The Science Behind Gene Therapy: Creating Breakthroughs One Gene at a Time

For more than 20 years, researchers at Children’s Hospital of Philadelphia and the University of Pennsylvania have been at the forefront of taking a system perfected by nature — a virus — and transforming it into breakthrough gene therapies for rare single-gene diseases. CHOP was the first pediatric research institution to develop chimeric antigen receptor T cell (CAR-T) therapy for acute lymphoblastic leukemia. In this approach, viral vectors are used to modify a patient’s own T cells, training them to track down and eliminate the circulating cancer cells. Research conducted at CHOP also built the foundation for a gene therapy treatment for Leber’s Congenital Amaurosis (LCA), a rare form of childhood blindness, that received FDA approval late last year. Many new therapies are also in development, including a gene therapy-based hemophilia B treatment, which has seen success in Phase I/II trials and began recruiting for phase III clinical trials in 2018.

So what goes into making a viral vector for gene therapy? It all starts with the virus. Gene therapy approaches typically use either a lentivirus or adeno-associated viruses (AAVs). The type of virus chosen generally depends on the type of treatment desired.

A lentivirus works well in applications where a gene needs to be delivered to cells that divide, such as stem cells, and this approach often is used for gene transfer to cells outside of the patient’s body. Hematopoietic stem cells (HSCs), cells that become all types of blood cells, have been engineered to express therapeutic genes to treat several diseases, including adrenoleukodystrophy, Wiskott–Aldrich syndrome, metachromatic leukodystrophy, and β-thalassemia.

Lentiviral vectors also are used in the production of CAR-T cells. In this case, T-cells are removed from the patient, treated with a vector that genetically engineers the cells to express chimeric antigen receptors (CARs), and then the cells are returned to the patient.

When the desired application requires targeting specific tissue and/or non-dividing cells within a patient, AAVs are useful. AAVs have been used in both the LCA and hemophilia B therapies to treat the eye and liver, respectively, with a single injection of vector. AAVs also have the benefit of being nonpathogenic, meaning they do not cause disease.

The virus needs some tweaking before it becomes a viral vector. Scientists within the Clinical Vector Core housed in the Raymond G. Perelman Center for Cellular and Molecular Therapeutics (CCMT) of the Research Institute are experts at this process. The genes that code for most viral functions, such as ones that would normally make a person sick, are removed. In their place, the gene that will be delivered to the patient, along with the elements needed for that gene to function, are added. Instead of a virus that infects someone with a particular disease, the resulting viral vector will “infect” the patient with a life-saving gene. Because of this, gene therapy has been most useful for diseases resulting from defects in a single gene.

Developing a successful gene therapy drug is not without its challenges. Simply reaching the target tissue can sometimes prove difficult, especially for neurogenetic diseases that require delivery of a gene to the entire brain. Another challenge is the lack of appropriate models for preclinical studies that mimic the human disease. It will be beneficial if gene editing approaches, such as CRISPR, can be used to develop models for diseases that currently do not have them; however, even when such models exist, the therapeutic effects observed in one species may not transfer to others.

On the clinical side, a critical challenge is the potential for the viral vector to stimulate an immune response. While it is normally beneficial for the immune system to respond to viral infection, the result in the case of gene therapy can mean reduced expression of the gene product, or even more severe adverse effects such as tissue damage. Triggering an immune response appears to be dependent on the amount of viral vector administered, so in some cases, the therapeutic goal may be a partial therapeutic response. For patients, this could mean going from severe disease to a more moderate, and perhaps more easily managed, disease.

One notable case is the hemophilia B gene therapy product, SPK-9001, which has benefited from the discovery of a hyperactive variant of factor IX. This supercharged factor IX allowed researchers to use a fraction of the amount of virus in patients.

So where does gene therapy go from here? Advancements continue to be made in the field, with the goal of improving both the safety and efficacy of viral vectors. At CHOP, the CCMT Clinical Vector Core is opening a new state-of-the-art facility where they will continue improving viral delivery, targeting gene expression to certain tissues, and minimizing the risk of triggering an immune response.

Thanks to their endeavors, and the tremendous support of CHOP, the future of gene therapy is bright. Continued work on developing these approaches will hopefully continue to produce many more breakthrough therapies in the years to come.