Non-invasive gut mucus analysis to functionally characterize the effects of GEMM and afford new IBD biomarkers.

Inflammatory bowel disease (IBD) affects ca. 300,000 Canadians with an annual burden of $1.3 billion in associated with treatments, medications, and lost productivity. Accurate biomarkers are required to distinguish between IBD from conditions with similar symptoms, to ascertain disease aggressiveness, predict complications or recurrence, and to evaluate the effectiveness of therapeutic interventions. Currently, endoscopic procedures are the clinical “gold standard” in IBD monitoring/diagnosis, but the invasiveness and cost of these tests prevents their routine application. The urgent need for effective, routine, and non-invasive IBD biomarkers is underscored by statistics indicating that one-in-three IBD patients fail to respond to the initially selected treatment with half losing response over time. This Mitacs proposal seeks to develop an untapped source of IBD biomarkers: the complex carbohydrates (called glycans) that make up the thick layer of mucus that protects the human gut, regulating and reflecting both the microbiome and the immune system. Simple monosaccharides can be biochemically sequentially combined in different ways (analogously to Lego blocks) to produce diverse glycans that are linked to an invariant protein backbone. Glycomic analyses has revealed that mucus may be up to 80% glycan by mass and thousands of glycan representing hundreds of unique structures either provide a nutrient source for microbes or keep them at bay, accomplishing activities both in structure-dependent ways. Although dynamic, research has shown that changes in the entire population of mucus-linked glycans may predispose to spontaneous colitis while other specific glycans are well-known hallmarks of inflammation; thus, glycans are linked to the etiology of IBD as well as representing putative markers of disease activity. Promising technology—called Genetically Engineered Microbial Medicines (GEMM)—developed by our Mitacs Life Sciences partner company Melius Microbiomics (MMB), seeks to use novel probiotics to repair the compromised gut barrier in IBD patients. We propose that evaluating the impact of GEMM on the protective gut mucus-glycans represents an ideal opportunity to establish glycans as non-invasive IBD biomarkers using the new high-throughput tools being developed in the Zandberg lab. Importantly, our research has demonstrated that gut mucus can be non-invasively collected from clinical stool samples and productively subjected to glycomic analyses.

This project has three aims:

1. Characterize how the mucus-borne glycans change in animal IBD models in the presence or absence of GEMM and correlate these changes with IBD disease metrics.
2. Develop a high-throughput glycan analyzer using repurposed Sanger Sequencers.
3. Characterize the stool-derived mucus-glycans in a longitudinal set of neonatal samples and correlating changes in the glycan populations with the microbiome and markers of inflammation.

The three aims afford three benefits to partner organization:

1. Tissues and mucus collected as part of previous and also future GEMM trials will be characterized by existing glycan-analysis techniques, generating knowledge required to establish stool-derived mucus-glycans as IBD biomarkers. These molecular details will inform MBB of the effects of their products at the mucosal interface between the microbiome and immune systems. In the long-term, we envision that MBB could use mucus-glycan biomarkers to predict which IBD patients will most optimally respond to GEMM treatment as well as providing direct functional evidence of gut mucosal healing.
2. A major outcome of the proposed research is a mucus-glycan profiling tool that can be used by MMB, ideally onsite.
3. The knowledge generated from the analysis of neonatal samples will enable MBB to develop important new markets for GEMM. Specifically, no routine screening tool or effective prophylactic currently exists for diseases like necrotizing enterocolitis (NEC), the most common and destructive gut disease in preterm infants.

Skills developed by intern(s) during this project include proficiency in several major analytical instruments that are currently in high demand in both academia and industry as well as data analytics skills. MBB expertise in market development, clinical trials, and bioengineering will afford the intern(s) with unique insights in these activities that are not normally possible in academia.