Novel sex‐specific candidate loci associated with Alzheimer disease identified through sex‐aware multi‐ancestry genome‐wide meta‐analysis

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BACKGROUND: Sex differences in progression and pathology of Alzheimer's disease (AD) suggest sex-specific factors influencing its development. While studies have established APOE-genotype as contributing to AD risk differently in men and women, few have searched for additional genetic sex differences in AD. To identify sex-specific AD genetic associations, we conducted genome-wide sex-aware meta-analyses in the Alzheimer's Disease Genetics Consortium (ADGC) and Alzheimer's Disease Sequencing Project (ADSP) datasets. METHOD: Sex-interaction and sex-stratified analyses were performed in multi-ancestry genome-wide imputed AD datasets from the ADGC (N = 25,284 cases, 60% female and 33,455 controls, 63% female; ancestry/ethnicity distribution: 63.7% European, 15.6% African, 15.2% Hispanic/Latino, 5.5% Asian). STAAR aggregation-based rare-variant testing was also conducted in coding and non-coding genomic regions on an ancestrally diverse sample of 8,697 AD cases and 14,758 controls with whole-genome sequencing from the ADSP. RESULT: Cross-ancestry sex-stratified analyses identified several loci with evidence of interaction (p <0.05) and suggestive significance in one sex (p <5x10-6) and not the other (p >0.05). These include male specific variants in STXBP6, MAP4K5 and the known AD locus PICALM. Genetic loci associated in females and not males include NPAS3, ZNF438 and a genome-wide result in NECTIN2 near the APOE locus. Top ancestry-specific results include associations at COL4A2 in Asian-ancestry males and C16orf96 in African-ancestry females. Cross-ancestry rare-variant aggregation-based testing revealed four novel genome-wide significant associations in females including with missense variants in SH3BP1. Five population specific associations were also discovered including with missense variants in SERTAD4 in a genetically-defined Hispanic/Amerindian/African ancestral population cluster and promoter variants of PSMA5 in a European population cluster. Seven male-specific effects were also discovered including genome-wide significant cross-ancestry associations with an enhancer region of MORC1 and a promoter of ITPKA. CONCLUSION: We identified sex-specific AD associations at loci with AD-relevant genes including STXBP6 (involved in AD relevant processes such as endolysosomal transport and synaptic transmission), NPAS3 (neurogenesis), COL4A2 (cerebral vasculature), ITPKA (learning/memory processes), PAQR3 (cholesterol homeostatis and neuronal function), and MORC1 (recently associated in a UK Biobank exome-wide sequencing study of dementia (Zhang et al. Alz & Dementia 2024). Understanding the nature of these associations could help explain sex differences in risk and progression for AD.

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