阿尔兹海默；微生物；类器官

阿尔茨海默病(Alzheimer disease, AD)是一种神经退行性疾病，主要表现为认知障碍。酒作为日常饮品虽能给人体带来益处，但过度饮酒将损害机体健康，目前研究成果展示由于酒精滥用会增加患AD的风险。为了探讨酒精对AD的作用机制，本文将通过AD的发病机制与酒精滥用对机体产生的危害进一步阐明酒精滥用对AD的影响。结果显示，酒精滥用将会导致机体产生炎症和氧化应激，而氧化应激又将进一步加重机体的炎症反应。此外，酒精滥用还会危害人体肠道微生物的数量及比例分布等，进而导致微生物生态失衡，不仅如此，肠道微生物还因酒精滥用导致炎症，这也将进一步危害机体的健康。又因氧化应激、炎症反应等又会加快AD的发病，所以由酒精滥用引起的氧化应激、炎症反应、肠道微生物失调等因素也能促进AD的发展。因此，控制酒精的摄取可能会在一定程度上减缓AD的发病，起到预防AD的作用。

阿尔茨海默病(Alzheimer’s disease，AD)是具有复杂病理特征的疾病，AD在病情发展过程中会对患者脑部造成不可逆的损害而导致记忆障碍，记忆缺失对正常生活有着影响，而且AD多发于老年人群体。对于日益加剧的人口老龄化现象，存在着极大的风险隐患。进行尸检样本的解剖研究对现阶段研究AD已经十分局限，进行动物模型研究可以寻求新突破口，在实验室中，可以通过细胞离体培养、转基因动物、特定环境设置、手术处理改变特定物质分泌等手段，直接明了地观测受试动物机体中各种有关物质的变化，例如淀粉样蛋白、神经原纤维缠结、γ分泌酶、炎症因子等与AD相关的物质的活性与水平，为后续开展针对性治疗奠定理论基础。此外，这些实验模型研究可帮助更好地理解该疾病的病理学机制，并为临床治疗提供思路。

肠道菌群对认知能力障碍的形成和进展具有显著影响。研究指出，调整肠道微生物群有助于缓解痴呆症的表现。传统中医学中的“脾胃”可类比肠道菌群在人体生命活动中生理及病理方面所发挥作用，通过调理脾胃来改善认知障碍的有效性已得到验证。截至当前，研究人员正处于初步阶段，利用中医药调整肠道菌群以预防和治疗痴呆症。本研究旨在通过调节肠道菌群，以传统医学脾胃生理病理特性为切入点，探索治疗认知障碍的机制，进而为认知功能障碍的干预提供新的思路。

阿尔茨海默病(Alzheimer’s disease, AD)的中医认识历史悠久，历代医家对本病的病因病机有不同的认识，随着AD的病因病机研究不断深入，我国医学专家对AD的病因病机把握越来越明晰。对AD的探讨研究发现，AD的病因病机主要包括髓海不足说、脾肾互赞说、痰浊蒙窍说、毒损脑络说、肝肠脑相维说等，这些学说各有理论依据及临床意义，但仍有不足之处有待商榷和补充，本文结合先贤所执之见，对AD的病因和病机进行了全面的梳理和归纳总结，以期为后续临床的诊疗提供参考。

肌少症与认知障碍是严重危害老年人健康的常见共病，二者相互影响，形成恶性循环。中医“筋为精神之外辅”理论深刻揭示了“筋”与“神”的辩证统一关系，为理解肌少症与认知障碍共病提供了中医理论依据。文章系统阐述了该理论的哲学内涵及筋与精神的生理联系，指出肌少症与认知障碍共病的核心病机为“精亏髓减，筋脑共损”。基于此，防治应遵循“以筋调神，以神驭筋”的原则，以易筋经、站桩等传统功法为实践手段，通过形、气、神协同调控干预肌脑轴，为防治老年筋神共病提供了中医思路。

