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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
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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...
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... in the F-MCs and M-MCs, respectively (Additional file 2: Table S3). Enrichment analyses of the genes upregulated in the F-MCs revealed sDEG overwhelmingly associated with GO terms relating to inflammation-associated pathways, including type I interferon signalling, positive regulation of NFκB activity, and response to lipopolysaccharide ( Fig. 2A). In contrast, genes upregulated in M-MCs were associated with pathways for protein translation and trafficking (Fig. ...Context 2
... in the F-MCs revealed sDEG overwhelmingly associated with GO terms relating to inflammation-associated pathways, including type I interferon signalling, positive regulation of NFκB activity, and response to lipopolysaccharide ( Fig. 2A). In contrast, genes upregulated in M-MCs were associated with pathways for protein translation and trafficking (Fig. ...Context 3
... 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 [41] (p = 0.002) upregulated-genes; none of the IR-AD gene sets were significantly enriched in the M-MCs (Fig. 2C). As AD is typically diagnosed around 75 years of age [9], we examined whether the expression of the IR-AD gene sets whose expression was enriched in monocytes from women were influenced by the age of the donor. No correlations with age were found for the enrichment of gene sets in the F-MC data (Fig. 2D); however, as the age range ...Context 4
... were significantly enriched in the M-MCs (Fig. 2C). As AD is typically diagnosed around 75 years of age [9], we examined whether the expression of the IR-AD gene sets whose expression was enriched in monocytes from women were influenced by the age of the donor. No correlations with age were found for the enrichment of gene sets in the F-MC data (Fig. 2D); however, as the age range employed here was narrow (59-83 years) these results need to be confirmed in a larger population including a wider age ...Context 5
... hormones are at their lowest (F lo ), and then during the predicted late follicular phase of the cycle when levels of 17β-oestradiol (E2, the primary circulating oestrogen [50]) peak (F hi ). Measurements of total serum E2 when blood was drawn for the monocyte isolations confirmed their associations with either F lo or F hi (Additional file 1: Fig. S2). Paired with those from age-matched men, the isolated monocytes were then differentiated in vitro into macrophages. None of the IR-AD gene sets were found to be significantly upregulated in the MDMs from men (M-MDMs) compared to those generated from monocytes of women sampled during menstruation (F lo -MDMs). However, the F lo -MDMs ...Context 6
... and box plots of the normalized expression counts of key microglial genes, including IBA1/AIF1, ITGAM (CD11b), ITGAX (CD11c), P2RY12, TMEM119, and CX3CR1 in male and female induced pluripotent stem cellderived microglial-like cells (MGLs). Figure S2. Sex labelling and identification of a population of post-menopausal female and age-matched male monocytes. ...Similar publications
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Citations
... Similar observations were made in a study of postmortem human brain tissue, where dysregulation of microglial gene signatures was shown to be more common in female patients than in male patients. 40 We were also interested in investigating the differences in gene expression in cell types that do not express Inpp5d. We used CellChat to infer differences in signaling between microglia and other cell types, which could help explain these findings. ...
INTRODUCTION
Inpp5d is genetically associated with Alzheimer's disease risk. Loss of Inpp5d alters amyloid pathology in models of amyloidosis. Inpp5d is expressed predominantly in microglia but its function in brain is poorly understood.
METHODS
We performed single‐cell RNA sequencing to study the effect of Inpp5d loss on wild‐type mouse brain transcriptomes.
RESULTS
Loss of Inpp5d has sex‐specific effects on the brain transcriptome. Affected genes are enriched for multiple neurodegeneration terms. Network analyses reveal a gene co‐expression module centered around Inpp5d in female mice. Inpp5d loss alters Pleotrophin (PTN), Prosaposin (PSAP), and Vascular Endothelial Growth Factor A (VEGFA) signaling probability between cell types.
DISCUSSION
Our data suggest that the normal function of Inpp5d is entangled with mechanisms involved in neurodegeneration. We report the effect of Inpp5d loss without pathology and show that this has dramatic effects on gene expression. Our study provides a critical reference for researchers of neurodegeneration, allowing separation of disease‐specific changes mediated by Inpp5d in disease from baseline effects of Inpp5d loss.
Highlights
Loss of Inpp5d has different effects in male and female mice.
Genes dysregulated by Inpp5d loss relate to neurodegeneration.
