Integrating Spatial Omics to Map the Biomolecular Fingerprint of Osteoarthritis Onset in the Mouse Knee

Osteoarthritis (OA) is a highly prevalent degenerative joint disease that causes pain and disability, resulting in a tremendous socioeconomic burden. Developing disease modifying treatments and early detection tools is a pressing need that remains unmet due to the challenging nature of working with joint tissues and the limited spatial context of previous molecular profiling technologies. This thesis addresses these challenges by adapting and integrating cutting-edge spatial molecular profiling omics technologies (MALDI-IMS and DSP) to study the molecular landscape of the healthy and osteoarthritic mouse knee. Chapter III outlines the development of a MALDI-IMS spatial omics analytical pipeline suitable for both paraffin-embedded and cryopreserved joint tissues. Presented are an array of technical considerations and adaptations carried out to optimise the data acquisition and analysis. In Chapter IV, the developed pipeline is applied to healthy and hypomineralised joint tissues in order to demonstrate its ability to detect biomarkers and track disease state. The healthy lipid signatures of marrow, cortical bone, articular cartilage, and the growth plate are established. A lipid atlas of over 120 lipids enriched in these tissues is generated. Abnormal PHOSPHO1-knockout growth plate tissues, characterised by reduced mineral deposition, are compared to healthy controls, uncovering over 600 lipid ions with differential growth plate zone-specific abundance. The presented results provide insights into the role of PHOSPHO1 in lipid homeostasis and the role of lipid biochemistry in the mineralisation process. In Chapter V, MALDI-IMS and DSP proteomics are integrated to uncover spatially-resolved biomarkers of OA onset and progression. A map of early OA molecular anatomy is presented, outlining significant alterations in apoptosis, autophagy, MAPK signalling, PI3K/AKT signalling, and immune cell signalling. For example, dysregulated autophagy and downregulation of MEK1 were early OA hallmarks in the articular cartilage. This resource requires further validation, but could aid the development of targeted tissue-specific disease-modifying therapeutics.