Symptoms such as fatigue, sleep disturbances, anxiety and depression are common in patients with IBD, but the cause is unknown. Understanding how these behaviors occur in IBD and their role in symptoms may help improve management of IBD. How IBD leads to changes in brain function remains unclear. Inflammation and dysfunction of blood flow may occur in patients with IBD, which may be linked to these symptoms. Patients with IBD also have an alteration or imbalance of gut bacteria which may play a role in the development of the disease, but the exact mechanism remains poorly understood;as a result, there are limited therapeutic options available clinically to address this issue. An approved therapy, anti-TNF α, may be useful in improving brain and gut activity as well as quality of life. The purpose of this research study is to better understand brain and gut activity in the context of IBD to possibly improve treatments for the disease. In patients taking anti-TNFα therapy as prescribed clinically as standard of care, the investigators will measure brain activity using NIRS; gut microbiome using stool analysis and quality of life using various questionnaires.

Hypothesis Conditions with acute systemic inflammation will correlate with changes in gut microbiome signatures, reduced cerebral oxygen saturation (StO2) and altered patterns of microvascular cerebral blood perfusion (as determined by near-infrared spectroscopy NIRS).

Rationale The investigators are investigating the ability of near-infrared spectroscopy (NIRS) to detect altered brain function and oxygenation under a range of clinically relevant medical conditions.

NIRS allows for non-invasive measurement of oxygenated (O2Hb) and deoxygenated hemoglobin (HHb) concentrations in cortical brain tissue. Therefore, NIRS can be used to quantify cortical tissue oxygen saturation (StO2), which reflects changing metabolic rate and perfusion. Furthermore, functional NIRS (fNIRS) can be used to probe brain activity in a similar fashion to functional MRI, by assuming that the measured changes in blood perfusion and oxygenation are due to functional hyperemia (i.e. hemodynamic changes caused by neural activity). Using NIRS in patients, altered patterns of brain blood perfusion and reduced brain oxygenation levels have been shown to correlate with fatigue and impaired cognition, linking reduced cortical perfusion to symptoms that have been reported to occur in patients with IBD.

Tight regulation of cerebral blood flow is critical to ensure normal brain oxygenation and function. Cerebrovascular dysfunction and hypoxia have been implicated in a range of neurodegenerative and neuroinflammatory disorders including Alzheimer's disease and multiple sclerosis (MS). In a recent study using fNIRS, the investigators found altered task associated hemodynamic responses and brain hypoxia in patients with the immune-mediated liver disease, primary biliary cholangitis (PBC). Moreover, the experimental work in mice suggests that these changes may be due to the actions of TNFα on the cerebral vasculature. It also showed that patients with multiple sclerosis had reduced inter-hemispheric coherence and hypoxia. These observations led to the question of whether general systemic inflammation or brain/gut interactions could link to abnormal brain function and hypoxia, as detectable by NIRS.

Supporting this hypothesis is a recent NIRS study by Fujiwara T et al in patients with IBD. They showed that during performance of a task, mean oxygenated hemoglobin concentration was significantly lower in the frontal lobe in IBD patients compared to healthy controls. However, changes in brain oxygenation have not been previously examined during resting state or in the context of markers of peripheral inflammation, quality of life measures and symptom burden, or gut microbiome signatures in IBD patients.

This currently proposed substudy is to examine patients with inflammatory bowel disease (IBD) for their level of hypoxia, fNIRS functional response and fNIRS coherence.

IBD is increasing in incidence and prevalence worldwide. Several factors have been implicated in the development of IBD, including a dysregulated immune response to altered microbiota in a genetically susceptible host exposed to inciting environmental factors, but the specific cause of IBD remains unknown. Comorbid maladaptive behaviors and pain are prevalent in patients with IBD20-26. These mental health comorbidities complicate management of IBD, adversely impacting patient outcomes and health, and increasing the resource burden to the health care system. However, comorbid mental health issues and symptoms in IBD patients are poorly understood and under-treated, paralleling unmet mental health treatment needs in the general Canadian population. Therefore, an improved understanding of how brain changes occur in association with IBD, and their potential role in symptom development and link to systemic inflammation and gut microbiome signatures is of significant importance to improve management of these patients.

