CIRM weekly stem cell roundup: stomach bacteria & cancer; vitamin C may block leukemia; stem cells bring down a 6’2″ 246lb football player

gastric

This is what your stomach glands looks like from the inside:  Credit: MPI for Infection Biology”

Stomach bacteria crank up stem cell renewal, may be link to gastric cancer.

The Centers for Disease Control and Prevention estimate that two-thirds of the world’s population is infected with H. pylori, a type of bacteria that thrives in the harsh acidic conditions of the stomach. Data accumulated over the past few decades shows strong evidence that H. pylori infection increases the risk of stomach cancers. The underlying mechanisms of this link have remained unclear. But research published this week in Nature suggests that the bacteria cause stem cells located in the stomach lining to divide more frequently leading to an increased potential for cancerous growth.

Tumors need to make an initial foothold in a tissue in order to grow and spread. But the cells of our stomach lining are replaced every four days. So, how would H. pylori bacterial infection have time to induce a cancer? The research team – a collaboration between scientists at the Max Planck Institute in Berlin and Stanford University – asked that question and found that the bacteria are also able to penetrate down into the stomach glands and infect stem cells whose job it is to continually replenish the stomach lining.

Further analysis in mice revealed that two groups of stem cells exist in the stomach glands – one slowly dividing and one rapidly dividing population. Both stem cell populations respond similarly to an important signaling protein, called Wnt, that sustains stem cell renewal. But the team also discovered a second key stem cell signaling protein called R-spondin that is released by connective tissue underneath the stomach glands. H. pylori infection of these cells causes an increase in R-spondin which shuts down the slowly dividing stem cell population but cranks up the cell division of the rapidly dividing stem cells. First author, Dr. Michal Sigal, summed up in a press release how these results may point to stem cells as the link between bacterial infection and increased risk of stomach cancer:

“Since H. pylori causes life-long infections, the constant increase in stem cell divisions may be enough to explain the increased risk of carcinogenesis observed.”

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Vitamin C may have anti-blood cancer properties

Vitamin C is known to have a number of health benefits, from preventing scurvy to limiting the buildup of fatty plaque in your arteries. Now a new study says we might soon be able to add another benefit: it may be able to block the progression of leukemia and other blood cancers.

Researchers at the NYU School of Medicine focused their work on an enzyme called TET2. This is found in hematopoietic stem cells (HSCs), the kind of stem cell typically found in bone marrow. The absence of TET2 is known to keep these HSCs in a pre-leukemic state; in effect priming the body to develop leukemia. The researchers showed that high doses of vitamin C can prevent, or even reverse that, by increasing the activity level of TET2.

In the study, in the journal Cell, they showed how they developed mice that could have their levels of TET2 increased or decreased. They then transplanted bone marrow with low levels of TET2 from those mice into healthy, normal mice. The healthy mice started to develop leukemia-like symptoms. However, when the researchers used high doses of vitamin C to restore the activity levels of TET2, they were able to halt the progression of the leukemia.

Now this doesn’t mean you should run out and get as much vitamin C as you can to help protect you against leukemia. In an article in The Scientist, Benjamin Neel, senior author of the study, says while vitamin C does have health benefits,  consuming large doses won’t do you much good:

“They’re unlikely to be a general anti-cancer therapy, and they really should be understood based on the molecular understanding of the many actions vitamin C has in cells.”

However, Neel says these findings do give scientists a new tool to help them target cells before they become leukemic.

Jordan reed

Bad toe forces Jordan Reed to take a knee: Photo courtesy FanRag Sports

Toeing the line: how unapproved stem cell treatment made matters worse for an NFL player  

American football players are tough. They have to be to withstand pounding tackles by 300lb men wearing pads and a helmet. But it wasn’t a crunching hit that took Washington Redskins player Jordan Reed out of the game; all it took to put the 6’2” 246 lb player on the PUP (Physically Unable to Perform) list was a little stem cell injection.

Reed has had a lingering injury problem with the big toe on his left foot. So, during the off-season, he thought he would take care of the issue, and got a stem cell injection in the toe. It didn’t quite work the way he hoped.

In an interview with the Richmond Times Dispatch he said:

“That kind of flared it up a bit on me. Now I’m just letting it calm down before I get out there. I’ve just gotta take my time, let it heal and strengthen up, then get back out there.”

It’s not clear what kind of stem cells Reed got, if they were his own or from a donor. What is clear is that he is just the latest in a long line of athletes who have turned to stem cells to help repair or speed up recovery from an injury. These are treatments that have not been approved by the Food and Drug Administration (FDA) and that have not been tested in a clinical trial to make sure they are both safe and effective.

In Reed’s case the problem seems to be a relatively minor one; his toe is expected to heal and he should be back in action before too long.

Stem cell researcher and avid blogger Dr. Paul Knoepfler wrote he is lucky, others who take a similar approach may not be:

“Fortunately, it sounds like Reed will be fine, but some people have much worse reactions to unproven stem cells than a sore toe, including blindness and tumors. Be careful out there!”

 

Brain stem cells unintentionally talk with brain tumors, allowing their spread

A stem cell’s capacity to lay quiet and, when needed, to self-renew plays a key role in restoring and maintaining the health of our organs. Unfortunately, cancer stem cells possess that same property allowing them to evade radiation and chemotherapy treatments which leads to tumor regrowth. And a CIRM-funded study published today in Cell shows the deviousness of these cancer cells goes even further. The Stanford research team behind the study found evidence that brain stem cells, which normally guide brain development and maintenance, unintentionally communicate with brain cancer cells in deadly tumors, called gliomas, providing them a means to invade other parts of the brain. But the silver lining to this scary insight is that it may lead to new treatment options for patients.

