The pathogen hypothesis of Alzheimer's disease (AD) proposes that viruses, bacteria, and other pathogens play a role in the etiology of AD. Most studies that have looked for pathogens in the AD brain have used sequencing, which detects nucleic acids but lacks the ability to pinpoint the location, morphology, and state of pathogens, important for probing how pathogens might couple to specific AD hallmark molecular pathologies (e.g., amyloid, hyperphosphorylated tau, and other hallmarks). Ideally one would be able to perform nanoscale resolution, molecularly multiplexed, mapping of pathogens with respect to AD hallmark molecular pathologies. We recently invented a new tool, expansion microscopy (ExM), which physically magnifies specimens so that molecular information can be imaged in a molecularly multiplexed fashion, with nanoscale precision, throughout intact tissues, on ordinary high-speed light microscopes. ExM is increasingly popular, with over 350 groups having undergone hands-on training on the procedure from us, and over 100 papers having performed ExM. Accordingly, we will in this study use ExM to systematically study the location, morphology, and state of the AD microbiome, thus yielding maps that can reveal how aspects of the AD microbiome relate to molecular pathologies associated with AD. We have assembled a complementary team of a half-dozen expert AD groups and technology-oriented groups, so that we can systematically probe this question from multiple angles. Specifically we will derive (Aim 1) a subcellular-resolution map of the AD microbiome in human brain specimens. We will then perform a (Aim 2) comparison of AD microbiomes to the temporal progression of AD molecular pathologies. Finally, we will examine the (Aim 3) spatial transcriptomics of microglia in relation to pathogens. Our hope is to reveal the fundamental organization of the AD microbiome and multiple AD hallmark molecular pathologies, so that it is possible to systematically generate specific hypotheses about mechanisms of, and targets for treating, AD.
Our research will advance human health by pinpointing, using a novel ultraprecise imaging technique, pathogens that may play a role in Alzheimer's disease. We will discover the spatial relationships between these pathogens and different molecular problems associated with Alzheimer's. These relationships will help reveal new mechanisms of, and treatment targets for, Alzheimer's disease.