Total loss of Inpp5d in female mice collapses a conserved gene co‐expression module.
Loss of microglial Inpp5d affects the transcriptome of other cell types.
... Aged females also possess a greater burden of senescent microglia, which may contribute to the development of neurodegenerative diseases and a more rapid and severe disease course in females (39, 42, 43). While research on sex differences in microglia in HD remains limited compared to other neurodegenerative diseases like Alzheimer's disease (AD), studies in AD have shown that aged female donors display higher expression of gene signatures related to inflammatory response and proinflammatory immune responses in microglia nuclei compared to males (44). Additionally, functional studies involving microglial transplants and analyses of microglial Ca 2+ signaling and process motility suggest that female mice exhibit more rapid aging of microglia than males (38, 45). ...
Huntington's disease (HD) is a debilitating neurodegenerative condition characterized by motor, cognitive and psychiatric abnormalities. Immune dysregulation, prominently featuring increased immune activity, plays a significant role in HD pathogenesis. In addition to the central nervous system (CNS), systemic innate immune activation and inflammation are observed in HD patients, exacerbating the effects of the Huntingtin (HTT) gene mutation. Recent attention to sex differences in HD symptom severity underscores the need to consider gender as a biological variable in neurodegenerative disease research. Understanding sex-specific immune responses holds promise for elucidating HD pathophysiology and informing targeted treatment strategies to mitigate cognitive and functional decline. This perspective will highlight the importance of investigating gender influence in HD, particularly focusing on sex-specific immune responses predisposing individuals to disease.
... Our subsequent analyses incorporating snRNA-seq data suggest that females do not have an increased abundance of microglia cells; rather that these cells are in a different state (Fig. 3C, D). Distinct microglia states are strongly implicated in Alzheimer's risk and progression through both human genetics and pathology [74,75]. For example, highthroughput analysis of microglial morphometrics in mice also indicated female microglia are in a more disease-like state, and more rapidly shift into this state in progress of disease models as well [76]. ...
Background:
Sex differences in the brain may play an important role in sex-differential prevalence of neuropsychiatric conditions.
Methods:
In order to understand the transcriptional basis of sex differences, we analyzed multiple, large-scale, human postmortem brain RNA-Seq datasets using both within-region and pan-regional frameworks.
Results:
We find evidence of sex-biased transcription in many autosomal genes, some of which provide evidence for pathways and cell population differences between chromosomally male and female individuals. These analyses also highlight regional differences in the extent of sex-differential gene expression. We observe an increase in specific neuronal transcripts in male brains and an increase in immune and glial function-related transcripts in female brains. Integration with single-nucleus data suggests this corresponds to sex differences in cellular states rather than cell abundance. Integration with case-control gene expression studies suggests a female molecular predisposition towards Alzheimer's disease, a female-biased disease. Autism, a male-biased diagnosis, does not exhibit a male predisposition pattern in our analysis.
Conclusion:
Overall, these analyses highlight mechanisms by which sex differences may interact with sex-biased conditions in the brain. Furthermore, we provide region-specific analyses of sex differences in brain gene expression to enable additional studies at the interface of gene expression and diagnostic differences.
... On the other hand, LHFPL2, and RTTN are DAM genes that we find are upregulated in female microglia compared to male 30 . Our data also remains consistent with a previous publication of AD-related transcriptional sex differences that identified ACSL1, ATP1B3, CD163, CREM, and SRGN as downregulated in female microglia cell nuclei compared to male 48 . The upregulation of genes APBB1IP, GLDN, LHFPL2, LRRK1, P2RY12, RASSF8, and RTTN in female microglia compared to male is also consistent with previous findings 48 . ...
Alzheimer’s Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD). It offers a broader spectrum of AD-related datasets, an optimized analytical pipeline, and improved usability. The database encompasses 1,053 samples (277 integrated datasets) from 67 AD-related scRNA-seq & snRNA-seq studies, totaling 7,332,202 cells. Additionally, it archives 381 ST datasets from 18 human and mouse brain studies. Each dataset is annotated with details such as species, gender, brain region, disease/control status, age, and AD Braak stages. ssREAD also provides an analysis suite for cell clustering, identification of differentially expressed and spatially variable genes, cell-type-specific marker genes and regulons, and spot deconvolution for integrative analysis. ssREAD is freely available at https://bmblx.bmi.osumc.edu/ssread/.