BACKGROUND & AIMS Tuft cells, a type of epithelial cell in the gut, play a pivotal role in regulating type 2 immunity and maintaining the gut barrier. However, their role in cognitive impairments remains unclear. METHODS We compared behavioral performance between male tuft cell-absent mice (Pou2f3-/-) and their wild-type littermates (WT). We analyzed gut microbiota using fecal 16S rRNA, measured gut permeability via FITC-dextran assay, and detected CD4+-T cells and type 2 innate lymphoid cells by flow cytometry in both genotypes. Co-housing and fecal microbiota transplantation (FMT) experiments were conducted to explore the role of gut microbiota in cognitive diseases. Single-cell RNA sequencing and fluorescence imaging were used to examine tuft cell changes in the colon of WT and Alzheimer's disease (AD) model mice. Colonic organoids were used to assess the effect of β-amyloid on tuft cell differentiation. Succinic acid, a promoter of tuft cells, was administered, and tuft cell-deficient AD mice were generated to evaluate its impact on behavior and gut homeostasis. RESULTS Increased gut permeability, immune imbalance, neuroinflammation, and cognitive dysfunction occurred in 10-month-old mice lacking tuft cells. These alterations were mediated by gut microbiota, evidenced by shifts in microbiota composition and abundance, and supported by co-housing and FMT experiments. AD model mice had fewer tuft cells and impaired type 2 immunity in the gut, potentially because of β-amyloid inhibiting tuft cell differentiation. Succinic acid, a tuft cell activator, restored cognitive function and gut homeostasis in AD mice. CONCLUSION Tuft cells may be necessary for maintaining gut homeostasis in cognitive disorders.

Gut microbiota dysbiosis is linked to Alzheimer’s disease (AD), but our understanding of the molecular and neuropathological bases underlying such association remains fragmentary. Using 16S rDNA amplicon sequencing, untargeted metabolomics, and multi-modal magnetic resonance imaging, we examined group differences in gut microbiome, fecal metabolome, neuroimaging measures, and cognitive variables across 30 patients with AD, 75 individuals with mild cognitive impairment (MCI), and 61 healthy controls (HC). Furthermore, we assessed the associations between these multi-omics changes using correlation and mediation analyses. There were significant group differences in gut microbial composition, which were driven by 8 microbial taxa (e.g., Staphylococcus and Bacillus) exhibiting a progressive increase in relative abundance from HC to MCI to AD, and 2 taxa (e.g., Anaerostipes) showing a gradual decrease. 26 fecal metabolites (e.g., Arachidonic, Adrenic, and Lithocholic acids) exhibited a progressive increase from HC to MCI to AD. We also observed progressive gray matter atrophy in broadly distributed gray matter regions and gradual micro-structural integrity damage in widespread white matter tracts along the AD continuum. Integration of these multi-omics changes revealed significant associations between microbiota, metabolites, neuroimaging, and cognition. More importantly, we identified two potential mediation pathways: (1) microbiota → metabolites → neuroimaging → cognition, and (2) microbiota → metabolites → cognition. Aside from elucidating the underlying mechanism whereby gut microbiota dysbiosis is linked to AD, our findings may contribute to groundwork for future interventions targeting the microbiota-metabolites-brain-cognition pathways as a therapeutic strategy in the AD continuum.

BACKGROUND Alzheimer's disease (AD), which is a chronic neurodegenerative disorder, is marked by the progressive deteriorations in learning and memory capabilities. The microbiota-gut-brain axis has come to be regarded as a crucial element in relation to the pathogenesis as well as the treatment of AD. Eucommiae cortex polysaccharides (EPs), being among the most plentiful substances present in the Eucommiae cortex, show the potential to exert immunomodulatory and neuroprotective function. However, whether EPs are protective against AD and their mechanism of action remain to be investigated OBJECTIVES: We hypothesize that EPs can regulate brain glutamine metabolism through gut microbiota and the butyric acid metabolized by them, improve oxidative stress and autophagy in the brain, and thus alleviate AD. METHODS In the present study, we used EPs (0.25 % w/w in food) and fecal microbiota transplantation, as well as butyrate supplementation (0.1 M in water), to intervene in AD mice. Multi-omics were used to determine the mechanism by which EPs improve AD-related learning and memory impairments. RESULTS Our results suggest that EPs, functioning as a prebiotic, alleviated learning and memory impairments in AD mice. Mechanistically, EPs are able to reshape the gut microbiota, promote the growth of gut microbiota involved in short-chain fatty acid metabolism, particularly butyrate-producing microbes. The butyrate produced by these microbes improves the brain microenvironment by modulating oxidative stress and autophagy mediated by brain glutamate metabolism, improving learning and memory impairments in AD mice, and inhibiting the formation and deposition of beta-amyloid proteins. Fecal microbiota transplantation (FMT) and butyrate supplementation further confirm this conclusion. CONCLUSIONS Our results highlighted that EPs can alleviate learning and memory impairments in AD with a gut microbiota-dependent manner and that butyric acid metabolized by butyric acid-metabolizing bacteria in the gut plays a central role in regulating brain glutamine metabolism to improve brain microenvironmental homeostasis. Meanwhile, the present study provides new insights into the treatment of AD with natural products.

Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer’s disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance. We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers. We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration. Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.

Ganoderma lucidum is a traditional Chinese medicine used to treat Alzheimer's disease (AD), whose main active ingredient is polysaccharides. A heteropolysaccharide named GLPZ-1 was isolated from Ganoderma lucidum. GLPZ-1 (6.608 kDa) predominantly consisted of Glc and minor Gal. The results of GC-MS and NMR analyses indicated that the backbone of GLPZ-1 was mainly composed of 1,4-α-D-Glcp, 1,4,6-α-Glcp and a minor amount of 1,3,4-β-D-Glcp, which was substituted with complex side chains at C-6 of 1,4,6-α-D-Glcp and at C-3 of 1,3,4-β-D-Glcp. GLPZ-1 demonstrated a protective effect on AD rats by improving behavioral abnormalities, alleviating pathological damage and ameliorating levels of IL-6, IL-1β, TNF-α and Th17, which were associated with GLPZ-1 modulating the microbiota-gut-metabolomics of AD rats. GLPZ-1 regulated the gut microbiota in AD rats by increasing the abundance of Bacteroides, unclassified_Lachnospiraceae, Lactobacillus, Pediococcus, Oscillibacter, Lachnoclostridium and Bifidobacterium, while simultaneously reducing the abundance of Pseudomonas and Desulfovibrio. GLPZ-1 could regulate fecal metabolites in AD rats tending towards the normal levels. These regulated fecal metabolites belonged to fatty acid metabolism, cholesterol and bile acid metabolism, neurotransmitters and aromatic amino acid metabolism. These findings provide a preliminary research basis for the exploitation of GLPZ-1 as an effective drug to prevent and delay AD.

Evidence indicates that Poria cocos polysaccharide (PCP) improves cognitive impairment in Alzheimer's disease (AD); however, its underlying mechanism, particularly its relationship with the gut microbiota, remains unclear. In the current study, we aimed to investigate the mechanism of PCP in improving cognitive impairment in AD. The results demonstrated that PCP markedly enhanced cognitive function and mitigated AD-related pathological alterations in 3 × Tg-AD mice. PCP treatment reversed the age-dependent gut microbiota dysbiosis in 3 × Tg-AD mice by 16S rDNA sequencing. The contents of propanoic acid, butanoic acid and isohexanoic acid were increased by short-chain fatty acid determination. In addition, PCP could restore both the intestinal barrier and the blood-brain barrier, as demonstrated by immunofluorescence staining of tight junction proteins. Furthermore, PCP alleviated systemic inflammation and neuroinflammation, as evidenced by reduced LPS levels in circulation and decreased IL-6 levels in the brain, likely by inhibiting the TLR4/NF-κB signaling pathway. In conclusion, PCP can reshape gut microbiota to regulate short-chain fatty acids and alleviate neuroinflammation-related cognitive impairment in AD mice.

No abstract available

Plant-based foods with low methionine contents have gained increasing interest for their potential health benefits, including neuroprotective effects. Methionine restriction (MR) linked to a plant-based diet has been shown to mitigate neurodegenerative diseases such as Alzheimer's disease (AD) through mechanisms that involve the gut microbiota. In this study, a 16-week MR diet (0.17% methionine, w/w) improved working memory and reduced neuronal damage exclusively in 4-month-old male APP/PS1 AD mice. Transcriptomic analysis revealed the activation of serum- and glucose-corticoid-regulated kinase 1 (SGK1) and peroxisome proliferator-activated receptor α (PPARα) pathways. Furthermore, metabolomics demonstrated increased serum indole-3-propionic acid (IPA) levels and an enhanced expression of gut barrier proteins Claudin-1 and MUC2 in male mice. MR significantly altered the gut microbiota composition, notably increasing indole-producing bacteria such as Lactobacillus reuteri (L. reuteri). Multiomics integration linked L. reuteri, IPA, and PPARα signaling to improved cognitive outcomes. Molecular docking and RT-qPCR analyses confirmed IPA's interaction with PPARα, leading to the activation of neuroprotective targets (Bdnf, Pparα, Acsbg1, Scd2, and Scd3). These results highlight the role of methionine restriction in modulating gut microbiota and metabolites, offering a promising dietary approach to managing neurodegenerative diseases with sex-specific effects.

