Identification and development of novel programmable nucleases for genome editing

This project is situated in the field of innovative CRISPR-Cas gene editing tools. The objectives are: (1) To develop novel, programmable nucleases for gene editing responding to the complexity of gene therapy applications. (2) Wide scale metagenomic assembly interrogation of yet unexplored programmable nucleases originating from the human gut microbiome. (3) To select candidate nucleases based on (i) in vitro and in vivo activity, (ii) editing efficiency in genomic loci and (iii) compatibility with vector delivery systems (rAAV, VLP, VesiCas). The project will involve both wet lab work including viral vector productions and bioinformatics. 

A successful project will result in: (1) Several candidate CRISPR-Cas and IscB nucleases based in bioinformatic analysis of the gut microbiome prioritised on small molecular weight and identified tracr/crRNA including PAM determination (either in silico or described in literature). (2) Full editing analysis (DeepSeq and GUIDE-Seq) of the novel gene editing nucleases by making use of the recently established HCA EGFP reporter platform. Both nuclease and non-nuclease activities are evaluated by fusing systems with deaminases domains to probe base-editing modifications. (3) rAAV and/or VLP engineered to deliver selected novel gene editing tools in cell culture and OoC.

Enrolment in Doctoral School: University of Trento

Planned secondments:

• INSERM/Université Côte D’Azure, France (M17-18): VLP production and transduction protocols 

• KU Leuven, Belgium (M26-27): Downstream bioprocessing 

• Mimetas, The Netherlands (M36-37): OoC technology and experimental procedures