Sex-dependent molecular landscape of Alzheimer's disease revealed by large-scale single-cell transcriptomics

Abstract

Introduction: Alzheimer's disease (AD) shows significant sex differences in prevalence and clinical manifestations, but the underlying molecular mechanisms remain unclear.

Methods: This study used a large-scale, single-cell transcriptomic atlas of the human prefrontal cortex to investigate sex-dependent molecular changes in AD. Our approach combined cell type-specific and sex-specific differential gene expression analysis, pathway enrichment, gene regulatory network construction, and cell-cell communication analysis to identify sex-dependent changes.

Results: We found significant sex-specific gene expression patterns and pathway alterations in AD. Male astrocytes showed changes in cell death pathways, with RPTOR as a key regulator, while female astrocytes had alterations in Wnt signaling and cell cycle regulation. Cell-cell communication analysis uncovered sex-specific intercellular signaling patterns, with male-specific impacts on apoptosis-related signaling and female-specific alterations in Wnt and calcium signaling.

Discussion: This study reveals sex-dependent gene expression patterns, pathway alterations, and intercellular communication changes, suggesting the need for sex-specific approaches in AD research.

Highlights: Single-cell transcriptomics reveals significant sex-specific molecular signatures in Alzheimer's disease (AD). Male astrocytes show enhanced modulation of apoptotic and cell death pathways in AD; female astrocytes exhibit distinct alterations in Wnt signaling and cell-cycle regulation. Sex-dimorphic changes in mitochondrial gene expression are observed in excitatory neurons, suggesting divergent energy metabolism profiles may contribute to AD sex differences. RPTOR is identified as a key regulator of male-specific changes in astrocytes, implicating the mechanistic target of rapamycin pathway in sex-dependent AD pathology. New cell-cell communication analyses reveal sex-specific patterns of intercellular signaling, providing insights into how cellular interactions may differentially contribute to AD pathology in males and females.

Keywords: Alzheimer's disease; apoptosis; cell death; network analysis; pathway analysis; sex differences; single‐cell sequencing; transcriptome analysis.

FIGURE 1

Dot plots showing the expression of key genes across specific cell types in AD patients and controls. The size of each dot represents the percentage of cells expressing the gene, while the color intensity indicates the average expression levels between females and males with AD across multiple cell types. The y axis shows the cell types, while the x axis displays the gene symbols. AD, Alzheimer's disease; ST, astrocytes; CTRL, healthy control; EX, excitatory neurons; F, female; Imm, immune cells; Inh, inhibitory neurons; M, male; Oli, oligodendrocytes; Vas, vascular cells.

FIGURE 2

Enriched GO terms in male astrocytes, representing the significant terms in males (P adjusted <  0.05) which do not approach significance in females (p  >  0.1). A, Enriched GO biological processes in males. B, Enriched GO molecular functions in males. GO, Gene Ontology.

FIGURE 3

Cell–cell communication analysis results for male astrocytes, highlighting the top 30 ligands and their downstream targets. Associated enriched gene ontology terms between the different cell type clusters are shown in Table S6 in supporting information. The cell–cell communication analysis results for female astrocytes are presented in Figure S3 in supporting information.

FIGURE 4

Graph representation of sub‐networks of the GRNs for male‐specific (A) and female‐specific (B) DEGs in astrocytes. As the complete networks are too large for interpretation, only the sub‐networks showing the upstream regulators of the key mediators RPTOR and LRP1 are presented. In the graphs, green lines represent activating interactions and red lines represent inhibitory interactions. The node colors indicate the gene expression log fold change in the respective phenotype, transitioning from red (overexpressed) to blue (underexpressed), as shown in the color legend on the right. DEG, differentially expressed gene; GRN, gene regulatory network.