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)

Don’t Be Afraid: High school stem cell researcher on inspiring girls to pursue STEM careers

As part of our CIRM scholar blog series, we’re featuring the research and career accomplishments of CIRM funded students.

Shannon Larsuel

Shannon Larsuel is a high school senior at Mayfield Senior School in Pasadena California. Last summer, she participated in Stanford’s CIRM SPARK high school internship program and did stem cell research in a lab that studies leukemia, a type of blood cancer. Shannon is passionate about helping people through research and medicine and wants to become a pediatric oncologist. She is also dedicated to inspiring young girls to pursue STEM (Science, Technology, Engineering, and Mathematics) careers through a group called the Stem Sisterhood.

I spoke with Shannon to learn more about her involvement in the Stem Sisterhood and her experience in the CIRM SPARK program. Her interview is below.


Q: What is the Stem Sisterhood and how did you get involved?

SL: The Stem Sisterhood is a blog. But for me, it’s more than a blog. It’s a collective of women and scientists that are working to inspire other young scientists who are girls to get involved in the STEM field. I think it’s a wonderful idea because girls are underrepresented in STEM fields, and I think that this needs to change.

I got involved in the Stem Sisterhood because my friend Bridget Garrity is the founder. This past summer when I was at Stanford, I saw that she was doing research at Caltech. I reconnected with her and we started talking about our summer experiences working in labs. Then she asked me if I wanted to be involved in the Stem Sisterhood and be one of the faces on her website. She took an archival photo of Albert Einstein with a group of other scientists that’s on display at Caltech and recreated it with a bunch of young women who were involved in the STEM field. So I said yes to being in the photo, and I’m also in the midst of writing a blog post about my experience at Stanford in the SPARK program.

Members of The Stem Sisterhood

Q: What does the Stem Sisterhood do?

SL: Members of the team go to elementary schools and girl scout troop events and speak about science and STEM to the young girls. The goal is to inspire them to become interested in science and to teach them about different aspects of science that maybe are not that well known.

The Stem Sisterhood is based in Los Angeles. The founder Bridget wants to expand the group, but so far, she has only done local events because she is a senior in high school. The Stem Sisterhood has an Instagram account in addition to their blog. The blog is really interesting and features interviews with women who are in science and STEM careers.

Q: How has the Stem Sisterhood impacted your life?

SL: It has inspired me to reach out to younger girls more about science. It’s something that I am passionate about, and I’d like to pursue a career in the medical field. This group has given me an outlet to share that passion with others and to hopefully change the face of the STEM world.

Q: How did you find out about the CIRM SPARK program?

SL: I knew I wanted to do a science program over the summer, but I wasn’t sure what type. I didn’t know if I wanted to do research or be in a hospital. I googled science programs for high school seniors, and I saw the one at Stanford University. It looked interesting and Stanford is obviously a great institution. Coming from LA, I was nervous that I wouldn’t be able to get in because the program had said it was mostly directed towards students living in the Bay Area. But I got in and I was thrilled. So that’s basically how I heard about it, because I googled and found it.

Q: What was your SPARK experience like?

SL: My program was incredible. I was a little bit nervous and scared going into it because I was the only high school student in my lab. As a high school junior going into senior year, I was worried about being the youngest, and I knew the least about the material that everyone in the lab was researching. But my fears were quickly put aside when I got to the lab. Everyone was kind and helpful, and they were always willing to answer my questions. Overall it was really amazing to have my first lab experience be at Stanford doing research that’s going to potentially change the world.

Shannon working in the lab at Stanford.

I was in a lab that was using stem cells to characterize a type of leukemia. The lab is hoping to study leukemia in vitro and in vivo and potentially create different treatments and cures from this research. It was so cool knowing that I was doing research that was potentially helping to save lives. I also learned how to work with stem cells which was really exciting. Stem cells are a new advancement in the science world, so being able to work with them was incredible to me. So many students will never have that opportunity, and being only 17 at the time, it was amazing that I was working with actual stem cells.

I also liked that the Stanford SPARK program allowed me to see other aspects of the medical world. We did outreach programs in the Stanford community and helped out at the blood drive where we recruited people for the bone marrow registry. I never really knew anything about the registry, but after learning about it, it really interested me. I actually signed up for it when I turned 18. We also met with patients and their families and heard their stories about how stem cell transplants changed their lives. That was so inspiring to me.

Going into the program, I was pretty sure I wanted to be a pediatric oncologist, but after the program, I knew for sure that’s what I wanted to do. I never thought about the research side of pediatric oncology, I only thought about the treatment of patients. So the SPARK program showed me what laboratory research is like, and now that’s something I want to incorporate into my career as a pediatric oncologist.

