Harnessing DNA as a programmable instruction kit for stem cell function

DNA is the fundamental molecule to all living things. The genetic sequences embedded in its double-helical structure contain the instructions for producing proteins, the building blocks of our cells. When our cells divide, DNA readily unzips into two strands and makes a copy of itself for each new daughter cell. In a Nature Communications report this week, researchers at Northwestern University describe how they have harnessed DNA’s elegant design, which evolved over a billion years ago, to engineer a programmable set of on/off instructions to mimic the dynamic interactions that cells encounter in the body. This nano-sized toolkit could provide a means to better understand stem cell behavior and to develop regenerative therapies to treat a wide range of disorders.


Instructing cells with programmable DNA-protein hybrids: switching bioactivity on and off Image: Stupp lab/Northwestern U.

While cells are what make up the tissues and organs of our bodies, it’s a bit more complicated than that. Cells also secrete proteins and molecules that form a scaffold between cells called the extracellular matrix. Though it was once thought to be merely structural, it’s clear that the matrix also plays a key role in regulating cell function. It provides a means to position multiple cell signaling molecules in just the right spot at the right time to stimulate a particular cell behavior as well as interactions between cells. This physical connection between the matrix, molecules and cells called a “niche” plays an important role for stem cell function.

Since studying cells in the laboratory involves growing them on plastic petri dishes, researchers have devised many methods for mimicking the niche to get a more accurate picture of how cells response to signals in the body. The tricky part has been to capture three main characteristics of the extracellular matrix all in one experiment; that is, the ability to add and then reverse a signal, to precisely position cell signals and to combine signals to manipulate cell function. That’s where the Northwestern team and its DNA toolkit come into the picture.

They first immobilized a single strand of DNA onto the surface of a material where cells are grown. Then they added a hybrid molecule – they call it “P-DNA” – made up of a particular signaling protein attached to a single strand of DNA that pairs with the immobilized DNA. Once those DNA strands zip together, that tethers the signaling protein to the material where the cells encounter it, effectively “switching on” that protein signal. Adding an excess of single-stranded DNA that doesn’t contain the attached protein, pushes out the P-DNA which can be washed away thereby switching off the protein signal. Then the P-DNA can be added back to restart the signal once again.

Because the DNA sequences can be easily synthesized in the lab, it allows the researchers to program many different instructions to the cells. For instance, combinations of different protein signals can be turned on simultaneously and the length of the DNA strands can precisely control the positioning of cell-protein interactions. The researchers used this system to show that spinal cord neural stem cells, which naturally clump together in neurospheres when grown in a dish, can be instructed to spread out on the dish’s surface and begin specializing into mature brain cells. But when that signal is turned off, the cells ball up together again into the neurospheres.

Team lead Samuel Stupp looks to this reversible, on-demand control of cell activity as means to develop patient specific therapies in the future:


Samuel Stupp

“People would love to have cell therapies that utilize stem cells derived from their own bodies to regenerate tissue. In principle, this will eventually be possible, but one needs procedures that are effective at expanding and differentiating cells in order to do so. Our technology does that,” he said in a university press release.



Stem cell stories that caught our eye: menstrual cycle on a chip, iPS cells from urine, Alpha Stem Cell Clinic Symposium videos

Say hello to EVATAR, a mini female reproductive system on a 3D chip. (Karen Ring)
I was listening to the radio this week in my car and caught snippets of a conversation that mentioned the word “Evatar”. Having tuned in halfway through the story, naturally I thought that the reporters were talking about James Cameron’s sequel to Avatar, and was slightly puzzled about the early press since the sequel isn’t expected to come out until 2020.

I was wrong in my assumption, but not that far off. It turns out that they were actually talking about a cutting edge new technology that generates artificial organs on 3D microfluidic chips. In the case of EVATAR, scientists have developed a functioning mini female reproductive system with all the essential components to recreate the female menstrual cycle. This sounds like science fiction, but it’s real. If you don’t believe me, you can read the publication in the journal Nature Communications.

EVATAR is a 3D organ-on-a-chip representing the female reproductive system. (Photo credit: Woodruff Lab, Northwestern University.)

 The chip consists of small boxes that each house an essential component of the reproductive system including the uterus, fallopian tubes, ovaries, cervix, and vagina. These tissues are generated from human stem cells except for the ovaries which were derived from mouse stem cells. The mini organs are connected to each other by tiny tubes and pumps that simulate blood flow and create a complete reproductive system. By adding specific hormones to this chip, the scientists stimulated the ovaries to produce the hormones estrogen and progesterone and even release an egg.

With EVATAR up and running, scientists are planning to use these personalized devices for various medical purposes including understanding reproductive diseases like endometriosis and testing how drugs affect specific people. The team is also developing a male version of this 3D reproductive chip called ADATAR and plans to study the two models side by side to understand differences in drug metabolism between men and women.

EVATAR is part of a larger project spearheaded by the National Institutes of Health to develop a “body-on-a-chip”. The lead author on the study, Teresa Woodruff from Northwestern University, explained in a news release how scaling down a human body to the size of a small chip that fits in your hand scales up the impact that the technology can have on developing personalized medicine for patients with various diseases.

“If I had your stem cells and created a heart, liver, lung and an ovary, I could test 10 different drugs at 10 different doses on you and say, ‘Here’s the drug that will help your Alzheimer’s or Parkinson’s or diabetes. It’s the ultimate personalized medicine, a model of your body for testing drugs.”

