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.