INTRODUCTION: The sortilin-related receptor (SORL1) directs APP and Aβ trafficking within the retromer pathway. Cleavage at the cell surface releases soluble SORL1 (sSORL1) into cerebrospinal fluid (CSF). We examined whether CSF-sSORL1 can serve as an in vivo marker of genetically impaired SORL1. METHODS: CSF-sSORL1 was quantified by enzyme-linked immunosorbent assay (ELISA) in 218 participants: 90 carriers of SORL1 variants, 78 SORL1-wildtype (WT) AD patients, and 50 SORL1-WT controls. RESULTS: sSORL1 concentrations were significantly lower in carriers of protein-truncating and damaging missense variants. In SORL1-WT patients, CSF-sSORL1 correlated with pTau181 but not with Aβ42 among AD patients, and did not differ between patients and controls. DISCUSSION: These findings suggest that impaired SORL1 trafficking reduces receptor delivery to the cell surface and thereby decreases sSORL1 shedding, supporting its potential use as a pathway-specific biomarker. Highlights: Enzyme-linked immunosorbent assay (ELISA) enables quantitative measurement of soluble sortilin-related receptor (sSORL1) in cerebrospinal fluid (CSF). sSORL1 levels are reduced in CSF from carriers of a pathogenic SORL1 variant. CSF-sSORL1 levels correlate with tau pathology in Alzheimer's disease. sSORL1 levels represent an in vivo biomarker of SORL1 function.

We constructed a polygenic protective score specific to Alzheimer’s disease (AD PPS) based on the current literature among the participants enrolled in five studies of healthy aging and extreme longevity in the USA, Europe, and Asia. This AD PPS did not include variants on apolipoprotein E (APOE) gene. Comparisons of AD PPS in different data sets of healthy agers and centenarians showed that centenarians have stronger genetic protection against AD compared to individuals without familial longevity. The current study also shows evidence that this genetic protection increases with increasingly older ages in centenarians (centenarians who died before reaching age 105 years, semi-supercentenarians who reached age 105 to 109 years, and supercentenarians who reached age 110 years and older). However, the genetic protection was of modest size: the average increase in AD PPS was approximately one additional protective allele per 5 years of gained lifetime. Additionally, we show that the higher AD PPS was associated with better cognitive function and decreased mortality. Taken together, this analysis suggests that individuals who achieve the most extreme ages, on average, have the greatest protection against AD. This finding is robust to different genetic backgrounds with important implications for universal applicability of therapeutics that target this AD PPS.

Traditional statistical approaches have advanced our understanding of the genetics of complex diseases, yet are limited to linear additive models. Here we applied machine learning (ML) to genome-wide data from 41,686 individuals in the largest European consortium on Alzheimer’s disease (AD) to investigate the effectiveness of various ML algorithms in replicating known findings, discovering novel loci, and predicting individuals at risk. We utilised Gradient Boosting Machines (GBMs), biological pathway-informed Neural Networks (NNs), and Model-based Multifactor Dimensionality Reduction (MB-MDR) models. ML approaches successfully captured all genome-wide significant genetic variants identified in the training set and 22% of associations from larger meta-analyses. They highlight 6 novel loci which replicate in an external dataset, including variants which map to ARHGAP25, LY6H, COG7, SOD1 and ZNF597. They further identify novel association in AP4E1, refining the genetic landscape of the known SPPL2A locus. Our results demonstrate that machine learning methods can achieve predictive performance comparable to classical approaches in genetic epidemiology and have the potential to uncover novel loci that remain undetected by traditional GWAS. These insights provide a complementary avenue for advancing the understanding of AD genetics.

