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Abstract or Project Description

Abstract or Project Description

It is now well recognized that IBD develops as a result of complex gene-environment interactions. Since there is no cure for IBD, treatment has focused on alleviating the symptoms. A better understanding of the fundamental mechanisms that drive the development and progression of IBD would allow for the design of more specific and effective treatments. Bacteria that naturally live in our intestine (called the microbiota) have been definitively linked to intestinal inflammation, but how this relationship is regulated is not well understood. Epigenetics refers to modifications that allow genes to be turned on or off and we have found unique epigenetic changes that occur in the intestine in response to signals from the microbiota. Further, we have identified similar epigenetic differences in intestinal cells of pediatric IBD patients. Based on these findings, studies in this proposal will use samples from pediatric IBD patients and mouse models to define how these newly-identified epigenetic changes are regulated by intestinal bacteria. We will also determine whether these targets enable us to predict patient prognosis and employ animal models and human intestine grown in culture to decipher their function. We anticipate that these studies will direct new approaches for preventing and treating IBD.

Abstract or Project Description

NOD2 was the first and to do date the most frequent gene associated with inflammatory bowel disease. The NOD2 protein functions as a sensor of bacteria by binding molecules (peptidoglycans) shed from the bacterial cell wall. The IBD mutations in NOD2 result in its inactivation or partial loss of function. In 2019 we reported that NOD2 requires the attachment of 2 fatty acids to be functional. This modification termed palmitoylation is mediated by the protein zDHHC5 and is missing from many of the mutant forms of NOD2 associated with Crohn’s disease. Palmitoylation is a reversible modification and while zDHHC5 is the “writer” that adds the modification, the “eraser” that removes it has not been identified. We believe that by blocking the eraser that we can restore function to at least some of the NOD2 mutants. Our unpublished work has identified the relevant acyl thioesterase which removes palmitate and inactivates NOD2. Through the use of chemical inhibitors we are able to rescue the function of several NOD2 mutant proteins. This proposal represents the next logical steps in our goal to characterize the relevant acyl thioesterase and to determine if any FDA approved drugs can restore function to NOD2 by inhibiting this eraser.

Abstract or Project Description

The intestine exerts the vital function of maximizing nutrient uptake from the diet we ingest, being constantly exposed to external stimulation by food components. Alterations in the timing of food intake and diet composition have been associated with the development of immune-related intestinal dysfunctions, including IBS. However, despite its profound biological and clinical relevance, there is a major gap in our understanding of how intestinal immune health is affected by diet. Recently, we uncovered that gut neurons are activated by the diet, and they can control intestinal immune responses. The long-term goal of this proposal is to determine how the diet is sensed by these neurons that have immune regulatory properties. Our studies are expected to uncover dietary and neuronal therapeutic targets to gut disturbances associated with a dysregulation in local immune responses, including IBS.

Abstract or Project Description

Colonization of the infant gut by commensal bacteria profoundly influences immune development and can thus have significant long-term consequences: promoting durable tolerance to environmental antigens or driving IBD. Despite the importance of this process for health, how immune responses to the microbiota are regulated during early life remain a significant gap in our knowledge. We discovered that antibodies targeting gut bacteria are transmitted from mother to offspring via breastfeeding where they restrain neonatal immune responses to beneficial gut bacteria. Antibodies are specialized immune proteins that bind to foreign particles, including harmful and helpful microbes. Healthy humans and mice produce distinct flavors, or ‘isotypes’, of antibodies that serve different functions in immunity. We revealed that the maternal antibody isotype required to restrain neonatal inflammatory responses is IgG, an isotype that has only recently been identified to participate in gut health. Human breastmilk also contains IgG, and a key role for maternal antibodies in dampening gut inflammatory responses has been described in breastfed humans. Here, we will combine new mouse models with cutting-edge approaches to define the mechanisms by which breastmilk antibodies instruct the neonate to avoid harmful responses to beneficial gut bacteria. This work will advance our ability to manipulate immune responses to gut bacteria and thus aid in the development of therapies to effectively curb the development or severity of IBD.

Abstract or Project Description

Besides the brain, the gastrointestinal tract has the highest number of neurons in the entire body. The enteric nervous system (ENS) is often referred to as the second brain as it commands all manner of intestinal function, from nutrient absorption to defecation control. In patients suffering from IBD, the ENS undergoes major disruption resulting in many debilitating complications impacting the quality of life. We have recently uncovered that the ENS also controls intestinal inflammation and regulates the balance of “good” vs. “bad” bacteria in the gut. As the ENS has the unique capacity to rapidly relay signals from the gut directly to the brain and, by extension, to all other organs, we hypothesized that ENS might act as front-line sensors of gut inflammation to warn the body of impending infections. Our preliminary data indicate that when intestinal neurons are activated, they can trigger inflammation in other organs to protect against bacterial invasion. This novel protective mechanism has never been reported before and in this project, we aim to elucidate this unknown pathway of inflammation. Going forward, we will further explore if this axis is aberrantly activated during chronic intestinal inflammation and if it directly contributes to non-intestinal inflammatory complications exhibited in patients with IBD to aid in novel therapeutic design.

