisco Bay Area, showed how these stories can be done in a way that balances hope, and accuracy.

Reporter Julie Haener followed the story of Jake Javier – we have blogged about Jake before – a young man who broke his spine and was then given a stem cell transplant as part of the Asterias Biotherapeutics clinical trial that CIRM is funding.

It’s a touching story that highlights the difficulty treating these injuries, but also the hope that stem cell therapies holds out for people like Jake, and of course for his family too.

If you want to see how a TV story can be done well, this is a great example.

T cell fate and future immunotherapies rely on a tag team of genetic switches

Imagine if scientists could build microscopic smart missiles that specifically seek out and destroy deadly, hard-to-treat cancer cells in a patient’s body? Well, you don’t have to imagine it actually. With techniques such as chimeric antigen receptor (CAR) T therapy, a patient’s own T cells – immune system cells that fight off viruses and cancer cells – can be genetically modified to produce customized cell surface proteins to recognize and kill the specific cancer cells eluding the patient’s natural defenses. It is one of the most exciting and promising techniques currently in development for the treatment of cancer.

Human T Cell (Wikipedia)

Human T Cell (Wikipedia)

Although there have been several clinical trial success stories, it’s still early days for engineered T cell immunotherapies and much more work is needed to fine tune the approach as well as overcome potential dangerous side effects. Taking a step back and gaining a deeper understanding of how stem cells specialize into T cells in the first place could go a long way into increasing the efficiency and precision of this therapeutic strategy.

Enter the CIRM-funded work of Hao Yuan Kueh and others in Ellen Rothenberg’s lab at CalTech. Reporting yesterday in Nature Immunology, the Rothenberg team uncovered a time dependent array of genetic switches – some with an ON/OFF function, others with “volume” control – that together control the commitment of stem cells to become T cells.

Previous studies have shown that the protein encoded by the Bcl11b gene is the key master switch that when activated sets a “no going back” path toward a T cell fate. A group of other genes, including Runx1, TCF-1 and GATA-3 are known to play a role in activating Bcl11b. The dominant school of thought is that these proteins gradually accumulate at the Bcl11b gene and once a threshold level is achieved, the proteins combine to enable the Bcl11b activation switch to flip on. However, other studies suggest that some of these proteins may act as “pioneer” factors that loosen up the DNA structure and allow the other proteins to readily access and turn on the Bcl11b gene. Figuring out which mechanism is at play is critical to precisely manipulating T cell development through genetic engineering.

To tease out the answer, the CalTech team engineered mice such that cells with activated Bcl11b would glow which allows visualizing the fate of single cells. We reached out to Dr. Kueh on the rationale for this experimental approach:

Hao Yuan Kueh, CalTech

Hao Yuan Kueh, CalTech

“To fully understand how genes are controlled, we need to watch them turn on and off in single, living cells over time.  As cells in our body are unique and different from one another, standard measurement methods, which average over millions of cells, often do not tell us the entire picture.”

The team examined the impact of inhibiting the T cell specific proteins GATA-3 and TCF-1 at different stages in T cell development in single cells. When the production of these two proteins were blocked in very early T cell progenitor (ETPs) cells, activation of Bcl11b was dramatically reduced. But that’s not what they observed when the experiment was repeated in a later stage of T cell development. In this case, blocking GATA-3 and TCF-1 had a much weaker impact on Bcl11b. So GATA-3 and TCF-1 are important for turning on Bcl11b early in T cell development but are not necessary for maintaining Bcl11b activation at later stages.

Inhibition of Runx1, on the other hand, did lead to a reduction in Bcl11b in these later T cell development stages. Making Runx1 levels artificially high conversely led to elevated Bcl11b in these cells.

Together, these results point to GATA-3 and TCF-1 as the key factors for turning on Bcl11b to commit cells to a T cell fate and then they hand off their duties to Runx1 to keep Bcl11b on and maintaining the T cell identity. Dr. Kuhn sums up the results and their implications this way:

“Our work shows that control of gene expression is very much a team effort, where some proteins flip the gene’s master ON-OFF switch, and others set its expression levels after it turns on…These results will help us generate customized T-cells to fight cancer and other diseases.  As T-cells are specialized to recognize and fight foreign agents in our body, this therapy strategy holds much promise for diseases that are difficult to treat with standard drug-based methods.  Also, these intricate gene regulation mechanisms are likely to be in play in other cell types in our body, not just T-cells, and so we believe our results will be widely relevant.”