ABSTRACT Effective therapies for Alzheimer’s disease (AD) are urgently needed. The existing approaches have largely failed to improve symptoms or modify disease progression, in part because of our incomplete understanding of the disease pathogenesis. Previous neuropathology and neuroimaging studies have been instrumental in establishing the histopathological hallmarks of AD and the involvement of specific brain regions. However, the selective vulnerability of distinct neuronal and non-neuronal cell types to AD and the underlying molecular mechanisms remain largely unknown. We hypothesize that subpopulations of neuronal and non-neuronal cell types contribute distinctively to AD and propose the use of single-cell transcriptomics in human brain to identify these cell types and the underlying molecular mechanisms leading to AD pathology. Although applying this innovative technology to human brain is challenging, human AD brain is crucial for understanding the contributions of distinct cell types to disease, identifying the earliest pathogenic events, uncovering neuroprotective pathways, and defining the spread of pathology. We will study early- and late-affected cerebral cortical regions, including entorhinal, association, and primary sensory cortices, from subjects encompassing the full spectrum of disease progression (Braak stages I–VI) and age-matched healthy controls. This strategy will provide a comprehensive landscape of the vulnerable and resilient cell types, their transcriptome changes, and the spread of changes over time and across cortical regions. In Aim 1 we will use single-nucleus RNA- sequencing for the unbiased identification and transcriptome profiling of neurons, glia (microglia, astrocytes, and oligodendrocytes), and blood vessel cells. In Aim 2 we will test the hypothesis that distinct molecularly defined subpopulations of cortico-cortical and cortico-thalamic projection neurons are selectively vulnerable to degeneration. In Aim 3 we will examine the molecular changes associated with tau pathology using our newly developed assay for purifying and profiling single neurons bearing neurofibrillary tangles. These studies will generate the first single-cell transcriptome profiling of human neurons with tangles and provide insight into the tau-mediated mechanisms of neurodegeneration. Together, our studies will provide an unbiased and robust identification of the vulnerable and resilient cell types in AD and insight into the molecular mechanisms underlying the selective vulnerabilities. These data will provide a valuable resource to the scientific community for improved cell-type-based disease modeling and drug discovery.