Mitochondrial DAMPs as Mechanistic Biomarkers of Mucosal Inflammation in Crohn's Disease and Ulcerative Colitis

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The hypothesis is that mitochondrial DAMPs are good mechanistic biomarkers for mucosal inflammation and healing in IBD. Complete mucosal healing (total resolution and absence of ulcerations in the gut) is the most sought-after treatment target with the best long-term implication in prognosis. Up to now IBD clinicians rely on (1) clinical symptoms (how patients feel, their bowel habit, presence of blood in stools), (2) clinical tests such as stool calprotectin (FC) and blood C-reactive protein (CRP) to inform both themselves and the patients, how well the drug treatment is working and importantly, whether the ulcers and inflammation seen in the gut lining have healed or not. Current evidence shows that these approaches are not fully informative. For example, 30% of patients with significant subjective improvement in their symptoms following treatment of active CD have evidence of active inflammation in their gut lining when further assessed with an ileo-colonoscopy. Blood and stool tests to predict mucosal healing are only useful in around 60-70% and very limited, in guiding the doctors in how severely inflamed the bowel wall is during active IBD. Direct visualisation using ileo-colonoscopy or flexible sigmoidoscopy is the most accurate approach to assess disease activity and mucosal healing in response to medical treatment. By knowing precisely, how the gut wall inflammation is responding to treatment, the clinician can accurately manage the IBD patient (by either changing the dose and type of treatment, and whether to carry on with expensive, strong medications with potentially serious side effects). However, in the real world, follow-up endoscopic tests are difficult to carry out as they are expensive and we lack the capacity to undertake these examinations within NHS. Project Goals The main goal for the MUSIC study is to investigate the role of mitochondrial DAMPs in the clinic as an indicator of gut inflammation and subsequent mucosal healing in response to medical treatment in IBD. Secondly, further scientific studies will be carried out using blood, stool, saliva and gut biopsy samples to investigate how mitochondrial DAMPs (and all known biomarkers and biological data such as genetics) contribute to the abnormal development of gut inflammation in IBD. Primary research questions: * Do mitochondrial DAMPs predict the activity and severity of IBD-inflammation? * Does normalisation of mitochondrial DAMPs reflect complete endoscopic mucosal healing in IBD? * How do mitochondrial DAMPs compare to current biomarkers (FC, CRP) and clinical symptoms (HBI/Mayo Score) in assessing IBD inflammation and mucosal healing? * Can a simple decision-making model be developed to predict mucosal healing based on mitochondrial DAMPs, together with relevant biological data such as genetics, blood transcriptomics, microbiome; and current clinical biomarkers such as calprotectin, faecal haemoglobin and blood CRP? Secondary research questions: * How are mitochondrial DAMPs released from cells in the IBD gut? * What types of cells are important in mitochondrial DAMP release? There are many forms of inflammatory cells in affected IBD gut (e.g. macrophage, epithelial, neutrophils). It is possible that different cell types may contain more inflammatory DAMPs. * Which type of mitochondrial DAMPs are important in causing inflammation? Can mitochondrial DAMPs pinpoint a specific underlying genetic susceptibility (e.g. autophagy) or inflammatory mechanism in IBD? Rationale The focus is to investigate mitochondrial DAMPs' utility in two clinically relevant scenarios: (a) How severe or active is the disease? (b) How well are we treating IBD? - with endoscopic endpoints of mucosal inflammation and healing respectively. The Simple Endoscopic Score for Crohn's Disease (SES-CD) and Endoscopic Mayo Score (eMS) will be used for CD and UC respectively. Both have been validated and used widely in research and in clinical trials. By using these objective endoscopic endpoints, mtDAMPs (and in combination with current biomarkers FC and CRP) can be tested across a range of mucosal inflammation (full healing to severe). In addition to this, it will be investigated if mitochondrial DAMPs can identify a subclinical pathogenic mechanism (e.g. \[a\] defective autophagy to clear damaged mitochondria; \[b\] de-regulated innate immune response to mitochondrial DAMPs.) These data will pave the way for future use of mitochondrial DAMP biomarkers as part of a stratified approach for new treatments targeted at mitochondrial DAMPs and their downstream inflammatory mechanisms in IBD. Study Population Presently within usual NHS care, all patients with active IBD, especially those to be initiated on biologic or immunomodulator treatment, are followed up where they will have documentation of disease activity (Harvey Bradshaw Index \[HBI\] or UC Mayo Score \[MS\], stool calprotectin, C-reactive protein, albumin and blood count) to assess their well-being and response to medical treatment. With MUSIC, patients will be followed up prospectively (aligning the usual NHS clinical care above) and will receive additional endoscopic follow-up to assess mucosal healing in response to medical treatment. Thus, the MUSIC study will incorporate a prospective endoscopic evaluation of mucosal inflammation and mucosal healing into IBD clinics. The recruitment and subsequent clinical data and sample collection will take place at 0, 3, 6, 9 and 12 months.