IMPORTANCE Older individuals without dementia often have amyloid-beta (Aβ) Thal phases similar to patients with Alzheimer disease (AD), suggesting that Aβ pathology may be a benign consequence of aging. OBJECTIVE To explore whether Aβ pathology in centenarians is associated with cognitive performance. DESIGN, SETTING, AND PARTICIPANTS This longitudinal cohort study used cross-sectional data on antemortem cognitive performance and postmortem neuropathology of participants in the Dutch 100-plus Study. Cognitive performance was measured a median of 10 (IQR, 3-13) months before postmortem brain donation. From January 2013 to July 2022, 1187 centenarians who self-reported being cognitively healthy, confirmed by proxy, were approached: 406 were included and 95 donated their brain. Centenarians were compared with patients with clinicopathologically confirmed AD from the Netherlands Brain Bank. Data were analyzed from June 2022 to October 2024. MAIN OUTCOMES AND MEASURES Aβ pathology was assessed with the Thal phase for Aβ progression and by determining quantitative Aβ loads (percentage positive area) in the frontal, parietal, temporal, and occipital neocortices, 3 parahippocampal, and 5 hippocampal subregions. Aβ pathology was associated with performance on 13 neuropsychological tests assessing memory, fluency, attention/processing speed, and executive functioning, as well as 4 measures of global cognition. RESULTS This study evaluated Aβ pathology in 95 centenarians (median age at brain donation, 103.5 [IQR, 102.3-104.7] years; 71 female [75%] and 24 male [25%]) and 38 patients with AD (median age, 84 [IQR, 78-90] years; 18 female [47%] and 20 male [53%]). Global cognition parameters were available for all 95 centenarians and complete cognitive assessment for 72 centenarians (76%). A fraction of the centenarians had no Aβ load (9 of 95 [9%]), most had low Aβ load (53 of 95 [56%]) and, despite high Thal phases, about one-third (33 of 95 [35%]) had high Aβ load comparable with patients with AD. Centenarians with no or low Aβ load had significantly higher cognitive performance than centenarians with high Aβ loads. Higher Aβ loads across all 4 neocortical regions, cornu ammonis 3, cornu ammonis 1/subiculum, and the entorhinal cortex specifically affected executive functioning. Interestingly, 5 resilient centenarians maintained high cognitive performance despite having high Aβ loads; they had significantly less tau pathology compared with centenarians with high Aβ loads and low cognitive performance. CONCLUSIONS AND RELEVANCE These results indicate that Aβ pathology is not a benign consequence of aging. Even in the oldest individuals, Aβ and tau pathology interaction was consistent with the amyloid cascade hypothesis.

Traditional statistical approaches have advanced our understanding of the genetics of complex diseases, yet are limited to linear additive models. Here we applied machine learning (ML) to genome-wide data from 41,686 individuals in the largest European consortium on Alzheimer’s disease (AD) to investigate the effectiveness of various ML algorithms in replicating known findings, discovering novel loci, and predicting individuals at risk. We utilised Gradient Boosting Machines (GBMs), biological pathway-informed Neural Networks (NNs), and Model-based Multifactor Dimensionality Reduction (MB-MDR) models. ML approaches successfully captured all genome-wide significant genetic variants identified in the training set and 22% of associations from larger meta-analyses. They highlight 6 novel loci which replicate in an external dataset, including variants which map to ARHGAP25, LY6H, COG7, SOD1 and ZNF597. They further identify novel association in AP4E1, refining the genetic landscape of the known SPPL2A locus. Our results demonstrate that machine learning methods can achieve predictive performance comparable to classical approaches in genetic epidemiology and have the potential to uncover novel loci that remain undetected by traditional GWAS. These insights provide a complementary avenue for advancing the understanding of AD genetics.

