Through their lens: Ray Solis created a prototype database to help speed stem cell research

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Ray Solis worked in the lab of Nicholas Schork at Scripps Research Institute.

Ray Solis working with his mentor. He submitted this image through Instagram to CIRMs #CIRMStemCellLab collection.

During the summer of 2013, I had the incredible opportunity to participate in a full time internship in the lab of Dr. Nicholas Schork at the Scripps Translational Science Institute, which is part of The Scripps Research Institute. During my internship, I personally worked alongside Dr. Schork on a very fascinating multidisciplinary stem cell research project. For my project, I designed and developed a unique, one-of-a-kind prototype database that consolidated high quality datasets, research and data analysis tools, articles and information about the current research being conducted on human induced pluripotent stem cells. To do this, I utilized and conducted a thorough analysis of multiple sources such as PubMed, Google Scholar, Gene Expression Omnibus, and other online resources.

In addition to engineering this prototype database, I showcased its utility by conducting a research and data analysis project on the current studies of various diseases and the intervention of induced pluripotent stem cells as a method to develop potential therapies and cures for these diseases. I analyzed the gene expression of these diseases and drew conclusions about potential therapies and diagnostic methods. These diseases can result from numerous factors, which in many cases are beyond the patient’s control. Biomedical researchers are currently investigating various diseases and the role of genetics within them in hopes of introducing clinical cures. Research of induced pluripotent stem cells is widely conducted due to their incredible potential in developing personalized medicine. Many scientists have a particular interest in these cells because they can be derived from the patient’s skin, therefore allowing them to analyze the genetic information of the individual and personalize their care.

By creating a prototype database, I am providing the scientific community around the world with instant access to the information they are looking for, as well as access to tools and methods they can use to analyze the information in the public domain, as well as data that is generated within their lab. Over time, my database will grow and evolve and eventually go live for public use. As time has progressed, we have been swimming in information and continue to be presented with new findings and data. My database provides everything a scientist needs in one convenient location and provides them with a “one stop shopping” research experience. My analysis on the genetic expression of various diseases will also contribute to the rapidly advancing world of biomedical and stem cell research. I will be analyzing the relationships between the genetic expression of diseased samples and comparing the genetic expression of induced pluripotent stem cells that have been generated as a potential therapy for those diseases. This will provide insight to potential cures for some of the most common and life-threatening conditions in existence.

This internship has provided me with an invaluable opportunity to obtain real lab research experience and gain exposure, skills, knowledge, and contacts in my field of interest that I plan to pursue in the future. The prospect of stem cells being used as a therapy for diseases has always fascinated me and made me want to pursue science further. The idea of finding therapies and cures for diseases and contributing to the betterment of human health is truly what drives me to learn as much as I can about the world of scientific research. I have gained an enormous amount of knowledge about stem cells and their potential, uses, and the experiments and trials that are being conducted to further their path to clinical use. I am extraordinarily grateful to have this amazing opportunity that will help me to achieve my goals in life and lead me to more great opportunities and experiences.

Ray Solis

Ray submitted this video about his experience:

Through their lens: Matt Wood learns that patience is a virtue in the lab

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Matt Wood worked in the lab of Jim Paulson at Scripps Research Institute.

Matt Wood learning lab techniques. He submitted this image through Instagram to CIRMs #CIRMStemCellLab collection.

When reflecting upon the many experiences I have had at The Scripps Research Institute, LSSI boot camp, and many other informational sessions, I am just amazed at how much knowledge can be learned in such a relatively small period of time. And I have been able to acquire such intensive understanding, because everyone in the scientific community has made themselves a resource to the younger generation of scientists.

Additionally, the most fulfilling aspect of the internship for me was the constant hands-on nature of the work, and opportunity for me, as a self identified kinesthetic learner, to feel, sense, and maneuver a variety of subjects, tissues, and projects. On an hourly basis, I am asked to analyze or identify a certain cell line or solution. Thankfully, I am not just referring to textbook information to figure out the specifics, I get to take it under the biosafety cabinet, stick it in an electronic reader, or immerse it in an indication solution.

