3D Printing Cells with DNA Velcro

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The complex, 3D micro-anatomy of the human liver. (Image source: WikiMedia Commons)

One of the Holy Grails of stem cell research is growing body parts to replace those damaged by disease or injury. Enormous strides have been made in a key first step: mastering recipes for maturing stem cells into various specialized cell types. But a lawn of, say, liver cells in a petri dish is not a functioning liver. Organs have complex, three-dimensional structures with intricate communication between multiple cell types.

Scientists are actively devising methods to overcome this challenge. For instance, cultivating cells onto biological scaffolds help mold the cells into the shape of a particular organ or tissue. And retooled 3D printers using “bio ink” can seed layers of different cells onto these scaffolds to create specified structures.

This week, a UCSF team added an ingenious new tool to this tissue engineering tool kit.  As reported on Monday in Nature Methods, the lab of Zev Gartner took advantage of DNA’s Velcro-like chemistry to build layers of different cell types in a specified pattern.

DNA – it’s not just for genetics anymore

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A DNA fragment is made of two complimentary strands that bind together with high specificity. (Image source: Visionlearning)

DNA is a molecule made of two thin strands. Each strand is specifically attracted to the other based on a unique sequence of genetic information. So if two strands of a short DNA fragment are peeled apart, they will only rejoin to each other and not some other fragment with a different sequence.  While DNA usually resides in the nucleus of a cell, the team worked out a method to temporarily attach copies of a strand of DNA on the outside of, let’s call it, “cell A”. The opposite strand of that DNA fragment was attached to “cell B”. When mixed together the two cells became attached to each other via the matching DNA sequences. Other cells with different DNA fragments floated on by.

The screen shot below from a really neat time-lapse video, which accompanies the research publication, shows how a rudimentary 3D cell structure could be built with a series of different cell-DNA fragment combinations. In this case, the team first attached DNA fragments onto a petri dish in a specific pattern. At the thirty-second mark in the video, you can see that cells with matching DNA fragments have attached to the DNA on the dish.

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This video demonstrates the assembly of 3D cell structures with the help of DNA “Velcro” (image source: Todhunter et al. Nature Methods 2015 Aug 31st)

The new technique, dubbed DNA programmed assembly of cells (DPAC), opens up a lot possibilities according to Gartner in a UCSF press release:

 “We can take any cell type we want and program just where it goes. We can precisely control who’s talking to whom and who’s touching whom at the earliest stages. The cells then follow these initially programmed spatial cues to interact, move around, and develop into tissues over time.”

The Quest still continues with possible victories along the way

 Of course, this advance is still a far cry from the quest for whole organs derived from stem cells. The cell assemblies using DPAC can only be grown up to about 100 microns, the thickness of a human hair. Beyond that size, the innermost cells get starved of oxygen and nutrients. Gartner says that obstacle is a current focus in the lab:

“We’re working on building functional blood vessels into these tissues. We can get the right cells in the right positions but haven’t figured out how to perfuse them with blood or a substitute efficiently yet.”

In the meantime, building these small 3D “organoids” from stem cells certainly could be put to good use as a means to test drug toxicity on human tissue or as a way to study human disease.

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Stem cell stories that caught our eye: regenerating limbs on scaffolds, self regeneration via a drug, mood stem cells, CRISPR

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.

Regenerating a limb, or at least part of it. Many teams have generated organs or parts of organs in animals by starting with a dead one. They literally wash away all the cells from the donor organ using a detergent so that they are left with a framework of the cells’ connective tissue. Then they seed that scaffold with stem cells or other cells to grow a new organ. A team at Massachusetts General Hospital has now used the same process to generate at least part of a rat limb.

The news cells growing on the donor limb scaffold in a bioreactor

The news cells growing on the donor limb scaffold in a bioreactor

It took a week to get the tiny little leg fully cleaned up and then another two weeks for the seeded cells to repopulate the scaffold left behind. That cellular matrix seems to send signals to the seeded cells on what type of tissue to become and how to arrange themselves. The team succeeded in creating an artificial limb with muscle cells aligned into appropriate fibers and blood vessels in the right places to keep them nourished. The researchers published their work in the journal Biomaterials and the website Next Big Future wrote up the procedure and provided some context on the limitations of current prosthetic limbs. The author also notes that the researchers have a lot more work to do, notably to prove they can get nerves to grow and connect at the point of transplantation to the “patient” animal. Discover also wrote a version of the story.

