Ulcerative colitis: Recent advances in the understanding of disease pathogenesis

Inflammatory bowel diseases are common, complex, immune-mediated conditions with a sharply rising global prevalence. While major advances since 2000 have provided strong mechanistic clues implicating a de-regulation in the normal interaction among host genetics, immunity, microbiome, and the environment, more recent progress has generated entirely new hypotheses and also further refined older disease concepts. In this review, we focus specifically on these novel developments in the pathogenesis of ulcerative colitis.


Introduction
The Inflammatory Bowel Diseases (IBDs), namely Ulcerative Colitis (UC) and Crohn's disease (CD) (Table 1), are chronic immune-mediated conditions with a high prevalence in developed countries (>0.3%) and rapidly increasing incidence in newly industrialised countries (annual percentage change +14.9%) 1,2 . Global prevalence is projected to affect up to 30 million individuals by 2025 3 . Since its original description by Samuel Wilks in Morbid appearances in the intestine of Miss Bankes in 1859, the notably consistent features of UC that at once appear to be such strong clues have not yet led to a clear understanding of disease pathogenesis 4 . These clinical features include the almost-universal involvement of the rectum (the lowest part of the colon) as the first site where inflammation starts and the distinctively confluent nature of inflammation that ends with an abrupt demarcation and transition into normal colonic mucosa. Smoking is protective, and UC often presents after smoking cessation 5 . Furthermore, the development of appendicitis is protective against UC. On the other hand, UC (like CD) is clinically heterogeneous: only 30% and 15% of patients have extensive (affecting more than half of the colon) or aggressive (patients rapidly become unwell with features of systemic upset) colitis, respectively 6 . Approximately half of patients may develop a more complicated disease course, some by virtue of not responding to drug treatments 7-9 . Hence, like many complex diseases, diverse aetiological factors shape the initiation of UC and impact subsequent disease course and severity ( Table 2).

The current platform of UC pathogenesis
A widely accepted framework suggests a complex contribution of environmental and host factors that increase the susceptibility of developing UC, and disease onset is triggered by events that perturb the mucosal barrier, alter the healthy balance of the gut microbiota, and abnormally stimulate gut immune responses. Here, we discuss the general aetiological factors that increase the risk of developing UC ( Figure 1) and review the molecular underpinnings of the abnormal inflammatory process in this disease ( Figure 2). We briefly cover the genetic, environmental, immune, and microbiome factors that currently frame our understanding of UC pathogenesis.

Genetics
Genetic studies (including genome-wide association [GWA], whole genome sequencing [WGS], and fine mapping studies) have been particularly successful in identifying 260 susceptibility

Sex
Higher incidence in females than in males Equal incidence in males and females Global prevalence High incidence of CD in developed countries with high prevalence UC emerged before CD in developed countries; UC is more prevalent in newly industrialised countries

Clinical presentation
Symptomology Chronic diarrhoea, abdominal pain, fever, malnourishment, fatigue, and weight loss Most commonly bloody diarrhoea with abdominal pain, urgency, and tenesmus; haematochezia is more common in UC

Serological markers
Antibodies to microbiota including anti-Saccharomyces cerevisiae antibodies; also, anti-OmpC, anti-I2, and anti-Cbir1 antibodies and antibodies against exocrine pancreas Anti-neutrophil cytoplasmic antibodies; also, antibodies to goblet cells

Gross pathology and histopathology
Affected areas Can affect the entire gastrointestinal tract (from mouth to anus); terminal ileum is often implicated Affects the colon with potential backwash ileitis or rectal sparing in longstanding disease

Epithelial barrier
• An impaired epithelial barrier is a pathogenic factor for UC • An innate "at risk" barrier-specific genetic phenotype where exposure to additional injurious stimuli, such as non-steroidal anti-inflammatories and dietary components such as emulsifiers, may be the second trigger that precipitates colitis Immune response • Neutrophils are "first responder" cells and undergo inflammatory cell death, which drives inflammation • Innate immune responses (neutrophils/macrophages) may promote a pathogenic adaptive (likely T-cell driven) response • How HLA allelic associations influence antigen presentation is not fully understood • UC immunity is more complex than simply a non-classical Th2 response given newly discovered Th19 and Th17 responses and effective interleukin (IL)-23 blockade therapy