The gastrointestinal tract serves as a dynamic and local ecosystem for gut microbiota. Dysbiosis, which is an alteration of the gut microbial composition that contributes to host disease, occurs in IBD patients. Specifically, IBD patients exhibit a lower microbial α-diversity and are enriched in several groups of bacteria compared with healthy controls. Recently, preclinical, translational, and clinical studies have indicated that alterations in the structural composition or function of the microbiome can contribute to the development of mental illness, including depression-like behavior, and thus, is a vital component linking the gut-brain axis. Consistent with this, strong correlations have been identified between alterations in gut microbiota and the development of chronic inflammatory disorders, such as IBD, suggesting that dysbiosis is an important factor in both gastrointestinal disorders and mental health. However, the precise mechanisms by which gut dysbiosis in IBD may alter behavior remains poorly understood.

How peripheral inflammation, as occurs in IBD, leads to remote changes in brain function remains unclear and, as a result, there are limited therapeutic options available clinically to address this issue. A number of general pathways have been described that link systemic inflammation to changes occurring in the brain, which in turn give rise to altered behavior. These pathways traditionally have included signaling via neural pathways (mainly vagal nerve afferents) and immune signaling (mainly via circulating cytokines like TNFα, which either enter the brain directly or activate cerebral endothelium). Recently, University of Calgary researchers described a novel inflammation signaling pathway which involves increased peripheral TNF-α production driving increased microglial activation, followed by monocyte recruitment into brain vasculature and brain parenchyma, which in turn drives the development of sickness behaviors. TNFα is a multifunctional cytokine that mediates a range of effects that can directly impact brain function (via modulating neurotransmission) and the gut (e.g. affecting intestinal barrier permeability) and modulate tissue inflammation (e.g. activate macrophages to induce cytokine and chemokine expression). Increased circulating levels of TNFα and elevated production by circulating leukocytes are commonly documented in patients with chronic inflammatory conditions associated with a high prevalence of sickness behaviors and mood disorders, including IBD. Hence, blockade of TNFα signaling has been extensively evaluated in clinical studies of IBD. In addition, improvement in symptoms by TNFα signaling inhibition are often evident in treated patients with chronic inflammatory diseases, prior to overt changes in disease activity. In patients with IBD, anti-TNFα therapy was associated with significant improvements in sleep, depression, and anxiety early after initiation of therapy, and these improvements were sustained. Moreover, another study assessed the effect of anti-TNFα therapy on interoceptive signaling in patients with Crohn's disease and demonstrated reductions in visceral sensitivity and improved cognitive-affective processing after anti-TNFα administration, paralleled by improved sense of well being. Changes in cognition were linked to changes in neural activity in prefrontal and limbic brain areas. Moreover, the rapid behavioral and neural changes observed were not associated with significant changes in fecal calprotectin levels (marker of gut inflammation) suggesting they were unlikely related to a simultaneous reduction in intestinal inflammation. Anti-TNFα therapy also alters the gut microbiome in patients with IBD. Specifically, anti-TNFα therapy in IBD patients increased gut microbial species richness and phylodiversity to levels similar to healthy controls. In addition, anti-TNF therapy decreased the relative abundances of proinflammatory bacteria Escherichia and Enterococcus in IBD patients, and increasing genera that produce short-chain fatty acids, which have well-established anti-inflammatory effects in the gut.