High grade gliomas do not end well
The most aggressive forms of glioma are called high grade gliomas and they carry devastating prognoses. For instance, the most common form of these tumors in children has a median survival of just 9 months with a 5-year survival of less than 1%. Surgery or anti-cancer therapies may help for a while but the tumor inevitably grows back.

MRI image of high grade glioma brain tumor (white mass on left). Image: Wikipedia

Researchers have observed that gliomas typically originate in the brain stem and very often invade a brain stem cell-rich area, called the subventrical zone (SVZ), that provides a space for the therapy-resistant cancer stem cells to hole up. This path of tumor spread is associated with a shorter time to relapse and poorer survival but the exact mechanism wasn’t known. The Stanford team hypothesized that SVZ brain stem cells release some factor that attracts the gliomas to preferentially invade that part of the brain.

To test this chemo-attraction idea, they mimicked cancer cell invasion in a specialized, dual compartment petri dish called a Boyden chamber. In the bottom compartment, they placed the liquid food, or media, that SVZ brain stem cells had been grown in. On the upper compartment, they placed the cancerous glioma cells. A porous, gelatin membrane between the two compartments acts as a barrier but allows the cells to receive signals from the lower compartment and migrate down into the media if a chemoattractant is present. And that’s what they saw: a significant glioma cell migration through the gelatin toward the brain stem cell media.

Boyden chamber assay. Image: Integr. Biol., 2009,1, 170-181

Pleiotrophin: an unintentional communicator with brain cancer cells
Something or somethings in the SVZ brain stem cell media had to be attracting the glioma cells. So, the Stanford team analyzed the composition of the media and identified four proteins that, when physically complexed together, had the same chemo-attraction ability as the media. They were pleased to find that one of the four proteins is pleiotrophin which is known to not only play a role in normal brain development and regeneration but also to increase glioma cell migration. And in this study, they showed that higher levels of pleiotrophin are present in the SVZ brain stem cell area compared to other regions of the brain. They went on to show that blocking the production of pleiotrophin in mice reduced the invasion of glioma cells into the SVZ region. This result suggests that blocking the release of pleiotrophin by brain stem cells in the SVZ could help prevent or slow down the spread of glioma in patients’ brains without the need of irradiating this important part of the brain.

The silver lining: hsp90 inhibitors have therapeutic promise

Michelle Monje, MD, PhD

To further explore this potential therapeutic approach, the team examined hsp90, one of the other three proteins complexed with pleiotrophin. Though it doesn’t have chemoattractant properties, it still is a necessary component and may act to stabilize pleiotrophin. It also turns out that inhibitors for hsp90 have already been developed in the clinic for treating various cancers. When the researchers in this study blocked hsp90 production in the SVZ region of mice, they observed a reduced invasion of glioma cells. Though clinical grade hsp90 inhibitors exist, team lead  Michelle Monje, MD, PhD – assistant professor of neurology, Stanford University – tells me that some tweaking of these drugs will be necessary to reach gliomas:

“Our challenge is to find an hsp90 inhibitor that penetrates the brain at effective concentrations.”

Once they find that inhibitor, it could provide new options, and hope, for people diagnosed with this dreadful cancer.

High school students SPARK an interest in stem cell research

SPARK students at the 2017 Annual Meeting at the City of Hope.

High school is a transformative time for any student. It marks the transition from childhood to adulthood and requires discipline, dedication and determination to excel and get into their desired college or university.

The barrier to entry for college now seems much higher than when I was eighteen, but I am not worried for the current generation of high school students. That’s because I’ve met some of the brightest young minds this past week at the 2017 CIRM SPARK meeting.

SPARK is CIRM’s high school education program, which gives underprivileged students in California the opportunity to train as stem cell scientists for the summer. Students participate in a summer research internship at one of seven programs at leading research institutes in the state. They attend scientific lectures, receive training in basic lab techniques, and do an eight-week stem cell research project under the guidance of a mentor.

At the end of the summer, SPARK students congregate at the annual SPARK poster meeting where they present the fruits of their labor. Meeting these students in person is my favorite time of the year. Their enthusiasm for science and stem cell research is contagious. And when you engage them or listen to them talk about their project, it’s hard to remember that they are still teenagers and not graduate level scientists.

What impresses me most about these students is their communication skills. Each summer, I challenge SPARK students to share their summer research experience through social media and blogging, and each time they go above and beyond with their efforts. Training these students as effective science communicators is important to me. They are the next generation of talented scientists who can help humanize research for the public. They have the power to change the perception of science as a field to be embraced and one that should receive proper funding.

It’s also inspiring to me that this young generation can effectively educate their friends, family and the public about the importance of stem cell research and how it will help save the lives of patients who currently don’t have effective treatments. If you haven’t already, I highly recommend checking out the #CIRMSPARKlab hashtag on Instagram to get a taste of what this year’s group of students accomplished during their internships.

Asking students, many of whom are learning to do research for the first time, to post on Instagram once a week and write a blog about their internship is a tall task. And I believe with any good challenge, there should be a reward. Therefore, at this year’s SPARK meeting held at the City of Hope in Duarte, California, I handed out prizes.

It was very difficult to pick winners for our presentation, social media and blogging awards because honestly, all our students were excellent this year. Even Kevin McCormack, Director of CIRM’s Communications, who helped me read the students’ blogs said,

“This was really tough. The standard of the blogs this year was higher than ever; and previous years had already set the bar really high. It was really difficult deciding which were really good and which were really, really good.”

Ok, enough with the hype, I know you want to read these award-winning blogs so I’ve shared them below. I hope that they inspire you as much as they have inspired me.


Amira Hirara

Amira Hirara (Children’s Hospital Oakland Research Institute)

It was a day like any other. I walked into the room, just two minutes past 10:30am, ready for another adventurous day in the lab. Just as I settle down, I am greeted by my mentor with the most terrifying task I have ever been asked to perform, “Will you passage the cells for me…alone?” Sweat begins to pour down my cemented face as I consider what is at stake.

