The APOE locus is the strongest genetic factor for Alzheimer's disease, with ε4 increasing and ε2 decreasing risk, yet the basis of these opposing effects remains unclear. Here we performed a multicohort proteomic analysis across plasma and cerebrospinal fluid in GNPC, BioFINDER-2, ADNI, UK BioBank, and PPMI. APOE-associated protein alterations are detectable before amyloid pathology and remain stable across age and disease progression. APOE2-associated proteins were enriched in pathways related to cellular maintenance and anti-inflammatory processes. By contrast, APOE4 showed a limited set of upstream mediators linked to cell-cycle and oligodendrocyte precursor cell biology, and a broader group of proteins reflecting vascular, immune, and proteostatic dysfunction shaped by downstream pathology. Comparative analyses highlighted allele-specific mediators and oppositely regulated proteins contributing to differential disease risk. Together, these findings reveal that APOE2 and APOE4 shape Alzheimer's disease risk through distinct molecular architectures and identify candidate biomarkers and targets for allele-specific interventions.

INTRODUCTION Genome-wide association studies (GWAS) have identified Bridging Integrator 1 ( BIN1 ) as the second-most significant genetic risk factor for Alzheimer’s disease (AD). We performed GWAS by proxy (GWAX) using UKBiobank and replicated this finding. However, the mechanism by which BIN1 impacts AD risk is largely unknown. METHODS To address this, we first measured the expression of BIN1 isoforms in a human induced pluripotent stem cells (hiPSC) model and further evaluated whether the BIN1 risk loci associated with the expression of BIN1 isoforms in a Phase 2 AD clinical trial. RESULTS Our data indicated BIN1 isoform expression patterns associated with the differentiation of hiPSC into neurons or microglia and found the variant rs35103166 impacts the expression of the BIN1 microglia-specific isoforms. DISCUSSION Given the strong association with susceptibility to AD, exploring the mechanisms of BIN1 genetic variants and their impacts on cell-type specific expression could serve as a valuable resource for novel drug discovery. Highlights ### Competing Interest Statement The authors have declared no competing interest. * GWAS : Genome-wide association study AD : Alzheimer’s disease BIN1 : Bridging integrator 1 SAIGE : Scalable and Accurate Implementation of Generalized Mixed Model hiPSC : Human induced pluripotent stem cells SNP : Single nucleotide polymorphism NPC : Neural progenitor cells PB : Peripheral blood

The ε4 and ε2 alleles of the Apolipoprotein E (APOE) gene confer opposite genetic risks for Alzheimer's disease (AD), but their underlying molecular mechanisms remain poorly characterized in humans. To resolve this, we systematically profiled APOE-associated proteomic alterations across five cohorts-including the Global Neurodegeneration Proteomics Consortium (GNPC), BioFINDER-2, the Alzheimer's Disease Neuroimaging Initiative (ADNI), the Parkinson's Progression Markers Initiative (PPMI), and UK Biobank (UKB)-using SomaLogic and OLINK platforms in plasma and cerebrospinal fluid (CSF) from over 10,000 individuals. Using GNPC (plasma SomaLogic, N=4,045), we mapped a comprehensive APOE-protein network and applied mediation modeling to classify genotype-related signals as upstream mediators, downstream consequences, or APOE-specific changes. We then leveraged CSF beta-amyloid (Aβ) biomarker data from BioFINDER-2 (plasma SomaLogic, N=1,421) to improve temporal resolution and isolate early, Aβ-independent proteomic programs. In the Aβ- individuals, APOE4 was linked to cell cycle and chromatin remodeling, while APOE2 was associated with mitochondrial regulation and DNA repair. Mediation analyses nominated proteins such as S100A13, TBCA, SPC25 for APOE4, and APOB, SNAP23 for APOE2 as candidate upstream effectors, supported by CSF validation (ADNI, SomaLogic, N=666), brain transcriptomic co-expression, and AD GWAS colocalization. Longitudinal CSF data from PPMI confirmed the temporal stability of several APOE-associated proteins. Cross-platform comparisons (UKB plasma OLINK, N=4,820, and BF2 CSF OLINK, N=1,475) revealed matrix- and assay-specific heterogeneity, underscoring challenges in reproducibility. Together, our results delineate allele-specific, temporally structured proteomic signatures that precede AD pathology, offering insight into APOE-driven molecular pathways and potential therapeutic targets for early intervention.

