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Gene editing transforms biology, raises ethical questions

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Jennifer and Dhanu with pigs

Senior research specialist Jennifer Meudt and Dhanu Shanmuganayagam, an assistant professor of physiology and nutrition, work with pigs to study human diseases at UW-Madison. Shanmuganayagam is using a gene editing technique called CRISPR-Cas9 to engineer pigs to be models of heart disease and neurofibromatosis, which causes tumors on nerve tissue. It's one of many ways in which UW-Madison scientists are using CRISPR, which is transforming biology.

JOHN HART -- State Journal

Dhanu Shanmuganayagam plans to use a new gene editing technique to engineer pigs with diabetes, obesity, high cholesterol and high blood pressure, to test treatments in animals with major risk factors for heart disease.

Heidi Kaeppler hopes to alter the DNA of corn, wheat and rice so the crops could grow nitrogen fertilizer naturally, as soybeans and alfalfa do.

Jill Wildonger is modifying genes in the nerve cells of fruit flies, which could better explain what goes wrong in Alzheimer’s and Parkinson’s diseases.

The UW-Madison researchers are joining scientists around the world in using a powerful gene editing tool that is transforming biology and could improve human health as much as anything since the first successful isolation of human embryonic stem cells, at UW-Madison, in 1998.

But, like embryonic stem cells, the new technology, called CRISPR-Cas9, raises ethical questions. It could affect the environment in unexpected ways or be used to alter the genes of future generations of humans — a line scientists generally have agreed shouldn’t be crossed but wasn’t feasible until now.

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Fruit flies in test tubes

Fruit flies are kept in test tubes in an incubator near the lab of Jill Wildonger at UW-Madison. Wildonger, an assistant professor of chemistry, is using the gene editing tool CRISPR-Cas9 to study nerve cells of fruit flies, which could better explain diseases such as Alzheimer's and Parkinson's.

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Alta Charo mug

Alta Charo

“It’s very easy to say you’re not going to cross the line when you don’t know how to do it,” said Alta Charo, a UW-Madison bioethicist who is co-chairwoman of a national committee studying the topic. “Now we have to face whether or not we’d ever want to do it.”

Two groups of scientists in China have come closest to crossing the line. In studies published a year ago and last month, the scientists edited genes of human embryos. But the embryos, which were not viable even before the gene editing, were destroyed, not implanted.

The Food and Drug Administration is considering the environmental risks of CRISPR in a proposal to release genetically engineered mosquitoes in the Florida Keys to try to prevent Zika virus and other diseases.

Meanwhile, achievements involving CRISPR are mounting.

In October, Harvard researchers said they used the technique to edit 62 genes involving immunity in pigs, a potential step toward using pig organs for human transplants.

In December, three research groups said they used CRISPR to treat muscular dystrophy in mice. Last month, the U.S. Department of Agriculture cleared the first CRISPR-modified food, a white button mushroom altered to resist browning.

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Flies with brush

Research specialist Dena Johnson-Schlitz uses a brush to manipulate and examine fruit flies under a microscope in Jill Wildonger's lab at UW-Madison. Wildonger, along with UW-Madison colleagues Melissa Harrison and Kate O’Connor-Giles, was among the first scientists to edit genes in fruit flies using CRISPR-Cas9, in 2013. They have shared their CRISPR fruit fly models with labs in other states and countries. 

CRISPR, which stands for “clustered regularly interspaced short palindromic repeats,” is based on a defense mechanism found in bacteria. It was discovered in 2012 by Jennifer Doudna of the University of California, Berkeley, and Emmanuelle Charpentier, a scientist in Germany.

Doudna has been among those calling for a moratorium on editing genes to make heritable changes in humans.

Amid the ethical debates, a growing number of researchers in Madison and elsewhere are using CRISPR in ways considered less worrisome.

Scientists have been able to sequence the DNA of humans and other species for years, but until CRISPR they didn’t have a quick, easy, cheap and precise way to alter genes to study disease mechanisms, potential therapies and agriculture methods in complete organisms.

“It’s like Microsoft Word,” said Dustin Rubenstein, who runs a lab on campus that has helped dozens of researchers use CRISPR in mice, rats and other animals to study cancer, stroke and other conditions.

“Not only are we reading the genome, we’re opening it up and cutting and pasting at will,” Rubenstein said.

Wildonger likens the process to the work of a car mechanic.

“Before, the mechanic couldn’t open up any part of your car, but only look at it and guess what was wrong,” she said. “Now, he or she can open up the hood, start changing components of the engine and see how it impacts how the car functions.”