I learned so much in such a short time period. Through SPARK, I was also able to connect with so many incredible, inspired young people. The students in my program and I still have a group chat, and we text each other about college and what’s new with our lives. It’s nice knowing that there are so many great people out there who share my interests and who are going to change the world.

Stanford SPARK students.

Q: What was your favorite part of the SPARK program?

SL: Being in the lab every day was really incredible to me. It was my first research experience and I was in charge of a semi-independent project where I would do bacterial transformations on my own and run the gels. It was cool that I could do these experiments on my own. I also really loved the end of the summer poster session where all the students from the different SPARK programs came together to present their research. Being in the Stanford program, I only knew the Stanford students, but there were so many other awesome projects that the other SPARK students were doing. I really enjoyed being able to connect with those students as well and learn about their projects.

Q: Why do you want to pursue pediatric oncology?

SL: I’ve always been interested in the medical field but I’ve had a couple of experiences that really inspired me to become a doctor. My friend has a charity that raises money for Children’s Hospital Los Angeles. Every year, we deliver toys to the hospital. The first year I participated, we went to the hospital’s oncology unit and something about it stuck with me. There was one little boy who was getting his chemotherapy treatment. He was probably two years old and he really inspired to create more effective treatments for him and other children.

I also participated in the STEAM Inquiry program at my high school, where I spent two years reading tons of peer reviewed research on immunotherapy for pediatric cancer. Immunotherapy is something that really interests me. It makes sense that since cancer is usually caused by your body’s own mutations, we should be able to use the body’s immune system that normally regulates this to try and cure cancer. This program really inspired me to go into this field to learn more about how we can really tailor the immune system to fight cancer.

Q: What advice do you have for young girls interested in STEM.

SL: My advice is don’t be afraid. I think that sometimes girls are expected to be interested in less intellectual careers. This perception can strike fear into girls and make them think “I won’t be good enough. I’m not smart enough for this.” This kind of thinking is not good at all. So I would say don’t be afraid and be willing to put yourself out there. I know for me, sometimes it’s scary to try something and know you could fail. But that’s the best way to learn. Girls need to know that they are capable of doing anything and if they just try, they will be surprised with what they can do.

Stem Cell Stories That Caught Our Eye: Three new ways to target cancer stem cells

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.

Targeting cancer stem cells. This week, three studies came out with novel ways for targeting cancer stem cells in different types of cancers. Here’s a brief run-down of this trifecta of cancer stem cell-crushing stories:

Take your vitamins! Scientists in the UK were experimenting on cancer stem cells and comparing natural substances to on-the-market cancer drugs to determine whether any of the natural substances were effective at disrupting the metabolism (the chemical reactions that keep cells alive and functioning) of cancer stem cells. Interestingly, they found that ascorbic acid, which you’ll know as Vitamin C, was ten times better at curbing cancer stem cell growth compared to a cancer drug called 2-DG.

Vitamin C has popped up as an anti-cancer treatment in the past when Nobel Laureate Linus Pauling found that it dramatically reduced the death rate in breast cancer patients. However this current study is the first to show that Vitamin C has a direct effect on cancer stem cells.

In coverage by ScienceDaily, the UK team hinted at plans to test Vitamin C in clinical trials:

“Vitamin C is cheap, natural, non-toxic and readily available so to have it as a potential weapon in the fight against cancer would be a significant step. Our results indicate it is a promising agent for clinical trials, and a as an add-on to more conventional therapies, to prevent tumour recurrence, further disease progression and metastasis.”

 

A gene called ZEB1 determines how aggressive brain tumors are. A team from Cedars-Sinai Medical Center was interested to know how cancer stem cells in aggressive brain tumors called gliomas survive, reproduce and affect patient survival. In a study published in Scientific Reports, they studied the genetic information of over 4000 brain tumor samples and found ZEB1, a gene that regulates tumor growth and is associated with patient survival.

They found that patients with a healthy copy of the ZEB1 gene had a higher survival rate and less aggressive tumors compared to patients that didn’t have ZEB1 or had a mutated version of the gene.

In coverage by ScienceDaily, the senior author on the study explained how their study’s findings will allow for more personalized treatments for patients with glioma based on whether they have ZEB1 or not:

“Patients without the gene in their tumors have more aggressive cancers that act like stem cells by developing into an uncontrollable number of cell types. This new information could help us to measure the mutation in these patients so that we are able to provide a more accurate prognosis and treatment plan.”