Mitochondria
• Mitochondriopathy is a pathogenic process in UC • Loss of mitochondrial homeostasis leads to defective energy production, increased oxidative stress, and the release of pro-inflammatory damage-associated molecular patterns Single-cell data • New colonic epithelial cell subsets have been identified that can sense colonic luminal pH and set the epithelial cGMP tone in response; goblet cell remodelling also has important implications • Strong compartmentalisation around inflammatory monocytes and novel network hubs around the poorly characterised CD8 + IL17 + T cells and microfold-like (M) cells are observed in UC • In some patients, inflammation-associated fibroblasts (IAFs) are expanded, enriched with many genes associated with colitis, fibrosis, and cancer • One of the most enriched genes in IAFs is oncostatin M (OSM); high mucosal OSM is associated with poor response to anti-tumour necrosis factor loci (both common and rare genetic variants) associated with IBD 10-14 . There are several key findings. Firstly, most genetic factors are shared between UC and CD. In an initial analysis of 15 GWA datasets, Jostins et al. showed that 110 out of 163 (67%) susceptibility loci were associated with both UC and CD 11 . These shared genes encode both innate and adaptive immune pathways, cytokine signalling, and immune sensing (e.g. IL23-R, IL-12, JAK2, CARD9, TNFSF18, and IL-10).
Many of these genes (70%) are also shared with other autoimmune diseases such as ankylosing spondylitis and psoriasis. Secondly, the strongest genetic signals within UC-specific loci are associated with the human leukocyte antigen (HLA) region in chromosome 6. Sixteen HLA allelic associations (mostly class II) are described for UC, including HLA DRB1*01*03 for IBD colonic involvement on deeper fine mapping genetic analysis 15 . Further analyses show that these are associated with colonic involvement for UC and CD 16 . It is of interest to note that HLA allelic associations with extensive and aggressive UC have been noted even prior to GWA studies 17 . Recent WGS of nearly 2,000 UC patients identified a new but rare missense variant (present in 0.6% of cases) in the adenylate cyclase 7 gene (ADCY7) that doubles the risk of UC 12 . Outwith the HLA region, the ADCY7 gene has the strongest genetic association observed with UC. ADCY7 is one of a family  of 10 enzymes that convert ATP to the ubiquitous second messenger cAMP. In addition to this, many UC-specific genes are involved in the regulation of epithelial barrier function (further discussed below). Thirdly, despite the identification of many susceptibility loci, genetics explain only 19% of disease heritability in UC 18 . The concordance rate amongst monozygotic twins for UC is only 6.3% (compared to nearly 60% in CD). Collectively, genetic factors confer a small but definite increase in susceptibility for UC. Many individuals, however, have no genetic predisposition when assessed by a polygenic risk score that accounts for all of the susceptibility loci 19 . This suggests a key role for aberrant adaptive immune responses and epithelial barrier dysfunction in UC disease pathogenesis. Non-genetic factors (notably epigenetics 20,21 ) may also play an important role.

Environmental factors
The rapid rise of UC incidence in newly industrialised countries suggests that environmental factors are important 1 . This parallels the patterns observed in the Western world during the early 20 th century. Specifically, UC appears first in urban areas, its incidence rising rapidly then slowing; subsequently, CD incidence rises and eventually approaches that of UC 22 . Westernisation is accompanied by new urban lifestyle, exposure to pollution, change in diet, access to antibiotics, better hygiene, and fewer infections, all considered as general contributory factors 23 . Notwithstanding this, more specific environmental factors associated with UC have been known for some time. The strongest example is seen in the protective effect of cigarette smoking and the notable observation of new-onset UC in individuals who stop smoking. The global patterns of smoking and IBD are changing; an increasingly large former smoker population with UC in China is suggestive of a rapid expansion of the at-risk population 24 . The anti-inflammatory effect conferred by cigarette smoking in UC is intriguing and may be mediated by carbon monoxide 25 . Further examples include the protective effect of appendicitis against future development of UC 26,27 , the bimodal incidence with a second peak associated with older age in men 28 , and, more recently, the curious association with Parkinson's disease (another condition associated with non-smoking and old age) 29,30 . These all provide more specific aetiological insights into the development of UC. Epidemiologic data have shown a potential protective effect of high dietary n-3 polyunsaturated fatty acids (PUFAs), present in oily fish 31 , and a diet high in red meat in the development of UC 32-34 .

