Biology subjects

Wilkins, H. M.

Publications and source records attributed to Wilkins, H. M..

6 recordsLinked to original sources

bioRxiv2026

Patient cerebral organoids capture Alzheimers disease proteomic biomarkers and drug targets

Patient iPSC-derived cerebral organoids are a leading human model of Alzheimers disease, yet their proteome has never been benchmarked against human disease. Clinical cohorts now nominate thousands of biomarkers and drug targets across three proteomic platforms, and whether patient organoids capture these candidates is unknown. Here, we profile AD and control cerebral organoids containing neurons, astrocytes, and microglia on the three platforms driving clinical discovery, mass spectrometry, SomaScan, and Olink, in both conditioned media and lysate. Benchmarked against 121 studies and clinical cohorts of over 17,000 plasma, CSF, and cortex samples, patient organoids detect almost every nominated candidate and reproduce the disease-associated change in roughly one in four of the most reproducible. This convergence spans plasma, CSF, and cortex, and extends to synaptic, mitochondrial, and proteostatic biology. We provide the first multi-platform reference proteome of a patient-derived AD model, establishing it as a translationally relevant system for studying AD.

neuroscience↗

bioRxiv2025

Mapping the circulating proteome across neurodegeneration: A harmonized, consortium-scale framework for uncovering molecular pathophysiology

Large-scale plasma proteomics offers unprecedented opportunities to investigate the systemic biology of neurodegeneration, yet technical heterogeneity, site-specific artifacts, and clinical confounding remain major barriers to reproducible discovery. Leveraging data from 13,733 individuals with Alzheimers disease (AD), Parkinsons disease (PD), frontotemporal dementia (FTD), Parkinsons disease dementia (PDD), amyotrophic lateral sclerosis (ALS), and non-impaired controls in the Global Neurodegeneration Proteomics Consortium (GNPC), we present a scalable and generalizable analytical framework for harmonizing and interpreting consortium-scale proteomic datasets. Using a high-dimensional perturbation framework, we systematically benchmark five commonly used batch correction methods across a range of realistic confounding structures, including site-disease imbalance, nonlinear effects, and heteroskedasticity. Empirical Bayes modelling via limma consistently emerged as the most robust method, optimally balancing removal of site-related technical variance with retention of disease-relevant biological signal. On this harmonized foundation, we resolve neurodegenerative disease plasma signatures, including a shared immune-metabolic axis in AD and PD, neuromuscular disruption in ALS, and proteostatic imbalance in PD. Tissue and cell-type enrichment highlight widespread immune-endocrine involvement in AD and hematopoietic activation in PD. Demographically matched analyses nominate distinct, candidate biomarkers across diseases, including lipid, redox, and complement factors in AD, lysosomal and cytoskeletal proteins in PD, and muscle-derived markers in ALS. This study establishes a scalable analytical framework for integrating real-world proteomic data and provides a disease-resolved catalogue of circulating signatures to inform biomarker development and targeted intervention across neurodegenerative diseases.

neuroscience↗

bioRxiv2025

AHA1 regulates Aβ production via modulation of APP expression and γ-secretase assembly

Deposition of amyloid {beta}-protein (A{beta}) is a hallmark of Alzheimers disease (AD), produced by {gamma}-secretase-mediated cleavage of amyloid precursor protein (APP). The 90-kDa heat shock protein (Hsp90) co-chaperone, activator of Hsp90 ATPase homolog 1 (AHA1), is known to promote the accumulation of toxic tau species; however, its effects on A{beta} production remain unclear. Here, we show that knockdown of endogenous AHA1 decreases A{beta} generation and reduces APP and {gamma}-secretase components, whereas AHA1 overexpression elevates A{beta} production and the expression of these proteins. The AHA1-E67K mutant, which has impaired Hsp90 binding, lowers A{beta} production and the levels of APP and {gamma}-secretase components compared with wild-type AHA1. AHA1 associates with APP and immature {gamma}-secretase components, including anterior pharynx-defective phenotype 1 (APH1), indicating its role in APP proteolysis and A{beta} production. Disruption of the AHA1/Hsp90 complex--through AHA1 knockdown, the E67K mutant, or a small-molecule inhibitor--reduces {gamma}-secretase assembly. Familial AD mutations in APP-C99 and presenilin-1 (PS1) increase AHA1, Hsp90, APP, and APH1 expression, enhancing A{beta} production. Importantly, AHA1 knockdown decreases abnormal A{beta} generation and C99, PS1-CTF, and APH1 levels in mutant APP cells, while AHA1 overexpression enhances A{beta} production in PS1 mutant cells. Collectively, these findings reveal that AHA1 regulates A{beta} production by modulating APP expression and {gamma}-secretase assembly, establishing AHA1 as a potential target for therapeutic intervention in AD.