 

Beating resistant tumors by squashing cancer stem cells. Our final cancer stem cell story today comes from the UCLA School of Dentistry. This team is studying another type of aggressive cancer called a squamous cell carcinoma that causes tumors in the head and neck. Often these tumors resist treatment and spread to a patient’s lymph nodes, which quickly reduces their survival rate.

The UCLA team thought that maybe pesky cancer stem cells were to blame for the aggressive and resistant nature of these head and neck tumors. In a study published in Cell Stem Cell, they developed a mouse model of head and neck carcinoma and isolated cancer stem cells from the tumors of these mice. When they studied these stem cells, they found that they expressed unique proteins compared to non-cancer cells. These included Bmi1, a well-known stem cell protein, and AP-1, a transcription factor protein that regulates other cancer genes.

At left, head and neck squamous cell carcinoma invasive growth, and at right, cancer stem cells (shown in red) in head and neck squamous cell carcinoma. (Image Demeng Chen and Cun-Yu Wang/UCLA)

After identifying the culprits, the team developed a new combination strategy that targeted the cancer stem cells while also killing off the tumors using chemotherapy drugs.

In a UCLA Newsroom press release, the lead scientist on the study Dr. Cun-Yu Wang explained the importance of their study for the future treatment of cancer and solid tumors:

“This study shows that for the first time, targeting the proliferating tumor mass and dormant cancer stem cells with combination therapy effectively inhibited tumor growth and prevented metastasis compared to monotherapy in mice. Our discovery could be applied to other solid tumors such as breast and colon cancer, which also frequently metastasizes to lymph nodes or distant organs.”

Curing the Incurable through Definitive Medicine

“Curing the Incurable”. That was the theme for the first annual Center for Definitive and Curative Medicine (CDCM) Symposium held last week at Stanford University, in Palo Alto, California.

The CDCM is a joint initiative amongst Stanford Healthcare, Stanford Children’s Health and the Stanford School of Medicine. Its mission is to foster an environment that accelerates the development and translation of cell and gene therapies into clinical trials.

The research symposium focused on “the exciting first-in-human cell and gene therapies currently under development at Stanford in bone marrow, skin, cardiac, neural, pancreatic and neoplastic diseases.” These talks were organized into four different sessions: cell therapies for neurological disorders, stem cell-derived tissue replacement therapies, genome-edited cell therapies and anti-cancer cell-based therapies.

A few of the symposium speakers are CIRM-funded grantees, and we’ll briefly touch on their talks below.

Targeting cancer

The keynote speaker was Irv Weissman, who talked about hematopoietic or blood-forming stem cells and their value as a cell therapy for patients with blood disorders and cancer. One of the projects he discussed is a molecule called CD47 that is found on the surface of cancer cells. He explained that CD47 appears on all types of cancer cells more abundantly than on normal cells and is a promising therapeutic target for cancer.

Irv Weissman

Irv Weissman

“CD47 is the first gene whose overexpression is common to all cancer. We know it’s molecular mechanism from which we can develop targeted therapies. This would be impossible without collaborations between clinicians and scientists.”

 

At the end of his talk, Weissman acknowledged the importance of CIRM’s funding for advancing an antibody therapeutic targeting CD47 into a clinical trial for solid cancer tumors. He said CIRM’s existence is essential because it “funds [stem cell-based] research through the [financial] valley of death.” He further explained that CIRM is the only funding entity that takes basic stem cell research all the way through the clinical pipeline into a therapy.

Improving bone marrow transplants

judith shizuru

Judith Shizuru

Next, we heard a talk from Judith Shizuru on ways to improve current bone-marrow transplantation techniques. She explained how this form of stem cell transplant is “the most powerful form of cell therapy out there, for cancers or deficiencies in blood formation.” Inducing immune system tolerance, improving organ transplant outcomes in patients, and treating autoimmune diseases are all applications of bone marrow transplants. But this technique also carries with it toxic and potentially deadly side effects, including weakening of the immune system and graft vs host disease.

Shizuru talked about her team’s goal of improving the engraftment, or survival and integration, of bone marrow stem cells after transplantation. They are using an antibody against a molecule called CD117 which sits on the surface of blood stem cells and acts as an elimination signal. By blocking CD117 with an antibody, they improved the engraftment of bone marrow stem cells in mice and also removed the need for chemotherapy treatment, which is used to kill off bone marrow stem cells in the host. Shizuru is now testing her antibody therapy in a CIRM-funded clinical trial in humans and mentioned that this therapy has the potential to treat a wide variety of diseases such as sickle cell anemia, leukemias, and multiple sclerosis.