Getting the body to regenerate itself. A strain of mice discovered 20 years ago has led a multi-institution team to a possible way to get the body to regenerate damaged tissue, something the mouse discovered two decades ago can do and other mammals cannot. The researchers found that those mice have one chemical pathway, HIF-1a, that is active in the adult mice but is normally only active in the developing embryo. When they pushed that chemical path to work in normal mice those mice, too, gained the power to regenerate tissue. Ellen Heber-Katz from the Lankenau Institute for Medical Research outside of Philadelphia was quoted in the institute’s press release on Health Medicine Network.

“We discovered that the HIF-1a pathway–an oxygen regulatory pathway predominantly used early in evolution but still used during embryonic development–can act to trigger healthy regrowth of lost or damaged tissue in mice, opening up new possibilities for mammalian tissue regeneration.”

Heber-Katz led the team that included researchers from the company Allergan and the University of California, Berkeley. In order to activate the HIF-1a pathway they basically took the natural brakes off it. Another cellular chemical, PHD normally inhibits the action of HIF-1a in adults. The researcher turned the table on PHD and inhibited it instead. The result, after three injections of the PHD inhibitor over five days the mice who had a hole punched in their ear healed over the hole complete with cartilage and new hair.

Regulating memory and mood. It turns out your brain’s hippocampus, the section responsible for both memory and mood, has not one type of stem cell replenishing nerves, but two. And those two types of stem cells give rise to different types of nerves, which may account for the highly varied function of this part of the brain. Researchers at the University of Queensland in Australia isolated the two types of stem cells and then let them grow into nerves but the nerves from each expressed different genes, which means they have different functions. The lead researcher on the study, Dhanisha Jhaveri, discussed the findings in a press release picked up by Science Daily:

“The two cell groups are located in different regions of the hippocampus, which suggests that distinct areas within the hippocampus control spatial learning versus mood.”

The research provides fodder for future work looking into the treatment of learning and mood disorders. Review of the now celebrity tool, CRISPR. I don’t think I have ever seen so much ink and so many electrons spilled over a science tool as I have seen for CRISPR, particularly for one few scientists can tell you what the acronym stands for: Clustered Regularly Interspaced Short Palindromic Repeats. It is basically a fluke in the genes of several bacteria in which some of the base pairs that make up their DNA get repeated at regular intervals. Their configuration confers the ability for CRISPR segments to be used to disrupt or change specific genes in other organisms. Heidi Ledford writing for Nature in the journal’s news section provides a great wrap-up of what the technology is and what it can do, but also provides some caveats about its efficiency, accuracy, ethical concerns, and occasionally just not understanding how it works. The Nature team provides some valuable infographics showing the history of the science and on the rapid adoption of the technology as shown in publications, patents and funding. They also published an infographic on using CRISPR for “gene drive,” a way to push a modified trait through a population quickly, such as a mutation that could stop mosquitos from transmitting malaria. This potential drives much of the concern about misuse of the tool. But scientists quoted in the piece also provide more mundane reasons for moving slowly in thinking about using the therapy for patients. One of those is that it can sometime cause a high rate of “off-target” gene edits; simply put, cutting DNA in the wrong place. But as a research tool, there is no doubt it has revolutionized the field of gene modification. It is so much faster and so much cheaper than earlier gene editing tools; it is now possible for almost any lab to do this work. The piece starts out with an anecdote from CIRM-grantee Bruce Conklin of the Gladstone Institutes, talking about how it completely changed the way his lab works.

“It was a student’s entire thesis to change one gene,” Conklin said, adding “CRISPR is turning everything on its head.”

