Single-cell transcriptomic and epigenomic analysis of brain cell vulnerabilities to tauopathies in early AD impacted brain regions

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Project Summary Alzheimer's disease (AD) is an age-related, progressive neurogenerative disease that leads to loss of brain cells and their connections. The existing literature provides a broad view of AD/ADRD-related molecular changes from heterogeneous cell populations. However, cell-specific and brain-region specific AD/ADRD-related loss of cells and connectivity is not yet resolved, particularly at a mechanistic level. In response to RFA-AG-23-028, we have assembled a strong multi-investigator team across multiple institutions with complementary expertise in single-cell transcriptomics and epigenomics analysis, neural circuit mapping, and next-generation AD mouse model development. We will use multiple complementary lines of tau mouse models, in conjunction with APOE genetic modulation or pathogenic triggers in targeted brain regions. 1) We will use the Tau P301S transgenic mice on either a human APOE4 knock-in background (TE4) or a mouse Apoe knock-out background (TEKO). TE4 knock-in markedly exacerbates tau-mediated neurodegeneration, while TEKO mice show largely attenuated neuronal loss and brain atrophy compared to P301S mice. 2) We will additionally use recently developed novel humanized Tau mouse models that replace the endogenous mouse MAPT gene with either a normal or pathogenic variant of the entire human MAPT gene (MAPT gene replacement, MAPT-GR), which express all isoforms of human tau at physiologic levels and ratios. We hypothesize that vulnerable cell types in early AD- impact brain regions (locus coeruleus, entorhinal cortex, and hippocampal CA1 and subiculum) show early maladaptive gene expression profiles and epigenomic signatures that define their molecular vulnerability during AD/ADRD pathogenesis. To test our hypothesis, in Aim 1 we will apply single-cell epigenomics and transcriptomics technologies to early AD-impacted brain regions in age-matched control and AD mice, creating cell-type-resolved multi-omic maps of gene expression and chromatin accessibility. Tauopathy progression unfolds in an age-dependent manner, thus we will compare control and pathological tau model mice at two different ages each for different mouse lines (4 months, 10 months for TE and TEKO; 6 months, 12 months for MAPT-GR lines) based upon their behavioral and neuropathological characterization. In Aim 2, we will use the multiplexed error-robust fluorescence in situ hybridization (MERFISH) technology to generate single-cell resolution spatial transcriptomic maps for the early AD-impacted brain regions. MERFISH will extend single-cell omics and spatial genomics to map neural circuits and pathologies at high spatial resolution. In Aim 3, we will use perform computational analysis to integrate single-cell multi-omics data, image-based anatomical and molecular gene expression maps from Aims 1-2, acquired from different mouse models at different ages, to fully characterize the neuronal circuits and AD-vulnerability at cellular level. The proposed research is well aligned to the RFA goals and is expected to provide new biological insights into AD/ADRD pathogenesis at unprecedented cellular and spatial resolution.