Editing genes in the microbiome to prevent and cure diseases

Plants and animals live in a biosphere dominated by bacteria and viruses. The human body is a complex ecosystem, containing not only human eukaryotic cells but also viruses, bacteria, archaea, fungi, protozoans, and other microorganisms. The human microbiome is the collection of all the microorganisms in the human body. The gut microbiome is especially important for one’s health and is part of the enteric nervous system ^1-2. Many human diseases (including asthma) can be caused by dysbiosis in the gut microbiome ^3-5. The gut microbiome of cattle produces methane, a dangerous greenhouse gas. Similarly, the microbiome in the rhizomes that are connected to the roots of rice produces methane. So, talented researchers are exploring ways of using CRISPR to edit genes in various microbiomes to support sustainable agriculture, reduce the production of methane, as well as to prevent and cure diseases ^6-7. The CRISPR editing technology has been described before in this journal ^8-9. CRISPR can be used by scientists to cut and paste almost any desired DNA sequence. Defective genes can be cut out and replaced with the desired, functioning gene, or to insert new genes that give the recipient better qualities.

Asthma is disease that causes a lifetime of difficult symptoms and is often fatal. Researchers have identified a biochemical called 12, 13-diHOME (12,13-dihydroxy-9Z-octadecenoic acid). It is produced by infant gut bacteria. It predicts the risk of allergy and asthma in childhood. Since the bacteria that make the molecule likely play other roles that are beneficial, eliminating them outright may not be the best approach. So, it is better to edit genes of microbes in the gut and airways that play a role in the disease. This will to prevent them from producing 12, 13-diHOME. It is the first step toward what researchers hope will become a new branch of medicine centered on the microbiome ¹.

CRISPR can also be used to treat and cure diseases that are not linked to the microbiome. It may be able to cure many types of cancer, as well as hemophilia, sickle cell disease, beta thalassemia, leukemia, childhood blindness, AIDS, cystic fibrosis, Duchenne’s muscular dystrophy, Huntington’s disease and Covid-19 ¹⁰. For example, Chinese scientists have started the first clinical trial using CRISPR to treat and possibly even cure lung cancer. They extract T cells from patients and remove the gene that codes for a protein called PD-1 that some tumor cells can bind to block an efficient immune response against cancer. This protein is found on the surface of immune cells. It is the target of some cancer drugs termed checkpoint inhibitors. Other scientists have used CRISPR to improve the efficacy and safety profiles of cancer immunotherapy, such as CAR-T cell and natural killer cell therapies. CRISPR Therapeutics is developing gene-edited T cell therapies using CRISPR, with two candidates in clinical trials. Earlier this year, the United States Food and Drug Administration (FDA) granted Orphan Drug designation to Intellia Therapeutics’ CRIPSR-based therapy for acute myeloid leukemia.

A CRISPR-based treatment is being developed by CRISPR Therapeutics and its partner Vertex Pharmaceuticals to treat and possibly cure beta-thalassemia and sickle cell disease. They are using something called exa-cel therapy, which is currently being tested in five clinical trials. They collect bone marrow stem cells from patients and use CRISPR technology to make them produce fetal hemoglobin. This is a natural form of the oxygen-carrying protein that binds oxygen much better than the conventional adult form. The modified cells are then reinfused into the patient. In September 2023, exa-cel was granted a rolling review by the FDA as a potential one-time treatment for sickle cell disease and transfusion-dependent beta-thalassemia. If approved, exa-cel will become the first CRISPR therapy to obtain regulatory approval for a genetic disease. Vertex also submitted a biologics licensing application for exa-cel and a marketing application to the European Medicines Agency.

CRISPR is also being used to develop treatments for many forms of blindness are caused by a specific genetic mutation. One of the opportunities presented by these forms of blindness is that the immune system is not very active in the eyes. This can prevent one’s body from rejecting the treatment. The company Editas Medicine is working on a CRISPR-based therapy to cure Leber congenital amaurosis, the most common cause of inherited childhood blindness, for which there is currently no treatment. The treatment aims to use CRISPR to restore the function of light-sensitive cells before the patient loses sight completely by fixing the most common genetic mutation behind the disease. In 2020, the company started a phase 1/2 clinical trial, which was the first trial to test an in vivo CRISPR treatment. That is, gene editing is performed directly inside the patient’s body rather than on cells extracted from their body. The treatment showed positive safety data in adults, so Editas Medicine used it on the first pediatric patient.