EVATAR has been popular in the press and was picked up by news outlets like NPR, STAT news and Tech Times. You can learn more about this technology by watching the video below provided by Northwestern Medicine.

Abracadabra: Researchers make stem cells from urine (Todd Dubnicoff)
I think one of the reasons the induced pluripotent stem cell (iPSC) technique became a Nobel Prize winning breakthrough, is due to its simplicity. All it takes is a slightly invasive skin biopsy and the addition of a few key factors to reprogram the skin cells into an embryonic stem cell-like state. The method is a game-changer for studying brain development disorders like Down Syndrome. Brain cells from affected individuals are not accessible so deriving these cells from iPSCs is critical in examining the differences between a healthy and Down Syndrome brain.

But skin biopsies are not “slightly invasive” when working with adults or children with an intellectual disability like Down Syndrome. The oversight committees that evaluate the ethics of a proposed human research study often denied such procedures. And even when they are approved, patients or caregivers have often dropped out of studies due to the biopsy method. This sensitive situation has hampered the progress of iPSC-based studies of Down Syndrome.

This week, a research team at Case Western Reserve University School of Medicine reported in STEM CELLS Translational Medicine that they’ve overcome this obstacle with a truly non-invasive procedure: collect cells via urine samples. But wait there’s more. It turns out that iPSCs derived from urine are more stable than their skin biopsy counterparts. The team believes it’s because skin cells, unlike cells found in urine, are exposed to the sunlight’s DNA-damaging UV radiation.

So far the team has banked iPSC lines from ten individuals with Down Syndrome which they will share with other researchers. Team lead Alberto Costa described the importance of these cell lines in a press release:

“Our methods represent a significant improvement in iPSC technology, and should be an important step toward the development of human cell-based platforms that can be used to test new medications designed to improve the quality of life of people with Down syndrome.”

ICYMI the CIRM Alpha Stem Cell Clinic Symposium Talks are Now on YouTube!
Last week, City of Hope hosted a fantastic meeting featuring the efforts of our CIRM Alpha Stem Cell Clinics. It was the second annual symposium and it featured talks from scientists, doctors, patients and advocates about the advancements in stem cell-based clinical trials and the impacts those trials have had on the lives of patients.

We wrote about the symposium earlier this week, but we couldn’t capture all the amazing talks and stories that were shared throughout the day. Luckily, the City of Hope filmed all the talks and they are now available on YouTube. Below are a few that we selected, but be sure to check out the rest on the City of Hope YouTube page.

CIRM President and CEO Randy Mills highlights the goals of the CIRM Alpha Clinics Network and what’s been achieved since its inception in 2014. 

CIRM’s Geoffrey Lomax talks about how the vision of the Alpha Clinics has turned into a reality for patients.

CIRM-funded UC Irvine Scientist, Henry Klassen, talks about his promising stem cell clinical trial for patients with a blinding disease called Retinitis Pigmentosa.

Even the early worm gets old: study unlocks a key to aging

A new study poses the question, ‘When does aging really begin?’ One glance in the mirror every morning is enough for me to know that regardless of where it begins I know where it’s going. And it’s not pretty.

But enough about me. Getting back to the question about aging, two researchers at Northwestern University have uncovered some clues that may give us a deeper understanding of aging and longevity, and even lead to new ways of improving quality of life as we get older.

The researchers were focused on C. elegans, a transparent roundworm. They initially thought that aging was a gradual process: that it began slowly and then picked up pace as the animal got older. Instead they found that in C. elegans aging begins just as soon as the animal reaches reproductive maturity. It hits its peak of fertility, and it is all downhill from there.

The researchers say that once C. elegans has finished producing eggs and sperm – ensuring its line will continue – a genetic switch is thrown by germline stem cells. This flipped switch begins the aging process by turning off the ‘heat shock response’; that’s a mechanism the body uses to protect cells from conditions that would normally pose a threat or even be deadly.

In a news release Richard Morimoto, the senior author of the study, says that without that protective mechanism in place the aging process begins:

C. elegans has told us that aging is not a continuum of various events, which a lot of people thought it was. In a system where we can actually do the experiments, we discover a switch that is very precise for aging. All these stress pathways that insure robustness of tissue function are essential for life, so it was unexpected that a genetic switch is literally thrown eight hours into adulthood, leading to the simultaneous repression of the heat shock response and other cell stress responses.”

You read that right. In the case of poor old C. elegans the aging process begins just eight hours into adulthood. Of course the lifespan of the worm is only about 3 weeks so it’s not surprising the aging process kicks in quite so quickly.

To further test their findings the researchers carried out an experiment where they blocked the genetic switch from flipping, and the worm’s protective mechanisms remained strong.

Now, taking findings from something as small as a worm and trying to extrapolate them to larger animals is never easy. Nonetheless understanding what triggers aging in C. elegans could help us figure out if a similar process was taking place at the cellular level in people.

Morimoto says that knowledge might help us develop ways to improve our cellular quality of life and delay the onset of many of the diseases of aging:

“Wouldn’t it be better for society if people could be healthy and productive for a longer period during their lifetime? I am very interested in keeping the quality control systems optimal as long as we can, and now we have a target. Our findings suggest there should be a way to turn this genetic switch back on and protect our aging cells by increasing their ability to resist stress.”

The study is published in the journal Molecular Cell.