Improving gene editing by modulating nucleotide metabolism

Background

Currently, most treatments for genetic blood-related disorders (both non-cancerous and cancerous) aim to alleviate symptoms, manage complications, and slow disease progression, rather than completely correcting the underlying genetic defect. In some cases, patients may qualify for a bone marrow transplant, which comes with the risk of many serious complications. Gene editing treatments are beginning to be considered as a possible cure; however, current gene therapies are in experimental/clinical trial stages and have a variety of limitations such as their lack of precision and accuracy with off-target mutations being a concern. These treatments can also be limited by the patient’s own immune system.

Technology Overview

To treat genetic blood-related disorders, Dr. Bauer’s group at Boston Children’s Hospital worked to develop a method to improve gene editing in hematopoietic stem and progenitor cells. In particular, prime editing, gene writing, retrotransposition, and retrons are gene editing technologies that depend on reverse transcription from an RNA template to synthesize DNA and depend on reverse transcriptase (RT) activity. Efficient prime editing remains challenging in primary hematopoietic cells due to the low concentration of nucleotides available for reverse transcription, and the markedly increased expression of SAMHD1, a triphosphohydrolase enzyme that depletes deoxyribonucleoside triphosphates (dNTPs).

The current study found existing genome-editing tools have been made more efficient by increasing nucleotides availability, for example, by directly providing supplemental nucleotides to cells. Alternatively, indirectly inhibiting cellular SAMHD1, such as by delivering a lentiviral-derived factor that degrades SAMHD1 (lentiviral Vpx) via virus-like particles, can also increase prime editing efficiency. This method improves the gene editing efficiency by successfully incorporating any desired genetic changes via RT-mediated systems with enhanced precision and accuracy, while minimizing off-target effects. Specifically, the study demonstrated enhanced prime editing in human hematopoietic stem and progenitor cell (HSPC)s as well as in resting and activated CD3+ T cells.

Applications

• Treatment of genetic blood-related disorders either non-cancerous (such as sickle cell disease, and thalassemia) or blood-related cancers.

Advantages

• This gene editing method could overcome current treatment limitations, specifically with more efficacy, precision, and accuracy.

Publications

• Levesque, S., Cosentino, A., Verma, A., Genovese, P., & Bauer, D. E. (2024). Enhancing prime editing in hematopoietic stem and progenitor cells by modulating nucleotide metabolism. Nature biotechnology, 10.1038/s41587-024-02266-4. Advance online publication. https://doi.org/10.1038/s41587-024-02266-4