Cell‐type deconvolution analysis of RNAseq data reveals cell‐specific glycosylation changes in the brains of Alzheimer’s Disease patients

Abstract Background Intriguing evidence that glycosylation is disrupted in Alzheimer’s Disease (AD) has emerged. However, our knowledge of cell‐specific alterations in the expression of genes involved in glycosylation in the brains of AD patients is limited. Method In this study, we conducted cell type deconvolution analysis of whole‐tissue RNAseq data to characterize cell type compositional differences and alterations in the expression of glycosylation related genes in the brains of AD patients and those with no cognitive impairment (NCI). Single‐cell human brain RNA‐seq data were obtained from the Allen Brain Map Atlas, consisting of 76,533 total nuclei derived from the cortical tissue of 2 humans. The identified cell types included GABAergic neurons, glutamatergic neurons, astrocytes, oligodendrocytes, oligodendrocyte precursor cells (OPC), microglia, endothelial cells, and vascular leptomeningeal cell (VLMC). The cell‐type deconvolution package CIBERSORT was applied in relative mode with S‐mode (single‐cell mode) batch correction to impute cell fractions and cell‐type‐specific gene expression profiles for NCI and AD samples in the ROSMAP dataset. The differences between cell type fractions of NCI and AD were analyzed by linear mixed regression model and t‐test. Result In the dorsolateral prefrontal cortex, neuronal cells represented the highest proportion of cells (∼30‐33%), followed by astrocytes (∼30%), and oligodendrocytes (∼20%), endothelial cells (∼7%), microglia (∼7%), VLMC (∼2‐3%), and OPC (<1%). The overall cell type composition was not significantly different between NCI and AD patients, however, the proportion of microglia, VLMC, and OPC was significantly higher in AD patients (p<0.05). The proportion of glutamatergic neuronal cells was significantly lower in female AD patients (p<0.05) compared with NCI controls, but not in males after controlling for age. Microglia‐associated expression of the glycosyltransferases MGAT1, ST6GAL1, and ST6GALNAC3 was observed in AD patients but not in NCI controls. Glutamatergic neuronal cells and VLMC cells associated with the expression of GALNT10 was observed in AD patients but not in NCI controls. In contrast, GALNT11 expression associated with astrocytes was observed in NCI controls but not in AD patients. Conclusion Our findings indicate changes in cell‐type proportions and cell‐specific changes in glycosyltransferase gene expression in the brains of AD patients compared with NCI controls.