... Females have a different gut microbiome composition from males (Shobeiri et al., 2022), and sex differences in immune cells and their responsivity have been reported in patients with AD. Specifically, peripheral blood leukocytes display a lower response to viral infection ex vivo in female compared to male AD patients (Coales et al., 2022;Sochocka et al., 2022). A study exploring gene expression in the brain and blood of patients with AD suggested AD immune dysregulation may be a specific feature to females (Paranjpe et al., 2021), and a preclinical study reported sex specific responsivity of microglia to antibiotic treatment in a mouse model of AD (Dodiya et al., 2019). ...
Alzheimer's disease is a complex and progressive condition that affects essential neurological functions such as memory and reasoning. In the brain, neuronal loss, synaptic dysfunction, proteinopathy, neurofibrillary tangles, and neuroinflammation are the hallmarks of Alzheimer's disease pathophysiology. In addition, recent evidence has highlighted that microbes, whether commensal or pathogenic, also have the ability to interact with their host and to regulate its immune system, therefore participating in the exchanges that lead to peripheral inflammation and neuropathology. Because of this intimate relationship, bacteria, viruses, fungi, and protozoa have been implicated in the development of Alzheimer's disease. Here, we bring together current and most recent evidence of the role of microbes in Alzheimer's disease, raising burning questions that need to be addressed to guide therapeutic approaches and potential prophylactic strategies.
... To investigate the potential influence of sex on differential expression, we applied a pseudo-bulk approach with a dedicated interaction term for sex and transgene status [102]. For generating sex-related molecular signatures in each cell type, we employed the voom [103] pipeline from the R package Limma [104] (version 3.56.1, ...
Alzheimer’s disease (AD) progression and pathology show pronounced sex differences, but the factors driving these remain poorly understood. To gain insights into early AD-associated molecular changes and their sex dependency for tau pathology in the cortex, we performed single-cell RNA-seq in the THY-Tau22 AD mouse model. By examining cell type-specific and cell type-agnostic AD-related gene activity changes and their sex-dimorphism for individual genes, pathways and cellular sub-networks, we identified both statistically significant alterations and interpreted the upstream mechanisms controlling them. Our results confirm several significant sex-dependent alterations in gene activity in the THY-Tau22 model mice compared to controls, with more pronounced alterations in females. Both changes shared across multiple cell types and cell type-specific changes were observed. The differential genes showed significant over-representation of known AD-relevant processes, such as pathways associated with neuronal differentiation, programmed cell death and inflammatory responses. Regulatory network analysis of these genes revealed upstream regulators that modulate many of the downstream targets with sex-dependent changes. Most key regulators have been previously implicated in AD, such as Egr1 , Klf4 , Chchd2 , complement system genes, and myelin-associated glycoproteins. Comparing with similar data from the Tg2576 AD mouse model and human AD patients, we identified multiple genes with consistent, cell type-specific and sex-dependent alterations across all three datasets. These shared changes were particularly evident in the expression of myelin-associated genes such as Mbp and Plp1 in oligodendrocytes. In summary, we observed significant cell type-specific transcriptomic changes in the THY-Tau22 mouse model, with a strong over-representation of known AD-associated genes and processes. These include both sex-neutral and sex-specific patterns, characterized by consistent shifts in upstream master regulators and downstream target genes. Collectively, these findings provide insights into mechanisms influencing sex-specific susceptibility to AD and reveal key regulatory proteins that could be targeted for developing treatments addressing sex-dependent AD pathology.
... While many studies have shown that DAM gene expression is elevated with aging (Coales et al., 2022;Riedel et al., 2016;Sala Frigerio et al., 2019;Sierksma et al., 2020), whether aging also elevates the function of the encoded proteins has not yet been determined. Here, for the first time we provide supportive evidence that active LPL is increased in aged female brains compared to males (Figure 4). ...
... 85 Although this is partially explained by the longer average lifespan of females, other factors, including post-menopausal changes in hormones and sex-specific differences in immune responses, are also implicated in this phenomenon. [86][87][88] However, comparatively little is understood with respect to the putative drivers of AD that might be unique to males. One possibility is raised by a metaanalysis of the impact of herpes zoster vaccination on dementia, which revealed that although vaccination is protective against the development of dementia later in life, this effect is stronger in females than in males. ...