All this movement stimulates me immensely, however, I have learned that when some procedures or assays get a little interesting, I tend to ensue with a haste that can end up causing problems for future steps. This was my hardest lesson that I have learned, and continue to learn: the value of patience. This balance between pursuing the project quickly while carefully following protocol is an act I have still yet to master. However, through some important mistakes, I have learned that failure can always be learned from in science, and seemingly so cliché, the tortoise really does win in research.

Regarding how my peers and family have responded to my work in research, I must say that they are more than excited for my involvement in such activities so early in my career. Even though most people in my support circle have not been to college, as I am a first generation, and most cannot understand the vocabulary that we speak with in the lab, the verbal and moral support has been unwavering. Furthermore, as a minority in science, I am traveling a path that has not been traveled by many. So I will admit, there is a pressure on me to succeed for the sake of my community, but this pressure just feeds my passion, and I will gladly continue with them in mind.

As someone who did not know anyone personally with a PhD, or even knew what a research lab looked like until recently, I can say that I am beyond grateful to CIRM, TSRI, and LSSI for making this all happen. With these experiences, I will take this knowledge to college, and from there, find my path in science.

Matt Wood

Matt submitted these videos of his experience:

Stem cell Stories that caught our eye: longevity, cell-virus combo for cancer, and cord blood

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.

Better trash collection and longer life. In order for cells to survive they need systems for getting rid of the debris that accumulates as they go about their normal function. Scientists call this trash collection system autophagy. In recent years, several teams have produced data that suggests a highly active autophagy system corresponds with longevity. Now a team at Sanford-Burnham Medical Research Institute in San Diego has found a genetic switch that can activate the trash collection system. The team currently is looking for potential therapies that could alter the functioning of this genetic switch that may have a role in many diseases of aging. The Institute’s press release was picked up on this web site.

Stem cells carry cancer-fighting virus. Some clinical trials have shown that certain viruses can selectively kill brain cancer cells. But it has been difficult to get the virus to the right spots in the brain to do its selective destruction. Since neural stem cells home to inflammation and they view cancer as inflammation, a team at the University of Chicago decided neural stem cells could be a great delivery system for the tumor killing virus. In mice with the brain tumor glioblastoma the stem cell-virus combo extended the lives of the animals. The research was published in Stem Cells Translational Medicine, and was detailed in this online news site.

CIRM funds a similar project. This one uses the neural stem cells to carry traditional chemotherapeutic agents to the glioblastoma. That team at the City of Hope outside Los Angeles expects to begin a clinical trial in the next year or two, and you can read about it, and other CIRM projects to treat glioma, on our web site.

Finding the right cord blood got easier. The use of donated umbilical cord blood stem cells increases every year. But so does the number of cord blood banks and databases, making finding the right genetic match for any one leukemia patient a cumbersome process. Now, a German company has deployed big data technology to create a search engine called CordMatch. The search ensures a good match for the genetic tags called HLA. The web site “datanami” described the new service here.

Bug found in cord blood Identified. In 2011 doctors began reporting cases of colitis, an inflammation of the colon, in patients that had received donated umbilical cord stem cells. Since the condition responded to antibiotics, doctors assumed it was caused by a bacteria, but the only tissue samples available from patients were already preserved, so would not have any live cells that could be grown, which is the usual way of identifying an infectious agent. So a team at Boston’s Dana-Farber Cancer Institute sequenced all of the DNA in the specimen, sorted out the human DNA, and started piecing together the remaining DNA fragments. When they compared those to known bacteria they resembled a bacteria associated with agriculture.

Since the disease was treatable with standard antibiotics, the research is more of a fun bit of science showing you can identify a new bug from DNA left behind in human tissue. The study appeared in this week’s New England Journal of Medicine and was described by Bloomberg News here.

Essay on the disruptive nature of science. GEN Genetic Engineering & Biotechnology News ran a thought-provoking essay by Zachary Russ about the fact that many breakthrough fields of science are disruptive to many in society. He starts by reflecting on the controversy surrounding the early days of in vitro fertilization (IVF). He notes that the eventual success of the procedure quelled some of the controversy, but much of it was just transferred to the new offshoot science: using left over IVF embryos to create embryonic stem cells (ESCs). Acknowledging that there are few ESC products today, he details the demonstrated worth of ESCs as a research tool and predicts that their eventual successes in therapy will quell much of the controversy.