Tackling stroke and heart disease

img_1327We also heard from two CIRM-funded professors working on cell-based therapies for stroke and heart disease. Gary Steinberg’s team is using human neural progenitor cells, which develop into cells of the brain and spinal cord, to treat patients who’ve suffered from stroke. A stroke cuts off the blood supply to the brain, causing the death of brain cells and consequently the loss of function of different parts of the body.  He showed emotional videos of stroke patients whose function and speech dramatically improved following the stem cell transplant. One of these patients was Sonia Olea, a young woman in her 30’s who lost the ability to use most of her right side following her stroke. You can read about her inspiring recover post stem cell transplant in our Stories of Hope.

Dr. Joe Wu. (Image Source: Sean Culligan/OZY)

Dr. Joe Wu. (Image Source: Sean Culligan/OZY)

Joe Wu followed with a talk on adult stem cell therapies for heart disease. His work, which is funded by a CIRM disease team grant, involves making heart cells called cardiomyocytes from human embryonic stem cells and transplanting these cells into patient with end stage heart failure to improve heart function. His team’s work has advanced to the point where Wu said they are planning to file for an investigational new drug (IND) application with the US Food and Drug Administration (FDA) in six months. This is the crucial next step before a treatment can be tested in clinical trials. Joe ended his talk by making an important statement about expectations on how long it will take before stem cell treatments are available to patients.

He said, “Time changes everything. It [stem cell research] takes time. There is a lot of promise for the future of stem cell therapy.”

Stem Cell Profiles in Courage: Karl’s Fight with Cancer

Karl Trede

Karl Trede

When I think of a pioneer I have an image in my head of people heading west across the Americans plains in the 18th century, riding in a covered wagon pulled by weary oxen.

Karl Trede doesn’t fit that image at all. He is a trim, elegant man who has a ready smile and a fondness for Hawaiian shirts. But he is no less a pioneer for all that. That’s why we profiled him in our 2016 Annual Report.

In 2006 Karl was diagnosed with cancer of the throat. He underwent surgery to remove his vocal chords and thought he had beaten the cancer. A few years later, it came back. That was when Karl became the first person ever treated in a CIRM-funded clinical trial testing a new anti-tumor therapy targeting cancer stem cells that so far has helped hold the disease at bay.

Here is Karl’s story, in his own words:

“I had some follow-up tests and those showed spots in my lungs. Over the course of several years, they saw those spots grow, and we knew the cancer had spread to my lungs. I went to Stanford and was told there was no effective treatment for it, fortunately it was slow growing.

Then one day they said we have a new clinical trial we’re going to start would you be interested in being part of it.

I don’t believe I knew at the time that I was going to be the first one in the trial [now that’s what I call a pioneer] but I thought I’d give it a whirl and I said ‘Sure’. I wasn’t real concerned about being the first in a trial never tested in people before. I figured I was going to have to go someday so I guess if I was the first person and something really went wrong then they’d definitely learn something; so, to me, that was kind of worth my time.

Fortunately, I lasted 13 months, 72 treatments with absolutely no side effects. I consider myself really lucky to have been a part of it.

It was an experience for me, it was eye opening. I got an IV infusion, and the whole process was 4 hours once a week.

Dr. Sikic (the Stanford doctor who oversees the clinical trial) made it a practice of staying in the room with me when I was getting my treatments because they’d never tried it in people, they’d tested it in mice, but hadn’t tested it in people and wanted to make sure they were safe and nothing bad happened.

The main goals of the trial were to define what the side effects were and what the right dose is and they got both of those. So I feel privileged to have been a part of this.

My wife and I (Vita) have four boys. They’re spread out now – two in the San Francisco Bay Area, one in Oregon and one in Nevada. But we like to get together a few times a year. They’re all good cooks, so when we have a family get together there’s a lot of cooking involved.

The Saturday after Thanksgiving, in 2015, the boys decided they wanted to have a rib cook-off for up to around 30 people and I can proudly say that I kicked their ass on the rib cook-off. I have an electric cooker and I just cook ‘em slow and long. I do a cranberry sauce, just some home made bbq sauces

I’m a beef guy, I love a good steak, a good ribeye or prime rib, I make a pretty mean Oso bucco, I make a good spaghetti sauce, baked chicken with an asparagus mousse that is pretty good.

I just consider myself a lucky guy.”

Karl Trede with CIRM President Randy Mills at the 2016 December Board meeting.