There are several ways that CRISPR could be used to treat and even cure AIDS. For example, CRISPR can be used to remove the DNA of the human immunodeficiency virus (HIV) inserts within the DNA of immune cells in patients. This approach could be used to attack the virus in its hidden, inactive form, which is what makes it impossible for most therapies to completely get rid of the virus. In September, the first ever individual with HIV was given a CRISPR-based gene-editing therapy in a phase 1/2 trial led by Excision Biotherapeutics and researchers at the Lewis Katz School of Medicine at Temple University in Philadelphia.

Cystic fibrosis is a genetic disease that causes severe respiratory problems. Although there are some treatments that are available to treat with the symptoms, the life expectancy is only about 40 years. Cystic fibrosis can be caused by multiple different mutations in the target gene coding for the protein called cystic fibrosis transmembrane conductance regulator, or CFTR. Over 700 mutations have been identified. This makes it difficult to develop a drug for each mutation. With CRISPR technology, mutations that cause cystic fibrosis can be individually edited. In 2020, researchers in the Netherlands used CRISPR to repair CFTR mutations in vitro in the cells of people with cystic fibrosis without creating damage elsewhere in their genetic code. In addition, companies such as Vertex Pharmaceuticals and CRISPR Therapeutics have plans to develop treatments for cystic fibrosis using CRISPR systems. However, these therapies are still being developed.

Duchenne’s muscular dystrophy (DMD) is caused by mutations in the DMD gene, which encodes for a protein necessary for the contraction of muscles. Children born with this disease suffer progressive muscle degeneration. Unfortunately, existing treatments are limited to a fraction of patients with the condition. Research in mice has shown that CRISPR could be used to fix the several genetic mutations that cause DMD. In 2018, a group of researchers used CRISPR to edit 12 strategic mutation hotspots that affect the majority of the estimated 3000 different mutations that cause this muscular disease. The company called Exonics Therapeutics started developing this method further. A year later, it was acquired by Vertex Pharmaceuticals for approximately $1 billion to accelerate drug development for DMD.

In 2018, researchers at the Children’s Hospital of Philadelphia revealed a version of CRISPR that includes a self-destruct mechanism. A group of Polish researchers then used CRISPR with an enzyme called nickase to edit the gene more precisely. More recently, researchers at the University of Illinois Urbana-Champaign used CRISPR to target and edit the messenger RNA (mRNA) that codes for the mutant proteins responsible for Huntington’s disease. This technique silences mutant genes while avoiding changes to the cell’s DNA. This minimizes permanent off-target mutations because RNA molecules are transient and degrade after a few hours.

Covid-19 may also become curable using CRISPR. Scientists at Stanford University have used it to remove some of the genetic material (RNA) in the SARS-CoV-2 virus to stop it from infecting lung cells. This approach, called PAC-MAN, was shown to reduce the amount of the virus in by more than 90 percent. So, editing genomes using CRISPR may be effective in curing several diseases.

In addition, CRISPR may be used to improve agricultural productivity and help stop global climate change caused by the production of methane, a greenhouse gas that is more potent than carbon dioxide ¹¹. For example, by editing genes that code for enzymes used in photosynthesis its efficiency can be increased, thus increasing crop yields. CRISPR can also be used to increase the efficiency of photosynthesis in tree leaves, thus increasing their removal of carbon dioxide from the atmosphere. Moreover, gene editing may be used to improve the yields of wheat, cassava, cacao, bananas, rice and sorghum. Rice is especially important. It is a staple food for more than 3.5 billion people, but bacteria in its roots produce 12 % of all the methane made by humans. Researchers are studying ways of editing the genes in the microbes that produce methane in rice. They are also trying to edit the genes in the gut microbiome of cows so that they don’t produce methane. It’s also hoped that microbes that have been edited so that they don’t produce methane can be added to landfills and become dominant and replace existing microbes that produce methane. One goal is to bring plant biologists and geologists together to modify plants to form soil aggregates and mineral-microbial complexes that will ensure long-term carbon storage in soil.

Also, in 2020, Japan approved marketing of a CRISPR-edited tomato that could purportedly lower blood pressure, while last month, researchers reported editing a tomato with CRISPR to increase vitamin D production. Earlier this year, the FDA approved a cow that had its genes edited so that it can withstand higher temperatures. CRISPR may also become used to minimize agricultural emissions, making crops more resilient to a more variable and extreme climate, and using crops and soil microbes to store more carbon. At the same time, others are studying sorghum because it is one of the most drought-tolerant crops anywhere. Learning how sorghum plants achieve this could direct breeders to genes in rice, wheat and corn that can be edited to reduce their need for water. So, CRISPR is becoming useful in improving crop yields and in reducing greenhouse gas emissions.