Background and ObjectivesIdentifying genetic causes of dementia in patients visiting memory clinics is important for patient care and family planning. Traditional clinical selection criteria for genetic testing may miss carriers of pathogenic variants in dementia-related genes. This study aimed identify how many carriers we are missing and to optimize criteria for selecting patients for genetic counseling in memory clinics.MethodsIn this clinical cohort study, we retrospectively genetically tested patients during 2.5 years (2010-2012) visiting the Alzheimer Center Amsterdam, a specialized memory clinic. Genetic tests consisted of a 54-gene dementia panel, focusing on Class IV/V variants per American College of Medical Genetics and Genomics guidelines, including APP duplications and the C9ORF72 repeat expansion. We determined the prevalence of pathogenic variants and propose new eligibility criteria for genetic testing in memory clinics. The eligibility criteria were prospectively applied for 1 year (2021-2022), and results were compared with the retrospective cohort.ResultsGenetic tests were retrospectively performed in in 1,022 of 1,138 patients (90%) who consecutively visited the memory clinic. Among these, 1,022 patients analyzed (mean age 62.1 ± 8.9 years; 40.4% were female), 34 pathogenic variant carriers were identified (3.3%), with 24 being symptomatic. Previous clinical criteria would have identified only 15 carriers (44% of all carriers, 65% of symptomatic carriers). The proposed criteria increased identification to 22 carriers (62.5% of all carriers, 91% of symptomatic carriers). In the prospective cohort, 148 (28.7%) of 515 patients were eligible for testing under the new criteria. Of the 90 eligible patients who consented to testing, 13 pathogenic carriers were identified, representing a 73% increase compared with the previous criteria.DiscussionWe found that patients who visit a memory clinic and carry a pathogenic genetic variant are often not eligible for genetic testing. The proposed new criteria improve the identification of patients with a genetic cause for their cognitive complaints. In systems without practical or financial barriers to genetic testing, the new criteria can enhance personalized care. In other countries where the health care systems differs and in other genetic ancestry groups, the performance of the criteria may be different.

BACKGROUND: Alzheimer's disease (AD) prevalence increases with age, yet a small fraction of the population reaches ages > 100 years without cognitive decline. We studied the genetic factors associated with such resilience against AD. METHODS: Genome-wide association studies identified 86 single nucleotide polymorphisms (SNPs) associated with AD risk. We estimated SNP frequency in 2281 AD cases, 3165 age-matched controls, and 346 cognitively healthy centenarians. We calculated a polygenic risk score (PRS) for each individual and investigated the functional properties of SNPs enriched/depleted in centenarians. RESULTS: Cognitively healthy centenarians were enriched with the protective alleles of the SNPs associated with AD risk. The protective effect concentrated on the alleles in/near ANKH, GRN, TMEM106B, SORT1, PLCG2, RIN3, and APOE genes. This translated to >5-fold lower PRS in centenarians compared to AD cases (P = 7.69 × 10⁻⁷¹), and 2-fold lower compared to age-matched controls (P = 5.83 × 10⁻¹⁷). DISCUSSION: Maintaining cognitive health until extreme ages requires complex genetic protection against AD, which concentrates on the genes associated with the endolysosomal and immune systems. Highlights: Cognitively healthy cent enarians are enriched with the protective alleles of genetic variants associated with Alzheimer's disease (AD). The protective effect is concentrated on variants involved in the immune and endolysosomal systems. Combining variants into a polygenic risk score (PRS) translated to > 5-fold lower PRS in centenarians compared to AD cases, and ≈ 2-fold lower compared to middle-aged healthy controls.

INTRODUCTION: Neuropathological substrates associated with neurodegeneration occur in brains of the oldest old. How does this affect cognitive performance?. METHODS: The 100-plus Study is an ongoing longitudinal cohort study of centenarians who self-report to be cognitively healthy; post mortem brain donation is optional. In 85 centenarian brains, we explored the correlations between the levels of 11 neuropathological substrates with ante mortem performance on 12 neuropsychological tests. RESULTS: Levels of neuropathological substrates varied: we observed levels up to Thal-amyloid beta phase 5, Braak-neurofibrillary tangle (NFT) stage V, Consortium to Establish a Registry for Alzheimer's Disease (CERAD)-neuritic plaque score 3, Thal-cerebral amyloid angiopathy stage 3, Tar-DNA binding protein 43 (TDP-43) stage 3, hippocampal sclerosis stage 1, Braak-Lewy bodies stage 6, atherosclerosis stage 3, cerebral infarcts stage 1, and cerebral atrophy stage 2. Granulovacuolar degeneration occurred in all centenarians. Some high performers had the highest neuropathology scores. DISCUSSION: Only Braak-NFT stage and limbic-predominant age-related TDP-43 encephalopathy (LATE) pathology associated significantly with performance across multiple cognitive domains. Of all cognitive tests, the clock-drawing test was particularly sensitive to levels of multiple neuropathologies.

