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HKUMed Revolutionises Genome Editing

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The LKS Faculty of Medicine at the University of Hong Kong (HKUMed) has achieved a significant breakthrough in overcoming the existing limitations in efficiently optimising precise genome editors on a large scale. Their research team has developed a novel method that enables the simultaneous engineering of hundreds or more base editor variants, eliminating the need for laborious individual testing.

This advancement allows researchers to identify the most suitable base editor variants for therapeutic genome editing and has been documented in a publication in Cell Systems. Furthermore, the team has filed a patent application based on their innovative work.

The emergence of base editing as a safer tool for correcting single-base mutations in genetic diseases has created a need for precise optimisation of base editor variants. However, current methods involve laborious one-by-one testing, leading to time-consuming processes and suboptimal outcomes.

The research team at HKUMed has developed a breakthrough method that enables parallel engineering of multiple base editor variants, significantly increasing throughput. This advancement helps identify the most suitable base editors for therapeutic genome editing, reducing the risk of incorrect edits and undesired effects.

The team’s innovative approach has been published in Cell Systems, highlighting the significance of their findings. By engineering hundreds or more base editor variants simultaneously, researchers can efficiently determine the best options for precise editing. This approach is particularly valuable for therapeutic loci without existing optimised base editors.

Previously, creating a new base editor could take months or even years using conventional methods. With the team’s method, the process is accelerated, offering a promising avenue for advancing base editing technology and its potential applications in treating genetic diseases. The team has also taken steps to protect their invention by filing a patent application based on their work.

The research team at HKUMed has made a significant achievement by developing a platform that combines a base editor reporter system with the advanced technology called CombiSEAL. This platform enables the parallel engineering of hundreds or more base editor variants by combining different enzymatic deaminase domains with CRISPR/Cas9-based DNA-recognition domains.

However, the performance and compatibility of these variants had not been thoroughly characterised and compared. To address this, the team used the platform to quantitatively assess the editing efficiency, purity, sequence motif preference, and the generation of single and multiple base conversions in human cells.

This evaluation helped identify the most suitable base editor variants for therapeutic targets, focusing on those that achieved the desired base conversions with high efficiency and minimal undesired edits.

In addition to characterising and screening base editor variants, the team extended the use of the platform to enhance the efficiency of the existing base editor system. They specifically focused on engineering the stem-loop-2 region of the sgRNA scaffold used in the base editor system.

Through this effort, they successfully identified two novel sgRNA scaffold variants, SV48 and SV240, which outperformed the wild-type scaffold and achieved significantly higher base editing efficiency, up to 2.2-fold greater.

Furthermore, the team demonstrated that the platform is not only applicable to base editors but also compatible with other precise genome editing systems like prime editors. This versatility expands the scope of the platform’s applications, enabling the search for suitable editors to correct genetic mutations at therapeutic targets where base editors may not be suitable.

The platform developed by HKUMed’s research team offers a powerful solution for accelerating the engineering of next-generation precise genome editors and their future application in therapeutics. The platform has been described as similar to an accelerated check-out process in stores.

Each base editor variant is tagged with a barcode, and at the check-out counter, all items can be placed in the basket together. The barcode scanner automatically identifies each item and completes the payment, which in this case refers to the analysis of base editing performance. This eliminates the need for individually assessing each base editor one-by-one, streamlining the process, and saving significant time and effort.

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