Omics approaches to identify potential biomarkers of inflammatory diseases in the focal adhesion complex

Inflammatory diseases such as inflammatory bowel disease require recurrent invasive tests, including blood tests, radiology and endoscopic evaluation for diagnosis, assessment of disease activity and to determine optimal therapeutic strategies. ‘Bedside’ simple biomarkers could be used in all phases of patient management to avoid unnecessary investigation and guide further management. The focal adhesion complex has been implicated in the pathogenesis of multiple inflammatory diseases including inflammatory bowel disease, rheumatoid arthritis and multiple sclerosis. Utilising ‘omics approaches has proven to be an efficient method to identify biomarkers from within the focal adhesion complex in the field of cancer medicine and predictive biomarkers are paving the way for the success of precision medicine for cancer patients, but inflammatory diseases have lagged behind in this respect. This review explores the current status of biomarker prediction for inflammatory diseases from within the focal adhesion complex using ‘omics techniques and looks forward to future potential avenues for biomarker identification

Exploring Genetic Susceptibility: Using a combined systems biology, in vitro and ex vivo approach to understand the pathology of ulcerative colitis

The overall aim of this PhD is to use a multidisciplinary approach to determine the function of Ulcerative Colitis (UC) associated SNPs, to help understand the role of SNPs in the pathogenesis of UC in general and in a patient specific context. UC is a chronic, relapsing inflammatory disease of the large bowel for which the aetiology is thought to be a trifecta of 1) dysregulation of the immune system in response to 2) an environmental trigger in a 3) genetically susceptible host. Genetic susceptibility or susceptibility loci for UC have been identified by Genome Wide Associations Scanning and subsequent fine mapping and deep sequencing. This work intended to further characterise these susceptibility loci at a global level and a patient specific level using both a systems biology approach and experimental validation of the in-silico work. Using publicly available datasets non exonic UC associated SNPs were functionally annotated to regulatory regions within the genome. Exonic SNPs were also analysed looking at impacts in protein linear motifs and splice enhancement motifs. Bioinformatics was used to identify interacting proteins and create a UC-interactome network. This suggested that UC was a disease of fine regulators as opposed to a disease of specific target proteins. Analysis of the UC-interactome identified the focal adhesion complex (FAC) that is involved in regulating wound healing as major component of the network. One member of the FAC, Leupaxin (LPXN), was identified as a potential target for validation. Using CRISPR-Cas9 technology, LPXN overexpressing cell lines and knock out cell lines were created. Wound healing assays and cytokine analysis identified that overexpression of LPXN impaired wound healing and reduced the secretion of MCP-1. In addition, using genotyped colonic biopsies from UC patients and control patients in a polarised in vitro organ culture (pIVOC) system we show that the LPXN risk allele may impact on cytokine production. Finally, UKIBD genetics consortium data was used to access a pilot dataset of 58 patients’ SNP profiles from Immunochip data who were patients at the Norfolk and Norwich University Hospital to create patient-specific UC-interactomes. Analysis of these footprints identified convergent interacting proteins affected by multiple SNPs and novel pathogenic pathways