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The X chromosome has long been an overlooked territory in Alzheimer disease (AD). Given the high density of X-linked genes expressed in the brain, exploring the X chromosome presents a compelling opportunity to uncover new genetic variations that may contribute to AD. The sex-specific nature of AD is well documented, with consistent findings of a greater prevalence of AD dementia in epidemiological cohorts, as well as higher levels of tau burden in older women relative to men, particularly in those with abnormal levels of amyloid burden. The recent study by Belloy et al, 1 published in this issue of JAMA Neurology, marks a significant advancement toward understanding the sex biological mechanisms at play by performing the first large-scale X chromosome-wide association study (XWAS) of AD dementia. Belloy et al 1 conducted an AD dementia case-control metaanalysis using genetic data from a multitude of cohorts, including the US Alzheimer's Disease Genetics Consortium (ADGC), Alzheimer's Disease Sequencing Project (ADSP), UK Biobank (UKB), the Finnish health registry (FinnGen), and the US Million Veterans Program (MVP). Their analysis, which included over 1.15 million participants, identified 6 loci with X chromosome-wide significance (P value <1 × 10 −5 ), with 4 showing causal support for an association with risk for AD. One locus, in the intron of SLC9A7 or CHST7, was of particular interest. The identified loci were involved in regulation of pH homeostasis in Golgi secretory compartments, and the authors argued that SLC9A7 may have downstream effects on β-amyloid accumulation.The X chromosome has remained enigmatic in AD research primarily due to technical challenges and complexities associated with its analysis. Traditional genome-wide association studies (GWAS) often exclude the X chromosome, focusing instead on autosomal chromosomes. In most studies, X-chromosome gene variants are discarded early in the quality control process. 2 They may also be improperly analyzed without accounting for unique issues associated with the X, such as mode of inheritance, X-chromosome inactivation escapism, 3 and consequent population genetic and evolutionary patterns. 4 This exclusion has left a gap in our understanding of sex-specific genetic contributions to AD via X-linked genes. Many human diseases, including AD, show some degree of sex specificity, which suggests an additional contribution of the X chromosome, which further highlights the major gap in the literature. Some major studies have demonstrated the importance of examining the X across a range of psychiatric and neurological conditions 5,6 ; however, the case for running an XWAS in AD dementia has remained underexplored, until now.
The X chromosome has long been an overlooked territory in Alzheimer disease (AD). Given the high density of X-linked genes expressed in the brain, exploring the X chromosome presents a compelling opportunity to uncover new genetic variations that may contribute to AD. The sex-specific nature of AD is well documented, with consistent findings of a greater prevalence of AD dementia in epidemiological cohorts, as well as higher levels of tau burden in older women relative to men, particularly in those with abnormal levels of amyloid burden. The recent study by Belloy et al, 1 published in this issue of JAMA Neurology, marks a significant advancement toward understanding the sex biological mechanisms at play by performing the first large-scale X chromosome-wide association study (XWAS) of AD dementia. Belloy et al 1 conducted an AD dementia case-control metaanalysis using genetic data from a multitude of cohorts, including the US Alzheimer's Disease Genetics Consortium (ADGC), Alzheimer's Disease Sequencing Project (ADSP), UK Biobank (UKB), the Finnish health registry (FinnGen), and the US Million Veterans Program (MVP). Their analysis, which included over 1.15 million participants, identified 6 loci with X chromosome-wide significance (P value <1 × 10 −5 ), with 4 showing causal support for an association with risk for AD. One locus, in the intron of SLC9A7 or CHST7, was of particular interest. The identified loci were involved in regulation of pH homeostasis in Golgi secretory compartments, and the authors argued that SLC9A7 may have downstream effects on β-amyloid accumulation.The X chromosome has remained enigmatic in AD research primarily due to technical challenges and complexities associated with its analysis. Traditional genome-wide association studies (GWAS) often exclude the X chromosome, focusing instead on autosomal chromosomes. In most studies, X-chromosome gene variants are discarded early in the quality control process. 2 They may also be improperly analyzed without accounting for unique issues associated with the X, such as mode of inheritance, X-chromosome inactivation escapism, 3 and consequent population genetic and evolutionary patterns. 4 This exclusion has left a gap in our understanding of sex-specific genetic contributions to AD via X-linked genes. Many human diseases, including AD, show some degree of sex specificity, which suggests an additional contribution of the X chromosome, which further highlights the major gap in the literature. Some major studies have demonstrated the importance of examining the X across a range of psychiatric and neurological conditions 5,6 ; however, the case for running an XWAS in AD dementia has remained underexplored, until now.
ImportanceThe X chromosome has remained enigmatic in Alzheimer disease (AD), yet it makes up 5% of the genome and carries a high proportion of genes expressed in the brain, making it particularly appealing as a potential source of unexplored genetic variation in AD.ObjectivesTo perform the first large-scale X chromosome–wide association study (XWAS) of AD.Design, Setting, and ParticipantsThis was a meta-analysis of genetic association studies in case-control, family-based, population-based, and longitudinal AD-related cohorts from the US Alzheimer’s Disease Genetics Consortium, the Alzheimer’s Disease Sequencing Project, the UK Biobank, the Finnish health registry, and the US Million Veterans Program. Risk of AD was evaluated through case-control logistic regression analyses. Data were analyzed between January 2023 and March 2024. Genetic data available from high-density single-nucleotide variant microarrays and whole-genome sequencing and summary statistics for multitissue expression and protein quantitative trait loci available from published studies were included, enabling follow-up genetic colocalization analyses. A total of 1 629 863 eligible participants were selected from referred and volunteer samples, 477 596 of whom were excluded for analysis exclusion criteria. The number of participants who declined to participate in original studies was not available.Main Outcome and MeasuresRisk of AD, reported as odds ratios (ORs) with 95% CIs. Associations were considered at X chromosome–wide (P &lt; 1 × 10−5) and genome-wide (P &lt; 5 × 10−8) significance. Primary analyses are nonstratified, while secondary analyses evaluate sex-stratified effects.ResultsAnalyses included 1 152 284 participants of non-Hispanic White, European ancestry (664 403 [57.7%] female and 487 881 [42.3%] male), including 138 558 individuals with AD. Six independent genetic loci passed X chromosome–wide significance, with 4 showing support for links between the genetic signal for AD and expression of nearby genes in brain and nonbrain tissues. One of these 4 loci passed conservative genome-wide significance, with its lead variant centered on an intron of SLC9A7 (OR, 1.03; 95% CI, 1.02-1.04) and colocalization analyses prioritizing both the SLC9A7 and nearby CHST7 genes. Of these 6 loci, 4 displayed evidence for escape from X chromosome inactivation with regard to AD risk.Conclusion and RelevanceThis large-scale XWAS of AD identified the novel SLC9A7 locus. SLC9A7 regulates pH homeostasis in Golgi secretory compartments and is anticipated to have downstream effects on amyloid β accumulation. Overall, this study advances our knowledge of AD genetics and may provide novel biological drug targets. The results further provide initial insights into elucidating the role of the X chromosome in sex-based differences in AD.
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