NDORMS DPhil & MSc by Research
Transcriptional networks and epigenetic regulation in Dupuytren’s Disease as a model system for fibrosis - the role of EBF2
OUTLINE OF RESEARCH PROPOSAL
Dupuytren's disease (DD - OMIM 126900) is a progressive fibroproliferative disease of the palmar fascia, which results in flexion contractures of the involved digits, and significant functional impairment. DD is very common, and affects males more commonly than females. In England alone, we perform over 15,000 operations for Dupuytren's Disease per year, and this number is increasing.
The pathophysiological basis of DD is complex and incompletely understood. The key pathological cell is thought to be the myofibroblast, though there is increasing evidence that inflammatory cells such as macrophages and mast cells are important. A genetic predisposition to DD is well recognised.
We have demonstrated a sibling recurrence risk of 4.5, and a recent twin study reported a heritability of 0.8. DD has been demonstrated to be a complex disease, where multiple genetic and environmental factors affect overall genetic predisposition. A pilot genome-wide association study (GWAS) in DD was published in 2011, wherein 9 loci predisposing to DD were identified, six of which harboured genes involved in WNT signalling.
We have recently completed a second phase GWAS in a total of 8220 cases and 12874 controls. We have identified 24 genetic loci predisposing to DD (in preparation). One of these 24 variants, rs10866846 (p=2.08 x 10-15), is present in an intron of the gene EBF2. EBF2 belongs to the COE (Collier/Olf/EBF) family of non-basic, helix-loop-helix transcription factors that have a well-conserved DNA binding domain. The COE family proteins play an important role in variety of developmental processes, including in the differentiation of osteoblasts, where it has been shown to act synergistically with beta-catenin - a key component of the WNT signalling pathway.
We hypothesise that variants controlling the expression or function of EBF2 pre-dispose to DD, and that EBF2 is therefore a key transcription factor in the development of fibrosis. Furthermore, we hypothesize that EBF2 expression is controlled by epigenetic factors, and modulation of this epigenetic network can influence EBF2 expression and the fibrotic response in DD tissue, leading to the potential development of new therapeutic options.
During your DPhil, you will re-analyse imputed genetic and ATAQseq data to generate a 99% credible set for the predisposing variant at this locus. The effect of these variants on EBF2 expression will be analysed in myofibroblast cell lines derived from DD patients. You will then undertake ChIPseq and RNAseq in myofibroblasts from DD patients in the resting state, and RNAseq after knockdown and overexpression of EBF2, to generate a signature motif of EBF2 responsive genes.
Finally, using our focused chromatin libraries (shRNA library targeting 400+ genes; small molecule inhibitor library (100+ compounds) that control epigenomic responses, you will determine the key components of chromatin regulation that influence EBF2 function and fibrotic response in these cells.
This DPhil will provide training in molecular biology techniques such as qPCR, shRNA and overexpression vectors, and more advanced techniques such as high throughput sequencing. Bioinformatic and statistical training will also be provided, as will training in transferrable generic skills such as data handling, presentation and writing skills, and time management.