Transcriptional analysis of chIFITM knock-out cell lines

Thesis

Interferon-inducible transmembrane (IFITM) proteins are restriction factors known to confer antiviral resistance against a wide range of viral pathogens. The chicken IFITM locus is found on Gallus gallus chromosome 5. It contains 4 genes of chIFITM family: chIFITM1, 2, 3, and 5. They have been shown to restrict avian influenza virus in vitro and significantly ameliorate clinical signs in animals in vivo. Here I hypothesise that chIFITM knock-out models could support higher viral titres due to the ablation of chIFITM genes. I develop two models: chIFITM KO DF-1 and chIFITM KO PGC. chIFITM KO DF-1 fibroblasts representing ubiquitous avian fibroblast line used in veterinary research and chIFITM KO PGC modelling an approximation to an animal model. chPGCs are chicken primordial germ cells: precursors of sperm and ova which are very amenable to gene editing and for that reason frequently used for production of transgenic animals in research. Subsequent to gene editing they were differentiated into fibroblasts to facilitate comparison with the DF-1 fibroblasts. The study focussed on the investigation of the effects of the chIFITM KO on the permissiveness of the cells to the influenza virus and their ability to support viral replication. Differential expression analysis and the subsequent pathway analysis was conducted on the differentially expressed genes in native conditions as well as during the influenza infection for both models to compare and contrast differentially regulated pathways for each model.

Authors: Hadrovic-Sinthalapadi, M

• DOI: 10.5287/ora-2rvnm1ga0
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: CRISPR; chIFITM; influenza; PGC; RNA-seq; DF-1
• Subjects: restriction factor; Infection; pathway analysis; Avian influenza; transcriptomics