Karl Trede with CIRM President Randy Mills at the 2016 December Board meeting.


Related Links:

Stem cell stories that caught our eye: designer socks for cancer patients, stem-cell derived stomachs and fighting off bone infections

Inspiring cancer patients with designer socks. (Karen Ring)
Here’s a motivating story we found in the news this week about a cancer survivor who’s bringing inspiration to other cancer patients with designer socks. Yes, you read that correctly, socks.

Jake Teitelbaum is a student at Wake Forest University and suffers from a rare form of blood cancer called Refractory Hodgkin’s lymphoma. Since his diagnosis, Jake has been admitted to hospitals multiple times. Each time he received a welcome package of a gown and a pair of beige, “lifeless” socks. After his fifth welcome package, this time to receive a life-saving stem cell treatment, Jake had had enough of the socks.

He explained in a story by USA Today College,

“[Those socks] represented chemotherapy and being in isolation. They were the embodiment of that experience.”

Jake ditched the hospital socks and started bringing his own to prove that his cancer didn’t define him. Even though his cancer kept coming back, Jake wanted to prove he was just as resilient.

Jake Teitelbaum

Jake Teitelbaum

Feeling liberated and in control, Jake decided to share his socks with other patients by starting the Resilience Project. Patients can go to the Resilience website and design their own socks that represent their experiences with cancer. The Resilience project also raises money for cancer patients and their families.

“We provide tangible benefits and create fun socks, but what we’re doing comes back to the essence of resilience,” said Jake. “These terrible circumstances where we’re at our most vulnerable also give us the unique opportunity to grow.”

Jake was declared cancer free in October of 2016. You can learn more about the Resilience project on their website and by watching Jake’s video below.

 

Feeding disease knowledge with stem cell-derived stomach cells.
Using educated guess work and plenty of trial and error in the lab, researchers around the world have successfully generated many human tissues from stem cells, including heart muscle cells, insulin-producing cells and nerve cells to name just a few. Reporting this week in Nature, stem cell scientists at Cincinnati’s Children Hospital have a new cell type under their belt. Or maybe I should say above their belt, because they have devised a method for coaxing stem cells to become stomach mini organs that can be studied in a petri dish.

Confocal microscopic image shows tissue-engineered human stomach tissues from the corpus/fundus region, which produce acid and digestive enzymes. Image: Cincinnati Children’s Hospital Medical Center

Confocal microscopic image shows tissue-engineered human stomach tissues from the corpus/fundus region, which produce acid and digestive enzymes. Image: Cincinnati Children’s Hospital Medical Center

With this method in hand, the team is poised to make new discoveries about how the stomach forms during human development and to better understand stomach diseases. In a press release, team lead Jim Wells pointed out the need to find new therapies for stomach disease:

“Diseases of the stomach impact millions of people in the United States and gastric [stomach] cancer is the third leading cause of cancer-related deaths worldwide.”

The cells they generated are those found in the corpus/fundus area of the stomach which releases enzymes and hydrochloric acid to help us break down and digest the food we eat. The team is particularly interested to use the mini organs to study the impact of H. pylori infection, a type of bacteria that causes ulcers and has been linked to stomach cancers.

In an earlier study, Wells’ group devised stem cell recipes for making cells from an area of the stomach, called the antrum, that produces hormones that affect digestion and appetite. Wells thinks having both tissue types recreated in a petri dish may help provide a complete picture of stomach function:

James Wells

James Wells

“Now that we can grow both antral- and corpus/fundic-type human gastric mini-organs, it’s possible to study how these human gastric tissues interact physiologically, respond differently to infection, injury and react to pharmacologic treatments.”

 

 

A silver bullet for antibiotic-resistant bone infections?
Alexander Fleming’s discover of penicillin in the 1920’s marked the dawn of antibiotics – drugs which kill off bacteria and help stop infections. Rough estimates suggest that over 200 million lives have been saved by these wonder drugs. But over time there’s been a frightening rise in bacteria that are resistant to almost all available antibiotics.

These super resistant “bugs” are particularly scary for people with chronic bone infections because the intense, long term antibiotic medication required to keep the infection in check isn’t effective. But based on research published this week in Tissue Engineering, the use of stem cells and silver may provide a new treatment option.

