Researchers Use Base Editing to Turn Pathogenic Gene Benign in Mice with SCD

Researchers were able to use a base editing approach to correct the mutation underlying the rare blood disorder sickle cell disease in patient blood cells and in mice by converting a pathogenic form of the hemoglobin gene to a benign variant.

Photo: David Liu, professor and director of the Merkin Institute of Transformative Technologies in Healthcare at the Broad Institute, professor at Harvard University, and Howard Hughes Medical Institute investigator

Sickle cell disease (SCD) is the most common deadly genetic disorder, affecting more than 300,000 newborns worldwide each year. It leads to chronic pain, organ failure, and early death in patients. The root of SCD is two mutated copies of the hemoglobin gene, HBB, which cause red blood cells to transform from a circular disc into a sickle shape — setting off a chain of events leading to organ damage, recurrent pain, and early mortality.

Currently, the only established method to cure SCD is a bone marrow transplant—but finding an appropriate bone marrow donor for a patient is difficult, and patients who undergo a transplant can suffer potentially life-threatening side effects. While there are a number of gene editing treatments under development that avoid these risks by modifying a patient’s own bone marrow directly, these experimental therapies rely on introducing new DNA or cleaving genomic DNA in cells, which can also cause adverse effects.

In a study published in Nature, researchers at the Broad Institute of MIT and Harvard and St. Jude Children’s Research Hospital used a base editing approach to correct the mutation underlying SCD in patient blood stem cells and in mice. This approach corrected the disease symptoms in animal models, enabling the long-lasting production of healthy blood cells.

“We were able to correct the disease-causing variant in both cell and animal models using a customized base editor, without requiring double-stranded DNA breaks or inserting new segments of DNA into the genome,” said co-senior author David Liu, professor and director of the Merkin Institute of Transformative Technologies in Healthcare at the Broad Institute, professor at Harvard University, and Howard Hughes Medical Institute investigator. “This was a major team effort, and our hope is that base editing will provide a promising basis for a therapeutic strategy down the road for sickle cell disease.”

The research team used what’s called an “adenine base editor,” a molecular tool developed in Liu’s lab that can target a specific gene sequence and convert the DNA base pair A-T to G-C, altering a gene at the level of a single pair of nucleotides. The base editor used in this study consists of a laboratory-evolved Cas9 variant — a CRISPR-associated protein that positions the base editor at the mutated HBB site in the genome — and a laboratory-evolved enzyme that converts the target A to a base that pairs like G. The base editor also guides the cell to repair the complementary DNA strand, completing the conversion of the target A-T base pair to G-C.

The single DNA mutation underlying sickle cell disease is an A in the healthy hemoglobin gene that has been altered to a T. While an adenine base editor cannot reverse this change, it can convert that T to a C. This edit transforms the dangerous form of hemoglobin into a naturally occurring, non-pathogenic variant called “hemoglobin Makassar.”

The team first introduced the adenine base editor into isolated blood stem cells from human SCD patients. In these experiments, up to 80 percent of the pathogenic hemoglobin variants were successfully edited into the benign Makassar variant, with minimal instances of the editor causing undesired changes to hemoglobin.

The researchers transferred these edited blood stem cells into a mouse model to observe how they functioned in live animals. After 16 weeks, the edited cells still produced healthy blood cells.

In a separate set of experiments, the researchers took blood stem cells from mice harboring the human sickle cell disease variant, edited them, and transplanted the edited cells into another set of recipient mice. Control mice transplanted with unedited cells showed typical symptoms: sickled red blood cells, consequences of short red blood cell lifetime, and an enlarged spleen. In contrast, mice transplanted with edited cells were improved compared to controls by every tested disease metric, with all measured blood parameters observed at levels nearly indistinguishable from healthy animals.

To confirm durable editing of the target blood stem cells, the researchers performed a secondary transplant, taking bone marrow from mice that had received edited cells 16 weeks previously and transferring the blood stem cells into a new set of mice. In the new animal cohort, edited cells continued to perform similarly to healthy blood stem cells, confirming that the effects of base editing were long-lasting. The team determined that editing at least 20 percent of pathogenic hemoglobin genes was sufficient to maintain blood metrics in the mice at healthy levels.

The researchers and other partners are working to conduct additional preclinical studies, with the eventual goal of reaching patients.

Author: Rare Daily Staff