Abstract or Project Description

Pain is a major component of inflammatory bowel diseases, increasing the suffering of patients and decreasing their quality of life. However, the underlying cellular basis for pain in IBD and the role of pain-mediating neurons in driving gut dysfunction are not well known. Our goal is to characterize the role of neurons that mediate pain in IBD, and to determine whether inhibiting or activating these neurons leads to changes in the gut that can treat pain and inflammation.

Abstract or Project Description

Ulcerative colitis (UC) is characterized by non-resolving pathological inflammation leading to erosion of the colon tissue. Recent studies analyzing gene expression signatures in UC patients highlighted specific colonic fibroblast populations that may contribute to inflammation and disease progression. While these studies emphasize the proinflammatory function of activated intestinal fibroblasts, it is unknown whether subsets of intestinal fibroblasts may fulfill protective regulatory functions required to limit intestinal inflammation. Our studies leverage a novel spatial transcriptomics method (MERFISH) to generate a detailed cellular and molecular atlas of the colon, with an emphasis on elucidating the function of fibroblasts in mouse and human colitis. We discovered a new population of regulatory fibroblasts (Fregs) that differentiate during colitis and suppress intestinal inflammation. In particular, we found that Fregs appear in non-inflammatory regions and promote the differentiation of regulatory B cells (Bregs) and tolerogenic dendritic cells (tolDCs). The goal of this project is to define the molecular framework governing Freg, Breg and tolDC interactions during colitis, and establish the nature of these interactions in human UC. These studies will demonstrate how Fregs orchestrate immune tolerance to colitis and whether failure of this mechanism may contribute to tolerance breakdown in UC.

Abstract or Project Description

Accumulating data supports the concept that IBD has a preclinical period that may be amenable to early diagnosis and intervention. Understanding the molecular underpinnings of this preclinical period in disease pathogenesis offers new opportunities in risk prediction and prevention. We have recently reported the first data from a large study using longitudinal pre-diagnostic samples from the US Department of Defense Serum repository, the PREDICTS study, where we assessed the predictive value of a panel of antimicrobial markers and a proteomic panel (>1100 proteins). Additional –omics data including glycan profiles, metabolome and exposome are currently generated on these same samples that span from up to 5 years before diagnosis to first clinical symptoms and confirmed diagnosis. We will integrate these massive multi-omics datasets to develop machine-learning (ML) based models predictive of future progression of CD and UC years before diagnosis, and to discover driver biomarkers and biological processes responsible for disease initiation. This will be achieved by constructing time-varying disease-specific networks capturing the associations across all biomarkers measured at different years before diagnosis available through the PREDICTS initiative. We will make all results publicly available via a user-friendly web-platform to facilitate the easy query, exploration and utilization of these data.

Abstract or Project Description

Up to 15% of patients with ulcerative colitis (UC) will require surgery, the most common of which is the total proctocolectomy (TPC) with ileal pouch-anal anastomosis (IPAA). Since 1980, the ‘J’ pouch has revolutionized the lives of thousands of patients, providing restoration of intestinal continuity and avoidance of a permanent end ileostomy. Unfortunately, pouchitis is common after surgery with cumulative incidence rates of 50% at two years. Patients with pouchitis experience increased bowel movement frequency, urgency, pelvic pain, rectal bleeding and/or incontinence – symptoms that are reminiscent of their disease before surgery. Antibiotics are the mainstay of acute pouchitis treatment, however approximately 20% of patients develop chronic pouchitis and require long-term antibiotic therapy or immunosuppressive therapy. The risk of surgical pouch removal and transition to a permanent end ileostomy is 5-10% in patients with chronic pouchitis. Fecal microbiota transplantation (FMT) has been successfully used in the treatment of recurrent Clostridiodes difficile infection and has shown benefit in the treatment of UC in clinical trials. The success of FMT in these patients is because of the reconstitution of the recipient’s unhealthy microbiome with the donor’s healthy microbiome. A number of studies have evaluated FMT in patients with chronic pouchitis, but have proven unsuccessful. This is likely because these studies have used stool from patients with a colon and transplanted it into patients with a pouch. This is problematic because the microbiome of the colon and pouch are not similar, and putting healthy stool from a colon may not reconstitute a healthy pouch microbiome. The specific purpose of this project is to transplant stool from patients with a healthy pouch to patients with an inflamed pouch. We hypothesize that the stool from patients with a healthy pouch is well suited to reconstitute the microbiome of patients with an inflamed pouch.