ABSTRACT Emerging clinical and experimental evidence highlight the involvement of gut microbiota in the onset and progression of neurodegenerative diseases such as Alzheimer’s disease (AD) via neuroinflammatory processes along the gut–brain axis. Despite this, the precise mechanisms governing gut microbial involvement in AD remain elusive. In this study, we observed that AppNL-G-F AD mice raised under germ-free (GF) conditions, display a reduced amyloid-β (Aβ) pathology, accompanied by a shift in microglial cells toward a less inflammatory state and increased phagocytotic efficiency. In addition, we demonstrate that gut microbiota depletion can protect against synaptic deficits in AD mice. Notably, administering bacterial extracellular vesicles (bEVs), i.e. nano-sized particles packed with bacterial components, derived from fecal slurry from specific pathogen-free housed AppNL-G-F AD mice, reversed the effects of GF conditions on both microglial activation and Aβ plaque accumulation. These findings reveal for the first time that commensal gut microbiota-derived bEVs have a major impact on AD pathology progression.

Introduction The gut microbiota composition and the expression profiles of microRNAs (miRNAs) in the brain tissue, cerebrospinal fluid, and blood of patients with Alzheimer’s disease (AD) differ significantly from those with normal cognition function. The study aimed to initially explore the relationship between plasma exosomal microRNAs, gut microbiota, and cognitive impairment, providing insights into the pathogenesis and treatment of AD. Methods The study enrolled 8 participants with AD and 8 participants with normal cognition. The Mini-Mental State Examination (MMSE) was utilized to evaluate cognitive function. High-throughput sequencing was used to identify differentially expressed miRNAs in plasma exosomes, while metagenomic sequencing was employed to detect differences in the abundance of gut microbiota. Furthermore, the associations among them were analyzed. Results Four exosomal miRNAs and 14 microbiota taxa, which exhibited differential expression and abundance, respectively, in comparison between AD group and normal cognition group, were identified to be significantly associated with MMSE scores. Notably, the abundance of potential probiotics, including Faecalibacterium prausnitzii, Roseburia intestinalis and Roseburia inulinivorans, which was decreased in AD patients, exhibited positive correlations with specific exosomal miRNAs: Roseburia intestinalis correlated with miR-3120-3p and miR-6529-5p; Roseburia inulinivorans correlated with miR-3120-3p, miR-6529-5p and miR-124-3p; Faecalibacterium prausnitzii correlated with miR-3120-3p. Discussion The study revealed a close association among gut microbiota, plasma exosomal miRNAs, and cognitive impairment in AD, and suggested that specific components of gut microbiota and exosomal miRNAs may serve as potential biomarkers and therapeutic targets for AD on the microbiota-gut-brain axis.

The gut microbiota may influence cognitive function via the gut-brain axis. This study aimed to investigate the gut microbiota profiles of 346 older Korean individuals with subjective cognitive decline but no symptoms (SCD), mild cognitive impairment (MCI), or Alzheimer’s disease (AD). Participants aged an average of 72.3 years underwent the profiling of cognitive function, amyloid-β (Aβ) deposition, apolipoprotein E (APOE) genetic variants, depression status, nutrition, and lifestyles. Human fecal bacterial FASTA/Q data (SCD, n = 24; MCI, n = 246; AD, n = 76) were processed using Quantitative Insights Into Microbial Ecology 2 (QIIME2) tools. Operational taxonomic units (OTUs) and their counts were assigned with the National Center for Biotechnology Information Basic Local Alignment Search Tool (BLAST). Machine learning models (random forest and XGBoost) identified key bacterial taxa differentiating groups. Redundancy analysis revealed associations between gut microbiota composition and cognitive function, age, gender, nutritional status, and body mass index. All three groups shared 71 common bacterial genera with distinct taxonomic profiles across cognitive states. The AD group uniquely harbored Hominisplanchenecus and Lentihominibacter, while the SCD group exclusively contained Anaerosacchariphilus and Anaerobutyricum. Phascolarctobacterium was shared between the AD and MCI groups, and Anaerostipes between the MCI and SCD groups. The SCD group showed significantly elevated Bifidobacterium catenulatum, Anaerobutyricum hallii, and Anaerostipes hadrus. Network analysis demonstrated greater microbial community complexity in the SCD group compared to the MCI and AD groups. Gut bacteria correlated with depression, Aβ deposition, APOE status, and cognitive scores. This study identified distinct gut microbiota profiles associated with different stages of cognitive impairment in older Korean adults. The observed associations between gut bacterial composition and cognitive function, neurodegeneration biomarkers, and related clinical factors suggest potential relationships that warrant further investigation. These findings contribute to the growing understanding of gut-brain interactions in cognitive aging.