Gut microbiota
The IBD gut microbiome is significantly less diverse and stable over time, as recently extensively characterised in the Integrative Human Microbiome Project ([iHMP], where 132 IBD and healthy individuals were followed up longitudinally for 1 year) 35 and demonstrated in a case-control study involving 1,800 IBD and irritable bowel syndrome patients 36 . A depletion of protective bacteria such as short-chain fatty acid (SCFA)producing Ruminococcaceae and Lachnospiraceae that coincides with an expansion of pro-inflammatory microbes such as Enterobacteriaceae, including Escherichia coli, and Fusobacteriaceae has been noted 37,38 . These changes, however, are less obvious in UC compared to CD 39 . It is not known if dysbiosis is a consequence of, or plays a causal role in, gut inflammation in UC. In this regard, the virome and mycobiome are also less diverse in UC 40-43 . In the longitudinal iHMP, microbiome patterns did not predict the likelihood of a disease flare. To add to the complexity, a further study in UC showed that microbial abundance did not necessarily correlate with transcriptional activity 44 . Therapeutically, however, faecal microbial transplantation (FMT) from healthy donors can treat UC. There are four controlled positive FMT clinical studies [45][46][47][48][49] . The restoration of microbial diversity, including bacterial species responsible for SCFA production in donor stool, has been suggested as an important contributor 46,50 . Hence, one of the main effects of dysbiosis in UC is likely to be a reduction in epithelial health or a state of epithelial dysfunction that further primes innate susceptibility to UC. In support of this, faecal diversion away from the rectum worsens inflammation, giving rise to "diversion colitis" in UC; the opposite is true for CD, where faecal diversion improves inflammation 51 .

Epithelial dysfunction
With the histologic observation of subepithelial inflammation, many studies implicate an impaired epithelial barrier as a pathogenic factor for UC. This is through either altered or impaired secretion (e.g. of antimicrobial peptides, damageassociated molecular patterns, or mucus) or physical defects (e.g. from disruption of epithelial tight junctions or defective regeneration or detoxification) (Text box 1) 52,53 . GWA studies show UC-specific susceptibility genes that regulate epithelial morphogenesis (hepatocyte nuclear factor 4 α, Hnf4α 54 ), adherens junction stability via E-cadherin (CDH-1), basement membrane anchoring and stability (via laminins, LAMB-1, and extracellular matrix, ECM1), tight junction assembly (guanine

Text box 1. Mucosal compartments of the gut wall
Secreted mucus barrier Mucus plays dual roles as a lubricant and a physical barrier between luminal contents and the intestinal epithelium. In the colon, an inner layer provides a bacteria-free environment adjacent to the epithelium, and the luminal less-viscous layer harbours the gut microflora.

Colonic epithelium
The single layer consists of intestinal epithelial cells (IECs), mostly absorptive colonocytes connected by tight junctions, interspersed with specialised epithelial lineages, including secretory goblet and enteroendocrine cells (EECs).

Lamina propria
The mucosal compartment beneath the epithelium supported by loose connective tissue and populated by resident immune cells such as macrophage and dendritic cells, along with mesenchymal cells.

Mesenchymal (stromal) cells
Mesenchymal cells of the intestinal lamina propria are a heterogeneous population of non-hematopoietic, non-epithelial cell types that contribute to the regulation of innate immunity and epithelial barrier maintenance with major intestinal tissue stromal cell subsets such as fibroblasts, α smooth muscle actin (α-SMA)expressing myofibroblasts, and perivascular pericytes.
ability to resolve inflammation, restore homeostasis, and repair the UC mucosa 81,82 .
Abnormal immune response: adaptive UC's strong genetic associations with HLA (mostly class II) suggest that abnormal antigen(s) driving the aberrant T-cell response, which then further shape the pathologic cytokine milieu, are likely to be a crucial causative factor. How HLA influences commensal and/or self antigen presentation (and the identities of these) to T cells and thereafter downstream pathogenic T-cell response remains unclear and challenging.
Approaches to study, screen, and define T-cell epitopes have improved considerably and progress is likely 83 . Traditionally, UC is associated with a Th2 response with high IL-4, IL-5, and IL-13, whereas CD has a more dominant Th1/Th17 response 84 . Earlier studies that show less IL-4 in UC, with CD1d-restricted natural killer T-cells producing IL-13, point to a non-classical Th2 response 85 . Some recent developments have overtaken this area. These include the identification of IL-23 as a key driver of Th17 responses 86 , genetic associations with IL-23 and its related genes 11,87 , and the presence of Th17 88 (and Th9 89 ) cells in UC. The Th2 angle becomes less clear where anrukinzumab (a drug that blocks IL-13 by binding with IL-4Ra, a shared subunit for IL-13 and IL-4 receptors) 90 and tralokinumab (a drug that blocks binding to both IL-13Ra and IL-13Ra2) are not effective in UC 91 . Blocking IL-23, however, is effective in UC, e.g. mirikizumab (anti-p19 subunit of IL-23) 92 and ustekinumab (anti-p40 subunit of IL-23) 93 . The example of anti-TNF treatment first used in CD and then shown to be equally effective in UC 94 demonstrates that basing a translational approach on pure Th-cytokine profile may be oversimplified. Furthermore, although CD4 T cells are considered to be more important in IBD pathogenesis, it is CD8 T cell transcriptomic signatures that have been found to influence whether UC and CD adopt a more aggressive disease course (in this study, CD4 T signatures were not useful) 95 . New data characterising the adaptive immune populations at a transcriptomic (and at a single cell) level 96 will yield many more new insights. The recent discovery of innate lymphoid cells (ILCs) 97,98 as a further mediator of IL-23-driven inflammatory response in the colon 99 is a further new dimension in UC.

