September 1, 2017 (Vol. 37, No. 15)

At University of Minnesota, the CGE’s Research Expands from ‘Sleeping Beauty’ Transposon System

In the 1980s, Minnesota’s then-Governor Rudy Perpich asked scientists at the University of Minnesota (UMN) if they could help the state’s fishing industry. When news of the request reached UMN geneticist Perry B. Hackett, Ph.D., he suggested that fish could be re-engineered to grow faster and larger. Soon, Dr. Hackett was reeling in $750,000 from the state and other institutions. With this money, Dr. Hackett assembled a research team dedicated to engineering salmon  that could grow up to three times normal size.

Frankenfish fears started circulating even though the super-sized fish were never meant to swim in the wild, just in laboratory tanks or aquaculture facilities. Undeterred by the outcry, Dr. Hackett’s team continued its work, identifying a gene in salmon that had been dormant for about 13 million years. This gene turned out to be a “jumping gene,” so named because it could move from one place to another in the genome. Once the gene was resurrected by the team it was used to introduce growth genes into a fish chromosome.

The mechanism behind the jumping gene became known as the Sleeping Beauty Transposon™ System. Just as Sleeping Beauty of fairy-tale fame was awakened from a long, long sleep, ,  the Sleeping Beauty of the genome was stirred from its evolutionary slumber. Instead of receiving a spell-lifting kiss, the transposon was reconstructed. Essentially, a synthetic version of the transposon was created. It was designed to confer new functions and replace defective genes by introducing new DNA into the chromosomes of cells. The Sleeping Beauty Transposon System, Dr. Hackett emphasized in a seminal 1997 paper, introduced the ability to alter the genome without the risks occasioned by viral vectors.

Further developing Sleeping Beauty was the goal when Dr. Hackett joined three UMN colleagues—Stephen C. Ekker, Ph.D., David A. Largaespada, Ph.D., and R. Scott McIvor, Ph.D.—to form the Beckman Center for Transposon Research. In 1999, the new center was off to a brisk start when it received a$2.5 million grant from the Arnold and Mabel Beckman Foundation.

Dr. McIvor has focused on adapting Sleeping Beauty to viral and nonviral delivery systems for gene therapy. Dr. Largaespada applied Sleeping Beauty as a mutagen to identify genes and pathways driving development and metastasis of diverse cancers. Dr. Ekker served as the center’s founding director and organized a zebrafish genetics lab focused on understanding how the vertebrate genome works.

New Name, Broader Mission

Before Dr. Ekker moved his lab to the Mayo Clinic in Rochester, MN, he recruited Daniel Voytas, Ph.D., a scientist who joined UMN in 2008 as a professor of genetics, cell biology, and development. Dr. Voytas succeeded Dr. Ekker the director of the Beckman Center for Transposon Research: “Bringing in Dan Voytas,” recalled Dr. Ekker, “was a deliberate strategy to add gene editing to the core toolbox of the [center’s] planning.”

Dr. Voytas led the center when it adopted a new name: The Center for Genome Engineering (CGE). The name change  indicated that the center intended to explore not just transposon research, but other approaches to gene therapy, gene discovery, and precision gene editing.

“As molecular biologists, we engineer genomes all the time, so it made logical sense to broaden the scope of the center to genome engineering and not simply just transposon research,” said Reuben S. Harris, Ph.D., a UMN 2017 Distinguished McKnight Professor who joined the center in 2003. His lab focuses on DNA deamination in both retrovirus and transposon restriction, as well as in cancer.

When Dr. Voytas arrived, the center was working on transposons for mutagenesis and DNA delivery. He was researching zinc finger nucleases. Before long, both the center and Dr. Voytas were expanding their activities.

“Shortly after I arrived in Minnesota, we discovered and invented the TALEN® (transcription activator-like effector nuclease) approach,” recalls Dr. Voytas. “CRISPR (clustered regularly interspaced short palindromic repeats)/Cas came about a year later. We wanted to broadly adopt technologies and develop strategies to implement them in human cells, plants, animals, and other organisms.”

Research Activities

Today, CGE’s research activities encompass the development of sequence-specific nuclease platforms (including platforms that employ zinc finger nucleases, TALENs, and CRISPR/Cas9 reagents); the optimization of vectors for delivery of gene-editing reagents to cells; the deployment of novel gene-editing enzymes such as cytosine deaminases; and the elucidation of DNA repair mechanisms.

