PhD opportunities – TRANS-AM Gene Therapy Program

Project 1: Understanding upstream AAV gene therapy manufacturing using single cell omics 

The study of cellular biology has been transformed by single cell analysis. Rapid technological advances in areas such as cell isolation methods using microfluidics or microwell devices, preparation of sequencing libraries from ultra-low quantities of nucleic acids have enabled the characterisation of DNA, RNA and proteins at single cell resolution. In particular, transcriptome analysis of single cells (scRNA-seq), has matured rapidly and the technique is now cost effective, highly accurate and capable of determining the distribution of expression levels in tens of thousands of single cells.  

Example publications from the Lab: 

• Detection of host cell microprotein impurities in antibody drug products. 2024 Nature Communications. Link 

• De novo DUOX2 expression in neutrophil subsets shapes the pathogenesis of intestinal disease. 2025 Proceedings of National Academy of Sciences. Link 

• Enhanced conversion of T cells into CAR T cells by modulation of the MAPK/ERK pathway. 2025 Cell Reports Medicine. Link 

• CAR Gene Delivery by T‐cell Targeted Lentiviral Vectors is Enhanced by Rapamycin Induced Reduction of Antiviral Mechanisms. 2023 Advanced Science. Link 

Project 2: Model-supported design of transient triple transfection for the biomanufacture of rAAV gene therapies 

Large-scale production of rAAVs is in the nascent stages and there are many significant challenges and bottlenecks to overcome to produce a safe, efficacious medicine reliably and robustly in a cost-effective manner for the patient. Transient triple transfection of HEK293 cells is the most common platform for rAAV production as this system does not require the use of a helper virus which can be challenging to remove.  However, it is characterized by low yield and high cost for several reasons: i) High requirement of expensive starting and raw materials particularly the three DNA plasmids (pDNA) required to produce the viral vector particles due to low uptake of the pDNA by the cells (<1 % reaches the nucleus of the cell ; ii) Typical reported maximum transfection efficiencies of 60 – 70% ; iii) Only a fraction of the viral capsids produced contain the therapeutic element; iv) Challenging downstream purification with low yields due to the similarity between the desired product and the product-related impurities . 

Project 3: Investigation of the prevalence of partially filled rAAV capsids 

rAAV vectors produced in current manufacturing processes often display a tendency to lack genomic content (the therapeutic cargo) within the viral particle. Determination of the full to empty ratio of AAV particles represents a standard quality assessment of these gene therapy vectors. While a variety of methods have emerged, some methods, such as analytical ultracentrifugation and forms of charge detection mass spectrometry (CDMS) where long acquisition times are required, report the presence of an additional species between the empty and full signals, commonly labelled as partially filled capsids.