Periodic Reporting for period 1 - GlycoMap (Integrated Glycomics for Cancer Precision Medicine)
Reporting period: 2023-09-01 to 2025-10-31
Tissue heterogeneity is fundamental for the development of multicellular organisms but presents considerable complexity for our understanding of biology and disease mechanisms, including cancer. One of the largest sources of tissue heterogeneity arises from post-translational glycosylation of proteins (attachment of a glycan structure during protein synthesis). Yet, substantial gaps remain in our knowledge of glycans. Proteoglycans are glycan-protein hybrids with long, linear glycan chains that govern multiple functions in biology. However, the structure and biochemical properties of these glycans provide significant challenges for their isolation and characterisation. Glycomics (the comprehensive study of the glycome) offers the potential to provide the global glycosylation status of a patient or sample and shed new light on disease mechanisms and treatment efficacy to guide precision medicine. The GlycoMap project aims to address the substantial knowledge gap in protein glycosylation data of proteoglycans by developing an integrated glycomics workflow from a single sample that includes proteoglycan analyses compatible with other glycomics. The mission and design of the GlycoMap project was to train the researcher, who has a background in proteoglycan biology and bioinformatics, with expanded skills and expertise in other glycan types (N-/O-glycomics), organoid biology, hi-resolution 3D imaging and advanced bioinformatics, augmenting her future career opportunities, as well as establishing an integrated glycomics workflow to support multiple glycan analyses (multi-glycomics), diagnostics and the development of novel treatments for human health and disease. The developed platform has high potential in the discovery of novel disease diagnostics and evaluation of treatment efficacies towards precision medicine for many diseases including cancer, sepsis, kidney and neurological diseases in addition to increasing our fundamental understanding of tissue development and organoid models.
In this project, the generation of the novel workflow coupled with advances in glycobioinformatics produced a solid foundation for multi-glycomics analyses of biological material enabling inter-relatable analyses from a single sample. Work package 1 addressed the development of integrated oliGAGomics (the study of glycosaminoglycan oligosaccharides) resulting in a of a novel, proteoglycan-enriched multi-glycomic workflow compatible with other glycomics analyses including: solubilization of proteins from organoid material, fractionation and enrichment of proteoglycans, application of enzymes to generate GAG oligosaccharides and their purification. Technology transfer and optimisation of the oliGAGomics was performed as part of method development. Evaluation of the potential use of xylanase to cleave glycosaminoglycans from core proteins was also addressed. Work package 2 focused on glycome identification and characterisation. It explored the expression of glycoenzymes and proteoglycans in organoid material in relation to metadata and the structure of glycans via mass spectrometry and bioinformatics. Work package 3 centered around the development and acquisition of new and advanced research and transferable skills, with the training of the researcher in N- and O-glycomics, 3D imaging, organoid culture and advanced bioinformatics as well as the two-way transfer of knowledge between the host and researcher.
The project results represent pioneering new research and the solid foundation of fundamental tools, techniques and infrastructure for the multi-glycomics field projecting towards a systems glycobiology approach to biological research that is applicable across multiple sectors. Main results beyond state-of-the-art achieved in this project: 1) Establishment of a novel multi-glycomics workflow compatible for proteoglycans and glycoproteins analysing N-glycans, O-glycans and glycosaminoglycans from a single sample, 2) generation of a multi-glycan dataset including proteoglycan and glycosaminoglycan oligosaccharide analysis for organoid material and 3) the development of advanced bioinformatics pathways for glycan analyses. Further research is required to expand the utility and impact of the workflow and pipelines for the evaluation of the impact of glycans in health and disease in specific contexts ie. cancer development and resistance, aging, immunology, host-pathogen interactions etc.