Search
Close this search box.

We are creating some awesome events for you. Kindly bear with us.

HKUMed Research Team Develops Novel Gene Editing Variants

Image Credits: HKU, Press Release

A research team from the LKS Faculty of Medicine at The University of Hong Kong (HKUMed) has developed more efficient CRISPR-Cas9 variants that could be useful for gene therapy applications. By establishing a new pipeline methodology that implements machine learning on high-throughput screening to accurately predict the activity of protein variants, the team has expanded the capacity to analyse up to 20 times more variants at once without needing to acquire additional experimental data, which vastly accelerates the speed in protein engineering.

The pipeline has been successfully applied in several Cas9 optimisations and engineered new Staphylococcus aureus Cas9 (SaCas9) variants with enhanced gene editing efficiency. The findings are now published in Nature Communications and a patent application has been filed based on this work.

Staphylococcus aureus Cas9 (SaCas9) is an ideal candidate for in vivo gene therapy owing to its small size that allows packaging into adeno-associated viral vectors to be delivered into human cells for therapeutic applications. However, its gene-editing activity could be insufficient for some specific disease loci.

Before it can be used as a reliable tool for the treatment of human diseases, further optimisations of SaCas9 are vital within precision medicine. These optimisations must comprise the boosting of its efficiency and precision by altering the Cas9 protein.

The standard protocol for modifying the protein involves saturation mutagenesis, where the number of possible modifications that could be introduced to the protein far exceeds the experimental screening capacity of even the state-of-art high-throughput platforms by order of magnitude.

In their work, the team explored whether combining machine learning with structure-guided mutagenesis library screening could enable the virtual screening of many more modifications to accurately identify the rare and better-performing variants for further in-depth validations.

The machine learning framework was tested on several previously published mutagenesis screens on Cas9 variants and the team was able to show that machine learning could robustly identify the best performing variants by using merely 5-20% of the experimentally determined data.

The Cas9 protein contains several parts, including protospacer adjacent motif (PAM)-interacting (PI) and Wedge (WED) domains to facilitate its interaction with the target DNA duplex. The research team married the machine learning and high-throughput screening platforms to design activity-enhanced SaCas9 protein by combining mutations in its PI and WED domains surrounding the DNA duplex bearing a (PAM). PAM is crucial for Cas9 to edit the target DNA and the aim was to reduce the PAM constraint for wider genome targeting whilst securing the protein structure by reinforcing the interaction with the PAM-containing DNA duplex via the WED domain.

In the screen and subsequent validations, the researchers identified new variants, including one named KKH-SaCas9-plus, with enhanced activity by up to 33% at specific genomic loci. The subsequent protein modelling analysis revealed the new interactions created between the WED and PI domains at multiple locations within the PAM-containing DNA duplex, attributing to KKH-SaCas9-plus’s enhanced efficiency.

Until recently, structure-guided design has dominated the field of Cas9 engineering. However, it only explores a small number of sites, amino-acid residues, and combinations. In this study, the research team was able to illustrate that screening with a larger scale and less experimental efforts, time and cost can be conducted using the machine learning-coupled multi-domain combinatorial mutagenesis screening approach, which led them to identify a new high-efficiency variant KKH-SaCas9-plus.

The Assistant Professor of the School of Biomedical Sciences, HKUMed stated that this approach will greatly accelerate the optimisation of Cas9 proteins, which could allow genome editing to be applied in treating genetic diseases more efficiently.

PARTNER

Qlik’s vision is a data-literate world, where everyone can use data and analytics to improve decision-making and solve their most challenging problems. A private company, Qlik offers real-time data integration and analytics solutions, powered by Qlik Cloud, to close the gaps between data, insights and action. By transforming data into Active Intelligence, businesses can drive better decisions, improve revenue and profitability, and optimize customer relationships. Qlik serves more than 38,000 active customers in over 100 countries.

PARTNER

As a Titanium Black Partner of Dell Technologies, CTC Global Singapore boasts unparalleled access to resources.

Established in 1972, we bring 52 years of experience to the table, solidifying our position as a leading IT solutions provider in Singapore. With over 300 qualified IT professionals, we are dedicated to delivering integrated solutions that empower your organization in key areas such as Automation & AI, Cyber Security, App Modernization & Data Analytics, Enterprise Cloud Infrastructure, Workplace Modernization and Professional Services.

Renowned for our consulting expertise and delivering expert IT solutions, CTC Global Singapore has become the preferred IT outsourcing partner for businesses across Singapore.

PARTNER

Planview has one mission: to build the future of connected work. Our solutions enable organizations to connect the business from ideas to impact, empowering companies to accelerate the achievement of what matters most. Planview’s full spectrum of Portfolio Management and Work Management solutions creates an organizational focus on the strategic outcomes that matter and empowers teams to deliver their best work, no matter how they work. The comprehensive Planview platform and enterprise success model enables customers to deliver innovative, competitive products, services, and customer experiences. Headquartered in Austin, Texas, with locations around the world, Planview has more than 1,300 employees supporting 4,500 customers and 2.6 million users worldwide. For more information, visit www.planview.com.

SUPPORTING ORGANISATION

SIRIM is a premier industrial research and technology organisation in Malaysia, wholly-owned by the Minister​ of Finance Incorporated. With over forty years of experience and expertise, SIRIM is mandated as the machinery for research and technology development, and the national champion of quality. SIRIM has always played a major role in the development of the country’s private sector. By tapping into our expertise and knowledge base, we focus on developing new technologies and improvements in the manufacturing, technology and services sectors. We nurture Small Medium Enterprises (SME) growth with solutions for technology penetration and upgrading, making it an ideal technology partner for SMEs.

PARTNER

HashiCorp provides infrastructure automation software for multi-cloud environments, enabling enterprises to unlock a common cloud operating model to provision, secure, connect, and run any application on any infrastructure. HashiCorp tools allow organizations to deliver applications faster by helping enterprises transition from manual processes and ITIL practices to self-service automation and DevOps practices. 

PARTNER

IBM is a leading global hybrid cloud and AI, and consulting services provider, helping clients in more than 175 countries capitalize on insights from their data, streamline business processes, reduce costs and gain the competitive edge in their industries. Nearly 3,800 government and corporate entities in critical infrastructure areas such as financial services, telecommunications and healthcare rely on IBM’s hybrid cloud platform and Red Hat OpenShift to affect their digital transformations quickly, efficiently, and securely. IBM’s breakthrough innovations in AI, quantum computing, industry-specific cloud solutions and business services deliver open and flexible options to our clients. All of this is backed by IBM’s legendary commitment to trust, transparency, responsibility, inclusivity, and service. For more information, visit www.ibm.com