The procedure was possibly thirty steps long and I have only executed it twice, with the supervision of my mentor of course. To be asked to do the task without the accompaniment of an experienced individual was unthought-of. I feel my breath begin to shorten as I mutter the word “Ok”. Yet it wasn’t just the procedure that left me shaking like a featherless bird, it was the location of my expedition as well. The dreaded tissue culture room. If even a speck of dirt enters the circulating air of the biosafety cabinet, your cells are at risk of death…death! I’ll be a cell murderer. “Alright”, she said, “I’ll just take a look at the cells then you’ll be on your way.” As we walk down the hallway, my eyes began to twitch as I try to recall the first steps of the procedure. I remember freezing our plates with Poly-ornithine and laminin, which essentially simulates the extracellular environment and allows adhesion between the cell and the plate itself. I must first add antibiotics to rid the frozen plate of potential bacteria. Then I should remove my cells from the incubator, and replace the old solution with accutase and new media, to nourish the cells, as well as unbind them from the plate before. Passaging is necessary when the cell density gets too high, as the cells must be relocated to a roomier environment to better promote survival. As we approach the tissue culture room, my jaw unclenches, as I realize the whirlwind of ideas meant I know more than I thought. My mentor retrieves our cells, views them under the microscope, and deems them ‘ready for passaging’.

“Good luck Amira” she says to me with a reassuring smile. I enter the room ready for battle. Placing first my gloves and coat, I then spray my hands and all things placed in the cabinet with 70% ethanol, to insure a sterile work environment. Back to the procedure, I’ll place the cellular solution of accutase and media into a covalent tube. After, I’ll centrifuge it for two minutes until a cellular pellet forms at the bottom, then dissolve the cells in fresh media, check its density using a cell counter, and calculate the volume of cellular solution needed to add to my once frozen plates. Wait, once I do that, I’ll be all done. I eagerly execute all the steps, ensuring both accuracy and sterility in my work. Pride swells within me as I pipette my last milliliter of solution into my plate. The next day, my mentor and I stop by to check on how our sensitive neural stem cells are doing. “Wow Amira, I am impressed, your cells seem very confluent in their new home, great job!” I smile slyly and begin to nod my head. I now walk these hallways, with a puffed chest, brightened smile, and eagerness to learn. My stem cells did not die, and having the amazing opportunity to master their treatment and procedures, is something I can never forget.

 

Gaby Escobar

Gaby Escobar (Stanford University)

Walking into the lab that would become my home for the next 8 weeks, my mind was an empty canvas.  Up to that point, my perception of the realm of scientific research was one-sided. Limited to the monotonous textbook descriptions of experiments that were commonplace in a laboratory, I wanted more. I wanted to experience the alluring call of curiosity. I wanted to experience the flash of discovery and the unnerving drive that fueled our pursuit of the unknown. I was an empty canvas looking for its first artistic stroke.

Being part of the CIRM Research program, I was lucky enough to have been granted such opportunity. Through the patient guidance of my mentor, I was immersed into the limitless world of stem cell biology. From disease modeling to 3D bioprinting, I was in awe of the capabilities of the minds around me. The energy, the atmosphere, the drive all buzzed with an inimitable quest for understanding. It was all I had imagined and so, so much more.

However, what many people don’t realize is research is an arduous, painstaking process. Sample after sample day after day, frustration and doubt loomed above our heads as we tried to piece together a seemingly pieceless puzzle.  Inevitably, I faced the truth that science is not the picture-perfect realm I had imagined it to be. Rather, it is tiring, it is relentless, and it is unforgiving. But at the same time, it is incomparably gratifying. You see, the innumerable samples, the countless gels and PCRS, all those futile attempts to fruitlessly make sense of the insensible, have meaning. As we traversed through the rollercoaster ride of our project, my mentor shared a personal outlook that struck very deeply with me: her motivation to work against obstacle after obstacle comes not from the recognition or prestige of discovering the next big cure but rather from the notion that one day, her perseverance may transform someone’s life for the good.  And in that, I see the beauty of research and science: the coming together of minds and ideas and bewildering intuitions all for the greater good.

As I look back, words cannot express the gratitude I feel for the lessons I have learned. Undoubtedly, I have made countless mistakes (please don’t ask how many gels I’ve contaminated or pipettes I have dropped) but I’ve also created the most unforgettable of memories. Memories that I know I will cherish for the journey ahead of me. Having experienced the atmosphere of a vibrant scientific community, I have found a second home, a place that I can explore and question and thrive. And although not every day will hold the cure to end all diseases or hand an answer on a silver platter, every day is another opportunity.  And with that, I walk away perhaps not with the masterpiece of art that I had envisioned in my mind but rather with a burning spark of passion, ready to ignite.

 

Anh Vo

Ahn Vo (UC Davis)

With college selectivity increasing and acceptance rates plummeting, the competitive nature within every student is pushed to the limit. In high school, students are expected to pad up their resumes and most importantly, choose an academic path sooner rather than later. However, at 15, I felt too young to experience true passion for a field. As I tried to envision myself in the future, I wondered, would I be someone with the adrenaline and spirit of someone who wants to change the world or one with hollow ambitions, merely clinging onto a paycheck with each day passing? At the very least, I knew that I didn’t want to be the latter.

The unrelenting anxiety induced by the uncertainty of my own ambitions was intoxicating. As my high school career reached its halfway mark, I felt the caving pressure of having to choose an academic path.

“What do you want to be?” was one of the first questions that my mentor, Whitney Cary, asked me. When I didn’t have an answer, she assured me that I needed to keep my doors open, and the SPARK program was the necessary first step that I needed to take to discovering my passion.