The dominant risk factors for late-onset Alzheimer’s disease (AD) are advanced age and the APOE4 genetic variant. To examine how these factors alter neuroimmune function, we generated an integrative, longitudinal single-cell atlas of brain immune cells in AD model mice bearing the three common human APOE alleles. Transcriptomic and chromatin accessibility analyses identified a reactive microglial population defined by the concomitant expression of inflammatory signals and cell-intrinsic stress markers whose frequency increased with age and APOE4 burden. An analogous population was detectable in the brains of human AD patients, including in the cortical tissue, using multiplexed spatial transcriptomics. This population, which we designate as terminally inflammatory microglia (TIM), exhibited defects in amyloid-β clearance and altered cell-cell communication during aducanumab treatment. TIM may represent an exhausted-like state for inflammatory microglia in the AD milieu that contributes to AD risk and pathology in APOE4 carriers and the elderly, thus presenting a potential therapeutic target for AD.
... contained in the edgeR pipeline 117 . Gene set variation analysis was performed using the GSVA package in R, as previously described 118 . ...
Multiple lines of evidence point to peripheral immune alterations in bipolar disorder (BD) although the activity of brain immune mechanisms remain largely unexplored. To identify the cell type-specific immune alterations in the BD brain, we performed a proteomic and single nuclear transcriptomic analysis of postmortem cingulate cortex samples from BD and control subjects. Our results showed that genes associated to the genetic risk for BD are enriched in microglia and astrocytes. Transcriptomic alterations in microglia point to a reduced proinflammatory phenotype, associated to reduced resistance to oxidative stress and apoptosis, which was confirmed with immunohistochemical quantification of IBA1 density. Astrocytes show transcriptomic evidence of an imbalance of multiple metabolic pathways, extracellular matrix composition and downregulated immune signalling. These alterations are associated to ADCY2 and NCAN, two GWAS genes upregulated in astrocytes. Finally, cell-cell communication analysis prioritized upregulated SPP1-CD44 signalling to astrocytes as a potential regulator of the transcriptomic alterations in BD. Our results indicate that microglia and astrocytes are characterized by downregulated immune responses associated to a dysfunction of core mechanisms via which these cells contribute to brain homeostasis.
... Many recent studies have investigated the sex-related differences affecting the abundance and activation states of microglia, from development to maturation, under various neuroinflammatory conditions [48][49][50]. Microglial cells isolated from female mouse models of AD shift from a homeostatic state towards an activated response (ARM) state faster than age-matched male mice [51]. This change involves more glycolytic activity and impaired phagocytosis in female mice, which causes reduced amyloid clearance in comparison with males. ...
Alzheimer’s disease (AD) is the most common form of dementia, which disproportionately affects women. AD symptoms include progressive memory loss associated with amyloid-β (Aβ) plaques and dismantled synaptic mechanisms. Perineuronal nets (PNNs) are important components of the extracellular matrix with a critical role in synaptic stabilisation and have been shown to be influenced by microglia, which enter an activated state during AD. This study aimed to investigate whether sex differences affected the density of PNNs alongside the labelling of microglia and Aβ plaques density.We performed neurochemistry experiments using acute brain slices from both sexes of the APPNL-F/NL-F mouse model of AD, aged-matched (2–5 and 12–16 months) to wild-type mice, combined with a weighted gene co-expression network analysis (WGCNA). The lateral entorhinal cortex (LEC) and hippocampal CA1, which are vulnerable during early AD pathology, were investigated and compared to the presubiculum (PRS), a region unscathed by AD pathology. The highest density of PNNs was found in the LEC and PRS regions of aged APPNL-F/NL-F mice with a region-specific sex differences. Analysis of the CA1 region using multiplex-fluorescent images from aged APPNL-F/NL-F mice showed regions of dense Aβ plaques near clusters of CD68, indicative of activated microglia and PNNs. This was consistent with the results of WGCNA performed on normalised data on microglial cells isolated from age-matched, late-stage male and female wild-type and APP knock-in mice, which revealed one microglial module that showed differential expression associated with tissue, age, genotype, and sex, which showed enrichment for fc-receptor-mediated phagocytosis. Our data are consistent with the hypothesis that sex-related differences contribute to a disrupted interaction between PNNs and microglia in specific brain regions associated with AD pathogenesis.