Clearing up chemobrain: cancer therapy-induced memory problems reversed by stem cells

You’d think receiving a cancer diagnosis and then suffering through chemo and/or radiation therapy would be traumatic enough. But as many as 75% of cancer survivors are afflicted by memory and attention problems long after their cancer therapy.

This condition, often called “chemobrain”, shouldn’t be misunderstood as being confined to cancers of the brain. A 2012 analysis of nearly 200 women who had been treated with chemotherapy for breast cancer showed they had ongoing memory and information processing deficits that persisted more than twenty years after their last round of treatment. And young cancer survivors are particularly vulnerable to reduced IQs, nonsocial behavior and an extremely lowered quality of life.

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CIRM grantee and UC Irvine professor Charles Limoli, PhD is senior author of this study

Chemotherapy drugs work by killing off cells that are dividing rapidly, a hallmark of cancer cells. But this brute force method also kills other rapidly dividing cells that are critical for normal bodily functions. In the case of chemobrain, it’s thought that damage to newly formed brain cells in the hippocampus, the memory center of the brain, is the culprit. A UC Irvine study published this week in Cancer Research supports that idea in experiments that test the effect of transplanting human nerve stem cells in rats. The research team leader Charles Limoli, a CIRM grantee and UC Irvine professor of radiation oncology, summarized the groundbreaking results in a press release (note: this study is not funded by CIRM):

“Our findings provide the first solid evidence that transplantation of human neural stem cells can be used to reverse chemotherapeutic-induced damage of healthy tissue in the brain.”

The novel place recognition test is evaluate memory function. Animal is initially presented with identical objects (red circles). Then a new object is introduced (blue square). A healthy mouse will investigate the blue square.

The novel place recognition test, one of several tests used in this study to evaluate memory function.  During training setup (left), the rodent is familiarized with identical objects (red circles). Later, rodent returns now in presence of a new object (blue square). A healthy mouse will investigate the new object during testing setup (right). Image credit: KnowingNeurons.com

So how the heck do you observe chemotherapy-induced cognitive problems in a rodent let alone show that stem cells can rescue the damage? In the study, the rats undergo a variety of recognition memory tasks after a typical chemotherapy drug treatment. For instance, in the novel place recognition test, an animal is familiarized with two identical objects inside a test “arena”. Later, the animal is returned to the arena but a new object is swapped in for one of the previous objects. Rats given chemotherapy treatment but no stem cell surgery (they’re implanted with a saline solution instead) do not show a preference for the novel object. But rats given chemotherapy and the human nerve stem cell surgery prefer the novel object. This novel seeking behavior is also seen in control rats given no chemotherapy. So these results demonstrate that the transplanted stem cells rescued normal memory recognition in the chemotherapy-treated rats.

The research team also saw differences within the brains of these groups of rats that match up with these behavioral results. First, they confirmed that the transplanted human stem cells had indeed survived and grafted into the rat brains and had matured into the correct type of brain cells. Next they looked at chemotherapy-induced inflammation of brain tissue. The brains of chemotherapy-treated rats with no stem cell transplantation showed increased number of active immune cells compared to the control and stem cell transplanted animals. In another experiment, a detailed analysis of the structure of individual nerve cells showed extensive damage in the chemotherapy treated rats compared to controls. Again, this damage was reversed in chemotherapy treated rats that also received the stem cell transplant.

Rat nerve cells (black structures) in memory center of the brain are damaged by chemotherapy (left); transplanting human nerve stem cells reverses the damage (right)

Rat nerve cells (black structures) in memory center of the brain are damaged by chemotherapy (left); transplanting human nerve stem cells reverses the damage (right). Image credit: Acharya et al. Cancer Research 75(4) p. 676

As many researchers can tell you, these exciting results in animals don’t guarantee a human therapy is around the corner. But still, says Limoli:

“This research suggests that stem cell therapies may one day be implemented in the clinic to provide relief to patients suffering from cognitive impairments incurred as a result of their cancer treatments. While much work remains, a clinical trial analyzing the safety of such approaches may be possible within a few years.”

For a more details about the role of stem cells in chemobrain, watch this recent presentation to the CIRM Governing Board by CIRM grantee and Stanford professor Michelle Monje.