Uncovering single‐nucleus RNA velocity variations in neuropathologic Alzheimer’s disease

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AbstractBackgroundDifferential single‐nucleus (snRNA‐seq) gene expression analyses in Alzheimer’s disease (AD) provide fixed snapshots of cellular alterations, failing to detect the temporal dynamics of genes at individual cells. To overcome this limitation, here we analyze single‐nucleus RNA velocities (RNA‐vel) from the prefrontal cortex to characterize dynamic genetic and cellular differences in neuropathological AD progression. RNA‐vel is the rate of change of gene expression obtained by comparing intronic and exonic sequence counts. Comparison of AD pathology associated gene expression with parallel RNA‐vel differences reveals sets of genes and molecular pathways that underlie the static and putative dynamic regimes of cell type‐specific dysregulations underlying the disease.MethodWe used snRNA‐seq data from the prefrontal cortex of 48 subjects1 with varied levels of AD pathology from ROSMAP2. We then calculated both the expression and RNA‐vel differences between low AD‐pathology and mild‐to‐severe AD‐pathology. These differences were cell‐specific across six major cell types: excitatory neurons, inhibitory neurons, astrocytes, microglia, oligodendrocytes, and oligodendrocyte progenitor cells.1. We characterized RNA‐vel differences associated with four AD neuropathology traits: neuritic plaque, neuronal neurofibrillary tangle, overall β‐amyloid load, and PHF tau tangle density.2. We demonstrated the reproducibility of the RNA‐vel differences in two independent datasets: dorsolateral prefrontal cortex (N = 24) from ROSMAP3 and superior frontal gyrus (N = 6) from GEO4.ResultOnly 10 of 843 (1.2%) genes overlap between the differential RNA expression and velocity analyses, suggesting substantial AD‐pathology related differences between these two RNA descriptors. The genes with only velocity differences relate to cell developmental and synaptic processes. Conversely, the genes with only differential expression are majorly associated with mitochondrial activity and ribosomal processes. Many genes were reproduced in the independent datasets; these overlapping genes are again associated with neural development and synaptic activities across many cell types, as well as vascular‐ and immune‐related processes in astrocytes and microglia, respectivelyConclusionWe use RNA velocity to characterize, for the first time to our knowledge, the dynamical multicellular processes underlying neuropathological AD progression. The results support the validity of the novel RNA‐vel concept for achieving a complementary molecular characterization of AD, which may be obscured by typical analysis of RNA abundance alone.