Gene engineering with protein barcodes

Department: Institute of Genetics and Cancer

Number of current Students: 1

Completed Supervisor training: Completed

Co Supervisors: Dr Alexander von Kriegsheim, Institute of Genetics and Cancer, Alex.VonKriegsheim@ed.ac.uk

Although genome sequencing is now routinely done in the NHS, diagnosis can be difficult because it is often unclear which mutations disrupt gene function and which are harmless. Our lab addresses this with Multiplex Assays of Variant Effects (MAVEs): experiments in which we construct thousands of mutated versions of a gene, put them into cells, and measure how each mutation affects the gene’s function. We apply this approach to disease genes (for example, in insulin resistance, Parkinson’s disease, and rare developmental diseases) and to genetic engineering, where we study how mutations change gene expression and RNA splicing.

MAVEs depend on being able to screen thousands of variants in one experiment, which is typically done using DNA barcodes. However, many mutations act at the protein level, for example by changing protein abundance or protein binding, and these effects are hard to capture with a DNA-level readout. To study them, we aim to develop a protein barcoding technology for MAVEs. Starting with a library of Green Fluorescent Protein genes available in the lab, we will design a collection of protein barcodes, integrate them into our genes, and analyse barcode levels with quantitative mass spectrometry. After validating the barcode analysis technique, we will apply it to gene and protein engineering, including context-dependent codon optimization and engineering of a therapeutic protein for increased stability.

BBSRC Remit Area: Transformative Technologies (within Advancing the Frontiers of Bioscience Discovery)