Development of a sample preparation protocol for 3D kidney ultrastructural analysis and immunolabeling by light microscopy

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Abstract The success of cohort studies such as the NIDDK Kidney Precision Medicine Project (KPMP) with its massive amount of samples depends on the cost and time-efficient evaluation of kidney biopsies at multiple scales. Assessing the structure of kidney tissue at the nanoscale (~10 nm) and evaluating the 3-D distribution of protein biomarkers in that context is, however, currently severely limited as it depends on expensive, time-consuming and extremely complex correlative light and electron microscopy (CLEM) as the only suitable tool. Panluminate has developed a proprietary new tissue expansion technology we call pan-Expansion Microscopy (pan-ExM), that directly addresses this challenge. By combining ~25-fold linear expansion of biological samples with novel bulk (pan) staining of amino acids, pan-ExM is capable of mapping the 3-D nanoscale distribution of specific biomarkers in the context of kidney ultrastructure. Hallmark ultrastructural features such as podocyte foot processes and cristae in mitochondria can now be resolved by their characteristic pan-staining pattern, analogous to heavy-metal stains in electron microscopy (EM). In contrast to EM/CLEM, however, pan-ExM is an all-optical method that allows researchers to interrogate tissue samples using standard confocal microscopes; this offers important advantages in terms of time, cost, complexity and sample preservation versus EM alternatives. Our proposed Phase I project is to develop and validate pan-ExM for kidney samples. Specifically we will: (1) optimize and validate a new antibody-labeling pan-ExM protocol in freshly fixed kidney tissue; and (2) develop and validate a novel ~25x tissue expansion protocol for archived FFPE kidney biopsies. This work is designed to lay the foundation for a Phase II project that will establish pan-ExM as a robust and powerful imaging technology in the kidney field by enabling every researcher in nephrology to locate multiple specific protein biomarkers within their 3D contextual compartments at the ~10 nm scale. Our long-term ambition is for pan-ExM to become a core imaging technology for kidney tissue atlases as well as a preferred technique for targeted research and diagnostic applications, thereby paving the road to precision medicine for nephrology.