Next-generation gene editing for sickle cell disease

Since its founding in 1962, St. Jude has been unwavering in its commitment to researching, understanding, and improving standards of care for people with sickle cell disease.

Sickle cell disease is a set of inherited blood disorders caused by mutations affecting red blood cells. Red blood cells contain hemoglobin, a protein that carries oxygen. Unlike healthy, round-shaped cells, the red blood cells of individuals with sickle cell disease have abnormal hemoglobin, which causes the cells to be rigid, sticky, and sickle- or crescent-shaped and die sooner than healthy red blood cells. 

The premature death of sickle-shaped red blood cells leads to complications caused by dead cells sticking and obstructing blood flow in small vessels. This blockage can trigger severe pain and give rise to other health issues, including infection and stroke. For a patient with sickle cell disease, acute pain is a predominant factor in their life. These pain crises vary in intensity and duration and can arise suddenly, affecting any body part. Sickle cell disease affects approximately 100,000 individuals in the United States alone, most prevalently African Americans and Hispanics. About 1 in 365 African Americans have the disorder.

The impact of sickle cell disease on patients’ lives underscores the urgent need for comprehensive research efforts to understand its intricacies and develop effective treatments. In recent years, groundbreaking advances in gene editing have opened new avenues for treating sickle cell disease. 

For 40 years, the only potential cure for sickle cell disease has been bone marrow transplantation. This option has its roots at St. Jude because, in 1982, a St. Jude patient with acute myeloid leukemia (AML) and sickle cell disease underwent bone marrow transplantation to treat her cancer — and it cured her sickle cell disease. The results, published in 1984 in the New England Journal of Medicine, marked a turning point in treating patients with sickle cell disease. Since then, clinicians have refined transplantation methods, yet challenges persist due to a lack of donor availability and potential side effects. Today, a new scientific era that applies leading-edge gene-editing technologies to human health and disease can potentially improve and expand treatment options for sickle cell disease.

Until recently, the primary method for editing human cells relied on nucleases like CRISPR–Cas9, which induce double-stranded breaks in DNA to disrupt target gene sequences. To improve standard gene-editing approaches, researchers continuously work to identify new strategies and techniques. For example, St. Jude scientists are investigating two new advanced techniques: base editing, a highly efficient method for directly altering single DNA bases, and prime editing, a more versatile technology capable of both base and gene edits. These innovations significantly broaden the possibilities and effectiveness of genome editing. Using these advanced approaches, scientists can directly convert the mutation underlying sickle cell disease by reverting the DNA to its healthy sequence. This work was conducted through the St. Jude Collaborative Research Consortium for Sickle Cell Disease, a multidisciplinary group of scientists from across the U.S. working together to develop new and effective treatments for this devastating disease.

St. Jude scientists Mitchell Weiss, MD, PhD, Department of Hematology chair, Jonathan Yen, PhD, Department of Hematology, and their collaborator David Liu, PhD, of the Broad Institute, explored adenine base editing to treat sickle cell disease and the blood disorder beta thalassemia. During fetal development, gamma-globin pairs with alpha-globin to create fetal hemoglobin. However, after birth, gamma-globin production decreases, allowing beta-globin to take over and form adult hemoglobin. Sickle cell disease and beta thalassemia arise from Hemoglobin subunit beta (HBB) mutations, which affect beta-globin. These conditions typically appear after birth when the body switches from relying on the fetal gamma-globin genes to the mutated genes that encode adult beta-globin. The study, published in Nature Genetics, used adenine base editing to induce fetal hemoglobin in red blood cells.

Through their research, Weiss and his colleagues discovered that one change made by adenine base editing was particularly potent for restoring fetal hemoglobin expression in red blood cells after birth. “The gamma-globin, or fetal hemoglobin, gene is a good target for base editing because there are very precise mutations that can reactivate its expression to induce expression after birth, which may provide a powerful ‘one-size-fits-all’ treatment for all mutations that cause sickle cell disease and beta thalassemia,” said Weiss.

The researchers found that, of the methods they tested to boost fetal hemoglobin levels in red blood cells, the adenine base editing generation of the gamma-globin –175A>G variant produced the most potent induction of fetal hemoglobin. “We used a base editor to create a new TAL1 transcription factor–binding site that causes powerful induction of fetal hemoglobin,” said Yen. “Creating a new transcription factor–binding site requires a precise base pair change — something that can’t be done using CRISPR–Cas9 without generating unwanted byproducts and other potential consequences from double-stranded breaks.”

Using adenine base editing at the most potent site in the gamma-globin promoter showed consistent and clinically relevant levels of editing in the DNA of human stem cells. In contrast, Cas9-generated genetic alterations resulted in variable fetal hemoglobin levels, suggesting that adenine base editing may be better suited for treating sickle cell disease because it creates more predictable and potent genetic changes.

“Ultimately, we showed that not all genetic approaches are equal,” Yen said. “Base editors may be able to create more potent and precise edits than other technologies. But we must do more safety testing and optimization.”

Besides adenine base editing, Weiss, Yen, and their colleagues are exploring a technique called prime editing that may be even more versatile. Prime editing allows modifications, including targeted small insertions, deletions, and base swapping without double-stranded DNA breaks. Prime editing expands the scope of base editing abilities to all 12 possible nucleotide combination swaps, making it a highly adaptable genetic modification tool. In a paper published in Nature Biomedical Engineering, Weiss, Yen, and Liu’s teams showed that the prime editing can convert the defective adult hemoglobin gene to the healthy DNA sequence, successfully modifying as much as 41% of the DNA in blood stem cells from patients with sickle cell disease.

“Prime editing is a promising approach because, in theory, we can directly correct disease mutations to specific healthy DNA sequences of our choosing,” said Yen.

As advancements in sickle cell disease research unfold, the urgency for more effective treatments — and even cures — heightens. St. Jude researchers are at the forefront of genome-editing ability with base and prime editing.

“We have identified what might be the next wave of therapies for genetic anemias,” said Weiss. “We took the newest cutting-edge genetic-engineering technology and showed that we could make meaningful gene edits for future therapies.”