Transcriptional analysis of chIFITM knockout technology for increased vaccine yields

Lead Research Organisation: University of Oxford
Department Name: Interdisciplinary Bioscience DTP


"Avian viruses are a major consideration in poultry health management as they cause disease and significant economic losses. Vaccines are the main tool used to mediate this problem. Due to the growth of the poultry industry, manufacturers are under considerable pressure to lower the costs of vaccines and to produce them more efficiently. As vaccines are predominantly produced in cell culture or embryonated chicken eggs, the host immune response poses a significant bottleneck in production, thereby reducing viral yields. Previous research has shown that transient ablation of restriction factors, namely Interferon Inducible Transmembrane Proteins (IFITMs), enables the virus to establish a more successful infection and consequently raises the yield of virus particles.

In this project we propose to employ CRISPR/Cas9 gene editing technology to stably knockout individual chicken IFITM (chIFITM) genes, as well as the entire chIFITM locus. To evaluate the outcomes of these gene edits, RNA sequencing will be used to identify differentially regulated immune signalling pathways. This will provide crucial information on the downstream effects of gene editing and determine whether this is a sustainable approach for vaccine production optimisation."



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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011224/1 01/10/2015 30/09/2023
1985950 Studentship BB/M011224/1 01/01/2018 31/03/2022 Martina Hadrovic Sinthalapadi
Description We studied the variability on mRNA level among clones of DF-1 chicken cell line during an infection with the influenza virus. We see the largest driver of variance in gene expression levels is the infection. Interferon signalling is not induced at the 6h time point when low quantity of virus is used as inoculum. The analysis confirmed upregulation of chIFITM genes during infection indicating their participation in the restriction of infection. Clones on average have similar transcriptomic profile indicating that cellular cloning does not affect the gene expression dynamics significantly. However, we did identify one deviant cell line that will be investigated further because it shows some interesting characteristics.
Exploitation Route Modern techniques of gene editing require cellular cloning as a step in the process. This step is stressful to the cells and can have an effect of the gene expression dynamics that can be difficult to distinguish from the effect of the gene editing that is being studied. Characterising the transcriptomic background will increase the resolution of the subsequent analysis because it informs about the level of noise that has to be taken into account as well as provide further information about DF-1 cell lines which are a widely used tool in avian immunology research.
Sectors Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology

Description Tillingbourne Junior School, Science day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact 120 7-year old children had a Science day organised for them by the school. Various play stations were organised, each dedicated to a biological concept. I was stationed at the microbiology one where we talked about microorganisms and how they grow and breathe. The children were very interested and knowledgeable showing great interest in science and the world around them.
Year(s) Of Engagement Activity 2019