Tweaking text in the book of life: What engineering genomes means for science and society

Scholars at UW-Madison lead the way in genome engineering research, as well as deliberations about responsible use of the technique.

This piece originially appeared at: Tweaking text in the book of life: What engineering genomes means for science and society

While humans certainly are composed of softer materials than steel and concrete, both bodies and buildings require multiple interacting systems to function harmoniously. Constructing each requires comprehensive specifications—and both contractors and living cells follow meticulous master plans.

However, while it’s relatively easy for an architect or engineer to edit blueprints, modifying the manuals for living beings—until recently—has been much more difficult.

Now, thanks to a revolutionary new gene-editing tool called CRISPR/Cas9, researchers have the ability to tweak life’s instruction manual with unprecedented ease and precision.

Why would scientists want to doctor nature’s directions? Mistakes in our biological blueprint cause a whole host of diseases and disorders, including sickle cell anemia, Parkinson’s disease, breast cancer and autism. Without a way to correct the underlying causes, physicians can only treat—but not cure—these and many other afflictions caused by abnormalities in an individual’s genetic code. Additionally, engineering genomes can give researchers tools to answer previously impossible questions about how life works.

DNA is made up of a long string of four different chemical components, called bases, represented by the letters A,T,C,G.
DNA is made up of a long string of four different chemical components, called bases, represented by the letters A,T,C,G.
(stock image)
Genes, genomes, and DNA—the coiled conductor for the symphony of life

Blueprints for buildings abound with line drawings, measurements, symbols and labels. In contrast, the instructions for living beings rely entirely on a limited four-letter alphabet—the chemical building blocks of DNA, called bases, and represented by the characters A, T, C, and G. More than three billion bases strung together one after another make up the human genome. Each individual base might be tiny, but unwound and stretched end-to-end, the tightly coiled DNA molecules inside each human cell would measure almost 6 feet long.

Sequences of bases in DNA, at first glance, appear to be gobbledygook—ATGGGAACTA doesn’t spell out anything meaningful to our human eyes, but cells can read the chemical letters and translate those instructions to grow and function. That particular stretch of letters comes from a region in the genome named BRCA1, which clinicians now know can contribute to malignant breast cancer when it malfunctions.

Segments of DNA, like BRCA1, that contain specific sets of directions, are called genes. One strand of DNA contains many thousands of genes. The collection of more than 20,000 genes that make up the human genome is divided among 23 separate DNA molecules, called chromosomes. Throughout the body, cells carry complete complements of chromosomes. However, different types of cells access specific genes, depending on their functions—for example, the plans for a liver aren’t useful for constructing an eye.

Genes dictate how and when to put together proteins, which make up the mechanical skeletons of our cells and also perform all of the chemical reactions and dynamic functions that spark life’s activity.

Mutations—or “typos”—in the genetic code can prevent one or more of those proteins from working or from being made at the proper place and time. Sometimes mutations cause catastrophic consequences, like genetic disorders and medical conditions.

Image of DNA sequencing gel
CRISPR allows scientists to rewrite genomes with unprecedented ease and accuracy.
(stock photo)
Rewriting DNA, redefining biology: The innovation of the century

It’s been possible to edit some genomes for years; researchers have been able to cut and paste segments of DNA between simple bacteria since the 1970s—but methods to modify genes en masse or make changes in more complicated organisms historically have been convoluted and expensive. In 2012, however, the field took a giant leap forward when groups of researchers at the University of California-Berkeley and in Sweden figured out that CRISPR/Cas9 could easily and inexpensively edit almost any DNA sequence.

In just a few short years, researchers applied the tool in some of science’s classic model organisms, starting with simple yeast, then progressing to complex creatures such as zebrafish and mice.

In 2013, scientists successfully used CRISPR to modify human cell lines growing in plastic dishes. Breaching that threshold caused celebration; what it meant was that CRISPR showed promise for correcting previously permanent genetic defects or, for example, removing HIV viruses integrated into the DNA of white blood cells. In late-December 2014, MIT Technology Review called CRISPR “the biggest biotech discovery of the century,” and in 2015, the journal Science hailed it as “the breakthrough of the year.

Scientists can now, in theory, correct the ruined recipes for proteins responsible for causing conditions like sickle-cell anemia. A host of new companies—including Editas, whose vice president of preclinical science received her PhD in oncology from UW-Madison—are rushing to develop CRISPR-based therapies and other technologies.

Ordinary origins for a transformative technology
Image of yogurt on spoon
CRISPR as a genome-editing tool spun out of basic research into bacteria used in yogurt production.
(stock photo)

This powerful—and, for researchers, easy-to-use—tool comes from surprisingly prosaic origins. In 1987, Japanese researchers first noticed a strange stretch of the E. coli genome. They called it “clustered regularly interspersed short palindromic repeats,” or CRISPR, after its unique sequence organization. However, nobody understood what function this odd region of DNA performed until 20 years later when dairy-industry scientists noticed that some microbes in their massive vats of fermenting milk seemed completely immune to attack from invading viruses. Intrigued, the researchers investigated and found that some bacteria inside the yogurt tanks carried a secret weapon for identifying and chopping up virus DNA inside their cells. That weapon was CRISPR.