Background: Many families with clinical early-onset Alzheimer’s disease (EOAD) remain genetically unexplained. A combination of genetic factors is not standardly investigated. In addition to monogenic causes, we evaluated the possible polygenic architecture in a large series of families, to assess if genetic testing of familial EOAD could be expanded. Methods: Thirty-six pedigrees (77 patients) were ascertained from a larger cohort of patients, with relationships determined by genetic data (exome sequencing data and/or SNP arrays). All families included at least one AD patient with symptom onset <70 years. We evaluated segregating rare variants in known dementia-related genes, and other genes or variants if shared by multiple families. APOE was genotyped and duplications in APP were assessed by targeted test or using SNP array data. We computed polygenic risk scores (PRS) compared with a reference population-based dataset, by imputing SNP arrays or exome sequencing data. Results: In eight families, we identified a pathogenic variant, including the genes APP, PSEN1, SORL1, and an unexpected GRN frameshift variant. APOE-ε4 homozygosity was present in eighteen families, showing full segregation with disease in seven families. Eight families harbored a variant of uncertain significance (VUS), of which six included APOE-ε4 homozygous carriers. PRS was not higher in the families combined compared with the population mean (beta 0.05, P = 0.21), with a maximum increase of 0.61 (OR = 1.84) in the GRN family. Subgroup analyses indicated lower PRS in six APP/PSEN1 families compared with the rest (beta −0.22 vs. 0.10; P = 0.009) and lower APOE burden in all eight families with monogenic cause (beta 0.29 vs. 1.15, P = 0.010). Nine families remained without a genetic cause or risk factor identified. Conclusion: Besides monogenic causes, we suspect a polygenic disease architecture in multiple families based on APOE and rare VUS. The risk conveyed by PRS is modest across the studied families. Families without any identified risk factor render suitable candidates for further in-depth genetic evaluation.

Introduction: With increasing age, neuropathological substrates associated with Alzheimer's disease (AD) accumulate in brains of cognitively healthy individuals—are they resilient, or resistant to AD-associated neuropathologies?. Methods: In 85 centenarian brains, we correlated NIA (amyloid) stages, Braak (neurofibrillary tangle) stages, and CERAD (neuritic plaque) scores with cognitive performance close to death as determined by Mini-Mental State Examination (MMSE) scores. We assessed centenarian brains against 2131 brains from AD patients, non-AD demented, and non-demented individuals in an age continuum ranging from 16 to 100+ years. Results: With age, brains from non-demented individuals reached the NIA and Braak stages observed in AD patients, while CERAD scores remained lower. In centenarians, NIA stages varied (22.4% were the highest stage 3), Braak stages rarely exceeded stage IV (5.9% were V), and CERAD scores rarely exceeded 2 (4.7% were 3); within these distributions, we observed no correlation with the MMSE (NIA: P = 0.60; Braak: P = 0.08; CERAD: P = 0.16). Discussion: Cognitive health can be maintained despite the accumulation of high levels of AD-related neuropathological substrates. Highlights: Cognitively healthy elderly have AD neuropathology levels similar to AD patients. AD neuropathology loads do not correlate with cognitive performance in centenarians. Some centenarians are resilient to the highest levels of AD neuropathology.

Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which involves advanced bioinformatic skills. We developed snpXplorer, an easy-to-use web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies, and displays regional information including SNP associations, structural variations, recombination rates, eQTL, linkage disequilibrium patterns, genes and gene-expressions per tissue. By overlaying multiple GWAS studies, snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. Given a list of SNPs, snpXplorer can also be used to perform variant-to-gene mapping and gene-set enrichment analysis to identify molecular pathways that are overrepresented in the list of input SNPs. snpXplorer is freely available at https://snpxplorer.net. Source code, documentation, example files and tutorial videos are available within the Help section of snpXplorer and at https://github.com/TesiNicco/snpXplorer.

