DNA methylation is a critical epigenetic mechanism involved in numerous physiological processes. Alterations in DNA methylation patterns are associated with various brain disorders, including dementias such as Alzheimer’s disease (AD) and frontotemporal dementia (FTD). Investigating these alterations is essential for understanding the pathogenesis and progression of these disorders. Among the various methods for detecting DNA methylation, DNA sequencing is one of the most widely employed. Specifically, two main sequencing approaches are commonly used for DNA methylation analysis: bisulfite sequencing and single-molecule long-read sequencing. In this review, we compared the performances of CpG methylation detection obtained using two popular sequencing platforms, Illumina for bisulfite sequencing and Oxford Nanopore (ON) for long-read sequencing. Our comparison considers several factors, including accuracy, efficiency, genomic regions, costs, wet-lab protocols, and bioinformatics pipelines. We provide insights into the strengths and limitations of both methods with a particular focus on their application in research on AD and FTD.

Alzheimer’s Disease (AD) and Frontotemporal Dementia (FTD) are the two major neurodegenerative diseases with distinct clinical and neuropathological profiles. The aim of this report is to conduct a population-based investigation in well-characterized APP, PSEN1, PSEN2, MAPT, GRN, and C9orf72 mutation carriers/pedigrees from the north, the center, and the south of Italy. We retrospectively analyzed the data of 467 Italian individuals. We identified 21 different GRN mutations, 20 PSEN1, 11 MAPT, 9 PSEN2, and 4 APP. Moreover, we observed geographical variability in mutation frequencies by looking at each cohort of participants, and we observed a significant difference in age at onset among the genetic groups. Our study provides evidence that age at onset is influenced by the genetic group. Further work in identifying both genetic and environmental factors that modify the phenotypes in all groups is needed. Our study reveals Italian regional differences among the most relevant AD/FTD causative genes and emphasizes how the collaborative studies in rare diseases can provide new insights to expand knowledge on genetic/epigenetic modulators of age at onset.

Monogenic forms of Alzheimer’s Disease (AD) and Frontotemporal Dementia (FTD) represent the two principal neurodegenerative disorders leading to early-onset dementia, primarily linked to mutations in key AD- and FTD-associated genes. The marked heterogeneity in age at onset and penetrance among carriers of pathogenic mutations suggests that monogenic variants act within a broader polygenic background. The combined impact of AD- and FTD-related genetic variation on disease incidence in monogenic forms remains largely unexplored. Herein, we investigate gene–gene interaction patterns in monogenic AD and FTD, with a focus on genetic variability in key AD (APP, PSEN1, PSEN2) and FTD (MAPT, GRN, C9orf72)-associated genes and their association with cumulative disease incidence. Within the GARDENIA Consortium, we studied 426 individuals from Italian pedigrees, including patients (n = 319) and presymptomatic (n = 107) carriers of causative variants in APP (n = 39), PSEN1 (n = 71), PSEN2 (n = 13), MAPT (n = 29), GRN (n = 188), and C9orf72 (n = 86). Age at symptoms onset, age at last follow-up and sex were recorded. Whole exome sequencing was performed, focusing on non-causative variants (n = 64) in the key AD (APP, PSEN1, PSEN2) and FTD genes (MAPT, GRN, C9orf72). Weighted genetic burden scores were derived using Fine–Gray competing risk models to estimate variant-specific effects on cumulative AD and FTD incidence, accounting for mutually exclusive outcomes and family clustering. Model fit was evaluated using Akaike Information Criterion. Higher AD-risk-weighted burden scores in AD-related genes were associated with a significantly increased cumulative incidence of AD, while higher FTD-risk-weighted scores in FTD-related genes showed a trend toward association with increased cumulative incidence of FTD. A significant interaction between burden scores was observed. AD and FTD burden scores showed a negative interaction for AD (~79% attenuation) but a modest synergistic effect for FTD (~6% increase). These findings could imply context-dependent pleiotropy rather than simple additive genetic effects. Our study suggests that even in carriers oh highly penetrant AD or FTD causative variants, genetic background could substantially modulate cumulative disease incidence. Integrating polygenic information with monogenic status may improve prognostic stratification and inform precision approaches in dementia research and clinical trials.