Image of bacteria
CRISPR protects bacteria from viruses.
(stock photo)

Fundamentally, CRISPR is a pair of programmable molecular scissors composed of two separate modules. One component of CRISPR does the cutting and the other guides the “scissors” to precise locations within the genome, allowing researchers to snip and replace a gene sequence. Scientists take advantage of the ways that cells normally fix broken DNA to write in whatever bases they want at the place where CRISPR makes a cut. The slice, dice and edit approach can correct disease-causing mutations, modify the functions of existing proteins, or introduce instructions to make entirely new products.

Easy to use; easy to abuse

Along with the excitement of this powerful new technology comes questions about its use: If life’s instruction manual is suddenly open for revisions, what’s to stop attempts at artificial improvements?

Three watershed moments for genome engineering dominated headlines in 2015. In early spring, a group of scholars instrumental in the development of CRISPR called for a worldwide moratoriumon any studies using it to manipulate human embryos. Yet, in the immediate aftermath of that announcement, a group of Chinese researchers announced that they had done exactly what everybody feared—attempting to correct the blood condition beta thassalemia in embryos obtained from in vitro fertilization clinics. Although the embryos had additional preexisting defects that would prevent them from ever developing into a viable pregnancy, the group’s announcement spooked the research community.

Photo of Krishna Saha
Krishnau Saha participated in the International Summit on Human Gene Editing.
(photo: Stephanie Precourt)

In late-2015, recognizing a need for open discussion of regulations, the U.S. National Academy of Sciences, the Chinese National Academy of Sciences, and the British Royal Academy of Science convened a three-day symposium in Washington, D.C., to discuss reasonable limits and future directions for the technology. The summit drew researchers across a range of fields, and several UW-Madison experts, including as Warren P. Knowles Professor of Law and Bioethics Alta Charo, John E. Ross Professor in Science Communication and Vilas Distinguished Achievement Professor Dietram Scheufele, and Biomedical Engineering Professor Krishanu Saha, participated in the discussions, and some played key leadership roles in the symposium. “The summit was a big first step,” says Saha. “There’s a big question as to what will happen next.”

During the symposium, geneticists, biochemists, microbiologists, ethicists, philosophers, historians, and legal scholars alike deliberated what CRISPR means for humanity. Panel sessions ranged from technical presentations on mechanistic biology to ethical concerns surrounding human enhancement, and attendees dove into discourse about what types of modifications to the human genome would be technically feasible and ethically and morally acceptable in the future.

The conference culminated with a commitment to keeping the conversation open. While research aimed at enhancing human beings falls outside acceptable ethical boundaries, most attendees agreed that efforts to correct disease-causing mutations merit further study. Overall, participants optimistically concluded that CRISPR could enable scientists to make leaps and bounds in clinical cures and basic research.

Saha's student examines stem cells under a microscope.
Saha’s student examines stem cells under a microscope.
(photo: Stephanie Precourt)
A robust research community

CRISPR is in wide use at UW-Madison; so much, in fact, that the university’s Biotechnology Centerhouses a full-service CRISPR facility for researchers here. And engineers are among the many researchers across campus who use CRISPR to study a vast array of topics ranging from toxicology to synthetic biology. CRISPR, for example, allowedSaha’s group to engineer a part of the cellular skeleton to glow red when viewed underneath a fluorescence microscope. The modification allows his team to observe minute-by-minute changes in the architecture of human stem cells, which they use to study cell development and toxicology.

Scientists also can use the tool to better understand organisms that cause human diseases. Megan McLean, an assistant professor of biomedical engineering, used CRISPR to modify the historically persnickety genome of the opportunistic human pathogen Candida albicans.

Because CRISPR is modular, researchers can alter how it interacts with the DNA, allowing them to modify how cells manage information. McLean uses a specially engineered version of CRISPR that doesn’t cut DNA to turn genes on and off on demand. Her group combined this non-cutting version of CRISPR with an activation signal that responds to light to stimulate specific sections of the genome as simply as flipping a light switch.

A $6 million multidisiplinary effort at broadening understanding of how environmental toxins affect the body also takes advantage of CRISPR. Led by William Murphy, the Harvey D. Spangler Professor in biomedical engineering, the UW-Madison team includes leading experts in human pluripotent stem cell biology, tissue development and microscale tissue engineering.

Beyond human health and well-being, the tool also can be applied in industrial-scale settings.Daniel Noguera, a Wisconsin Distinguished Professor in civil and environmental engineering, used the technique to improve the yield of biofuel reactors, increasing the energy bang for the cellulosic biomass buck by modifying a microbe that breaks down the biomass to produce fewer toxic byproducts as it works.

Alongside ongoing conversations about how far is too far, Saha sees beneficial applications of the technology continuing to blossom over the coming decade. “I do see it in the clinic,” he says. “People have started trying to alter T-cells (a type of white blood cell) to have them attack cancer in smart ways. I see that type of functionality being engineered into the body—be it in the blood system, the skin, or the eye.”

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