GENE EDITITING AND REGULATION TO IMPROVE IMMUNE SYSTEM

FROM:  NATIONAL SCIENCE FOUNDATION
Rewriting genetic information to prevent disease

Breakthrough Prize winner harnesses CRISPR to improve immune system
For the last few years, scientists have been studying an ancient but only recently understood mechanism of bacterial immunity that has the potential to provide immeasurable benefits to plant and animal health.

The phenomenon known as CRISPR (for Clustered Regularly Interspaced Short Palindromic Repeats) is a natural immune system found in many bacteria with the ability to identify and destroy the genomes of invading viruses and plasmids.

Researchers are trying to harness this system for gene editing and regulation, a process that could transform "the genome of plants or animals in ways that will improve their health, or introduce genetic changes that will resist disease of climate change," says Jennifer Doudna, a Howard Hughes Medical Institute investigator and professor of biochemistry, biophysics and structural biology at the University of California, Berkeley. "The explosion of research using this technique has been amazing."

Doudna, collaborating with Emmanuelle Charpentier of Sweden's Helmholtz Center for Infection Research and Umeå University, identified how the system works and engineered it in new ways that broadened its scope. The two researchers, who described their work in a 2012 paper in the journal Science, developed a technique that enables the rewriting of genetic information and the correction of mutations that otherwise can cause disease, and also can knock out the cell's ability to make harmful proteins, she says.

"Many labs have shown in principle that this can be used to correct such mutations as those that occur in cystic fibrosis, or sickle cell disease," she says. "They are showing it in cell lines and lab animals. We're still some period of time away from using this in humans, but the pace in the field has been truly remarkable, and really exciting to see."

Many bacteria have this CRISPR-based immune system capable of identifying and destroying hostile invaders. Doudna and Charpentier showed that, in doing so, CRISPR produces the protein Cas9, a DNA-cutting enzyme guided by RNA, which relies on two short RNA guide sequences to find foreign DNA, then cleaves, or cuts, the target sequences, thereby muting the genes of the invaders.

Cas9 has evolved to provide protection against viruses that could infect the bacterium, and uses pieces of RNA derived from CRISPRS to direct its activity. The system is specific and efficient enough to stave off viral infections in bacteria.

Doudna and her colleagues programmed the process so that it can be directed by a single short RNA molecule; researchers who use it to edit genomes can customize the RNA so that it sends Cas9 to cleave, like "scissors," at their chosen location in the genome.

"When we figured out how it worked, we realized we could alter the design of RNA and program Cas9 to recognize any DNA sequence," she says. "One can therefore target Cas9 to any region of a genome simply by providing a short guide RNA that can pair with the region of interest. Once targeted, different versions of Cas9 can be used to activate or inhibit genes, as well as make target cuts within the genome. Depending on the experimental design, research can use these latter cuts to either disrupt genes or replace them with newly engineered versions."

Recently Douda and Charpentier and four other scientists received the Breakthrough Prize in life sciences, which honors transformative advances toward understanding living systems and extending human life. The prizes recognize pioneering work in physics, genetics, cosmology, neurology and mathematics, and carry a $3 million award for each researcher. The Breakthrough committee specifically cited Doudna and Charpentier for their advances in understanding the CRISPR mechanism.

Doudna has been the recipient of several National Science Foundation (NSF) grants to support her research in recent years totaling more than $1.5 million. In 2000, she received NSF's prestigious $500,000 Alan T. Waterman Award, which recognizes an outstanding young researcher in any field of science or engineering supported by NSF.

She also was a founder of the Innovative Genomics Initiative, established in 2014 at the Li Ka Shing Center for Genomic Engineering at UC Berkeley. Its goal is to promote and support genome editing research and technology in both academic and commercial research communities.

"We have a team of scientists working with various collaborative partners," she says. "We want to ensure that the technology gets into as many hands as possible, and explore ways to make it even better. We are trying to bring about fundamental change in biological and biomedical research by enabling scientists to read and write in genomes with equal ease. It's a bold new effort that embraces a new era in genomic engineering."

-- Marlene Cimons, National Science Foundation
Investigators
Jennifer Doudna
Related Institutions/Organizations
University of California-Berkeley

HOX GENES AND OUR FUTURE

FROM:  NATIONAL SCIENCE FOUNDATION 
Understanding how our genes help us develop

Hox genes are the master regulators of embryonic development for all animals, including humans, flies and worms. They decide what body parts go where. Not surprisingly, if something goes wrong with these genes, the results can be disastrous.

In Drosophila, the fruit fly, a Hox mutation can produce profound changes--an extra pair of wings, for example, or a set of legs, instead of antennae, growing from the fly's head.

"The job of the Hox genes is to tell cells early on in embryonic development what to become--whether to make an eye, an antenna or wings," says Robert Drewell, associate professor of biology at Harvey Mudd College in Claremont, Calif. "Just a single mutation in the Hox gene can produce these dramatic anomalies."

Humans have Hox genes too. For this reason, Drewell is trying to understand the molecular function of Hox genes in the fruit fly, including what happens when they work properly and what happens when they don't, in order to learn more about their behavior in humans.

Genetically, humans and fruit flies are very much alike; in fact, many known human disease genes have a recognizable match in the genetic code of the fruit fly. Thus, the information researchers gain from studying flies could provide insights into certain birth defects, such as extra ribs and extra digits, and potentially serious diseases.

"We have exactly the same genes, and use them in exactly the same way," he says. "By understanding them in Drosophila, we can understand them in humans."

Drewell is conducting his research under a National Science Foundation Faculty Early Career Development (CAREER) award, which he received in 2009. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education, and research within the context of the mission of their organization. He is receiving about $600,000 over five years.

Hox genes have been entirely conserved throughout animal evolution, meaning "since around 530 million years ago, when many complex animal life forms appeared, they had Hox genes," Drewell says.

Fruit flies are model organisms for studying genetics since they have a short lifespan--several generations can be studied in a matter of weeks--and are small and easy to grow. More importantly, they can provide a wealth of information for computational analysis because scientists have deciphered their entire genetic blueprint.

"We live in this post-genomic era, so we can do comparisons across species to look at exactly how the regulatory regions at Hox genes are changing over time," Drewell says.

Drewell's lab uses several different approaches, applying biology, genetics and computational methods to learn more about the behavior of Hox genes.

"We make what are called 'reporter' genes," he says. "We construct these artificial genes in the lab, then reintroduce them back into Drosophila. This allows us to measure what is happening to those genes. The genes we are putting in are combinations of fragments from Hox genes--different DNA regions--and we are testing if these different regions are responsible for regulating when and where the Hox gene is turned on and off."

Through their experiments, "We can look at what genes are turned on and off, and can detect exactly which DNA elements regulate the process, and how they regulate it."

Because the fruit fly's genome is available, "we are able to do comparisons across species to look at exactly how these regulatory regions are changing over time," using computational biology methods, he says. Moreover, "through that process, we can essentially start to get a handle on the role that Hox genes play in controlling cell identify in the developing embryo. We can do this in all animals, including humans."

The educational component of his CAREER grant has allowed Drewell to incorporate new elements to the curriculum, including mathematical and computational approaches, and provides undergraduate students the opportunity to conduct research that typically would not be available to them.

"Harvey Mudd doesn't have a graduate program, so all the research, essentially, is done by undergraduates," Drewell says. "They get an opportunity to do something they might not otherwise get to do. Each student is fully encouraged to take ownership of his or her own project. In this way, this often exposes them to a research field for the very first time and establishes a great foundation for their future endeavors in research."

-- Marlene Cimons, National Science Foundation