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CRISPR: Everything you wanted to know, but were afraid to ask

“CRISPR is a revolutionary gene-editing tool, but it’s not without risk.” Mark Shwartz

If you are a regular reader of Germ Gems, you know by now that the blogs are aimed at intellectually curious people who are interested in what’s in the news about germs (aka microbes). Little background in microbiology or infectious diseases is required to understand the blogs. That said, this blog deals with a technically sophisticated subject that many experts believe is the single biggest scientific breakthrough in the past decade—the development of the gene-editing tool called CRISPR. Its implications span all of medicine, including the field of infectious diseases. Therefore, I believe everyone needs to know something about it.



As was pointed out in an earlier blog, the explosive emergence of antibiotic-resistant microbes around the globe is viewed by many public health authorities as our single biggest infectious disease threat. Thus, an article in the October 29, 2019, New York Times was entitled: “Is Crispr the Next Antibiotic?” suggests that a general readership would be interested in this topic. But before getting to the application of CRISPR to this and other infectious disease-related challenges, a little background information is needed.


Who gets credit for the discovery of CRISPR-Cas9 and how does it work?


In 2012, University of California, Berkeley scientist Jennifer Doudna and Emmanuelle Charpentier of Umea University were the first to propose that CRISPR (clustered regularly interspaced short palindromic repeats) and an accompanying Cas9 protein could be used as a gene editing tool—an idea considered to be one of the most significant discoveries in the history of biology. To give you some sense of how quickly this work is moving along, on September 3, 2019, the U.S. Patent and Trademark Office awarded these researchers and several associates the 12th CRISPR-Cas9 patent. It seems highly likely that this discovery is headed for a Nobel Prize of Physiology or Medicine.


But before giving these scientists all of the credit, it should be noted that this breakthrough was based on their recognition that CRISPR-Cas9 are enzymes used by microbes (bacteria and archaea) to protect themselves against infection by viruses called bacteriophages. About 40% of the bacterial cells in the oceans and on land are killed every day by these viruses, so the immunity conferred by CRISPR-Cas9 is of paramount importance to their survival. (It almost seems unfair that the microbial world won’t be credited the Nobel Prize.)


The CRISPR-Cas9 system consists of two molecules that introduce a change (mutation) in DNA. The enzyme called Cas9 acts as a pair of molecular scissors that can cut both strands of DNA at a specific location in the genome so that bits of DNA can be added or removed. The second molecule is a piece of RNA called guide RNA (gRNA) that “guides” Cas9 to the right part of the genome. The gRNA is designed to find and bind to a specific sequence in the DNA. When Cas9 makes its cut, the cell recognizes that the DNA is damaged and tries to repair it. Scientists use this DNA repair machinery to introduce changes to one or more genes of interest in the genome. By taking advantage of the repair process, genes that cause disease can be knocked out, or the repair process can be hijacked to add DNA—even an entire gene.


While the CRISPR-Cas9 system currently stands out as the fastest, cheapest, and most reliable system for editing genes, other gene editing technologies recently have been developed to improve gene targeting methods. One newfangled CRISPR developed by David Liu, a chemist at the Broad Institute in Cambridge, dubbed “prime editing,” offers more targeting flexibility and precision with less collateral damage to other areas of the genome.


The gene editing tool CRISPR-Cas9 also has the capability of acting as a “gene drive.” In sexually reproducing organisms, most DNA sequences have a 50% chance of being inherited. Gene drives, however, manage to rig the game so that they are inherited more frequently—up to 100% of the time. This type of technology affords us, for the first time, the power to alter or eliminate entire populations of pests in the wild, such as particularly nasty mosquitoes.


What are the applications and implications of CRISPR-Cas 9?


CRISPR-Cas9 has a lot of potential for treating a range of medical conditions that have a genetic component, including cancer, sickle cell anemia, cystic fibrosis, muscular dystrophy, Huntington’s disease, and even high cholesterol. For the first time in the U.S., researchers at the University of Pennsylvania announced this week that they had used CRISPR-Cas9 to delete genes in T-cells from three patients with advanced cancer. The genes that were edited are known to interfere with the cell’s ability to fight cancer. When the T-cells were infused back into the patients their numbers expanded. The procedure was found to be safe, which was the main goal of this small study.


Many of the proposed applications of CRISPR-Cas9 involve editing the genomes of somatic (non-reproductive) cells, but there has been a lot of interest in, and as you would imagine debate about, editing germline (reproductive) cells, such as the egg and sperm. (Currently, gene editing in germline cells is illegal in the US, UK, Canada, and many other countries.)

What are the applications and implications of CRISPR-Cas9 in infectious diseases?


The first successful application of CRISPR-Cas9 in humans was announced on November 28, 2018. The Chinese scientist He Jiankul used this gene editing tool in the embryos of twins to knock out a gene that makes a protein that allows HIV to enter cells. Thus, their cells were made resistant to infection by HIV. But because human germline cells were used, the accomplishment was widely condemned by many scientists and ethicists. And it fueled the worldwide movement to make this type of gene editing illegal.


Mosquitoes are one of the most promising targets of CRISPR-Cas9 gene editing technology. More than 200 million people contract malaria per year, and almost half a million die annually of this mosquito-borne disease, most of whom are children in Africa. Since 2014, scientists have engineered CRISPR-based gene drive systems that would eradicate a mosquito species that carries the parasite that causes malaria. Target Malaria, a non-profit international research consortium seeking to use gene-drive mosquitoes for malaria control in Africa appears to be only a few years away from testing this approach in Burkina Faso. But such an approach to the elimination of entire populations of pests, be they mosquitoes, rodents, and even microbes has raised concerns among environmentalists as well as ethicists.


Image shows a Malaria parasite connecting to a red blood cell

CRISPR-Cas9 and related gene editing systems are rapidly improving. Expanded applications of this technology to the development of rapid and accurate diagnostics as well as prevention and treatment of infectious diseases are on the horizon. As mentioned earlier, one such target is antibiotic-resistant bacteria. Another especially important target of emerging CRISPR-based therapeutics is persistent viral infections, including HIV, herpes simplex virus, and hepatitis B.


What’s the future of CRISPR-Cas9?


Application of CRISPR-Cas9 for the treatment and prevention of many infectious diseases, as well as of cancer and a host of genetic disorders, is highly promising. Nevertheless, significant technical and ethical hurdles must still be cleared before the promise can be realized. At this time, it appears likely to be years before this gene-editing tool is used in humans. But given the extraordinary needs, as well as investments by both non-profit organizations and private enterprises, let’s hope this timeline is considerably shortened.

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