At the time this article was written, the CGE website listed 21 faculty members. According to this website, the faculty members try to combine research and educational activities. For example, they attend the center’s twice-monthly seminars, which give students and postdocs opportunities to present their most recent research findings. In addition to educating trainees, the seminars are designed to spark new collaborations and research projects.

“The seminars provide a mechanism for everyone who is interested in gene editing and manipulating nucleic acids in vivo, brings them all together, whether you’re working on plants, animals, or human cells,” Dr. Voytas said.

The Center also holds monthly interinstitutional webinars and annual meetings. Originally, the annual meetings were held at UMN. Now, they constitute an international conference series. Every other year, an annual meeting is sponsored by the Federation of American Societies for Experimental Biology (FASEB).

CGE co-sponsored the first conference of the Genome Writers Guild, “Realizing the Future: Genome Engineering 2017,” which was held July 13–15 at UMN. In addition to a plenary address from scientist-turned author David Bring, Ph.D., the conference combined scientific presentations with broader discussions involving researchers as well as physicians, members of Congress, and the public.

Licensing and Spinning Out

Arguably, CGE’s most important activities are the licensing of its technologies and the “spinning out” of new companies. Sleeping Beauty was among technologies sublicensed in 2015 by The University of Texas MD Anderson Cancer Center under a licensing agreement with Intrexon and its oncology partner Ziopharm Oncology toward development of nonviral adoptive cellular cancer immunotherapies.

CGE faculty members co-founded Recombinetics, a company that uses “precise gene editing” in diverse applications, some of which are managed by dedicated subsidiaries. The Acceligen and Surrogen subsidiaries, for example, aim to commercialize gene-edited animal models for agricultural and biomedical uses, respectively, by applying TALEN and CRISPR/Cas9 technologies. 

Spinout companies include Discovery Genomics, Inc. (DGI), formed by the center’s co-founders to commercialize morpholino oligomers (for drug discovery guided by functional genomics) and Sleeping Beauty (for gene therapy). DGI was acquired by Seattle-based Immusoft last year.

Calyxt—founded in 2010 and now a wholly owned subsidiary of Cellectis—uses TALEN gene-editing technology developed by Dr. Voytas’ lab at CGE to create specialty food ingredients and food crops with traits sought by farmers, such as herbicide tolerance. Dr. Voytas is a co-founder and CSO for Calyxt, which on July 20 launched a $56 million initial public offering.

ApoGen Biotechnologies, another CGE spinout, develops cancer therapies targeting drivers of cancer genomic mutation led by APOBEC3B (A3B), a DNA cytosine deaminase.

Other CGE spinouts include:

  • ApoGen Biotechnologies, a developer of cancer therapies targeting drivers of cancer genomic mutation led by APOBEC3B (A3B), a DNA cytosine deaminase.
  • B-Mogen Biotechnologies, a provider of gene delivery and gene editing solutions for antibody validation, human disease research, gene transfer, and mitochondrial DNA editing.

Focus on Minnesota

“We’ve seen a really impressive array of companies emerge,” says Dr. Voytas. He adds that in many of these companies, economic activity is focused in the Midwest and Minnesota.”

Expanding on that activity is a key priority for Dr. Hackett, who earlier this year was honored for his research by UMN with its Impact Award. Dr. Hackett is winding down his current projects while he focuses on promoting biotech in Minnesota. He intends to develop funding sources other than the U.S. government. He also plans to advocate “rational” regulation of genome-edited organisms, saying taxpayers should benefit from decades of precision genetics research funding.

Although UMN and the Mayo Clinic are perhaps Minnesota’s best-known biotech research co-anchors, Dr. Hackett says that the CGE has also enhanced the “North Star State” by pioneering and building a presence in genome engineering.

“Over the past five years or so at international meetings on genome engineering, no place has had more representation than Minnesota,” Dr. Hackett observes. “I think that’s because of the Sleeping Beauty system and the places it led to, plus Dan Voytas’ TALEN technology that preceded CRISPRs and thus had an earlier takeoff for exploitation of site-specific nucleases. I want to build on this.”

“There are so many young investigators that have the need, the energy, and the creativity to pursue some of the avenues we pioneered,” Dr. Hackett adds.

Continue reading the complete set of Genome Engineering articles.

CRISPR Proving More User-Friendly
Many Ways to Beat Genome Writer’s Block
A Guild for Sharing Genomic Know-How

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