GlycoWeb

Glycosaminoglycans (GAGs) are linear sugars that decorate most cells in the body and are ubiquitous components of the extracellular matrix. Many of their functions are mediated via the interaction of protein ligands with structural motifs encoded within the sugar chains. These motifs (often comprising families of related structures) are the result of coordinated enzymatic activity and can be highly specific for particular proteins. However, we still lack knowledge of how the GAG biosynthetic machinery is regulated and controlled at the cellular level, and therefore cannot universally link the regulation of biosynthesis with resulting GAG structure. Moreover, without defining the rules governing the relationship between GAG structure and GAG function (e.g. protein binding) and defining how this influences cell behaviour, for example during development and disease, we are missing crucial knowledge on a major class of biomolecules which are critical for understanding the fundamental rules of life.

We will address this major knowledge gap with GlycoWeb, named to reflect the project's interconnectivity, combining complementary approaches to validate results. We will use early embryonic development, modelled without animals using gastruloids (3D aggregates of embryonic stem cells that recreate many aspects of early mammalian development) as an exemplar system. GAGs are known to play a critical role in these processes, and changes in GAG structure are linked to discrete functions such as the response to specific growth factors.

Our first major goal (objective 1) will be to correlate transcriptomic, proteomic and GAG structural analyses at specific developmental stages and detect how these link to the altering structure and function of GAGs as development progresses. By integrating datasets, we will build predictions of how GAG structure is regulated at the transcriptional and protein level and then return to the 3D gastruloid system to test and refine our hypotheses. As part of the structural characterisation, our second goal (objective 2) is to create a new library of GAG-binding 'probes' for sensitive spatiotemporal localisation of GAGs in the gastruloid model (and more widely, e.g. in human tissue). These novel probes can be combined with similar technologies for RNA, proteins and other glycans providing a much-needed additional layer of knowledge. The GlycoWeb team will therefore build the first network of mechanistic rules connecting the regulation of GAG synthesis at the transcriptional and protein level with their structure and function (objective 3).

We have assembled an experienced, innovative, multidisciplinary team supported by strong research culture. Expertise in the gastruloids is provided by two groups instrumental in creating the technology. We will combine well established and complementary new methods for the structural analysis of GAGs as well as proteins and phosphoproteins, with contributing groups expert in all these areas. The new, well characterised, GAG-binding probes will also be made freely available to the wider research community. We have also recruited additional support from two leading global centres in glycobiology, specifically for their expertise with transcriptional regulation of glycan biosynthesis and mapping these complex processes, using bioinformatics, to build predictive models. A commercial partner, InterReality Labs will work with us to enhance how we interact with those models, including when working remotely.

By removing current barriers preventing the understanding and application of GAGs by the wider scientific community, GlycoWeb will enhance knowledge and provides new opportunities for commercial and societal benefit. Our approach will transform control of GAG structure and function into an accessible web of predictable processes that can be understood and exploited by researchers across biological sciences, extending to biomaterials and pharmaceutical production.

Glycosaminoglycans (GAGs) are polysaccharides present on the surface of most cells and in the extracellular matrix (ECM) of all tissues that influence how cells interact with their pericellular environment. GAG activities are mediated via the binding of protein ligands (growth factors, cytokines, matrix components etc.) to motifs encoded within the GAG chains. The chains are constructed through the action of multiple enzymes which themselves are under transcriptional, metabolic, and epigenetic control. Currently, we lack a thorough understanding of how the functional activity of a GAG links to its structure and, critically, how GAG structure is controlled by cells. This prevents the harnessing of GAGs for multiple bioscience applications: it is currently impossible to predict changes in GAG motifs/activity from transcriptomic datasets, or to select which enzymes should be combined to synthesise a GAG with a specific function. We have assembled an interdisciplinary team with complementary approaches, including the use of 3D in vitro models of development (gastruloids) to provide material for coordinated analyses, creating an interconnected web of information that we will then use to generate and test hypotheses. Transcriptomic and proteomic analyses linked to detailed structural and spatial analysis of GAGs will allow us to build and then refine models of how the biosynthetic machinery creates particular GAG structures, allowing us to generate and apply a novel toolbox of GAG-binding probes. Coordinating this information with defined developmental stages and responses to known GAG-dependent ligands (e.g., BMP, FGF family members etc.) will directly link structure to function. To test emergent hypotheses, we will use gene editing to target key regulatory hotspots in the 3D gastruloid models, allowing the refinement of our understanding of the critical factors controlling GAG structure and function and how this maps onto molecular and biological function.