New progress in the pathogenesis of UC
The mitochondria and UC Recent progress has been driven by a strong focus on direct studies on the inflamed mucosa specifically in newly diagnosed or drug-naïve individuals 38,100,101 . Of interest, using a bulk RNAseq approach in 206 newly diagnosed paediatric UC individuals (PROTECT study), Haberman et al. showed a significant reduction in the expression of mitochondrial genes that encode the oxidative phosphorylation chain (responsible for energy production) and nuclear encoded genes such as PPARGC1A (responsible for mitochondrial biogenesis), implicating mitochondriopathy as a pathogenic process in UC 100 . Mitochondria are intracellular double-membrane-bound organelles with many essential physiological roles such as in energy production and the regulation of cell death and immune responses 102 . In the last 10 years, many seminal studies have nucleotide binding protein alpha 12, GNA12), ion transport (solute carrier family-26, SLC26A3) 55 , and epithelial health via endoplasmic reticulum stress (orsomucoid-1-like gene 3, ORMDL3) 56 . Of interest, a protein truncating genetic variant in RNF186, a single-exon ring finger E3 ligase with strong colonic epithelial expression, protects against UC; however, the underlying mechanism is not yet clear 14,57 . Hence, there is a potentially innate "at risk" phenotype where exposure to additional injurious stimuli such as non-steroidal anti-inflammatories 58 (that reduce the synthesis of protective prostaglandins) and dietary components such as emulsifiers (that reduce the thickness of the mucus layer) 59 may be the second trigger that precipitates colitis. As discussed earlier, dysbiosis results in loss of SCFA production 35 , which is essential for epithelial energy provision, mucus production, and proliferation in the colon. Hence, clinical trials involving butyrate 60 , propionic acid 61 , prebiotics 62-66 , and L-carnitine 61 , which facilitate SCFA transport, have demonstrated some efficacy in treating UC 67 . During active UC, key pro-inflammatory cytokines such as tumour necrosis factor-alpha (TNF-α), interferon (IFN)-γ, and interleukin (IL)-13 have direct deleterious effects on epithelial barrier integrity 68,69 . Drugs that maintain remission in UC, such as mesalazine, may exert some of their therapeutic effect by maintaining epithelial health 67 . Hence, protecting the "at risk" or restoring colonic epithelial health may be a viable strategy to maintain long-term remission in UC.

