The CRISPR Gene-Editing Revolution

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In its brief five years of existence, the gene-editing tool CRISPR-Cas9 has revolutionized medical research with its precision and ease of use.

While not the first gene-editing “scissors,” CRISPR (clustered regularly interspaced short palindromic repeats) allows scientists to conduct exhaustive genetic research in a fraction of the time such work would have taken just a few years ago. Probing, altering, and understanding genomes was never as easy and efficient.

“It might take you months to knock out one gene” by older methods, said Nicholas P. Restifo, MD, director of the Center for Cell-Based Therapy at the National Cancer Institute. “What would take a big lab a lifetime of work can now be done as part of a PhD student’s thesis work.”

CRISPR refers to repeated bits of DNA discovered in bacteria. Researchers used that discovery to develop a tool to locate a DNA sequence and then use Cas9, a RNA-guided enzyme, to cut both strands of the DNA helix. A DNA base pair can be removed (knocked out) or new genetic information can be inserted.

CRISPR has accelerated research that may someday enable scientists to edit out genetic defects such as muscular dystrophy and to develop more effective cancer treatments.

In Restifo’s research published in August 2017 in Nature, he was able to identify more than 100 mutations in human melanoma cells that enable the cancer to evade the body's immune system. He used CRISPR-Cas9 to alter DNA at 123,000 locations in the cells. Making so many experimental changes to the melanoma genome wouldn’t have been possible without CRISPR.

“The CRISPR platform doesn’t do anything that the other platforms dont do. The advantage to CRISPR is that it’s easy to use,” said Dana Carroll, PhD, professor in the Department of Biochemistry at the University of Utah School of Medicine and a member of the Nuclear Control of Cell Growth and Differentiation Program at the Huntsman Cancer Institute.

“What would take a big lab a lifetime of work can now be done as part of a PhD student’s thesis work.”

Nicholas P. Restifo, MD
National Cancer Institute

“Labs around the world have adopted [CRISPR] because of its simplicity ... Genome modifications can be accomplished in anyone’s garage,” Carroll quipped.

While that’s an exaggeration, CRISPR has become the go-to method for gene editing.

Researchers are using CRISPR to develop modifications to cell and animal models to mimic or correct human genetic diseases. Thanks to cutting and pasting with CRISPR, many academic medical centers now have core laboratories where mice can be ordered with pre-specified genetic alterations created. Researchers are engineering chimeric antigen receptor (CAR)-T cells to battle cancer, and even repairing genetic defects and lab animals with the goal of doing the same, someday, in people.

“The next level will be using CRISPR in the context of human diseases,” said Ross McKinney, MD, chief scientific officer for the AAMC. “Cells are being removed from affected people, the cells modified with CRISPR, and then reinfused into patients to treat their conditions. That’s the technique behind the CAR-T cells, developed at Penn Medicine using ideas that originated with James Allison, currently at MD Anderson Cancer Center.”

Researchers across academic medicine have been working toward the creation of potent therapies drawing on CRISPR. In the summer of 2017, a team at Memorial Sloan Kettering Cancer Center used CRISPR to engineer more powerful CAR-T cells, similar to those approved by the U.S. Food and Drug Administration (FDA) to treat children with acute lymphoblastic leukemia.

In August 2017, researchers at the Center for Embryonic Cell and Gene Therapy at Oregon Health & Science University reported the first use of CRISPR in human embryos to correct a pathogenic gene mutation. Their work, about correcting a genetic cardiomyopathy, was published in Nature.

Applying CRISPR           

The uses for CRISPR are wide open. The technology has altered the genomes of crops and livestock to produce desirable traits (such as faster growth, disease resistance, or more nutrients). Scientists are even contemplating the creation of “gene drives” that would spread a deleterious trait through a population of insect pests to wipe out a population of, say, mosquitoes carrying the malaria or Zika virus.

The potential for using CRISPR to make changes in inheritable genetic traits in humans, however, has raised concerns about possible “off-target” effects. Tinkering with inheritable human traits has raised ethical questions as well. These issues, combined with the ease of applying CRISPR, have caused worry about potential misuse of the technology.