Scanning Electron micrograph of methicillin-resistant Staphylococcus aureus (MRSA, brown spheres) surrounded by cellular debris. MRSA, the bacteria examined in this study, is resistant by many antibiotics

Scanning Electron micrograph of methicillin-resistant Staphylococcus aureus (MRSA, brown spheres) surrounded by cellular debris. MRSA, the bacteria examined in this study, is resistant by many antibiotics. (Wikimedia)

It’s been known for many years that silver in liquid form can kill bacteria and scientists have examined ways to deliver a controlled release of silver nanoparticles at the site of the bone infection. But there has been a lot of concern, including by the Food and Drug Administration (FDA), about the toxicity of silver nanoparticles to human cells.

In this study, a team led by Elizabeth Loboa from the University of Missouri instead looked at the use of silver ions which are safer than the nanoparticles. The team developed a three-dimensional cell culture system that resembles bone by growing human bone-forming stem cells on a tissue engineered scaffold, which also slowly releases silver ions.

The researchers stimulated the stem cells within the scaffold to specialize into bone cells and included a strain of bacteria that’s resistant to multiple antibiotics. They found that the silver ions effectively killed the bacteria and at the same time did not block the bone-forming stem cells. If this work holds up, doctors may one day use this silver ion-releasing, biodegradable scaffold to directly treat the area of bone infection. And to help prevent infection after joint replacement procedures, surgeons may rely on implants that are coated with these scaffolds.

How stem cells are helping change the face of medicine, one pioneering patient at a time

One of the many great pleasures of my job is that I get to meet so many amazing people. I get to know the researchers who are changing the face of medicine, but even more extraordinary are the people who are helping them do it, the patients.

Attacking Cancer

Karl

Karl Trede

It’s humbling to meet people like Karl Trede from San Jose, California. Karl is a quiet, witty, unassuming man who when the need arose didn’t hesitate to put himself forward as a medical pioneer.

Diagnosed with throat cancer in 2006, Karl underwent surgery to remove the tumor. Several years later, his doctors told him it had returned, only this time it had spread to his lungs. They told him there was no effective treatment. But there was something else.

“One day the doctor said we have a new trial we’re going to start, would you be interested? I said “sure”. I don’t believe I knew at the time that I was going to be the first one, but I thought I’d give it a whirl.”

Karl was Patient #1 in a clinical trial at Stanford University that was using a novel approach to attack cancer stem cells, which have the ability to evade standard anti-cancer treatments and cause the tumors to regrow. The team identified a protein, called CD47, that sits on the surface of cancer stem cells and helps them evade being gobbled up and destroyed by the patient’s own immune system. They dubbed CD47 the “don’t eat me” signal and created an antibody therapy they hoped would block the signal, leaving the cancer and the cancer stem cells open to attack by the immune system.

The team did pre-clinical testing of the therapy, using mice to see if it was safe. Everything looked hopeful. Even so, this was still the first time it was being tested in a human. Karl said that didn’t bother him.

“It was an experience for me, it was eye opening. I wasn’t real concerned about being the first in a trial never tested in people before. I said we know that there’s no effective treatment for this cancer, it’s not likely but it’s possible that this could be the one and if nothing else, if it doesn’t do anything for me hopefully it does something so they learn for others.”

It’s that kind of selflessness that is typical of so many people who volunteer for clinical trials, particularly Phase 1 trials, where a treatment is often being tried in people for the first time ever. In these trials, the goal is to make sure the approach is safe, so patients are given a relatively small dose of the therapy (cells or drugs) and told ahead of time it may not do any good. They’re also told that there could be some side effects, potentially serious, even life-threatening ones. Still, they don’t hesitate.

Improving vision

Rosie Barrero certainly didn’t hesitate when she got a chance to be part of a clinical trial testing the use of stem cells to help people with retinitis pigmentosa, a rare progressive disease that destroys a person’s vision and ultimately leaves them blind.

Rosalinda Barrero

Rosie Barrero

“I was extremely excited about the clinical trial. I didn’t have any fear or trepidation about it, I would have been happy being #1, and I was #6 and that was fine with me.”

 

Rosie had what are called retinal progenitor cells injected into her eye, part of a treatment developed by Dr. Henry Klassen at the University of California, Irvine. The hope was that those cells would help repair and perhaps even replace the light-sensing cells damaged by the disease.

Following the stem cell treatment, gradually Rosie noticed a difference. It was small things at first, like being able to make out the colors of cups in her kitchen cupboard, or how many trash cans were outside their house.

“I didn’t expect to see so much, I thought it would be minor, and it is minor on paper but it is hard to describe the improvement. It’s visible, it’s visible improvement.”

These are the moments that researchers like Henry Klassen live for, and have worked so tirelessly for. These are the moments that everyone at CIRM dreams of, when the work we have championed, supported and funded shows it is working, shows it is changing people’s lives.

