Alzheimer's disease-related transcriptional sex differences in myeloid cells

Abstract

Sex differences have been identified in many diseases associated with dysregulated immune responses, including Alzheimer's disease (AD), for which approximately two-thirds of patients are women. An accumulating body of research indicates that microglia may play a causal role in the pathogenesis of this disease. We hypothesised that sex differences in the transcriptome of human myeloid cells may contribute to the sex difference observed in AD prevalence. To explore this, we assessed bulk and single-nuclear RNA sequencing data sets generated from four human derived myeloid cell populations: post-mortem microglial nuclei, peripheral monocytes, monocyte-derived macrophages (MDMs) and induced pluripotent stem cell derived microglial-like cells (MGLs). We found that expression of AD risk genes, gene signatures associated with the inflammatory response in AD, and genes related to proinflammatory immune responses were enriched in microglial nuclei isolated from aged female donors without ante-mortem neurological disease, relative to those from males. In addition, these inflammation-associated gene sets were found to be enriched in peripheral monocytes isolated from postmenopausal women and in MDMs obtained from premenopausal individuals relative to age-matched males. Expression of these gene sets did not differ in MDMs derived from women whose blood was sampled across the menstrual cycle or in MGLs cultured with 17β-oestradiol. This suggests that the observed gene set enrichments in myeloid cells from women were not being driven by acute hormonal influences. Together, these data support the hypothesis that the increased prevalence of AD in women may be partly explained by a myeloid cell phenotype biased towards expression of biological processes relevant to AD.

Keywords: Microglia; Neurodegeneration; Neuroinflammation; Sex.

Fig. 1

Sex differences in the transcriptome of post-mortem microglial nuclei isolated from non-disease controls. A Box plots showing the enrichment of the Alzheimer’s disease GWAS signal (− log10P) between the F-MGN and M-MGN from previously published data sets [39, 41]. B, C Dot plots showing the enriched gene ontology (GO) biological processes in the upregulated sDEG in the B F-MGN (blue) and C M-MGN (red) isolated post-mortem from non-diseased brains. Significance of sDEG was determined via MAST analysis using an FDR < 0.05. The size of the dots corresponds to the size of the gene set, whereas the intensity of the colour denotes the FDR value of the overrepresentation of the corresponding biological pathway in the sDEGs. D Bar chart showing the enrichment of IR-AD gene sets. A negative log fold change (logFC) shows enrichments in the female nuclei whilst a positive logFC denotes enrichment in males

Fig. 2

Sex differences in the transcriptome of aged ex vivo monocytes. A, B Dot plots showing the enriched gene ontology biological processes in the significantly sDEG upregulated in the nuclei of A F-MC (blue) and B M-MC (red). Significance of sDEG was determined via MAST analysis using an FDR < 0.05. C Bar chart showing the enrichment of IR-AD gene sets. A negative log fold change (logFC) denotes enrichment in F-MCs whilst a positive logFC denotes enrichment in M-MCs. D Correlation of the gene set enrichment scores for all IR-AD gene sets significantly enriched in the female samples with age. These data were derived from the re-analysis of the publicly available microarray data set E-GEOD-56047

Fig. 3

Sex differences in the transcriptomic profile of monocyte-derived macrophages from women (F_lo) and men. A Bar chart showing the enrichment of IR-AD gene sets. A negative log fold change (logFC) denotes enrichment in F_lo-MDMs whilst a positive logFC denotes enrichment in M-MDMs. Significantly enriched gene sets are shown in colour, with blue indicating enrichment in F_lo-MDMs. B Volcano plot showing the number of significantly differently expressed Reactome and XiE (genes known to escape X-chromosome inactivation) gene sets between the M- and F_lo-MDMs. Each dot represents one of the total 382 gene sets. C Dot plot showing a collection of significantly sexually differentially expressed gene sets (sDGS)  between M-MDMs and F_lo-MDMs.  For plots B and C, p values were calculated via mixed-effects models with Benjamin-Hochberg multiple test corrections.

Fig. 4

Overlapping leading edge genes for the female-enriched Alzheimer’s disease associated gene sets (AD-GS). Venn diagrams showing the overlapping and unique leading-edge genes for each of the IR-AD found significantly enriched in the myeloid cells isolated from women in the A MDMs, B MCs, and C MGLs