Background Analysis of cerebrospinal fluid (CSF) facilitates the understanding of brain-specific molecular changes that may associate with disease progression. Proximity extension assays (PEA) have been deployed in several CSF studies, however the validation of the assay and impact of freeze-thaw cycles on the protein signal has not been documented. We sought to ([1][1]) validate the assay on the PEA platform and ([2][2]) evaluate the effect of freeze-thaw cycles on the detectability of analytes on the PEA platform. Results We have validated the PEA with Next Generation Sequencing (NGS) readout assay and report on the detectability and coefficient of variation observed in CSF samples. We have also evaluated proteomic signals with a minimum of 3 and a maximum of 9 freeze thaw cycles and detected very minimal change in signal with increasing cycle number. Conclusion Our study is the first to validate PEA using NGS readout platform with CSF samples. We report lower protein detection rates and higher variability in the expansion panels compared to the original 4 panels, with acceptable variation above detectability threshold. In addition, our work demonstrates that the proteomic signal is robust and continues to be stable across multiple freeze thaw cycles. This is highly impactful to the processing and analysis of clinical samples and facilitates the investigation of samples with variable pre-analytical conditions. ### Competing Interest Statement The authors have declared no competing interest. * ALS : Amyotrophic lateral sclerosis CNS : Central nervous system CSF : Cerebrospinal fluid CV : Coefficient of variation PEA : Proximity Extension Assay LOD : Limit of detection NPX : Normalized protein expression NGS : Next Generation Sequencing F/T : freeze/thaw [1]: #ref-1 [2]: #ref-2

Alzheimer’s disease (AD) is an increasing societal burden globally, with an urgent need for early screening strategies to improve disease management. Multiomics profiling represents a promising approach for identifying biomarkers and stratifying disease risk. We analysed data from a cohort of 391 individuals (mean age: 73.6 ± 6.7 years) enrolled in the Australian Imaging, Biomarkers, and Lifestyle (AIBL) study. Multi-Omics Factor Analysis (MOFA) was employed to integrate and identify key axes of variation (latent factors) across three omics datasets: RNA sequencing (N = 19259), single nucleotide polymorphisms (SNPs, N = 298516), and DNA methylation (N = 154846). Latent factors were subsequently assessed with PET Amyloid (Spearman’s Rho) and time to progression (accounting for age), using Cox proportional hazards models. Time to event was derived as time for a participant to progress from MCI to AD, or time the participant remained MCI (censored). The unsupervised integration using MOFA showed that the principal axes of variation captured combined contributions from all three omics datasets. DNA methylation explained the largest proportion of variance, followed by RNA sequencing and SNP genotype data (31.8%, 13.9%, and 0.9% cumulative variance explained across the first 10 factors, respectively). Post hoc analyses showed that one of the factors was correlated with PET Amyloid levels (Rho = 0.20, controlling for age and APOE ε4). This factor also significantly predicted time to event, with participants exhibiting higher scores progressing to AD more quickly (Figure 2). This study demonstrates the utility of multiomics integration for uncovering biologically relevant patterns in AD and its potential application disease risk stratification. Future research should focus on validating these patterns in larger, independent cohorts and exploring their utility in clinical applications.

The Alzheimer's Disease Neuroimaging Initiative (ADNI) Private Partners Scientific Board (PPSB) Diversity, Equity, and Inclusion Working Group (DE&I WG) was established to work with the ADNI3 Diversity Task Force to provide an industry perspective on increasing the representation of diverse participants in ADNI3 and to build precompetitive cross-industry knowledge in engagement and recruitment of under-represented participants (URPs). In this article, we review and highlight the role and ongoing activities within the ADNI PPSB DE&I WG and provide a cross-industry perspective on areas where precompetitive collaboration can improve the inclusiveness in clinical trials, drawing on examples from ADNI4.

