DNA Methylation Signature of LINE1, SATα and Alu elements in Alzheimer’s Disease: Tracing NeuroEpigenetics by a Sex-specific Approach

Alzheimer's disease (AD) is a neurodegenerative disorder caused by Aβ accumulation leading to cognitive decline. APOE ε4 confers the strongest genetic risk for AD since it lowers Aβ clearance. Beyond APOE, there are no informative biomarkers. Female sex and age are other risk factors sharing mutual relationships with neuromethylome, making DNA methylation a potential biomarker. LINE1, Alu and SATα elements cover about 45% of the human genome, so their methylation changes can impact host gene expression and stability accelerating AD progression. Our study aims to identify global methylation signature, which may be crucial to unmask AD molecular bases and discover new druggable targets. We examined methylation levels of 214 AD patients through LINE1, Alu and SATα bisulfite pyrosequencing. We correlated age, sex, MMSE (Mini-Mental State Examination), APOE haplotypes to methylation. Females (68%) had significantly lower mean MMSE (F:21.09; M:23.03; P=0.0002) at any age considered. LINE1 and SATα methylation are inversely related with age (P=0.028; P=0.035), with females showing lower LINE1 values (P=0.029). Linear regression demonstrated a direct relationship between LINE1 methylation and MMSE score (P=0.0002) with females having a lower methylation-dependent trend (r²F:0.038 vs r²M:0.077; P=0.10). When stratified by APOE, ε4-carriers (38%) had slightly higher methylation of LINE1 and SATα compared to noncarriers, with a consequent higher age-dependent decline in LINE1 (P=0.08) more evident in SATα (P=0.015). Direct relationship between LINE1 methylation and MMSE ascribes to ε4-carriers a higher slope (r²=0.08; r²=0.05; P=0.05). No significant changes were found in Alu levels. Our findings highlight correlation between epigenetic variation and cognitive decline, ascribing to females or ε4-carriers the worst phenotype (MMSE 21.09; 20.72). Hence, the combination of female sex and ε4 reserves the lowest score (MMSE 20.5) although they show an opposite methylation trend. Lower methylation is found in females but not for all ε4-carriers, speculating unmodifiable risk factors may cause compensatory epigenetic rearrangements to counteract environment and reduce AD risk. Thus, ascribing methylation a useful tool for genetic and clinical data to identify early at-risk individuals.