One year ago this month our governing Board approved a new Strategic Plan, a detailed roadmap of where we want to go in the coming years. The plan laid out some pretty ambitious goals, such as funding 50 new clinical trials in the next 5 years, and at our Board meeting next week we’ll report on how well we are doing in terms of hitting those targets.

People like Karl and Rosie help motivate us to keep trying, to keep working as hard as we can, to achieve those goals. And if ever we have a tough day, we just have to remind ourselves of what Rosie said when she realized she could once again see her children.

“Seeing their faces. It’s pretty incredible. I always saw them with my heart so I just adore them, but now I can see them with my eye.”


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Buildup of random mutations in adult stem cells doesn’t explain varying frequency of cancers

To divide or not to divide?

 It’s a question every cell in your body must constantly ask itself. Cells in your small intestine, for instance, replace themselves about every three days so the cells in that tissue must divide frequently to replenish the tissue. Liver cell are less active and turn over about once a year. And on the other extreme, the cells in the lens of the eye are kept over a life time.

The cell cycle, an exquisitely controlled process.

The cell cycle, an exquisitely controlled process. (Source wikipedia)

It’s no wonder that the process of cell division, also called the cell cycle, is exquisitely controlled by many different proteins and signaling molecules. It also makes sense that mutations in genes that produce the cell cycle proteins, could cause the regulation of cell division to go awry.

Mutations pave a path to cancer

Accumulation of enough mutations over a lifetime can lead to uncontrolled cell growth and eventually cancer. Adult stem cells are thought to be especially vulnerable to cell cycle mutations since these cells already have the capacity to self-renew and can pass mutations to their daughter cells.

Now, gene mutations can be inherited from one’s parents or caused by environmental factors like UV rays from the sun or acquired by random mistakes that occur as DNA replicates itself during cells division. Studying how the accumulation of these different mutation types impact cell division is important for understanding the formation of cancers. Results from a study in early 2015 indicated that mutations caused by random mistakes in DNA replication had a bigger impact on many cancers than mutations arising from lifestyle and environmental factors.

“Bad luck” mutations may not be the most harmful

But a new research publication in Nature suggests that, while these “bad luck” mutations can drive the development of cancer, they probably are not the main contributors. To reach this conclusion, the research team – which hails from the University Medical Center Utrecht in the Netherlands – directly measured mutation rates in human adult stem cells collected from donors as young as three years and as old as 87. In particular, stem cells from the liver, small intestine and colon were obtained. Individual stem cells were grown in the lab into mini-organs, or organoids, that resemble the structures of the source tissue. After studying these organoids, they determined that the frequency of cancer is very different in these organs, with the incidence cancer in the colon being much higher than in the other two organs.

Mutation rate the same, despite age, despite organ type

Through a various genetic analyses, the team found that an interesting pattern: the mutation rate was the same – about 40 mutations per year – for all organ types and all ages despite the higher incidence of colon cancer and older age-related cancers. Dr. Ruben van Boxtel, the team leader, expressed his reaction to these results in an interview with Medical News Today:

“We were surprised to find roughly the same mutation rate in stem cells from organs with different cancer incidence. This suggests that simply the gradual accumulation of more and more ‘bad luck’ DNA errors over time cannot explain the difference we see in cancer incidence – at least for some cancers.”

Still, the team did observe that different types of random mutations were specific to one organ over the other. These differences may help explain why the colon, for example, has a higher cancer incidence than the liver or small intestine. Van Boxtel and his team are interested in examining this result further:

“It seems ‘bad luck’ is definitely part of the story but we need much more evidence to find out how, and to what extent. This is what we want to focus on next.”

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.”

Multi-Talented Stem Cells: The Many Ways to Use Them in the Clinic

CIRM kicked off the 2016 International Society for Stem Cell Research (ISSCR) Conference in San Francisco with a public stem cell event yesterday that brought scientists, patients, patient advocates and members of the general public together to discuss the many ways stem cells are being used in the clinic to develop treatments for patients with unmet medical needs.

Bruce Conklin, Gladstone Institutes & UCSF

Bruce Conklin, Gladstone Institutes & UCSF

Bruce Conklin, an Investigator at the Gladstone Institutes and UCSF Professor, moderated the panel of four scientists and three patient advocates. He immediately captured the audience’s attention by showing a stunning video of human heart cells, beating in synchrony in a petri dish. Conklin explained that scientists now have the skills and technology to generate human stem cell models of cardiomyopathy (heart disease) and many other diseases in a dish.