Determining the genetic architecture of Alzheimer's disease pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we perform a genome-wide association study of cortical tau quantified by positron emission tomography in 3046 participants from 12 independent studies. The CYP1B1-RMDN2 locus is associated with tau deposition. The most significant signal is at rs2113389, explaining 4.3% of the variation in cortical tau, while APOE4 rs429358 accounts for 3.6%. rs2113389 is associated with higher tau and faster cognitive decline. Additive effects, but no interactions, are observed between rs2113389 and diagnosis, APOE4, and amyloid beta positivity. CYP1B1 expression is upregulated in AD. rs2113389 is associated with higher CYP1B1 expression and methylation levels. Mouse model studies provide additional functional evidence for a relationship between CYP1B1 and tau deposition but not amyloid beta. These results provide insight into the genetic basis of cerebral tau deposition and support novel pathways for therapeutic development in AD.

Alzheimer's disease (AD) is the most common global dementia and is universally fatal. Most late-stage AD disease-modifying therapies are intravenous and target amyloid beta (Aβ), with only modest effects on disease progression: there remains a high unmet need for convenient, safe, and effective therapeutics. Senescent cells (SC) and the senescence-associated secretory phenotype (SASP) drive AD pathology and increase with AD severity. Preclinical senolytic studies have shown improvements in neuroinflammation, tau, Aβ, and CNS damage; most were conducted in transgenic rodent models with uncertain human translational relevance. In this study, aged cynomolgus monkeys had significant elevation of biomarkers of senescence, SASP, and neurological damage. Intermittent treatment with the senolytic navitoclax induced modest reversible thrombocytopenia; no serious drug-related toxicity was noted. Navitoclax reduced several senescence and SASP biomarkers, with CSF concentrations sufficient for senolysis. Finally, navitoclax reduced TSPO-PET frontal cortex binding and improved CSF biomarkers of neuroinflammation, neuronal damage, and synaptic dysfunction. Overall, navitoclax administration was safe and well tolerated in aged monkeys, with meaningful changes in biomarkers relevant to human neurodegenerative disease.

Alzheimer’s disease (AD) is the most common global dementia and is universally fatal. Most late-stage AD disease-modifying therapies are intravenous and target amyloid beta (Aβ), with only modest effects on disease progression: there remains a high unmet need for convenient, safe, and effective therapeutics. Senescent cells (SC) and the senescence-associated secretory phenotype (SASP) drive AD pathology and increase with AD severity. Preclinical senolytic studies have shown improvements in neuroinflammation, tau, Aβ, and CNS damage; most were conducted in transgenic rodent models with uncertain human translational relevance. In this study, aged cynomolgus monkeys had significant elevation of biomarkers of senescence, SASP, and neurological damage. Intermittent treatment with the senolytic navitoclax induced modest reversible thrombocytopenia; no serious drug-related toxicity was noted. Navitoclax reduced several senescence and SASP biomarkers, with CSF concentrations sufficient for senolysis. Finally, navitoclax reduced TSPO-PET frontal cortex binding and showed trends of improvement in CSF biomarkers of neuroinflammation, neuronal damage, and synaptic dysfunction. Overall, navitoclax administration was safe and well tolerated in aged monkeys, inducing trends of biomarker changes relevant to human neurodegenerative disease.

