In the 1980s, pig farmers started seeing their herds come down with a viral infection causing severe breathing problems, a disorder that became known as porcine reproductive and respiratory syndrome, or PRRS. The disease is particularly rough on young pigs, and in sows it can cause early pregnancy terminations or stillbirths of entire litters. PRRS today results in annual losses among pork producers in the U.S. of $650 million and €1.5 billion in Europe.
Livestock researchers in the U.S. and Europe traced PRRS to an inherited condition that makes some pigs more susceptible to the disease. The condition results from a particular gene mutation that weakens some white blood cells in the immune system, so they not only cannot fight the infections, but also become infected themselves, making the disorder even more difficult to treat.
Up to recently, people or farm animals with genetic diseases had few treatment options, with managing their symptoms being the best hope. After all, one's genetic code is as permanent and immutable as it gets, right?
Maybe not. An emerging technology promises to edit out from DNA disease-causing genetic mutations, and correct inherited disorders, where before few treatments existed. The technology is called CRISPR, short for clustered regularly interspaced short palindromic repeats. For PRRS, researchers in the U.K. reported in February 2017 that CRISPR could edit out key protein-coding mutations in the DNA of pigs embryos, making the animals less susceptible to the disease. Initial tests showed immune system cells from DNA-edited pigs resist PRRS viral infections.
Guided by RNA
CRISPR is based on bacterial defense mechanisms that use RNA -- genetic material producing basic proteins in the body -- to identify and monitor precise locations in DNA. The actual editing of genomes with CRISPR in most cases uses an enzyme known as CRISPR-associated protein 9 or Cas9. With this approach to CRISPR, RNA molecules guide Cas9 proteins to specific genes needing repair, making it possible to address root causes of many diseases.
For biomedical scientists, CRISPR opens up possibilities for new diagnostics and treatments that previously seemed a pipe dream. CRISPR is being developed to treat, for example, inflammation in cartilage causing arthritis and the genetic eye disease retinitis pigmentosa, while CRISPR can simplify diagnostics for infectious diseases, like the Zika virus. And returning to pigs, the technology is being adapted by a start-up company to make organs from pigs suitable for human transplantation.
Genome editing isn't brand new, but the advantages of CRISPR over earlier genome-editing methods are its simplicity and accuracy, since specific RNA molecules home in on the corresponding region in the genetic code to be edited. CRISPR is so simple that do-it-yourself CRISPR kits are now on the market to alter the genomes of bacteria or brewer's yeast for as little as $150.00.
As one might imagine, a simple and accessible way to change genetic codes sets off all kinds of ethical alarms. Earlier this year, a committee of the National Academies in the U.S. cautiously recommended genome editing to remove or replace disease-causing genetic variations passed on from parents' DNA to children, known as germ line or reproductive cell editing. The committee said this kind of genome editing should be restricted only to serious and disabling medical conditions, and not used to produce enhanced physical or mental capabilities. Genome editing to correct somatic, or non-inherited, mutations such as sickle cell disease raises fewer ethical hackles.
CRISPR is also forcing regulatory authorities to confront the implications of easy, off-the-shelf genome editing. Another National Academies group concluded that the rate of change in biotechnology is accelerating at rate that threatens to leave current regulatory mechanisms behind. Not only is the quantity of new biotech discoveries increasing, the reach of these discoveries is extending into new types of organisms and biological processes, and in some cases, in disruptive ways.
In 2016, the U.S. Congress prevented federal funds from being used "in research in which a human embryo is intentionally created or modified to include a heritable genetic modification." But since then, the prospect of simple genome-editing is raising alarms of CRISPR falling into the hands of bio-terrorists.
Heavyweight patent bout
Yet another disruption is associated with CRISPR, but in this case it's a patent fight that threatens further development of CRISPR itself. This dispute pits two academic heavyweight institutions against each other: University of California in Berkeley against the Broad Institute, a medical research center at Harvard University and MIT.
University of California bases its CRISPR claims on the work of UC-Berkeley molecular and cell biologists Jennifer Doudna and Emmanuelle Charpentier, now director of the Max Planck Institute for Infection Biology in Berlin. At the time of their patent filing, Charpentier was on the faculty at University of Vienna in Austria that shares in the patent. The California patent claims the rights to CRISPR using Cas9 editing enzymes applied to cells from all organisms, from bacteria and other single-cell organisms to more complex plants and animals, where cells have a nucleus containing the DNA.
Broad Institute geneticist Feng Zhang also works with CRISPR and develops techniques similar to Doudna's and Charpentier's, but focusing solely on more complex species, not bacteria or other single-cell organsims. When Broad Institute filed its patent applications, University of California claimed Zhang interfered with, or took unfair advantage of Doudna's and Charpentier's earlier patents for its inventions. Broad Institute, however, pointed out that Zhang’s and colleagues’ discoveries are sufficiently different from Doudna’s and Charpentier’s to be considered a separate technology. In February of this year, the U.S. Patent and Trademark Office sided with Zhang and Broad Institute, dismissing UC-Berkeley's interference claims.
But Doudna, Charpentier, and UC-Berkeley aren't backing down. Not only is UC-Berkeley appealing USPTO's ruling, they took their case to the European Patent Office, which in March granted the UC-Berkeley team a European patent for CRISPR using Cas9 enzymes for editing, the leading editing method.
The financial stakes in this dispute are enormous. Both Doudna and Zhang founded spin-off enterprises attracting hundreds of millions of dollars in investment capital and licensing fees from pharmaceutical, biotechnology, and agricultural companies. Plans for clinical trials of CRISPR therapies are in final stages.
But at the end of May, a team from Stanford, Columbia, and University of Iowa raised serious questions about CRISPR with Cas9 enzyme editing, the method patented by Doudna and Charpentier. The research team found CRISPR-Cas9 to introduce hundreds of unintended mutations in the genomes of lab animals beyond the desired edits. While the unintended mutations did not noticeably change the health of the animals, the researchers say the findings indicate CRISPR with Cas9 editing does not translate from lab dish to living species as cleanly and easily as forecast.
At the same time, Zhang and colleagues at Broad Institute developed other CRISPR editing techniques they say are more accurate than Cas9. Zhang's lab found another enzyme known as Cpf1 that the researchers say is smaller and simpler than Cas9, making it easier to deliver to cells and tissues.
This dispute is far from over, and may even be decided by scientists, not lawyers.