As I reflected on my experience, the SPARK program was undoubtedly the “first step”. It was the first step into a lab and above all, into a community of scientists, who share a passion for research and a vehement resolve to contribute to scientific merit. It was the integration into a cohort of other high school students, whose brilliance and kindness allowed us to forge deeper bonds with each other that we will hold onto, even as we part ways. It was the first nervous step into the bay where I met the Stem Cell Core, a team, whose warm laughter and vibrancy felt contagious. Finally, it was the first uncertain stumble into the tissue culture room, where I conceived a curiosity for cell culture that made me never stop asking, “Why?”

With boundless patience, my mentor and the Stem Cell Core strove to teach me techniques, such as immunocytochemistry and continually took the time out of their busy day to reiterate concepts. Despite my initial blunders in the hood, I found myself in a place without judgement, and even after discouraging incidents, I felt a sense of consolation in the witty and good-humored banter among the Stem Cell Core. At the end of every day, the unerring encouragement from my mentor strengthened my resolve to continue improving and incited an earnest excitement in me for the new day ahead. From trembling hands, nearly tipping over culture plates and slippery gloves, overdoused in ethanol, I eventually became acquainted with daily cell culture, and most importantly, I gained confidence and pride in my work.

I am grateful to CIRM for granting me this experience that has ultimately cultivated my enthusiasm for science and for the opportunity to work alongside remarkable people, who have given me new perspectives and insights. I am especially thankful to my mentor, whose stories of her career journey have inspired me to face the future with newfound optimism in spite of adversity.

As my internship comes to a close, I know that I have taken my “first step”, and with a revived mental acquisitiveness, I eagerly begin to take my second.

Other 2017 SPARK Awards

Student Speakers: Candler Cusato (Cedars-Sinai), Joshua Ren (Stanford)

Instagram/Social Media: Jazmin Aizpuru (UCSF), Emily Beckman (CHORI), Emma Friedenberg (Cedars-Sinai)

Poster Presentations: Alexander Escudero (Stanford), Jamie Kim (CalTech), Hector Medrano (CalTech), Zina Patel (City of Hope)


Related Links:

Have scientists discovered a natural way to boost muscle regeneration?

Painkillers like ibuprofen and aspirin are often a part of an athlete’s post-exercise regimen after intense workouts. Sore muscles, aches and stiffness can be more manageable by taking these drugs – collectively called non-steroidal anti-inflammatory drugs, or NSAIDS – to reduce inflammation and pain. But research suggests that the anti-inflammatory effects of these painkillers might cause more harm than good by preventing muscle repair and regeneration after injury or exercise.

A new study out of Stanford Medicine supports these findings and proposes that a component of the inflammatory process is necessary to promote muscle regeneration. Their study was funded in part by a CIRM grant and was published this week in the Proceedings of the National Academy of Sciences.

Muscle stem cells are scattered throughout skeletal muscle tissue and remain inactive until they are stimulated to divide. When muscles are damaged or injured, an inflammatory response involving a cascade of immune cells, molecules and growth factors activates these stem cells, prompting them to regenerate muscle tissue.

Andrew Ho, Helen Blau and Adelaida Palla led a study that found drugs like aspirin and ibuprofen can inhibit the ability of muscle tissue to repair itself in mice. (Image credit: Scott Reiff)

The Stanford team discovered that a molecule called Prostaglandin E2 or PGE2 is released during the inflammatory response and stimulates muscle repair by directly targeting the EP4 receptor on the surface of muscle stem cells. The interaction between PGE2 and EP4 causes muscle stem cells to divide and robustly regenerate muscle tissue.

Senior author on the study, Dr. Helen Blau, explained her team’s interest in PGE2-mediated muscle repair in a news release,

“Traditionally, inflammation has been considered a natural, but sometimes harmful, response to injury. But we wondered whether there might be a component in the pro-inflammatory signaling cascade that also stimulated muscle repair. We found that a single exposure to prostaglandin E2 has a profound effect on the proliferation of muscle stem cells in living animals. We postulated that we could enhance muscle regeneration by simply augmenting this natural physiological process in existing stem cells already located along the muscle fiber.”

Further studies in mice revealed that injury increased PGE2 levels in muscle tissue and increased expression of the EP4 receptor on muscle stem cells. This gave the authors the idea that treating mice with a pulse of PGE2 could stimulate their muscle stem cells to regenerate muscle tissue.

Their hunch turned out to be right. Co-first author Dr. Adelaida Palla explained,

“When we gave mice a single shot of PGE2 directly to the muscle, it robustly affected muscle regeneration and even increased strength. Conversely, if we inhibited the ability of the muscle stem cells to respond to naturally produced PGE2 by blocking the expression of EP4 or by giving them a single dose of a nonsteroidal anti-inflammatory drug to suppress PGE2 production, the acquisition of strength was impeded.”

Their research not only adds more evidence against the using NSAID painkillers like ibuprofen and aspirin to treat sore muscles, but also suggests that PGE2 could be a natural therapeutic strategy to boost muscle regeneration.

This cross-section of regenerated muscle shows muscle stem cells (red) in their niche along the muscle fibers (green). (Photo courtesy of Blau lab)

PGE2 is already approved by the US Food and Drug Administration (FDA) to induce labor in pregnant women, and Dr. Blau hopes that further research in her lab will pave the way for repurposing PGE2 to treat muscle injury and other conditions.

“Our goal has always been to find regulators of human muscle stem cells that can be useful in regenerative medicine. It might be possible to repurpose this already FDA-approved drug for use in muscle. This could be a novel way to target existing stem cells in their native environment to help people with muscle injury or trauma, or even to combat natural aging.”