Healthy cerebral endothelial cells (CECs) are critically important for brain blood flow regulation, as well as the normal function of the blood-brain barrier (BBB). Cytokines, including TNFα, originating from within the central nervous system or present in the peripheral blood circulation, can induce CEC dysfunction and increase BBB permeability, which is known to be associated with many neurological disorders including Alzheimer's and MS, as well as peripherally induced neuroinflammation. Indeed, CECs exposed to TNFα express fewer interendothelial proteins and have greater reactive oxygen species generation, leading to increased BBB permeability. Furthermore, CECs can be activated by cytokines that are either present in the blood or released by circulating immune cells in intimate contact with CECs, to produce secondary signaling molecules (e.g., additional cytokines, prostaglandin E2, nitric oxide) which interact with cells within the brain to alter NVC responses. Consistent with this suggestion, in a mouse model of peripheral inflammation, it was shown that activated monocytes within the cerebral circulation adhere to CECs and induce CEC activation through TNFα-TNF receptor-1 interactions. This immune cell and TNFα-driven CEC activation up-regulates inducible nitric oxide synthase expression within CECs and was directly linked to activation of microglia within the brain (especially those cells in close proximity to blood vessels), and ultimately to altered behavior. These previous findings from this group provide a mechanism by which peripheral inflammation can impact the function of CECs, thereby altering cerebrovascular function. Blocking activated immune cells within the circulation from adhering to CECs increases task-induced cortical blood flow (i.e., NVC)66, suggesting that immune cell-CEC adhesive interactions can lead to neurovascular uncoupling. CECs can also play an essential role in the regulation of cerebral blood flow by passively allowing vessel smooth muscle to relax and contract. Interestingly, activated leukocytes have been shown to promote endothelial cell-dependent vasospasticity and reduce arterial relaxation in vitro and in vivo. Further, endothelial cell-dependent vasospasticity is heightened in the presence of protein aggregates in the blood, which would effectively reduce the dynamic range of vasodilation. This is particularly interesting considering previous findings that peripheral inflammation leads to increased CEC presentation of the adhesion molecule P-selectin, which in turn promotes leukocyte and platelet adhesion to CECs. Taken together, these findings suggest that increased leukocyte-CEC interactions associated with peripheral inflammation may significantly contribute to altered cerebrovascular dynamics and potential neurovascular uncoupling in the setting of peripheral inflammatory disease, which is manifest as altered cerebral oxygenation.

Considered in the context of neuroinflammation associated with chronic peripheral inflammation, alterations in cortical perfusion and oxygenation may contribute, at least in part, to the behavioral symptoms associated with IBD and disease-associated reductions in health related quality of life (QoL).

The IBD clinic is routinely testing new treatments for IBD. They have agreed to integrate NIRS into a pilot protocol to determine if there is sufficient evidence to warrant a longer trial of NIRS as a biomarker of neurological involvement in IBD.

The investigators propose the following series of experiments, using NIRS, to determine (A) whether patients with IBD exhibit reduced cortical oxygen saturation and altered patterns of microvascular cerebral blood perfusion; (B) whether NIRS findings of oxygen saturation and perfusion correlate with clinical disease activity markers, a disease-specific gut microbiome signature, and/or symptom and quality of life scores in patients with IBD; (C) the impact of anti-TNF therapy (administered as clinically indicated, as standard of practice) on NIRS changes, the fecal microbiome, markers of systemic inflammation, and symptom severity.

Inclusion Criteria:

Eligible patients will be:

• > 18 years of age with moderate-to-severe UC or (partial Mayo score [excluding endoscopy] ≥5 with rectal bleeding subscore ≥1; or total Mayo subscore 6-12 with RBS ≥1) or CD (Harvey-Bradshaw index [HBI] of 7 or greater, and active CD confirmed on POC bowel ultrasound (defined by bowel wall thickness >3mm and positive Color doppler signal and a fecal calprotectin > 50 μg/g ).
• based on their active disease status patients cannot be taking > 20 mg prednisone daily and
• must be eligible for anti-TNF therapy as per standard of care (clinical decision made by IBD specialist caring for the patient).

Exclusion Criteria:

• patients with severely active UC (clinical signs of fulminant colitis or toxic megacolon) or CD (HBI > 16), requiring > 20 mg of prednisone daily at induction, suicidal ideation or psychosis.

Participants will have either Ulcerative Colitis or Crohn's Disease