Ken Diffenderfer
Stem cell core facilities are driving advanced therapeutics
TEDxSanDiego 2018

Imagine a day when a small piece of skin or a few milliliters of blood could dramatically change how scientists study and understand the human condition. Imagine a paradigm shifting resource that could unlock the mysteries of aging and development and provide previously unattainable insights into the foundational mechanisms that cause disease.

Imagine that that same starting material could also provide a therapeutic solution to a wide variety of diseases that affect the human population.

The reality is that this is not some intangible future. Scientists throughout an international research community have been rapidly developing the techniques needed to generate and utilize patient-specific stem cells for well over a decade. Stem cells that have the power to drive disease research and therapeutic discovery.

Very early in human development there is an incredibly unique stem cell that is poised to develop or differentiate into all of the unique cell types in the human body. Stem cell biologists described this unique developmental state as pluripotency. Through the process of differentiation, pluripotent stem cells ultimately give rise to the diverse cell types that comprise tissues, tissues that make up organs, organs that interact in organ systems, and organ systems that ultimately result in the biological complexity that is us.

For the longest time, the predominating thought in the scientific world was that this developmental process only happens in one direction. Essentially, as stem cells are exposed to small chemical messengers, they commit to a specific developmental path and cannot revert back to an earlier state.

Imagine a stem cell as a ball at the top of a large and undulating hill. As that ball is nudged from its perch, it rolls downhill, hitting key developmental transition points along the way. Eventually the ball comes to rest at the bottom of the hill, never to return to the top to repeat the ride back down.

In 2006, a small group of Japanese scientists led by Shinya Yamanaka shocked the biological world by turning this notion of one-way human development on its head. Through the simple introduction of four key genes, Yamanaka and colleagues showed that you could reverse a permanently developed cell all the way back to the earliest stages of development.

For the first time, a permanently developed, permanently mature, permanently differentiated cell was reprogrammed all the way back to the pluripotent state. Yamanaka named these cells induced pluripotent stem cells, or IPSCs.

IPSCs have since revolutionized the way scientists study and understand the human condition and have also provided a specialized source of cells to treat disease. For this groundbreaking discovery, Yamanaka was awarded the 2012 Nobel Prize in medicine.

What does this reprogramming process look like? At first glance, the routine of generating induced pluripotent stem cells from skin and blood is relatively straightforward. First, donated biopsy materials are processed to isolate the cells of interest. For example, a small piece of your skin can be broken apart within enzymes into individual cells.

The four key genes are then introduced, and cells are grown in specialized conditions to help them transition towards the pluripotent state. After approximately three to four weeks, stem cells start to emerge as small circular cell structures called colonies. Colonies are then manually isolated, rigorously tested to ensure quality, and finally they’re frozen and banked.

After two to three months of work involving manual hands-on techniques, we’re left with a small seemingly insignificant vial of cells. As this material originated from an individual with a unique genetic background, and these cells have the power to differentiate into any cell type in the human body, we’re actually left with an incredibly powerful tool to study disease, to model disease in a dish.

In a nutshell, all of the cells in your body have the exact same genetic information. If I were to take a small piece of your skin and reprogram it to induced pluripotent stem cells, the resulting IPSCs would retain all the genetic information that makes you unique.

If those stem cells were then differentiated into neurons, heart muscle, or any other cell type, the final cell product would also retain the same genetic information as the skin cells we started with.

If we imagine this in the context of an individual with a diagnosed disease, the power of this technology becomes clear. If the induced pluripotent stem cells were generated from a patient that has Alzheimer’s disease and then differentiated into neurons, we would be left with a dish full of neurons that have the genetic characteristics associated with Alzheimer’s disease. We would be left with a dish full of neurons that behaved like Alzheimer’s disease neurons.

A fantastic example of early work in the disease modeling field comes from the lab of Rusty Gage here at the Salk Institute. In a 2011 publication, Gage Lab researchers showed that when induced pluripotent stem cells were generated from patients with schizophrenia and then differentiated into neurons, the resulting neural networks lacked the complex cell to cell connections seen in neurons differentiated from healthy cells.

When those exact same schizophrenic neurons were treated with a commonly used FDA approved anti-psychotic, researchers observed that those cell to cell connections could be rescued back to levels seen in healthy cells.

This disease modeling approach is by no means limited to schizophrenia. Researchers here at the Salk Institute have utilized patient-specific stem cells to study a wide variety of diseases, including Alzheimer’s, Parkinson’s, multiple sclerosis, autism, depression, hemophilia, cystic fibrosis, diabetes, and more.

