Investigating functional consequences of disease-specific genomic enhancers in ankylosing spondylitis
- Project No: #OxKEN-2022/9
- Intake: OxKEN 2022
Ankylosing spondylitis (AS) is the archetypal spondyloarthropathy, characterised by inflammatory arthritis of the spine and sacroiliac joints that frequently results in bony fusion. The polygenic associations with AS are well documented, and to date more than 100 genetic associations have been characterised, however, the exact mechanisms and SNPs involved remain poorly understood. In a handful of examples, such as the IL-23 receptor, and the aminopeptidase ERAP1, coding polymorphisms have been documented, but in the majority of cases it is likely that the functional SNP lies within a non-coding regulatory region such as gene enhancers or promoters. A recent unpublished study in the Knight lab in collaboration with Professor Bowness and Professor Wordsworth has used epigenomic profiling in subsets of immune cells from AS patients and healthy volunteers to identify hundreds of putative regulatory genomic regions that are specifically activated or repressed in cells from patients with active disease. These regulators typically act in a cell-type specific manner and are hypothesised to activate proximal genes or work over large genomic distances, as mediated by chromosome looping events. Consequently this work has identified a number of genomic regions that are strong candidates for further functional follow up, in order to define their role in disease pathogenesis and define new therapeutic targets in AS. This is essential if we are to capitalise on the results of genome wide association studies, using knowledge of the genes modulated by specific regulatory regions containing disease associated variants.
The aims of this DPhil project are:
- to perform chromosome looping experiments (such as Capture-C) to identify and confirm interactions between disease-specific regulatory elements and cognate genes
- to perform reporter gene assays to confirm that putative regulatory regions have enhancer or suppressor activity in appropriate model systems
- to use genomic editing methods involving CRISPR-Cas9 to experimentally manipulate putative regulatory regions, and identify effects on gene regulation
- to perform functional immunological assays to establish the role of prioritised genes identified in earlier parts of the project
- to take forward targets for drug development in collaboration with colleagues in NDORMS and the Centre for Medicine Discovery
The analysis outlined in Aims (i)-(iii) will initially be performed on a small number of regions while the candidate becomes proficient in the relevant methods. However there is potential for medium-high throughput screening in later stages of the DPhil. These experiments will be performed in cell line model systems, complimented by application in primary human immune cells from AS patients and healthy volunteers (ethical approval is in place).
This project presents an exciting opportunity for a student undergoing medical training to become proficient in the field of functional genomics which has wide ranging applications in rheumatology and beyond.
This project presents the opportunity for the student to train in relevant core molecular and genetic laboratory methods, along with cutting edge techniques such as using CRISPR-Cas9. This will be done through local training with senior postdoctoral researchers experienced in these methods. Additionally, appropriate bioinformatics training will be provided so that the student can gain competency in analysing genomic datasets in statistical packages such as R. There will be opportunities to work alongside senior clinical rheumatologists, enabling the student to develop an understanding of how genomics research can be applied in the clinic. The establishment of the NHS genomic medicine service highlights the need for capacity building in genomics with cross disciplinary training and expertise. The Knight lab offers an excellent opportunity for medical students to gain this and become future leaders in the field.
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- Fairfax, B.P., P. Humburg, S. Makino, V. Naranbhai, D. Wong, E. Lau, L. Jostins, K. Plant, R. Andrews, C. McGee, and J.C. Knight, Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression. Science, 2014. 343(6175): p. 1246949.
- Roberts, A.R., M. Vecellio, L. Chen, A. Ridley, A. Cortes, J.C. Knight, P. Bowness, C.J. Cohen, and B.P. Wordsworth, An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation. Ann Rheum Dis, 2016. 75(12): p. 2150-2156.