“People may get a little aggressive in their use, even with good intentions, and start using the technology before its really ready for medical application,” said Carroll. “Someone with access to an in vitro fertilization clinic might try to make germline modifications in human embryos and then try to get the embryo implanted and to initiate a pregnancy. And the technology is absolutely not ready for that yet. Its not safe enough, its not effective enough.”

CRISPR_NIH_3D_Printing.jpg
Cas9 from CRISPR (Clustered Regularly-Interspaced Short Palindromic Repeats). Cas9 is a nuclease, an enzyme specialized for cutting DNA. Credit: NIH 3D Print Exchange, National Institutes of Health

“CRISPR has become an incredibly powerful tool, but we are still working through the ethical ramifications of gene editing, to assure that it will be a force for good,” said McKinney. “There are many single-gene defect diseases such as sickle cell or cystic fibrosis, and it would be great to have better strategies to treat them. Much of this work will involve fixing genes so that individuals who might have had a disease don’t get it and their children don’t either.”

“The fact that the research will require working in embryonic cells to learn how to do the editing makes this as much a political issue as an ethical and scientific one,” McKinney continued. “Our society will need to resolve it thoughtfully.”

As yet, federal research policy has not caught up to navigating the ethical considerations related to editing the human genome.

The need for federal oversight policies

The federal government has two “negative policies” in regard to gene editing, said Robert Cook-Deegan, MD, professor at the School for the Future of Innovation in Society and the Consortium for Science, Policy, and Outcomes at Arizona State University. First, the National Institutes of Health (NIH) has declared it won’t fund gene-editing research that would produce inheritable changes in a human embryo that would result in a pregnancy. Second, Congress has said the FDA can’t spend federal money on proposals “to modify a human organism in such a way that it would transmit an inherited change.”

These prohibitions “kind of take the NIH and FDA out of the regulatory framework. But we don’t actually have any formal policies about what we should be doing,” Cook-Deegan said. “It’s a stark contrast with how policy is beginning to evolve in the United Kingdom, for example, where they’ve got licensing authority. In order to do an experiment, you’ve got to get a license. And in order to get a license, you have to show what you’re going to do and go through an approval process. So it’s a very rational framework.”

Cook-Deegan said such an approach looks unlikely in the United States “because of the politics on embryo research and the politics of abortion, which are intermingled. It makes it very difficult to have a productive political debate in the United States.”

“CRISPR is an incredibly powerful tool, but we are still working through the ethical ramifications of gene editing, to assure that it will be a force for good.”

Ross McKinney, MD
AAMC

In February 2017, a panel of experts from the National Academy of Sciences (NAS) recommended “existing regulatory processes [local and national oversight committees] to oversee human genome editing laboratory research” that “does not involve transfer of embryos for gestation.”

The NAS panel also advised against going forward with genome editing to enhance “physical traits and capacities beyond those considered typical of adequate health.”

Finally, the panel recommended the United States consider allowing germline (heritable) genome editing in the absence of reasonable alternatives, if it prevents a serious disease and if the treatment is directed at “genes that have been convincingly demonstrated to cause or strongly predispose to that disease or condition.”

In a 2016 commentary in Molecular Therapy, Carroll imagined a public debate on the issue involving a push and pull between those who accuse researchers and doctors of “playing God” and “patient advocates and disease-specific organizations that will promote any therapy that improves the prospects for potential sufferers of devastating conditions.”

To be continued

A complicated battle over intellectual property rights, centered around an ongoing patent dispute between the University of California and the Eli and Edythe L. Broad Institute of MIT and Harvard, could hamper medical research in the future—or not. The rights to license the use of CRISPR is being claimed by at least three companies, two in the United States and one in Europe.

“The intellectual property situation is really complicated,” said Cook-Deegan. “It may or may not emerge as a major issue.”

Despite the policy and commercial uncertainties, CRISPR is revolutionizing health and medical research with its rapid spread and utility. “I think it’s wonderful that we have the technology, and I hope people will continue to use it wisely,” Carroll summed up.