Baseball’s loss is CIRM’s gain as Stanford’s Linda Boxer is appointed to Stem Cell Agency Board

Boxer

Dr. Linda Boxer: Photo courtesy Stanford University

One of the things that fascinates me is finding out how people end up in the job they have, the job they love. It is rare that the direction they started out on is the one they end on. Usually, people take several different paths, some intended, some unintended, to get to where they want to be.

A case in point is Dr. Linda Boxer, a renowned and respected researcher and physician at the Stanford School of Medicine, and now the newest member of the CIRM Board (you can read all about that in our news release).

In Dr. Boxer’s case, her original career path was a million miles from working with California’s stem cell agency:

“The first career choice that I recall as a young child was professional baseball—growing up in Minnesota, I was a huge Twins fan—I did learn fairly quickly that this was not likely to be a career that was available for a girl, and it wasn’t clear what one did after that career ended at a relatively young age.”

Fortunately for us she became interested in science.

“I have always been curious about how things work—science classes in grade school were fascinating to me. I was given a chemistry kit as a birthday gift, and I was amazed at what happened when different chemicals were mixed together: color changes, precipitates forming, gas bubbles, explosions (small ones, of course).

Then when we studied biology in middle school, I was fascinated by what one could observe with a microscope and became very interested in trying to understand how living organisms work.

It was an easy decision to plan a career in science.  The tougher decision came in college when I had planned to apply to graduate school and earn a PhD, but I was also interested in human health and disease and thought that perhaps going to medical school made more sense.  Fortunately, one of my faculty advisors told me about combined MD/PhD programs, and that choice seemed perfect for me.”

Along the way she says she got a lot of help and support from her colleagues. Now she wants to do the same for others:

“Mentors are incredibly important at every career stage.  I have been fortunate to have been mentored by some dedicated scientists and physicians.  Interestingly, they have all been men.  There were really very few women available as mentors at the time—of course, that has changed for the better now.  It never occurred to me then that gender made a difference, and I just looked for mentors who had successful careers as scientists and physicians and who could provide advice to someone more junior.

One of the aspects of my role now that I enjoy the most is mentoring junior faculty and trainees.  I don’t think one can have too many mentors—different mentors can help with different aspects of one’s life and career.  I think it is very important for established scientists to give back and to help develop the next generation of physicians and scientists.”

Dr. Boxer is already well known to everyone at CIRM, having served as the “alternate” on the Board for Stanford’s Dr. Lloyd Minor. But her appointment by State Controller Betty Yee makes her the “official” Board member for Stanford. She brings a valuable perspective as both a scientist and a physician.

The Minnesota Twins lost out when she decided to pursue a career in science. We’re glad she did.

 

Stanford scientists devise an algorithm that identifies gene pairs associated with cancer

Using data from human tumor samples, Stanford scientists have developed a new computer algorithm to identify pairs of genes that cause cancer. Their research aims to identify alternative ways to target cancer-causing mutations that have thus far evaded effective clinical treatment.

The study, which was published this week in Nature Communications, was led by senior authors Dr. Ravi Majeti and Dr. David Dill and included two CIRM Bridges interns Damoun Torabi and David Cruz Hernandez.

Identifying Partners in Crime

Cancer cells are notorious for acquiring genetic mutations due to the instability of their genomes and errors in the machinery that repairs DNA. Sometimes these errors create what are called synthetic lethal genes. These are pairs of genes that can cause a cell to die if both genes are defective due to acquired mutations, but a defect in only one of the genes allows a cell to live.

Cancer cells rely on pairs of genes with similar functions for their survival. If one gene is mutated, then the cancer cell depends on the other functional gene, aka its “partner in crime”, to keep it doing its mischief. Scientist are interested in targeting this second partner gene in synthetic lethal pairs in the hopes of developing less toxic cancer therapies that only kill cancer cells instead of healthy ones too.

The Stanford team went on the hunt for synthetic lethal partner genes in data from 12 different human cancers using an algorithm they developed called Mining Synthetic Lethals (MiSL). David Dill explained their strategy in a Stanford Medicine news release:

“We were looking for situations in which, if gene A is mutated, gene Y is amplified to compensate for the loss of function of gene A. Conversely, gene Y is only ever deleted in cells in which gene A is not mutated.”

David Dill. (Credit: L.A. Cicero/Stanford News Service)

They identified a total of 3,120 cancer-causing mutations and over 145,000 potential synthetic lethal partner genes associated with these mutations. Some of these partnerships were identified in other studies, validating MiSL as an effective tool for their purposes, while other partnerships were novel.

Targeting Partners in Crime

One of the new partnerships they discovered was between a mutation in the IDH1 gene, which is associated with acute myeloid leukemia, and a gene called ACACA. The team validated this pair with experiments in the lab proving that defects in both IDH1 and ACACA blocked leukemia cell growth. MiSL identified 89 potential synthetic lethal partners for the leukemia-causing IDH1 mutation, 17 of which they believe could be targeted by existing cancer drugs.

The authors concluded that using computer algorithms to sift through mountains of biological data is a powerful strategy for identifying genetic relationships leveraged by tumors and could advance drug development for different types of cancers.

Ravi Majeti concluded,

“We’re entering a new era of precision health. Using data from real human tumors gives us important, fundamental advantages over using cancer cell lines that often don’t display the same mutation profiles. We’ve found that, although many known cancer-associated mutations are difficult to target clinically, their synthetic lethal partners may be much more druggable.”

Ravi Majeti (Credit: Steve Fisch)

Keeping intestinal stem cells in their prime

Gut stem cells (green) in the small intestine of a mouse.

The average length of the human gut is 25 feet long. That’s equivalent to four really tall people or five really short people lined up head to toe. Intestinal stem cells have the fun job of regenerating and replacing ALL the cells that line the gut. Therefore, it’s important for these stem cells to be able to self-renew, a process that replenishes the stem cell population. If this important biological process is disrupted, the intestine is at risk for diseases like inflammatory bowel disease and cancer.

