Directed evolution of engineered virus-like particles with improved production and transduction efficiencies

Aditya Raguram; Meirui An; Paul Z Chen; David R Liu

doi:10.1038/s41587-024-02467-x

Directed evolution of engineered virus-like particles with improved production and transduction efficiencies

Nat Biotechnol. 2024 Nov 13. doi: 10.1038/s41587-024-02467-x. Online ahead of print.

Authors

Aditya Raguram^{1

2

3

4}, Meirui An^{5

6

7}, Paul Z Chen^{5

6

7

8}, David R Liu^{9

10

11}

Affiliations

¹ Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA. araguram@wi.mit.edu.
² Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. araguram@wi.mit.edu.
³ Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. araguram@wi.mit.edu.
⁴ Whitehead Institute for Biomedical Research, Cambridge, MA, USA. araguram@wi.mit.edu.
⁵ Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁶ Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
⁷ Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
⁸ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁹ Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA. drliu@fas.harvard.edu.
¹⁰ Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu.
¹¹ Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. drliu@fas.harvard.edu.

PMID: 39537813
DOI: 10.1038/s41587-024-02467-x

Abstract

Engineered virus-like particles (eVLPs) are promising vehicles for transient delivery of proteins and RNAs, including gene editing agents. We report a system for the laboratory evolution of eVLPs that enables the discovery of eVLP variants with improved properties. The system uses barcoded guide RNAs loaded within DNA-free eVLP-packaged cargos to uniquely label each eVLP variant in a library, enabling the identification of desired variants following selections for desired properties. We applied this system to mutate and select eVLP capsids with improved eVLP production properties or transduction efficiencies in human cells. By combining beneficial capsid mutations, we developed fifth-generation (v5) eVLPs, which exhibit a 2-4-fold increase in cultured mammalian cell delivery potency compared to previous-best v4 eVLPs. Analyses of v5 eVLPs suggest that these capsid mutations optimize packaging and delivery of desired ribonucleoprotein cargos rather than native viral genomes and substantially alter eVLP capsid structure. These findings suggest the potential of barcoded eVLP evolution to support the development of improved eVLPs.

Abstract

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