Key Takeaways
- St. Jude Children’s Research Hospital has developed a new method called Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing Base Editors (CHANGE-seq-BE) to assess precision genome editing technology.
- CHANGE-seq-BE is an unbiased, sensitive, and resource-efficient method that can find off-target edits in the genome, outperforming conventional approaches.
- The technique has already been used to support clinical work, including a case study of an emergency application to the Food and Drug Administration (FDA) for a base editor treating a genetic immune disease.
- CHANGE-seq-BE has the potential to advance the development of genome editing therapies and has already been adopted by researchers and clinicians.
Introduction to CHANGE-seq-BE
Scientists and physicians can now better assess precision genome editing technology using a new method made public by St. Jude Children’s Research Hospital. The new method, called Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing Base Editors (CHANGE-seq-BE), is an unbiased, sensitive, and resource-efficient way to find off-target edits in the genome. This is a significant development, as identifying small off-target sites that pose a safety risk has been a major challenge in improving CRISPR gene editing technology. CHANGE-seq-BE has the potential to advance the development of genome editing therapies and has already been used to support clinical work.
The Need for CHANGE-seq-BE
Traditional genome editing technology uses CRISPR-Cas9 to cut a small segment of DNA from the genome, but scientists have continued to develop more precise versions, including base editors, which can find and replace individual DNA base pairs. However, assessing the safety of base editors has been a challenge, as conventional methods have had to choose between comprehensive coverage and efficient resource use. Some techniques require whole genome sequencing, which can be prohibitively expensive and time-consuming, while others pre-select suspected off-targets, which can miss unexpected off-target edits. St. Jude researchers addressed this problem by creating CHANGE-seq-BE, which captures the best of both approaches: a comprehensive solution that is also resource-efficient.
How CHANGE-seq-BE Works
CHANGE-seq-BE starts with a whole genome, but instead of immediately sequencing it, scientists split the genome into tiny circles of DNA. They then take those circles and expose them to the base editor being tested. Afterward, they treat the DNA with a special enzyme that detects if base editing occurred, opening those – and only those – DNA circles with evidence of base editing into linear strands. The linear strands of DNA are then selectively sequenced, requiring far fewer resources than competing techniques. This approach allows CHANGE-seq-BE to detect off-target edits with high sensitivity and specificity, while using only a fraction of the resources required by conventional methods.
Clinical Applications of CHANGE-seq-BE
CHANGE-seq-BE is already being adopted to support clinical research. The paper published today includes a case study of an emergency application to the Food and Drug Administration (FDA) for a base editor treating CD40L-deficient X-linked Hyper IgM (X-HIGM) syndrome, a genetic immune disease that base editing may be able to correct. CHANGE-seq-BE was able to confirm 95.4% on-target specificity from the base editor used, with no significant off-target activity, providing valuable safety data to help push forward the patient’s treatment. This is a significant example of how CHANGE-seq-BE can be used to support clinical work and advance the development of genome editing therapies.
Advantages of CHANGE-seq-BE
CHANGE-seq-BE has several advantages over conventional methods. It is an unbiased approach that can detect off-target edits with high sensitivity and specificity, while using only a fraction of the resources required by conventional methods. This makes it a more efficient and cost-effective way to assess precision genome editing technology. Additionally, CHANGE-seq-BE is a simple and streamlined way to understand the global activity of base editors, enabling researchers to select highly specific and active editor and target combinations for research or therapeutics. The technique has already been used to characterize the first patient-specific in vivo genome editing treatment and has been adopted by researchers and clinicians alike.
Future Directions for CHANGE-seq-BE
The development of CHANGE-seq-BE has the potential to advance the development of genome editing therapies. By providing a more efficient and cost-effective way to assess precision genome editing technology, CHANGE-seq-BE can help researchers and clinicians to quickly understand and find the base editors with the highest potential activity and specificity. This can help to push forward the development of new therapies and bring them to patients more quickly. As the field of genome editing continues to evolve, techniques like CHANGE-seq-BE will play an important role in advancing our understanding of the technology and its potential applications.