CRISPR-Cas9 has many applications especially in agriculture and animal breeding.
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James Kozubek, author of “Modern Prometheus: Editing the Human Genome with CRISPR-Cas9.

“I think there will be an ability for agriculture technology developers to get more crops through the pipeline without as much resistance, because I think there will be fewer regulatory hurdles,” James Kozubek, author of “Modern Prometheus: Editing the Human Genome with CRISPR-Cas9,” told World Grain.

Whoever wins the CRISPR-Cas9 patent case — either the University of California-Berkeley or the Broad Institute of Harvard University and the Massachusetts Institute of Technology — will begin to make good on what observers contend are billions of dollars in licensing fees as CRISPR-Cas9 becomes widely used in gene-editing plants and animals.

Eventually, the technique may be applied to humans to knock out   diseases like malaria or sickle-cell anemia.   Experiments using CRISPR-Cas9 on human genes so far have remained confined to laboratories and are considered controversial.

CRISPR is the shorthand name for “clustered regularly interspaced short palindromic repeats,” which are a set of DNA sequences first found in the E. coli bacterium by Japanese researchers in 1987. Further investigation showed they were part of the DNA of every living being that was tested, including humans. They functioned as “bookends,” indicating where individual genes start and stop in a long chain of DNA. They also were a place where DNA from invading viruses was stored in the host organism. If an identical virus attacked again, CRISPR had the ability to mobilize an enzyme to cut out the unwelcome DNA and end the threat.

Interest in laboratory applications of CRISPR began to blossom after scientific papers were published in 2012 and later described how a specific protein — in this case Cas9 — could cut a DNA chain and remove a  gene  responsible for an undesirable trait or disease. Other similar proteins also have been discovered recently, said Kozubek, that may further influence the realm of gene-editing.

CRISPR also may make specific mutations by adding desired DNA sequences and either enhance or suppress the expression of certain genes. The possibilities for genetic improvements to plants and animals began to grow dramatically, at least in the imagination of researchers.

“It is an elegant, amazingly accurate gene editing method that bacteria have used for billions of years, but humans have only understood and deployed for about 36 months,” wrote Laurie Garrett, a science journalist and senior fellow for global health at the Council on Foreign Relations, in April 2016.

CRISPR-Cas9 already is changing the terms of the debate about genetically modified foods, as highly specific and subtle alterations of edible plant and animal genomes appeared capable of supplanting older, clumsier transgenic techniques that led to widespread criticism of bioengineered foods in the United States and especially in Europe. Visions of another Green Revolution — where crop yields could improve significantly and worries fade about how to feed a potential world population of nine billion people in 2050 — have given CRISPR a powerful halo as a possible solution to problems such as agricultural disease threats and negative effects of climate change. An important additional development is the ability of plants and animals bioengineered using CRISPR-Cas9 to avoid the public relations pitfalls of the so-called GMO wars.

“We’re creating new categories now — we’re calling these things ‘precision crops’… CRISPR crops can actually be classified as organic because the alterations we are creating, the gene modification systems are so subtle that they don’t involve what you would call transgenic modifications,” Kozubek said.

The tidy way CRISPR-Cas9 works is invaluable to those seeking a better way to make genetic changes in organisms and plants. Instead of requiring consumers to wrap their heads around the notion of a vegetable incorporating pieces of DNA from another organism such as a bacteria or even from an animal, they can contemplate a technique that quickly and inexpensively removes or silences unwanted genetic material or adds in better traits by the tweak of a tiny protein.

At the same time, though, there are concerns about a sci-fi future of animal and plant alterations proliferating by a technology whose boundaries are not fully understood. The use of CRISPR may mean a wide variety of plants, crops and livestock would see their genetic footprint change, not just in the current generation, but into the infinite future.

Scientists are exploring the characteristics of the gene drive, the mechanism that moves a chosen gene throughout a population and imbeds in future generations. Many observers have questioned the possible danger to the ecosystem of such alterations and have cautioned that interference in a species’ genomes is a recipe for negative unintended consequences.

As the National Academies of Sciences said in a recent report, “Powerful new tools, such as CRISPR-Cas9, allow researchers with basic knowledge of molecular biology to precisely modify the genetic makeup of any living organism. The possible applications of such technologies are many. We are at a critical juncture in genetic research. What is needed now is guidance that is based on an in-depth review of the science underlying gene editing and an understanding of the potential benefits as well as the valid concerns raised by this research.”

Kozubek added, “Don’t forget that pathogens evolve. If you introduce some species into the environment that are resistant, say, to Lyme disease or different types of viruses in the ocean or parasites in the ocean, they are going to evolve again. We’re not done with evolution.”

His comments underscore one of the key elements of gene-editing using CRISPR: human interference with the trajectory of evolution in generations to come and the possibility of unpredictable collateral damage to the ecosystem.

“You don’t want to compromise genetic diversity in the food chain,” Kozubek said. “I’m just very skeptical that, when people say that things they’re going to do is going to improve something, that they actually are, without some other kinds of consequences happening.

“What if you have a new evolved strain of something like Lyme disease that is even more pernicious than the original one?”

Kozubek’s mention of Lyme disease referred to efforts using CRISPR-Cas9 to disrupt immune system genes and bioengineer mice resistant to Lyme disease in New England.

Lyme-resistant mice leading to Lyme-free deer and humans are one example of a panoply of possible applications of CRISPR-Cas9. Kozubek also said efforts are afoot to grow larger pigs with better fat marbling. Crops such as tobacco, rice, wheat, soybeans, potatoes, sorghum, oranges and tomatoes all have been involved in experiments using CRISPR-Cas9 to create, among other things, varieties of wheat to resist mildew and corn and wheat strains edited to resist drought.

In the realm of animal breeding, CRISPR has been used to raise cattle that don’t grow horns, a benefit in the feedlot, where animals can butt heads and cause injuries with their horns. Experiments also have been conducted in which pig cells were engineered with CRISPR-Cas9 to inactivate the 62 Porcine Endogenous Retroviruses (PERV) in the pig genome, making it impossible for those pigs to infect humans.

A scientist in Sweden even altered cabbage seeds using CRISPR-Cas9 and ate the resulting plant in a pasta dish.  Other genetic changes have been made in the laboratory, including breeding mushrooms that resist browning. Industrial yeast has also been gene-edited by CRISPR-Cas9.

Indications are that regulatory agencies in the United States may take a somewhat more relaxed view of species modified by CRISPR-Cas9 than by transgenic bioengineering. The U.S. Department of Agriculture said it has no plans to regulate a starchier corn hybrid altered by CRISPR-Cas9.

In the meantime, some observers contend it is only a matter of time before scientists will press to explore CRISPR-Cas9 in humans. In October 2016, a team of Chinese doctors injected genes modified by CRISPR-Cas9 into the cells of a patient with lung cancer as part of a clinical trial.

 For now, though, most of the world medical community is advocating a moratorium on experiments involving humans. But that doesn’t keep scientists from envisioning a day when CRISPR may be used to snip out genes causing conditions such as malaria, cystic fibrosis and hemophilia.

In the meantime, prospects for crops with better drought tolerance and higher yields and livestock with less disease will continue to be balanced against concerns about maintaining genetic variety in a world of ever-increasing knowledge about the intricacies of plant and animal genomes.