BACKGROUND: Dementia in families can be caused by one genetic variant. Identifying these so-called monogenic causes of dementia is important, because it explains the origin of dementia in families and raises the possibility of predictive testing for relatives. Still, we do not know how frequent these monogenic causes are, due to strict selection criteria for DNA testing based on age at onset and a positive family history. We aimed to identify the mutation frequency of monogenetic dementia by screening a large, unselected cohort of patients from a memory clinic specialized in early onset dementia. METHOD: Between 1-1-2010 and 1-7-2012, 1,138 patients visited the Alzheimer Center Amsterdam and all patients underwent the same diagnostic trajectory (van der Flier et al 2018). Of these, 1,093 (96%) consented to research and donated blood. An additional 73 patients (7%) were excluded because suboptimal DNA quality. Whole exome sequencing and C9orf72-repeat length analysis was performed in the remaining 1,020 patients (90% of all patients). All variants in 54 dementia related genes were analysed and classified. C9orf72 repeat length >30 repeat units was considered pathogenic. Variants classified as likely pathogenic and pathogenic were considered a monogenic cause of dementia. RESULT: The average age at presentation was 62(±6SD) years and 419(41%) were female. We found a monogenic cause of dementia in 34 (3.4%) patients. The most frequently occurring (likely) pathogenic variants were found in the genes C9orf72, PSEN1, NOTCH3 and MAPT. These genes explained 65% of the (likely) pathogenic variants. The clinical characteristics of the patients screened positive; 50% were diagnosed with dementia and 50% had a first degree relative with dementia; and 40% had an age at presentation of <60 years and 44% was between 60 to 70 years, the remainder was older. Surprisingly, only 47% of the patients with a (likely) pathogenic variant fulfilled our current criteria (based on diagnosis, age and familial history) for offering diagnostic genetic testing (21% of patients). CONCLUSION: In our large unselected cohort of patients from a memory clinic specialized in early onset dementia, the majority of the patients with a monogenetic predisposition for dementia did not fulfill our current criteria for genetic testing.

BACKGROUND: Several collaborative genome-wide-association studies (GWAS) have characterized the genetic landscape of Alzheimer's disease (AD), which now counts >70 single-nucleotide polymorphisms (SNPs) associated with AD-risk. METHOD: We linked these SNPs to their affected biological pathways, and combined the effect of multiple SNPs into pathway-specific polygenic-risk-scores (PRS). Using a genetically homogeneous dataset of 2,458 AD-patients (age=70.2±10.4), 3,848 healthy controls (age=61.1±14.8), 343 cognitively healthy centenarians (age=101.1±1.8) and 705 individuals with mild-cognitive-impairment (MCI, age=69.1±8.9), we studied the association between pathway-PRS and AD-risk, MCI-to-AD conversion, and resilience against AD. RESULT: With an integrative strategy, we linked 72 AD-associated SNPs to 5 clusters of biological pathways: beta-amyloid cluster, immune cluster, vascular cluster, endocytosis cluster and a trafficking cluster (Figure 1). A PRS comprising all 72 SNPs (excluding APOE-SNPs) was significantly associated with AD-risk (OR=1.53, p<2e-16), progression of MCI to AD dementia (OR=1.45, p=5.5e-4), and, albeit in the opposite direction, resilience against AD in healthy centenarians (OR=0.82, p=6.4e-4) (Figure 2, Figure 3). At the pathway level, all pathway-PRS significantly associated with increased AD-risk while specifically the vascular-, endocytosis- and trafficking-PRS associated with resilience against AD (p<0.05) (Figure 4). Interestingly, the beta-amyloid-, endocytosis and trafficking-PRSs were significantly associated with MCI-to-AD progression (p<0.05), with a higher-PRS leading up to 1.5-year shorter conversion time. CONCLUSION: Our results add on the efficacy of pathway-specific PRSs to identify individuals at highest or the lowest risk for the development of AD. Further, our results suggest that specific biological pathways are more important at different stages of the disease or in fact, associate with the escape of disease. AD diagnostic procedures may benefit from the identification of individual, pathway-specific vulnerabilities. In the future, pathway-specific PRSs may contribute to the selection of patients who may benefit most from pathway-specific treatment strategies.