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Jill Wildonger looking through microscope

Jill Wildonger, an assistant professor of biochemistry at UW-Madison, works with fruit flies in her lab.

"Molecular scissor"

CRISPR-Cas9 is a “molecular scissor” that cuts DNA at specific sequences and allows the body’s DNA repair process to insert a new gene if desired, said Krishanu Saha, a UW-Madison biomedical engineer.

The technology includes a “guide RNA” that targets gene sequences and a protein to cut them, called Cas9.

Saha uses CRISPR in stem cells derived from people with fragile X syndrome, a condition in which an inactive gene causes intellectual disability.

In the lab, Saha snips the gene, adds a luminescent tag and screens potential drugs to see which ones turn it on. He’s had two hits so far.

He plans to work with Dr. David Gamm, a UW-Madison ophthalmologist, to use CRISPR to correct genetic mistakes that cause vision loss, in cells from patients and, eventually, if possible, directly in the eye.

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Red filter fruit flies

Fruit flies are seen under fluorescent light and through a red filter in Jill Wildonger's lab at UW-Madison. The flies' eyes glow because of a marker that indicates the presence of the enzyme Cas9, used in the CRISPR-Cas9 gene editing technique.

Ethical questions surrounding CRISPR’s human applications are not limited to altering embryos, Saha said. Gene-editing treatments could spur gene-editing enhancements to give people stronger muscles, quicker growth spurts or greater intelligence.

An international summit on CRISPR that Saha attended in December in Washington, D.C., even floated the idea of a gene-edited sleep cycle — less time sleeping but with more recovery.

“What assistant professor wouldn’t like that going through the tenure process?” Saha, an assistant professor, said during a town hall discussion about CRISPR on campus last month.

Charo said there could be good reasons to make genetic changes to future generations of people. One would be eliminating diseases such as Tay Sachs, a progressive, congenital condition that weakens muscles and typically kills children by age 4.

“Is there any reason why we shouldn’t just wipe this out if we can?” Charo asked.

But CRISPR could have unintended consequences, such as in trying to control mosquitoes, she said.

“Wiping out one pest could allow a different pest to explode,” she said.

The committee she is co-chairing, formed by the National Academy of Sciences and the Institute of Medicine, is expected to issue a report this year with recommendations for the responsible use of CRISPR.

The committee met last month in Paris with European representatives to discuss regulatory approaches.

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Dhanu walking on campus

Dhanu Shanmuganayagam, walking near his lab at UW-Madison, said the gene editing tool CRISPR-Cas9 has made it much easier to develop animal models for human diseases. "It's a game changer," he said.

CRISPR in the lab

Shanmuganayagam said CRISPR makes it much easier to develop animal models to study human diseases, such as the pig model for heart disease.

He’s also using CRISPR to make a pig model of neurofibromatosis, which causes tumors on nerve tissue.

The pig models will resemble human diseases better than mouse models, he said. Previously, he said, it was very difficult to design such pig models.

“We want to test therapies in a more accurate background,” he said.

Kaeppler said CRISPR could help allow corn, wheat and rice to be capable of nitrogen fixation, a process found in soybeans and alfalfa, in which the plants acquire nitrogen through a symbiotic relationship with bacteria.

“That would be a great addition if you could add that to other crops,” she said.

She and others at the Great Lakes Bioenergy Research Center on campus are also using CRISPR to try to increase the yield of corn for biofuels.

Wildonger, along with UW-Madison colleagues Melissa Harrison and Kate O’Connor-Giles, was among the first scientists to edit genes in fruit flies using CRISPR, in 2013.

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Fruit fly neuron microscope image

A laser microscope image of a fruit fly neuron, on a computer screen, shows many connections, in Jill Wildonger's lab at UW-Madison.

They have distributed their fruit fly CRISPR models to other labs around the world. Madison-area companies, such as Aldevron and Promega, also sell products used in CRISPR.

In fruit flies, Wildonger is altering nerve cell proteins that control movement, mirroring human conditions collectively known as spastic paraplegia. She’s also studying mutations associated with Alzheimer’s and Parkinson’s.

Since CRISPR has been available for only a few years, it may take a while for the general public to see any tangible benefits. But for researchers, the benefits are already real, Wildonger said.

“CRISPR-Cas9 is going to revolutionize science,” she said. “This a technique to pay attention to.”

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David Wahlberg is the health and medicine reporter for the Wisconsin State Journal.