Abstract or Project Description

Patients with inflammatory bowel disease (IBD) have dysfunctions in gut motility (the movement of muscles in the gastrointestinal tract). Currently, most available therapeutics developed to directly target the gut fail to stabilize symptoms, suggesting that dysfunctions in gut motility could arise from pathological changes occurring outside the gut. Intriguingly, gut motility problems also occur at high frequencies in patients with neurological disorders, including neurodegenerative, neurodevelopmental and neuropsychiatric diseases, associated with dysregulated neural activity in a specific region of the brain—the cerebral cortex. We propose that dysregulated neural activity in the cortex contributes to the emergence of gut dysfunction. We will test this hypothesis by first identifying specific regions in the cortex that are anatomically connected to the gut and then determining if modulating neural activity within these regions alters gut function. Additionally, we will use established mouse models of various neurological disorders and IBD to ask whether restoring homeostatic levels of neural activity to the cortex improves gut phenotypes. Our study will provide anatomical and functional evidence to support the concept that cortical modulations regulate gut motility. Furthermore, the insight gained from the study can lead to novel therapeutics for ameliorating gut motility symptoms in IBD patients.

Abstract or Project Description

Despite medical advances, a significant proportion of inflammatory bowel disease (IBD) patients are resistant to therapies, with CD4 T cells being consistently activated. Analysis of inflamed tissues from a cohort of refractory IBD patients reveals an enrichment of metabolism gene transcripts in CD4 T cells. Exploring the mechanisms, our preliminary data demonstrate that several proinflammatory cytokines can independently trigger metabolic phenotypes which we believe reinvigorates the pathogenic function of CD4 T cells. This led us to formulate the hypothesis that IBD CD4 T cells, governed by metabolic cues, utilize common intracellular metabolites to drive inflammatory response that results in disease pathogenesis. Thus, our research goal is to identify the metabolic vulnerabilities of IBD CD4 T cells, which will consequently guide strategies for developing efficacious therapies.

Abstract or Project Description

In IBD, the microbes within the intestinal tract, collectively known as the microbiota, are targeted by inappropriate immune responses. There are also a number of changes in the microbiota composition that are thought to drive or amplify IBD pathology. One of these is the expansion of E. coli. However, our preliminary data has identified select E. coli isolates that limit intestinal pathology in mouse models of colitis by activating intestinal macrophages that either limit inflammation or promote barrier repair, two therapeutic endpoints for IBD. These results indicate that while some E. coli may amplify disease, others may protect against it. Understanding these differences will allow us to develop novel therapeutics.

Abstract or Project Description

Patients with inflammatory bowel diseases (IBD) require timely and efficacious therapeutic intervention. When conventional medications such as corticosteroids or 5-aminosalicylates fail to alleviate the disease, biologics that block a critical inflammatory molecule called tumor-necrosis-factor alpha (TNF_) are commonly used. Several drugs targeting TNF_ are currently used to treat IBD, which include Infliximab, Adalimumab, Etanercept, and Certolizumab Pegol. Unfortunately, one third of treated patients still fail to respond to these drugs. We and others have established in the past a role of immune cells called Neutrophils in IBD pathology. Neutrophils are professional phagocytes with primary role in bacterial killing and host defense; however, they also shape the inflammatory environment in the colon and are responsible for IBD disease severity. More recent studies have correlated Neutrophil presence and activity in the colon with reduced therapeutic response. Importantly, we and others have identified diverse neutrophil subsets in inflamed tissue with both protective and detrimental functions. Thus, the goal of this study is to use state of the art molecular and genetic tools to establish whether distinct Neutrophil subsets drive unresponsiveness to TNF_ biologics and define specific gene signatures that can help predict clinical response and aid in designing of future therapeutics to maintain durable clinical response in severe IBD.

Abstract or Project Description

Inflammatory Bowel Diseases (IBDs) are typified by bouts of inflammation-induced epithelial damage and repair. By take cues from their microenvironment or “niche”, intestinal stem cells (ISCs) direct these fluctuating pathological and reparative states in IBD. Yet, we do not understand which cells comprise the inflamed ISC niche and how they switch on programs of repair. To track evolving ISC niches, we are proposing the development of a new cutting-edge Niche-labeling system. Our ultimate goal is to understand how ISC niches change over the course of disease and leverage this information to reprogram an “inflammatory ISC niche” into a “regenerative ISC niche” and achieve lasting remission in IBD.