Conklin went on to highlight four main ways that stem cells are contributing to human therapy. First is using stem cells to model diseases whose causes are still largely unknown (like with Parkinson’s disease). Second, genome editing of stem cells is a new technology that has the potential to offer cures to patients with genetic disorders like sickle cell anemia. Third, stem cells are known to secrete healing factors, and transplanting them into humans could be beneficial. Lastly, stem cells can be engineered to attack cancer cells and overcome cancer’s normal way of evading the immune system.

Before introducing the other panelists, Conklin made the final point that stem cell models are powerful because scientists can use them to screen and develop new drugs for diseases that have no treatments or cures. His lab is already working on identifying new drugs for heart disease using human induced pluripotent stem cells derived from patients with cardiomyopathy.

Scientists and Patient Advocates Speak Out

Malin Parmar, Lund University

Malin Parmar, Lund University

The first scientist to speak was Malin Parmar, a Professor at Lund University. She discussed the history of stem cell development for clinical trials in Parkinson’s disease (PD). Her team is launching the first in-human trial for Parkinson’s using cells derived from human pluripotent stem cells in 2016. After Parmar’s talk, John Lipp, a PD patient advocate. He explained that while he might look normal standing in front of the crowd, his PD symptoms vary wildly throughout the day and make it hard for him to live a normal life. He believes in the work that scientists like Parmar are doing and confidently said, “In my lifetime, we will find a stem cell cure for Parkinson’s disease.”

Adrienne Shapiro, Patient Advocate

Adrienne Shapiro, Patient Advocate

The next scientist to speak was UCLA Professor Donald Kohn. He discussed his lab’s latest efforts to develop stem cell treatments for different blood disorder diseases. His team is using gene therapy to modify blood stem cells in bone marrow to treat and cure babies with SCID, also known as “bubble-boy disease”. Kohn also mentioned their work in sickle cell disease (SCD) and in chronic granulomatous disease, both of which are now in CIRM-funded clinical trials. He was followed by Adrienne Shapiro, a patient advocate and mother of a child with SCD. Adrienne gave a passionate and moving speech about her family history of SCD and her battle to help find a cure for her daughter. She said “nobody plans to be a patient advocate. It is a calling born of necessity and pain. I just wanted my daughter to outlive me.”

Henry Klassen (UC Irvine)

Henry Klassen, UC Irvine

Henry Klassen, a professor at UC Irvine, next spoke about blinding eye diseases, specifically retinitis pigmentosa (RP). This disease damages the photo receptors in the back of the eye and eventually causes blindness. There is no cure for RP, but Klassen and his team are testing the safety of transplanting human retinal progenitor cells in to the eyes of RP patients in a CIRM-funded Phase 1/2 clinical trial.

Kristen MacDonald, RP patient

Kristen MacDonald, RP patient

RP patient, Kristen MacDonald, was the trial’s first patient to be treated. She bravely spoke about her experience with losing her vision. She didn’t realize she was going blind until she had a series of accidents that left her with two broken arms. She had to reinvent herself both physically and emotionally, but now has hope that she might see again after participating in this clinical trial. She said that after the transplant she can now finally see light in her bad eye and her hope is that in her lifetime she can say, “One day, people used to go blind.”

Lastly, Catriona Jamieson, a professor and Alpha Stem Cell Clinic director at UCSD, discussed how she is trying to develop new treatments for blood cancers by eradicating cancer stem cells. Her team is conducting a Phase 1 CIRM-funded clinical trial that’s testing the safety of an antibody drug called Cirmtuzumab in patients with chronic lymphocytic leukemia (CLL).

Scientists and Patients need to work together

Don Kohn, Catriona Jamieson, Malin Parmar

Don Kohn, Catriona Jamieson, Malin Parmar

At the end of the night, the scientists and patient advocates took the stage to answer questions from the audience. A patient advocate in the audience asked, “How can we help scientists develop treatments for patients more quickly?”

The scientists responded that stem cell research needs more funding and that agencies like CIRM are making this possible. However, we need to keep the momentum going and to do that both the physicians, scientists and patient advocates need to work together to advocate for more support. The patient advocates in the panel couldn’t have agreed more and voiced their enthusiasm for working together with scientists and clinicians to make their hopes for cures a reality.

The CIRM public event was a huge success and brought in more than 150 people, many of whom stayed after the event to ask the panelists more questions. It was a great kick off for the ISSCR conference, which starts today. For coverage, you can follow the Stem Cellar Blog for updates on interesting stem cell stories that catch our eye.

CIRM Public Stem Cell Event

CIRM Public Stem Cell Event