Limited understanding of the diversity of variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene across ancestries hampers efforts to advance molecular diagnosis of cystic fibrosis (CF). The consequences pose a risk of delayed diagnoses and subsequently worsened health outcomes for patients. Therefore, characterizing the spectrum of CFTR variants across ancestries is critical for revolutionizing molecular diagnoses of CF. We analyzed 454,727 UK Biobank (UKBB) whole-exome sequences to characterize the diversity of CFTR variants across ancestries. Using the PanUKBB classification, the participants were assigned into six major groups: African (AFR), American/American Admixed (AMR), Central South Asia (CSA), East Asian (EAS), European (EUR), and Middle East (MID). We segregated ancestry-specific CFTR variants, including those that are CF-causing or clinically relevant. The ages of certain CF-causing variants were determined and analyzed for selective pressure effects, and curated phenotype analysis was performed for participants with clinically relevant CFTR genotypes. We detected over 4000 CFTR variants, including novel ancestry-specific variants, across six ancestries. Europeans had the most unique CFTR variants [n = 2212], while the American group had the least unique variants [n = 23]. F508del was the most prevalent CF-causing variant found in all ancestries, except in EAS, where V520F was the most prevalent. Common EAS variants such as 3600G > A, V456A, and V520, which appeared approximately 270, 215, and 338 generations ago, respectively, did not show evidence of selective pressure. Sixteen participants had two CF-causing variants, with two being diagnosed with CF. We found 154 participants harboring a CF-causing and varying clinical consequences (VCC) variant. Phenotype analysis performed for participants with multiple clinically relevant variants returned significant associations with CF and its pulmonary phenotypes [Bonferroni-adjusted p < 0.05]. We leveraged the UKBB database to comprehensively characterize the broad spectrum of CFTR variants across ancestries. The detection of over 4000 CFTR variants, including several ancestry-specific and uncharacterized CFTR variants, warrants the need for further characterization of their functional and clinical relevance. Overall, the presentation of classical CF phenotypes seen in non-CF diagnosed participants with more than one CF-causing variant indicates that they may benefit from current CFTR modulator therapies.

Introduction: Elezanumab (EZB), a monoclonal antibody specific to repulsive guidance molecule A (RGMa), is under investigation to treat acute ischemic stroke. Biomarker evidence in ischemic stroke and for the RGMa pathway is limited. Methods: This blinded, in-study analysis from a 52-week phase 2a, multicenter, randomized (1:1; EZB:placebo) clinical trial (NCT04309474) included patients aged 30-90 years with an acute ischemic stroke (onset ≤ 24 hours before baseline), and a NIHSS score of 7-21. Blinded analyses did not distinguish between treatment arms. Healthy adult controls were procured outside this trial. Blood samples were taken post-stroke across 52 weeks, or 1 time (baseline) for healthy adults. Plasma concentrations of neurodegenerative markers neurofilament light chain protein (NfL) and glial fibrillary acidic protein (GFAP) were measured (validated Simoa Human Neurology 4-Plex A assay; Quanterix). Protein, mRNA, and miRNA were assessed with omics approaches. Results: This preliminary analysis included 34 patients with stroke (mean [SD] age 67.1 [12.3] years, 58.8% male) and 31 healthy adults (61.8 [8.0] years, 71.0% male). The mean (SD) baseline NIHSS total score was 10.9 (4.3). NfL and GFAP concentrations were elevated on day 1 in patients with stroke vs healthy adults (healthy adults are included for reference only). Mean concentrations of NfL were 48.7 pg/mL vs 13.9 pg/mL, respectively; mean concentrations of GFAP were 746.0 pg/mL vs 137.2 pg/mL, respectively. In patients with stroke, agnostic to treatment, peak NfL and GFAP elevations occurred at day 28 and days 2-4, respectively; NfL and GFAP concentrations were lower at week 52 than day 1. Conclusions: Preliminary blinded analysis of plasma markers of neurodegeneration confirm increased NfL and GFAP levels during acute stroke, which diminish over time with different temporal patterns. Final unblinded results will provide a robust natural time course of specific biomarkers of neurodegeneration including GAP43. Forthcoming analyses evaluate broad panels of proteins, mRNA, and miRNA markers. Identifying relevant post stroke biomarkers with directed and exploratory omics may allow development of validated assays to assess efficacy and support decision making in clinical trials.

PDF file, 83K, RNA-Sequencing of Vector and DNMT3B7 expressing LA1-55n cells.

PDF file, 83K, DNMT3B7 expression in LA1-55n transduced cells by RNA-Sequencing.

PDF file, 56K, Relative DNA methylation by mass spectrometry.

<p>PDF file, 58K, Establishment of KCNR neuroblastoma cells overexpressing DNMT3B7.</p>

Supplementary Methods, Figures 1-10, Tables 1-8 from DNMT3B7, a Truncated DNMT3B Isoform Expressed in Human Tumors, Disrupts Embryonic Development and Accelerates Lymphomagenesis