Abstract or Project Description

How do immune responses of the intestinal lining contribute to inflammatory bowel diseases (IBD)? The goals of this project are to determine how cells of the intestinal epithelium are “hardwired” to respond to immune stimuli and how stable changes to these responses are related to IBD. It is known that multiple inflammatory factors produced by the immune system are present in the intestinal tissue during IBD flares, and neutralization the inflammatory molecule TNF is among the most successful current treatment strategies. However, TNF neutralization is frequently insufficient to ameliorate disease. Studies from our lab and others have established that other immune signals called interferons can cooperate with TNF to promote epithelial cell damage. Additionally, there is evidence that interferon response may be amplified in diseased epithelial cells. We will use cutting edge genomic approaches and organoid cultures to determine how the inflammatory “wiring” of response genes in epithelial stem cells of IBD patients differ from healthy controls. Additionally, we will compare the amount of damage in response to inflammatory signals and determine the efficacy of novel inhibitors in preventing toxicity. These studies have the potential to reveal new targets that complement existing TNF therapeutics.

Abstract or Project Description

Recently there has been increased evidence that patients with Crohn’s disease (CD) commonly have disrupted sleep, and disrupted sleep correlates with the risk of disease flare. The sleep/wake cycle, immune function, and multiple biological processes are orchestrated by the circadian clock. The central circadian clock in the brain entrains these processes to the environment by light exposure, and CD subjects have evidence of misaligned circadian rhythms that correlate with subclinical inflammation. The long-term goal of this research proposal is to show that bright light therapy in CD improves barrier integrity, reduces markers of subclinical inflammation, and modifies the microbial structure/function to an anti-inflammatory state. To test this hypothesis, we will conduct a randomized crossover trial of morning bright light therapy (60 min) given by a wearable device (Re-timer™). We will do three assessments in inactive CD subjects at: 1) baseline; 2) after four weeks of wearable glasses with bright light therapy; and 3) after four weeks of wearable glasses without bright light therapy. The results of this innovative proposal will improve quality of life in CD subjects, reduce the risk of disease flare, and identify novel circadian regulated targets for the treatment of CD.

Abstract or Project Description

Patients with inflammatory bowel diseases (IBD) can experience many years of inflammation and remission in the gastrointestinal tract. As a result, the intestines can undergo a structural change known as fibrosis, which narrows the inside. This narrowing is a major, and sometimes life-threatening, health issue for patients because it can block the passage of digested food and stool. Unfortunately, the only treatment for this condition consists of invasive surgical procedures to either widen the opening or remove the affected areas of the intestine. Therefore, there is an urgent need to develop less invasive therapies such as drug-based treatments. Preliminary studies carried out in our laboratory have pointed to a potential role for the molecule serine, an amino acid, in the development of intestinal fibrosis. For example, we have found that serine is produced in areas of fibrosis in the intestines of IBD patients and in our mouse model of intestinal fibrosis, suggesting that it may play a role in the development of this condition. The work proposed in this application will determine if in fact serine is largely responsible for intestinal fibrosis and establish methods to limit its production and thus prevent fibrosis development. Carrying out the proposed work can lead to the development of novel treatments for intestinal fibrosis and significantly improve the lives of patients with IBD.

Abstract or Project Description

The microbes that flourish within our guts are central to many aspects of human health. Which microbes are present can dictate susceptibility to a number of acute and chronic diseases, including IBD. This proposal will use a mouse model with a defined and stable set of bacteria to probe how mice interact with specific members of their microbiota in health and during disease. First, each microbe will be tested for its ability to elicit an immune response in healthy mice. Once we have established the baseline response in normal healthy mice, we will use chemicals to disrupt the gut lining to elicit an inflammatory response, or we will disrupt genes known to limit intestinal inflammation. We will then investigate how immune recognition of the microbiota changes under these altered conditions. This system will enable us to track responses to the microbiota with unprecedented precision and will provide clues regarding which microbes drive immune activation during dysregulated responses to the microbiota. Such studies will pave the way for future work aimed at manipulating responses to key members of the microbiota responsible for inflammatory diseases of the gut.

Abstract or Project Description

Diet is thought to be a major environmental factor contributing to inflammatory bowel disease (IBD) and represents a non-invasive path to improve this debilitating condition. To leverage diet to treat IBD the precise ways that dietary components influence development or healing of inflammation need to be determined. We discovered that different dietary protein sources have variable effects on intestinal inflammation and these effects are dependent on the community of microorganisms (microbiome) that inhabit the human colon. In particular, we discovered that soy protein promotes production of a beneficial metabolite called isobutyrate that reduces inflammation in a mouse model of IBD that we developed to mimic low fiber diet- and microbiome-driven inflammation. Isobutyrate is only produced by some bacteria and is derived from the dietary amino acid L-valine via at least two different metabolic pathways. Because soy protein specifically promotes isobutyrate, our model is that it is better at delivering L-valine-containing peptides to the colon after digestion, leading to bacterial isobutyrate production. The proposed experiments will uncover the specific component(s) of soy protein that promotes isobutyrate as well as the bacteria that produce this metabolite so that dietary protein can be optimized in the context of patients’ microbiomes to reduce inflammation.