Don Gibbons

Through their lens: Heather Macomber investigated the possibility of immune rejection of iPS and embryonic stem cells

This summer we’re sponsoring high school interns in stem cell labs throughout California. We asked those students to contribute to our Instagram photos and YouTube videos about life in the lab, and write about their experiences.

Heather Macomber worked in the lab of Jeanne Loring at Scripps Research Institute.

Heather Macomber working in the lab. She submitted this photo through Instagram to CIRM’s #CIRMStemCellLab collection.

This summer CIRM has given me an astonishing opportunity to study the immunology of induced pluripotent stem cells (iPSCs). These cells have the potential to create more accurate and patient specific drug screening, and replace damaged cells and organs within the body without the risk of immune rejection. To study this exciting possibility, under the mentorship of Victoria Glenn I’m working to investigate the expression of the Major Histocompatibility Complex, MHC, within two stem cell lines. MHC is a molecule of the human immune system; it is used in hospitals as the main indicator if a donor organ will be rejected by a patient’s immune system. Because iPSCs are a relatively new cell type, we decided to investigate the levels of expression of MHC. There has been some argument that differentiated human pluripotent stem cells do not express any MHC. If this were true, doctors wouldn’t need to worry about matching immune systems from donor iPSCs to patients. My mentor’s previous work has provided evidence contrary to this notion. It has shown that when stem cells are in their undifferentiated, pluripotent state they do not express MHC, but when they are differentiated towards a linage expression does rise. She specifically tested cardiac and neural progenitors. These data indicate that immune profiles do need to be considered when looking at induced pluripotent stem cells for transplant.

To continue this research, I differentiated two lines of human pluripotent stem cells, the h9 (embryonic stem cells) line and an internally created induced pluripotent stem cell line, into cardiac progenitor cells. We decided to stop differentiation at this stage because it is most promising for clinical application. When implanted into mouse models, multipotent progenitors are more successful then either undifferentiated or fully differentiated cells at repairing damaged tissue. For reasons still unknown, the multipotent progenitors appear to be in the “goldilocks” zone for regenerative ability. To understand the gene expression of cells from both E9 and iPSC lines, I will analyze them using real time PCR and immunocytochemistry. By using ICC, I expect to prove that these cells have properly differentiated into the cardiac progenitors we’re looking for. Additionally, by comparing an E9 line to an iPSC line, I hope to add to a body of evidence that shows these cell types to be clinically indistinguishable. Through PCR, I will investigate the expression levels of MHC as well as confirming the cardiac progenitor state of my cells. This step will help us evaluate the expression of proteins, which are known to interact with the immune system. These data will be used in further research to investigate various other immune system responses.

CIRM and the Loring lab have provided me with an opportunity that has taught me indefinite amounts of information in a short time. By being immersed in a lab culture, I have quickly learned a variety of terms and soaked up knowledge about stem cells, so that I can converse fluently with fellow researchers. By carrying out real world experiments on the frontier of modern science with highly relevant impacts, I have been further inspired to become a research scientist. In addition, my exposure to stem cell research and induced pluripotent stem cells in particular has peaked my interest in this emerging and exciting field. I hope to further explore this field as I move forward in my scientific and creative endeavors.

Heather Macomber

Heather submitted this video of her experience:

By any measure; a fine man, a great loss. Remembering Duane Roth

What is the true measure of a man? That’s a question that has been on the minds of many of us these last few days as we struggle to come to terms with the sudden and untimely death of our friend and colleague Duane Roth.

Duane died last weekend of injuries he suffered in a bicycle accident on July 21. He was riding with a group from the Challenged Athletes Foundation, an organization dedicated to supporting people with physical disabilities, providing them the help and support they need to lead an active lifestyle. It was typical of Duane to be doing something to help others. He appreciated his own good fortune and tried to use it to give back to those less fortunate.