Over the last decade, the routine of developing induced pluripotent stem cells from skin and blood has been well established. Current protocols are fairly robust, allowing most labs experienced with cell culture techniques the ability to reprogram a handful of patient cells with limited difficulty.

Things get interesting, however, when six patients turn into 50, 100, or 200. As with most tasks, scale changes everything. Much like grandma’s secret cookie recipe, those delicious oatmeal chocolate morsels are never quite the same when we try a double batch. As we moved towards doing more, it becomes incredibly difficult to maintain a high-quality product.

With the power of induced pluripotent stem cells becoming widely known, the demand for these specialized cells makes it incredibly difficult for individual labs to keep up. This is exactly where core facilities come in. Core facilities are specialized resource centers built into modern research institutes that allow for the development and dissemination of specialized techniques and technologies.

Here at the Salk Institute we have 13 such core facilities that provide access to everything from the advanced imaging technologies that allow researchers to peer into the depths of cells with mind boggling clarity to the next generation sequencing technologies that allow for unlocking the mysteries of the genetic code.

We also have the facility that I call home, our Stem Cell Core facility, where we focus on providing human stem cell models primarily to researchers here at the Salk, but also a larger local, national, and international community.

In 2012, the Stem Cell Core was presented with an opportunity to generate induced pluripotent stem cells from over 200 individuals through a collaboration with researchers here at Salk and UC San Diego.

Armed with an intimate hands-on knowledge of the reprogramming process, we were able to identify key transition points and bottlenecks in the reprogramming workflow, allowing us to break a complicated three-month process down into individual functional steps that patient cells can be staggered through in small manageable groups. A process that enabled a team of researchers to generate induced pluripotent stem cells from over 222 individuals ranging from the ages of 9 to 88 and encompassing 41 distinct family groups.

At the center of this induced pluripotent stem cell collection, there are 39 individuals with diagnosed cardiac disease. In many cases representation from the parents, siblings, and children of these individuals.

Ultimately, this resource provides the scale and variation needed to connect small genetic changes to actual cellular and molecular dysfunction that can be observed when stem cells are differentiated into medically relevant cell types, like the beating muscle cells of the heart.

One hundred percent of these stem cell lines have been shared with a world-leading stem cell banking facility and are immediately available to an international cardiac disease and broader research community.

Is the reprogramming process still time consuming? Yes. Is the process still hands on? Absolutely, it is. But with a little bit of Core ingenuity and a dedicated and experienced staff, we have developed a process that works just as well for 800 as it does for 8.

Beyond issues of scale, Stem Cell Cores also play a crucial role in pushing the boundaries of the field by helping to develop new and novel applications for stem cell models. A fantastic example of this is organoid technologies.

Traditionally, stem cell modeling involved growing cells, most often a single cell type, on a flat two-dimensional surface. While this approach has been incredibly fruitful in expanding our understanding of disease, it never truly captured the complexity of human biology, and therefore has limited our opportunity for discovery.

While a dish full of just neurons can tell us a lot about Alzheimer’s disease, a small highly organized cluster of cells that more accurately captured the layered complexity of the human brain could tell us a great deal more.

Scientists throughout the stem cell research community have been well aware of this limitation and have been working to develop protocols to generate these 3-D clusters of cells that mimic organs and also implement them into new and novel disease modeling approaches.

Here at the Salk Institute, researchers have made groundbreaking discoveries in this arena with protocols to develop both kidney and brain organoids. In the Stem Cell Core, we’re actively investigating ways to improve the efficiency and variability of the organoid modeling process.

It’s awe-inspiring to consider the last decade of induced pluripotent stem cell research. A fledgling technique to generate patient-specific stem cells has grown into a highly robust and reproducible technology, allowing for the development of thousands upon thousands of unique patient-specific stem cell lines worldwide.

Through the power of scale, large and well-characterized collections of induced pluripotent stem cells are allowing researchers to connect small genetic variations to actual mechanisms that cause disease. The field has also started to push traditional two-dimensional disease modeling approaches into 3-D organoids that more accurately capture the complexity of human biology.

Where will this exciting technology take us next? Will fully automated reprogramming systems create a highly efficient production process that makes IPS cell therapies as routine as prescription medicine? Will organoids make the leap toward actual organs, providing an opportunity for rejection-free transplantation?

Will large, widely available banks of induced pluripotent stem cells generated from super donors end up taking the personal out of personalized cell therapies?

While the future is not crystal clear, what is clear is that induced pluripotent stem cell technologies represent a critical tool for the development of advanced therapies. With Stem Cell Core facilities driving efficiency and innovation, the possibilities are limitless.

Thank you.