neuroscience↗

bioRxiv2025

Loss of ovarian function and estrogen therapy remodel the brain's synaptic and metabolic proteome

Menopause is linked to cognitive decline and reduced brain metabolism, while estrogen (E2) therapy has been shown to mitigate these effects. Understanding the molecular mechanisms by which ovarian hormones and E2 influence neuroprotection is essential for developing strategies to maintain brain health in women. In this study, we examined how the loss of ovarian hormones, with or without E2 treatment, affects the brain proteome and mitochondrial energy production in aged female C57BL/6J mice (36-40 weeks). The mice underwent sham or ovariectomy (OVX) surgery and were fed a high-fat diet for 10 weeks; six weeks after surgery, OVX mice received either sesame oil or E2 treatment for four weeks. Proteomic analysis of brain homogenates revealed 4,992 proteins regulated by E2, with pathway analysis showing increased signaling proteins related to synaptogenesis. OVX reduced proteins involved in synaptic function, branched-chain amino acid and ketone metabolism, the TCA cycle, and oxidative phosphorylation (Complexes I, IV, and V), while E2 restored protein expression within these pathways. Despite alterations in OxPhos proteins, basal and state 3 mitochondrial respiration remained unchanged, although notable impairments to Complex IV enzymatic activity were apparent in OVX, but not following E2 replacement. Overall, these results indicate that E2 supports brain health by maintaining proteins crucial for synaptic integrity and metabolism, and by reducing the decline in mitochondrial bioenergetics associated with menopause.

neuroscience↗

bioRxiv2025

Proteomic and metabolic profiling reveals APOE4-dependent shifts in whole brain, neuronal, and astrocytic mitochondrial function and glycolysis

Apolipoprotein E (APOE) genetic variation is the strongest genetic risk factor for late onset Alzheimers disease (LOAD). Studies on APOE genotype dependent changes have largely focused on amyloid beta (A{beta}) aggregation, disease pathology, and lipid metabolism. Recently, there has been increased interest in the relationship between metabolic function and APOE genetic variation. In this study, we examined how APOE genotype can alter metabolism in the brains of young male and female APOE3 and APOE4 targeted replacement (TR) mice. In combination with this, we also examined cell type-specific differences using induced pluripotent stem cell (iPSC) derived astrocytes and neurons. We found sex and genotype dependent changes to metabolism in the brains of young APOE TR mice. Specifically, APOE4 mice show signs of metabolic stress and compensatory mechanisms in the brain. Using proteomics and stable isotope tracing metabolomics, we found that APOE4 iAstrocytes and iNeurons exhibit signs of inflammation, mitochondrial dysfunction, altered TCA cycle and malate-aspartate shuttle activity, and a metabolic shift toward glycolysis. Taken together, this data indicates APOE4 causes early changes to metabolism within the central nervous system. While this study establishes a relationship between APOE genotype and alterations in bioenergetics, additional studies are needed to investigate underlying mechanisms.

neuroscience↗

bioRxiv2024

Cerebrospinal fluid proteome profiling using machine learning shows a unique protein signature associated with APOE4 genotype

INTRODUCTIONProteome changes associated with APOE4 variant carriage that are independent of Alzheimers disease (AD) pathology and diagnosis are unknown. This study investigated APOE4 proteome changes in people with AD, mild cognitive impairment, and no impairment. METHODSClinical, APOE genotype, and cerebrospinal fluid (CSF) proteome and AD biomarker data was sourced from the Alzheimers Disease Neuroimaging Initiative (ADNI) database. Proteome profiling was done using supervised machine learning. RESULTSWe found an APOE4-specific proteome signature that was independent of cognitive diagnosis and AD pathological biomarkers, and increased risk of progression to cognitive impairment. Proteins were enriched in brain regions including the caudate and cortex and cells including endothelial cells, oligodendrocytes, and astrocytes. Enriched peripheral immune cells included T cells, macrophages, and B cells. DISCUSSIONAPOE4 carriers have a unique CSF proteome signature associated with a strong brain and peripheral immune and inflammatory phenotype that likely underlies APOE4 carriers vulnerability to cognitive decline and AD.

neuroscience↗