A memorial service is being held for Duane today at the Church of the Immaculata on the University of San Diego campus. There’s more information about the memorial on the CONNECT website.

On our online memorial, CIRM leaders and members of the public wrote their memories of Duane. CIRM’s President Alan Trounson remembers Duane’s “engaging smile, the crinkle and twinkle in his eyes, his dapper appearance and his willingness to stop and help.”

“He was my friend,” Alan says. “He gave so much – to his wife Renee and other close family, his work mates at Connect, to the growing national life science industry, to advocates for disease and injury, to his work for charity.“

“He was always committed to doing the right thing, even when it wasn’t the easy thing, or the politically expedient thing, or the popular thing,” says Claire Pomeroy, who served with Duane on the stem cell agency’s governing Board, the ICOC.

“After CIRM meetings we often got together to debrief at the bar. I remember him acknowledging that he was often the only Republican at the table – outnumbered by emphatic democrats. Yet, our discussions found great areas of agreement as well as some areas of respectful differences. He never minded being in the minority because his core values and beliefs were constant, well articulated, and compassionate. And Duane liked a good time. He often treated the whole group to wine- always accompanied by a smile and delight with the opportunity to be together.” 

For CIRM Board Chair, Jonathan Thomas, Duane was: “Thoughtful, caring, humble and brilliant- a true leader- we won’t be the same without him.”

“Duane and I talked on a regular basis about a whole range of issues affecting CIRM, often on short notice and at odd hours. We’d always laugh because he invariably was coming from a meeting of one business or charitable organization or another that he either ran or for whom he was a key player. I could never figure out how somebody could do such a great job on so many fronts at once or how he ever had enough hours in the day to get it all done.” 

Pompey, in Shakespeare’s Measure for Measure, says “Good counsellors lack no clients.” Duane, by all accounts was a wise and good counselor.

Art Torres, his co-Vice Chair at the agency, says “Duane was a no-nonsense person. He had the experience of a lifetime in the health care field and it was that background which made him so invaluable to CIRM and as an advisor and friend to me.”

Art says he and Duane shared a love of politics and recalls one interview in the La Jolla Light newspaper where Duane was asked who he would invite to a dinner party for 8. “JFK, Reagan, Thatcher, Churchill, Lincoln, Teddy Roosevelt, my wife Renee to sit next to JFK, and my brother Ted Roth who is a Democrat.”

Jeff Sheehy, a former colleague of Duane’s on the Board, says he came to “deeply respect Duane as a friend, colleague, teacher and mentor.”

“What I loved about Duane, besides his unflappable good humor, was his patient and carefully considered exposition of his viewpoints. I learned so much from Duane, not just his views about the issues we debated, but also how to respectfully meld diverse viewpoints to find common ground and tons about the art of management. I can’t measure how much good sense and good judgment rubbed off on me, just from listening to and learning from Duane. California has suffered a terrible loss.” 

For another former Board colleague, Leeza Gibbons, the shock of his loss is still only just hitting home.

 “I just keep seeing that smile, that ‘just-walked-off-the-pages-of-a- fashion-magazine’ look, and those intelligent eyes that always saw the best in everything and everyone (even when we, ourselves, couldn’t). Duane was one of those who reached out to people and met them where they were…seeing what was important to them and always interested in helping. I had barely begun my term at CIRM when Duane showed up like a big brother to inspire me and guide me.” 

Bishop Robert South once wrote: “If there be any truer measure of a man than by what he does, it must be by what he gives.” By any measure Duane gave generously.

“He put his heart and soul into his life and his friendship with all of us,” Alan says. “It’s difficult to think of anyone who contributed more of himself for others. We miss him terribly.”

“That was Duane,” says Jonathan. “So much giving on so many fronts doing so much good for so many people. It is very rare to find people like him. We were extraordinarily lucky to have him for seven years and will carry on in his memory going forward.”

The family has suggested that anyone wishing to honor Duane’s memory can make a donation to the Otterson Legacy Fund the Challenged Athletes Foundation, or the Copley-Price Family YMCA.

Please feel free to leave your own memories of Duane on our online memorial.

Kevin McCormack