Search Grantees

Abstract or Project Description

Males and females with Inflammatory Bowel Disease (IBD) differ in terms of incidence of disease, symptoms and response to treatments. The underlying reasons are largely unknown. Understanding why these sex differences exist could reveal why many patients develop IBD as they enter young adulthood. Sex hormones such as testosterone surge during adolescence and then circulate at very different levels in males and females. These hormones are powerful signaling molecules that regulate diverse aspects of physiology and may play a role in IBD. Clinical studies hint that testosterone signaling is protective in IBD, but it is largely unclear which cells this hormone signals to in the gut and how this signaling might influence intestinal inflammation. We have discovered that testosterone signals to an important population of nerve cells along the gut-brain axis, called nociceptors, that communicate information about the gut to the brain and regulate local immune responses. Using mice in which we can specifically disable testosterone signaling in nociceptors without altering it in the rest of the body, we will determine how testosterone influences inflammation and tissue repair in colitis. The results will advance the understanding of how sex hormones impact disease activity in IBD, potentially explain sex-dependent outcomes and inform therapeutic strategies.

Abstract or Project Description

Inappropriate and chronic inflammatory responses underly the development of Inflammatory Bowel Diseases (IBD), including both ulcerative colitis and Crohn’s disease. This process is an intertwined, inter-cellular cascade among diverse immune cells and tissue stroma. The interactions between immune and stromal cells not only propagate inflammatory responses but also regulate resolution of inflammation. Yet, we do not understand how immune cells interact with tissue stroma when intestinal inflammation occurs and resolve. We propose to first develop cutting-edge technologies that discover interacting partners of immune cells in vivo in a high-throughput and unbiased manner. We will then apply these new tools to identify the interactomes of immune cells over the course of intestinal inflammation. Funding from the Kenneth Rainin Foundation will support our program to map out the path of immune-stromal interactions from a healthy intestine to an inflamed tissue to recovery and repair. Targeting immune-stromal interactions that cause inflammatory propagation as well as the resolution will establish a new strategy to alleviate inflammation. Our long-term goal is to leverage this knowledge to switch “inflammatory interactions” to “resolving interactions” in order to restore intestinal homeostasis, which will ultimately curtail IBD and its devastating health implications.

Abstract or Project Description

The epithelial cells lining the intestine control responses to gut bacteria, limiting intestinal damage in Crohn’s disease. A critical gene in this pathway is DUOX2, which is up-regulated in response to bacteria, and helps maintain intestinal health. We discovered that Crohn’s disease patients who carry genetic variants in DUOX2 are more likely to progress to fibrotic disease complications requiring surgery. We tested an intestinal gene signature for refractory pediatric Crohn’s disease in a database containing 2000 small molecules, identifying 140 which might be more effective therapies. Our studies will now utilize a novel Human Intestinal Organoid, or “mini-gut” model system for refractory pediatric Crohn’s disease that we have developed informed by genetic factors like DUOX2. We have prepared stem cells from pediatric Crohn’s disease patients who did or did not have DUOX2 genetic variants, and will differentiate them into white blood cells and human intestinal organoids. This novel model system will be used to test ways to modulate pathways linked to fibrosis in patients, by screening the top small molecules which we have identified as potentially beneficial. Our studies will advance precision medicine, by developing a platform to screen new therapies in patient-derived intestinal organoids with clinically important genetic variants.

Abstract or Project Description

Our gut microbiome has a strong influence on a variety of diseases, including Inflammatory Bowel Disease (IBD). Fungi form an integral part the human gut microbiome, and studies in mice showed that fungi may have a substantial influence on inflammation and IBD development, while antibody responses against fungi constitute important clinical IBD diagnostic tools. However, the functional roles of fungi in modulating IBD, and whether they can be harnessed towards new treatments, remain elusive to date. In this study, we plan to uncover the role of fungi in IBD by taking biopsy samples of the gastrointestinal tract from IBD patients. From the biopsies, we plan to grow mini-guts, called organoids, in petri dishes. We have previously shown that it is possible to use these organoids cultured with microbes to study the interactions between bacteria and the gut cells. Thus, using IBD-patient derived gut organoids and specific IBD-relevant fungi, we will be able to identify mechanisms of the interactions between the diseased gut cells and the fungi. Interesting fungal candidates will be further validated in IBD-like mouse models. This combination of different approaches will allow us to better understand the influence of fungi on IBD progression and develop new intervention strategies for treating IBD.