This week, Stanford Medicine researchers published new findings about the biological processes responsible for regulating the regenerative capacity of intestinal stem cells. Their work, which was partially funded by CIRM, was published in the journal Nature.

Priming gut stem cells to self-renew

Scientists know that the self-renewal of intestinal stem cells is very important for a happy, functioning gut, but the nuances of what molecules and signaling pathways regulate this process have yet to be figured out. The Stanford team, led by senior author and Stanford Professor Dr. Calvin Kuo, studied two signaling pathways, Wnt and R-Spondin, that are involved in the self-renewal of intestinal stem cells in mice.

Dr. Calvin Kuo, Stanford Medicine.

“The cascade of events comprising the Wnt signaling pathway is crucial to stem cell self-renewal,” Dr. Kuo explained in an email exchange. “The Wnt pathway can be induced by either hormones classified as “Wnts” or “R-spondins”.  However, it is not known if Wnts or R-spondins cooperate to induce Wnt signaling, and if these Wnts and R-spondins have distinct functions or if they can mutually substitute for each other.   We explored how Wnts and R-spondins might cooperate to regulate intestinal stem cells – which are extremely active and regenerate the 25-foot lining of the human intestine every week.”

The team used different reagents to activate or block Wnt or R-spondin signaling and monitored the effects on intestinal stem cells. They found that both were important for the self-renewal of intestinal stem cells, but that they played different roles.

“Our work revealed that Wnts and R-spondins are not equivalent and that they have very distinct functions even though they both trigger the Wnt signaling cascade,” said Dr. Kuo. “Both Wnts and R-spondins are required to maintain intestinal stem cells.  However, Wnts perform more of a subservient “priming” function, where they prepare intestinal stem cells for the action of R-spondin, which is the active catalyst for inducing intestinal stem cells to divide.”

The authors believe that this multi-step regulation, involving priming and self-renewal factors could apply to stem cell systems in other organs and tissues in the body. Some of the researchers on this study including Dr. Kuo are pursuing this idea through a new company called Surrozen, which produces artificial bioengineered Wnt molecules that don’t require activation like natural Wnt molecules. These Wnt molecules were used in the current study and are explained in more detail in a separate Nature article published at the same time.

The company believes that artificial Wnts will be useful for understanding stem cell biology and potentially for therapeutic applications. Dr. Kuo explained,

“The new surrogate Wnts are easily produced and can circulate in the bloodstream, unlike natural Wnts.  There may be medical applications of these bioengineered Wnt surrogates in stimulating various stem cell compartments of the body, given the wide range of stem cells that are governed by natural Wnts.”

Stem cell-derived, 3D brain tissue reveals autism insights

Studying human brain disorders is one of the most challenging fields in biomedical research. Besides the fact that the brain is incredibly complex, it’s just plain difficult to peer into it.

It’s neither practical nor ethical to access the cells of the adult brain. Patrick J. Lynch, medical illustrator; C. Carl Jaffe, MD, cardiologist.

For one thing, it’s not practical, let alone ethical, to drill into an affected person’s skull and collect brain cells to learn about their disease. Another issue is that the faulty cellular and molecular events that cause brain disorders are, in many cases, thought to trace back to fetal brain development before a person is even born. So, just like a detective looking for evidence at the scene of a crime, neurobiologists can only piece together clues after the disease has already occurred.

The good news is these limitations are falling away thanks to human induced pluripotent stem cells (iPSCs), which are generated from an individual’s easily accessible skin cells. Last week’s CIRM-funded research report out of Stanford University is a great example of how this method is providing new human brain insights.

Using brain tissue grown from patient-derived iPSCs, Dr. Sergiu Pasca and his team recreated the types of nerve cell circuits that form during the late stages of pregnancy in the fetal cerebral cortex, the outer layer of the brain that is responsible for functions including memory, language and emotion. With this system, they observed irregularities in the assembly of brain circuitry that provide new insights into the cellular and molecular causes of neuropsychiatric disorders like autism.

Recreating interactions between different regions of the development from skin-derived iPSCs
Image: Sergui Pasca Lab, Stanford University

Holy Brain Balls! Recreating the regions of our brain with skin cells
Two years ago, Pasca’s group figured out a way grow iPSCs into tiny, three-dimensional balls of cells that mimic the anatomy of the cerebral cortex. The team showed that these brain spheres contain the expected type of nerve cells, or neurons, as well as other cells that support neuron function.

Still, the complete formation of the cortex’s neuron circuits requires connections with another type of neuron that lies in a separate region of the brain. These other neurons travel large distances in a developing fetus’ brain over several months to reach the cortical cortex. Once in place, these migrating neurons have an inhibitory role and can block the cortical cortex nerve signals. Turning off a nerve signal is just as important as turning one on. In fact, imbalances in these opposing on and off nerve signals are suspected to play a role in epilepsy and autism.

So, in the current Nature study, Pasca’s team devised two different iPSC-derived brain sphere recipes: one that mimics the neurons found in the cortical cortex and another that mimics the region that contains the inhibitory neurons. Then the researchers placed the two types of spheres in the same lab dish and within three days, they spontaneously fused together.

Under video microscopy, the migration of the inhibitory neurons into the cortical cortex was observed. In cells derived from healthy donors, the migration pattern of inhibitory neurons looked like a herky-jerkey car being driven by a student driver: the neurons would move toward the cortical cortex sphere but suddenly stop for a while and then start their migration again.

“We’ve never been able to recapitulate these human-brain developmental events in a dish before,” said Pasca in a press release, “the process happens in the second half of pregnancy, so viewing it live is challenging. Our method lets us see the entire movie, not just snapshots.”