Abnormal immune response: innate
In active UC, there is a complex inflammatory milieu of innate and adaptive immune cells infiltrating the lamina propria. Neutrophils, the short-lived "first responder" cells, are recruited in abundance with characteristic histology of "crypt abscesses" in UC, where neutrophils transmigrate across the colonic epithelium and die within the colonic crypts 70 . The UC inflammatory environment promotes neutrophil survival (potentially via HIF-1 and hypoxia) 71,72 . This increased survival escalates its inflammatory action and tissue damage (via many means, including the release of serine and matrix metalloproteases, reactive oxygen species, and pro-inflammatory cytokines) 73 . The high number of neutrophils undergo uncontrolled pro-inflammatory cell death (necrosis, necroptosis, and NETosis), which potentiates and amplifies the pro-inflammatory environment 74,75 . This is supported by high levels of s100a8/9 proteins (or calprotectin), usually found in neutrophils, that are released in blood and stool 76-78 and a prominent serological response to self perinuclear anti p-neutrophil cytoplasmic antibodies (pANCA) in UC, both likely indirect indicators of uncontrolled neutrophil cell death 79 . Neutrophil extracellular traps (NETs) can act as a sump for immunogenic molecules that sustain the inflammatory response 75 . Hence, there is a rational paradigm that, following disease initiation, the preceding wave of innate inflammatory neutrophils and monocytes (with their pro-inflammatory cytokine repertoire, e.g. IL-1 family, IL-6, and TNF-α) creates an inflammatory milieu (nutritional, metabolic, and cytokine) that promotes a pathologic adaptive (likely T-cell) immune response 80 . Such a milieu can also shape newly arriving inflammatory monocytes, monocyte-macrophage function, their survival, and their phenotype, and further factors that influence the host's highlighted the mitochondria as the major previously unknown "jigsaw piece" in inflammation 103 . Mitochondrial dysfunction has long been implicated in UC, as far back as 1980 104,105 (reviewed by Novak et al. 106 ), but new data from the last 3 years have re-focused this concept 100,107,108 . Such dysregulation of genes that control mitochondrial function have been shown in earlier colonic microarray studies in UC 109 .
Functional studies show that mitochondria are sited in a uniquely damaging environment (in the colon, more so than other tissue sites) 107,110 . Loss of mitochondrial homeostasis (including mitophagy and the autophagic removal of damaged mitochondria-IBD GWAS susceptibility genes PARK7 and LRRK2) can lead to defective energy production 111 , increased mitochondrial oxidative stress 107 , and even the release of mitochondrial products (mitochondrial DNA) as pro-inflammatory DAMPs 108,112 . These lines of evidence contribute to key UC themes such as epithelial dysfunction, the pro-inflammatory mucosal milieu, and direct triggers of the inflammatory response. Such convergence of data has culminated in new approaches in targeting the pro-inflammatory mitochondria, for example mitochondrial anti-oxidant therapy in active UC.
Single cell profiling of the inflamed UC mucosa Single cell RNA sequencing (scRNA) technology was developed in 2009 before becoming more widely available in 2014. It provides a comprehensive analysis and census of the cell populations ("who is all there?") in a complex inflamed UC mucosal milieu 113 . In UC, three recent scRNA studies (Parikh et al. 114 ,Smillie et al. 96 ,and Kinchen et al. 115 -scRNA analyses on colonic epithelium, whole layer, and mesenchyme, respectively) have provided some compelling insights 96,114 . These studies have identified new and rare cell types, unique cell-type-specific expression, and deep cell-cell interaction and cell lineage relationships. Secondly, mucosal compartments that have previously received less attention-notably, the colonic mesenchyme-are now implicated as key mediators of inflammation 116 . Thirdly, they show entirely new disease angles and have unexpectedly reinvigorated some older mechanistic theories. We highlight the key findings below.