Abstract or Project Description

Monogenic forms of Inflammatory Bowel Disease (IBD) offer valuable insights into key regulators of intestinal inflammation. Building on our previous advancements in characterizing very early onset IBD (VEO-IBD) patients with monogenic CASP8 and RIPK1 deficiencies, we aim to elucidate the key factors and molecular mechanisms of disrupted cell death responses (necroptosis) in these life-threatening conditions.

Our hypothesis proposes that unbiased and simultaneous exploration of thousands of genes by employing discovery-oriented pooled CRISPR screens will illuminate the signaling network governing perturbed inflammatory and cell death responses, shedding light on novel therapeutic targets for RIPK1 and CASP8 deficiencies. In the proposed CRISPR screen, we will assess the enrichment of guide RNAs from genome-wide libraries that are capable of rescuing uncontrolled LPS-induced necroptosis and inflammatory responses in RIPK1- and CASP8-deficient macrophages using next-generation sequencing and bioinformatics analysis. A set of prioritized targets will be characterized in advanced genetically engineered induced pluripotent stem cell-derived human disease models.

Given the potency of monogenic IBD as a powerful model for defining key regulators of intestinal homeostasis, we anticipate uncovering critical insights into the molecular pathomechanisms and druggable targets of inflammation, contributing valuable knowledge for rare and common forms of IBD according to the translational genomics principle bedside-to-bench and back.

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 Inflammatory Bowel Disease (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

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

Intestinal fungi, collectively known as the mycobiota, have emerged as significant contributors to intestinal disease severity. Our prior research demonstrated the efficacy of fecal microbiota transplantation in inducing clinical responses in ulcerative colitis (UC) patients associated with decreased fungal colonization over time. Further investigations in mouse models and UC patients revealed that fungi exacerbate disease severity through the production of a toxin called candidalysin. Utilizing an array of approaches, we determined a wide fungal genetic variation within the gut of UC patients. With this proposal we will explore innovative approaches for fungal targeting in UC employing dietary approaches.

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

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

Despite advances in understanding Inflammatory Bowel Disease (IBD), research has been constrained by the inability to sample the intestinal microenvironment under physiological conditions. Current methods utilize fecal specimens, constraining our comprehension of regional differences within the gut, or use invasive biopsies from colonoscopy-accessible areas, which represent less than 25% of the intestine. Furthermore, these biopsies are usually performed in fasted, sedated patients who have undergone rigorous bowel preparation. Unfortunately, all of these actions significantly change the intestinal microenvironment and limit our knowledge of how the microbiome influences IBD pathology.

Utilizing CapScan, a novel sampling device the size of a common vitamin pill, and our team’s expertise in integrating multi-omics investigations, we aim to fill crucial knowledge gaps, particularly in understanding the intricate interplay between the human microbiome and IBD pathophysiology. This pill technology passively samples the colon and crucially, the largely unexplored small intestine under physiologic conditions.
For the first time, we can directly assess the regional gut microenvironment (including the microbiome, inflammatory proteins, drug metabolites/levels, as well as host and bacterial metabolites) under natural conditions.

Leveraging our expertise in machine learning, we will correlate changes in the intestinal microenvironment with clinical characteristics including medical/dietary exposures. Our approach will address the pressing need for a more comprehensive understanding of IBD pathology, laying the groundwork for improved diagnostic/prognostic biomarkers and personalized treatments.