New insights into Timothy Syndrome may also uncover molecular basis of autism
To study the migration of the inhibitory neurons in the context of a neuropsychiatric disease, iPSCs were generated from skin samples of patients with Timothy syndrome, a rare genetic disease which carries a wide-range of symptoms including autism as well as heart defects.

The formation of brain spheres from the patient-derived iPSCs proceeded normally. But the next part of the experiment revealed an abnormal migration pattern of the neurons.  The microscopy movies showed that the start and stop behavior of neurons happened more frequently but the speed of the migration slowed. The fascinating video below shows the differences in the migration patterns of a healthy (top) versus a Timothy sydrome-derived neuron (bottom). The end result was a disruption of the typically well-organized neuron circuitry.

Now, the gene that’s mutated in Timothy Syndrome is responsible for the production of a protein that helps shuttle calcium in and out of neurons. The flow of calcium is critical for many cell functions and adding drugs that slow down this calcium flux restored the migration pattern of the neurons. So, the researchers can now zero in their studies on this direct link between the disease-causing mutation and a specific breakdown in neuron function.

The exciting possibility is that, because this system is generated from a patient’s skin cells, experiments could be run to precisely understand each individual’s neuropsychiatric disorder. Pasca is eager to see what new insights lie ahead:

“Our method of assembling and carefully characterizing neuronal circuits in a dish is opening up new windows through which we can view the normal development of the fetal human brain. More importantly, it will help us see how this goes awry in individual patients.”

Could revving up stem cells help senior citizens heal as fast as high school seniors?

All physicians, especially surgeons, sport medicine doctors, and military medical corps share a similar wish: to able to speed up the healing process for their patients’ incisions and injuries. Data published this week in Cell Reports may one day fulfill that wish. The study – reported by a Stanford University research team – pinpoints a single protein that revs up stem cells in the body, enabling them to repair tissue at a quicker rate.

Screen Shot 2017-04-19 at 5.37.38 PM

Muscle fibers (dark areas surrounding by green circles) are larger in mice injected with HGFA protein (right panel) compared to untreated mice (left panel), an indication of faster healing after muscle injury.
(Image: Cell Reports 19 (3) p. 479-486, fig 3C)

Most of the time, adult stem cells in the body keep to themselves and rarely divide. This calmness helps preserve this important, small pool of cells and avoids unnecessary mutations that may happen whenever DNA is copied during cell division.

To respond to injury, stem cells must be primed by dividing one time, which is a very slow process and can take several days. Once in this “alert” state, the stem cells are poised to start dividing much faster and help repair damaged tissue. The Stanford team, led by Dr. Thomas Rando, aimed to track down the signals that are responsible for this priming process with the hope of developing drugs that could help jump-start the healing process.

Super healing serum: it’s not just in video games
The team collected blood serum from mice two days after the animals had been subjected to a muscle injury (the mice were placed under anesthesia during the procedure and given pain medication afterwards). When that “injured” blood was injected into a different set of mice, their muscle stem cells became primed much faster than mice injected with “uninjured” blood.

“Clearly, blood from the injured animal contains a factor that alerts the stem cells,” said Rando in a press release. “We wanted to know, what is it in the blood that is doing this?”

 

A deeper examination of the priming process zeroed in on a muscle stem cell signal that is turned on by a protein in the blood called hepatocyte growth factor (HGF). So, it seemed likely that HGF was the protein that they had been looking for. But, to their surprise, there were no differences in the amount of HGF found in blood from injured and uninjured mice.

HGFA: the holy grail of healing?
It turns out, though, that HGF must first be chopped in two by an enzyme called HGFA to become active. When the team went back and examined the injured and uninjured blood, they found that it was HGFA which showed a difference: it was more active in the injured blood.

To show that HGFA was directly involved in stimulating tissue repair, the team injected mice with the enzyme two days before the muscle injury procedure. Twenty days post injury, the mice injected with HGFA had regenerated larger muscle fibers compared to untreated mice. Even more telling, nine days after the HGFA treatment, the mice had better recovery in terms of their wheel running activity compared to untreated mice.

To mimic tissue repair after a surgery incision, the team also looked at the impact of HGFA on skin wound healing. Like the muscle injury results, injecting animals with HGFA two days before creating a skin injury led to better wound healing compared to untreated mice. Even the hair that had been shaved at the surgical site grew back faster. First author Dr. Joseph Rodgers, now at USC, summed up the clinical implications of these results :

“Our research shows that by priming the body before an injury you can speed the process of tissue repair and recovery, similar to how a vaccine prepares the body to fight infection. We believe this could be a therapeutic approach to improve recovery in situations where injuries can be anticipated, such as surgery, combat or sports.”

Could we help senior citizens heal as fast as high school seniors?
Another application for this therapeutic approach may be for the elderly. Lots of things slow down when you get older including your body’s ability to heal itself. This observation sparks an intriguing question for Rando:

“Stem cell activity diminishes with advancing age, and older people heal more slowly and less effectively than younger people. Might it be possible to restore youthful healing by activating this [HGFA] pathway? We’d love to find out.”

I bet a lot of people would love for you to find out, too.

Could the Answer to Treating Parkinson’s Disease Come From Within the Brain?

Sometimes a solution to a disease doesn’t come in the form of a drug or a stem cell therapy, but from within ourselves.

Yesterday, scientists from the Karolinska Institutet in Sweden reported an alternative strategy for treating Parkinson’s disease that involves reprogramming specific cells in the brain into the nerve cells killed off by the disease. Their method, which involves delivering reprogramming genes into brain cells called astrocytes, was able to alleviate motor symptoms associated with Parkinson’s disease in mice.

What is Parkinson’s Disease and how is it treated?

