Regulatory Landscape of Neurodegeneration by Single-Cell Spatial Multiomics - SUMMARY Alzheimer’s disease (AD), the most common form of dementia, is a looming crisis that imposes huge healthcare, economic and social burden in the US. AD progression is associated with neurodegeneration while the pathogenetic mechanisms underlying neuronal death and dysfunction remain unclear. This neurodegenerative process involves complex interactions of AD hallmarks β-amyloid (Aβ) and tau with the localized inflammation contributed by glial cells. But little is known about how the cells near AD hallmarks regulate themselves and respond to the microenvironment. Recently, chromatin accessibility has been recognized as a dynamic central regulator of transcription since chromatin remodeling enables access of cis-regulatory elements, while closed chromatin regions impair the accessibility of promoters and enhances. AD-associated chromatin signatures show brain region and cell-type specificity, implicating noncoding regulatory regions within AD genetic risk loci that participate in a variety of biological pathways as well as changes in TF regulation. Another layer of cell regulation is through signaling transduction and activation of transcription factors at the protein level. The outcomes of epigenetic regulation should be better described by protein measurements since proteins predominantly represent cell identity, drug target, clinical biomarkers, signaling networks, transcriptional factors, functional readouts of proliferation, cell cycle status, metabolism regulation and apoptosis makers. However, these two layers of regulatory machinery have not been integrated before for spatially distributed heterogeneous tissue cells. The current single-cell omics tools often lack spatial information, and the spatial omics tools frequently lack single-cell resolution. Integration of single-cell spatial proteomics is particularly difficult as most state of the art can only detect a few proteins. Based on our multiplex in situ tagging (MIST) microchip technique, we have successfully measured hundreds of critical proteins in cell identification, signaling transduction and transcription from single brain cells. This technique is also compatible with chromatin accessibility assays. With that, we propose to (1) Sequentially measure functional proteome and epigenome by MIST-seq with high accuracy and spatial resolution; (2) Determine molecular signatures and regulation of cells near amyloid plaques in the early AD stages. Through the unique single-cell spatial omics technology, we will not only uncover the regulatory landscape of damaged neurons in AD onset and progression, but also reveal the contribution of the inflammatory microenvironment near Aβ plaques. The success of this project will advance our understanding of neuronal loss in the early stages of AD, assist identification of drug targets and biomarkers, and uncover the complex relationship between inflammation and neurodegeneration.