Colonic epithelium: novel cell population and cell-specific changes.
A main question is whether there are specific subsets of colonic epithelial cells that display intrinsic molecular pathology that can be pathogenic drivers in UC. Both scRNA studies identified a previously unknown epithelial cell population characterised by distinct expression of the calcium-sensitive chloride channel bestrophin-4 (BEST4), the protease cathepsin E, and the OTOP2 gene. Intriguingly, this colonocyte likely has the ability to sense pH in the luminal environment and to set the epithelial cGMP tone in response. Smillie et al. showed that BEST4 + enterocytes are distinct from epithelial cells and they are also enriched in genes including otopetrins 2 and 3 (OTOP2/3), proton channels that detect pH and underlie sour taste perception, and carbonic anhydrase VII (CA7). In another novel finding, Parikh et al. demonstrated a positional remodelling of goblet cells that coincides with downregulation of WFDC2, an anti-protease molecule that is expressed by goblet cells and inhibits bacterial growth. In vivo, WFDC2 preserves the integrity of tight junctions between epithelial cells and prevents invasion by commensal bacteria and mucosal inflammation. WFCD2 has been proposed as a regulator of innate immunity through inhibition of serine and cysteine proteases 117 .
Colonic epithelium: intrinsic changes associated with UC inflamed and non-inflamed mucosa. The sharp demarcation between inflamed and non-inflamed UC mucosa in the colon provides the unique opportunity for scRNA approaches to find distinct changes that may explain this transition from normal to affected mucosa. Interestingly, both areas exhibit many similar dysregulated gene expressions. This suggests a role for mucosal epigenetics: the transcriptional signature of UC precedes inflammation, arises as the result of a dominance of regenerative over damage cues or even as a protective mechanism in anticipation of damage, and persists after resolution. All epithelial subtypes in the inflamed UC mucosa showed upregulation of several inflammatory pathways, notably IFN-γ signalling and cytokine production. Epithelial cells downregulated metabolic processes and induced genes that are needed to produce reactive oxygen species and for microbial killing. Absorptive and secretory progenitor cells upregulated differentiation and cell migration pathways, which suggests an active attempt to repair colitisinduced damage. Smillie et al.'s study that explored the overall colonic immune cell population, cell-cell interaction analyses in the inflamed UC mucosa showed strong compartmentalisation around inflammatory monocytes and novel network hubs around the poorly characterised CD8 + IL17 + T cells and microfold-like (M) cells that are usually rarely found in the healthy colon. CD8 + IL17 + T cells induce IL17A/F, IL23R, and cytotoxic, co-stimulatory, and co-inhibitory programs in UC. M cells are typically associated with lymphoid tissue in the human small intestine, where they are important for recognition of the gut microbiota but are rarely found in the healthy colon 118 . A further striking cell-cell interaction hub is centred on a mesenchymal subset of inflammation-associated fibroblasts (IAFs) 96 . In some UC patients, IAFs are expanded nearly 190-fold and enriched with many genes associated with colitis, fibrosis, and cancer (including IL13RA2).

Colonic mesenchyme: a newly identified inflammatory component contributing to an anti-tumour necrosis factor response.
In the mesenchyme-focused scRNA study, Kinchen et al. identified a distinct activated mesenchymal cell population that expressed TNF superfamily member 14 (TNFSF14), fibroblastic reticular cell-associated genes, IL-33, CCL19, and lysyl oxidases 115 . One of the most enriched genes in IAFs is oncostatin M (OSM), a putative risk gene, and its receptor OSMR 10 . In an earlier study 38,119 , West and colleagues identified significant overexpression of OSM in inflamed IBD mucosa 116 . OSM is part of the IL-6 cytokine family that can induce JAK-STAT, phosphatidylinositol-3-kinase (PI3K), and mitogenactivated protein kinase (MAPK) downstream signalling pathways. Further characterisation showed that OSMR is highly expressed in the mesenchyme (as later also shown to be the case). Using UC clinical trial datasets on anti-TNF treatment (infliximab and golimumab), high mucosal OSM expression is associated with poor response to anti-TNF 120,121 .
Future insights from scRNA studies. These recent studies provide a vast "library reference" level amount of data that the IBD research community is only beginning to assimilate and understand. Tantalising new discoveries such as epithelial pH sensing, the roles of new enterocytes marked by BEST4 + , and colonic anti-bacterial responses mediated by WFDC2 and CD8 + IL17 + T cells will require more detailed studies. These are early days of moving from census to understanding function and biology. Other leads such as OSMR blockade and CCL9 inhibition are nearer to translation as potential therapeutic targets. The International Human Gut Atlas Project (https:// helmsleytrust.org/rfa/gut-cell-atlas) will generate an even larger compendium of scRNA data in the next 5 years. Rationalising these enormous data (with other -omics datasets, e.g. genetics and microbiome), or, in lay-terms, how we combine the knowledge of "what and where are the cells?" with "what genes?" and "what bacteria?", will be both challenging and exciting 122 .

Concluding remarks
The rise of deep data encompassing all aspects of molecular and clinical phenotypes in increasingly larger human cohorts, allied with the rapid development of powerful computational analytical approaches, provides a platform to prioritise the directions of mechanistic studies. Original clinical questions 123 such as "why is there a near-universal involvement of the rectum?", "why is mucosal inflammation different to CD?", and "how does smoking protect?" and scientific ones such as "is there a specific antigenic trigger?", "what is the relative importance of adaptive vs. innate immunity?", and "what are the main mucosal factors that maintain the state of non-resolving inflammation in UC?" will emerge again and hopefully lead to better informed deductive (top-down logic) alongside the inductive (bottom-up logic) processes derived from these big datasets to fully understand the pathogenesis of UC.

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