Parkinson’s disease (PD) is a progressive neurodegenerative disease that’s characterized by the death of dopamine-producing nerve cells (called dopaminergic neurons) in an area of the brain that controls movement.

Dopaminergic neurons grown in a culture dish. (Image courtesy of Faria Zafar, Parkinson’s Institute).

PD patients experience tremors in their hands, arms and legs, have trouble starting and stopping movement, struggle with maintaining balance and have issues with muscle stiffness. These troublesome symptoms are caused by a lack dopamine, a chemical made by dopaminergic neurons, which signals to the part of the brain that controls how a person initiates and coordinates movement.

Over 10 million people in the world are affected by PD and current therapies only treat the symptoms of the disease rather than prevent its progression. Many of these treatments involve drugs that replace the lost dopamine in the brain, but these drugs lose their effectiveness over time as the disease kills off more neurons, and they come with their own set of side effects.

Another strategy for treating Parkinson’s is replacing the lost dopaminergic neurons through cell-based therapies. However this research is still in its early stages and would require patients to undergo immunosuppressive therapy because the stem cell transplants would likely be allogeneic (from a donor) rather than autologous (from the same individual).

Drug and cell-based therapies both involve taking something outside the body and putting it in, hoping that it does the right thing and prevents the disease. But what about using what’s already inside the human body to fight off PD?

This brings us to today’s study where scientists reprogrammed brain cells in vivo (meaning inside a living organism) to produce dopamine in mice with symptoms that mimic Parkinson’s. Their method, which was published in the journal Nature Biotechnology, was successful in alleviating some of the Parkinson’s-related movement problems the mice had. This study was funded in part by a CIRM grant and received a healthy amount of coverage in the media including STATnews, San Diego Union-Tribune and Scientific American.

Reprogramming the brain to make more dopamine

Since Shinya Yamanaka published his seminal paper on reprogramming adult somatic cells into induced pluripotent stem cells, scientists have taken the building blocks of his technology a step further to reprogram one adult cell type into another. This process is called “direct reprogramming” or “transdifferentiation”. It involves delivering a specific cocktail of genes into cells that rewrite the cells identity, effectively turning them into the cell type desired.

The Karolinska team found that three genes: NEUROD1, ASCL1 and LMX1A combined with a microRNA miR218 were able to reprogram human astrocytes into induced dopaminergic neurons (iDANs) in a lab dish. These neurons looked and acted like the real thing and gave the scientists hope that this combination of factors could reprogram astrocytes into iDANs in the brain.

The next step was to test these factors in mice with Parkinson’s disease. These mice were treated with a drug that killed off their dopaminergic neurons giving them Parkinson’s-like symptoms. The team used viruses to deliver the reprogramming cocktail to astrocytes in the brain. After a few weeks, the scientists observed that some of the “infected” astrocytes developed into iDANs and these newly reprogrammed neurons functioned properly, and more importantly, helped reverse some of the motor symptoms observed in these mice.

This study offers a new potential way to treat Parkinson’s by reprogramming cells in the brain into the neurons that are lost to the disease. While this research is still in its infancy, the scientists plan to improve the safety of their technology so that it can eventually be tested in humans.

Bonus Blog Interview for World Parkinson’s Day

Ernest Arenas, Karolinska Institutet

In honor of World Parkinson’s day (April 11th), I’m providing a bonus blog interview about this research. I reached out to the senior author of this study, Dr. Ernest Arenas, to ask him a few more questions about his publication and the future studies his team is planning.

Q) What are the major findings of your current study and how do they advance research on Parkinson’s disease?

The current treatment for Parkinson’s disease (PD) is symptomatic and does not change the course of the disease. Cell replacement therapies, such as direct in vivo reprogramming of in situ [local] astrocytes into dopamine (DA) neurons, work by substituting the cells lost by disease and have the potential to halt or even reverse motor alterations in PD.

Q) Can you comment on the potential for gene therapy treatments for Parkinson’s patients?

We see direct in vivo reprogramming of brain astrocytes into dopamine neurons in situ as a possible future alternative to DA cell transplantation. This method represents a gene therapy approach to cell replacement since we use a virus to deliver four reprogramming factors. In this method, the donor cells are in the host brain and there is no need to search for donor cells and no cell transplantation or immunosuppression. The method for the moment is an experimental prototype and much more needs to be done in order to improve efficiency, safety and to translate it to humans.

Q) Will reprogrammed iDANs be susceptible to Parkinson’s disease over time?

As any other cell replacement therapy, the cells would be, in principle, susceptible to Parkinson’s disease. It has been found that PD catches up with transplanted cells in 15-20 years. We think that this is a sufficiently long therapeutic window.

In addition, direct in vivo reprogramming may also be performed with drug-inducible constructs that could be activated years after, as disease progresses. This might allow adding more cells by turning on the reprogramming factors with pharmacological treatment to the host. This was not tested in our study but the basic technology to develop such strategies currently exist.

Q) What are your plans for future studies and translating this research towards the clinic?

In our experiments, we used transgenic mice in order to test our approach and to ensure that we only reprogrammed astrocytes. There is a lot that still needs to be done in order to develop this approach as a therapy for Parkinson’s disease. This includes improving the efficiency and the safety of the method, as well as developing a strategy suitable for therapy in humans. This can be achieved by further improving the reprogramming cocktail, by using a virus with a selective tropism [affinity] for astrocytes and that do not incorporate the constructs into the DNA of the host cell, as well as using constructs with astrocyte-specific promoters and capable of self-regulating depending on the cell context.

Our study demonstrates for the first time that it is possible to use direct reprogramming of host brain cells in order to rescue neurological symptoms. These results indicate that direct reprogramming has the potential to become a novel therapeutic approach for Parkinson’s disease and opens new opportunities for the treatment of patients with neurological disorders.