Alzheimer’s disease (AD) is a neurodegenerative disorder often preceded by a prodromal stage of Mild Cognitive Impairment (MCI). Previous research suggests that gut microbiota (GMB) dysbiosis may contribute to cognitive decline via the microbiota-gut-brain axis (MGBA). Notably, GMB composition patterns can vary across populations and stages of dementia. This study aimed to characterize the GMB in a cohort of older adults from Tarragona (Spain) diagnosed with AD or MCI, or presenting a healthy cognitive status (HC), all of whom follow a Mediterranean lifestyle (ML). The present cross-sectional, multicenter case–control study analyzed fecal samples from 99 individuals,including 31 with AD, 30 with MCI, and 38 HC,aged 60–85 years, recruited from seven hospitals and specialized cognitive centers in the province of Tarragona, Spain. Shotgun metagenomic sequencing was conducted with taxonomic profiling using Kraken2. APOE genotyping was performed from fecal DNA using TaqMan assays. Richness, alpha and beta diversity, differential abundance, multivariate linear modeling, and Jonckheere–Terpstra trend tests were conducted to identify GMB species signatures associated with MCI and AD. Richness, alpha and beta diversity did not differ across groups. Differential abundance analysis identified 109 taxa, of which ten microbial species were shared across comparisons. Notably, several species, including Coprococcus comes and Odoribacter splanchnicus, emerged as replicable candidates, showing both discriminatory value and severity-related declines, alongside taxa with context-dependent or adverse associations. Overall GMB diversity did not differ across cognitive groups, but specific taxa, particularly short-chain fatty acid producers, showed consistent associations with cognitive decline in this ML cohort. These findings support a role for the GMB in AD pathology and suggest that targeting key microbial species may provide novel avenues for prevention and intervention.

Emerging evidence implicates gut microbiota (GM), shaped by diet, in Alzheimer's disease (AD) pathogenesis. However, the association between the dietary index for GM (DI‐GM) and AD remains unclear.

Background No effective drug treatment is currently available for Alzheimer's disease (AD), highlighting the urgent need to develop efficient therapeutic options. We have developed a formula based on medicine and food homology (MFH) consisting of egg yolk oil, perilla seed oil, raphani seed oil, cinnamon oil, and noni puree (EPRCN), and demonstrated that it can treat AD by alleviating neuroinflammation and oxidative stress. However, whether EPRCN can improve AD by regulating gut microbiota remains unknown. Objective The current study aimed to evaluate the effect of EPRCN on regulating gut microbiota and neuroprotection. Methods 16S rRNA sequencing was used to assess the structure of gut microbiota. Hematoxylin-eosin (HE) staining, qRT-PCR, and ELISA were used to evaluate gut inflammation. Detected indexes associated with cholinergic dysfunction and neuronal damage to investigate the neuroprotective effects of EPRCN. Results 16S rRNA gene analysis revealed that EPRCN remodeled the gut microbiota, inhibited gut metabolic disorders, and promoted CoA biosynthesis in scopolamine-induced mice. EPRCN can ameliorates gut inflammation by activating the cholinergic anti-inflammatory pathway. The results further indicated that EPRCN improved cholinergic dysfunction by inhibiting the activity of acetylcholinesterase and restoring cholinergic receptors. Additionally, EPRCN administration suppressed the neuronal loss and elevated brain derived neurotrophic factor expression in hippocampus. Correlation analysis found that alteration of several gut microbes was associated with indexes improved by EPRCN. Conclusions These findings suggest that EPRCN may serve as a promising dietary intervention for treating AD by regulating the microbiota-gut-brain axis and exerting neuroprotective function.

Background Euchromatic histone-lysine N-methyltransferase 2 (EHMT2), a neuroinflammatory histone methyltransferase, has been proposed as a therapeutic target for Alzheimer's disease (AD), potentially via modulation of gut microbiota. However, causality remains unclear due to confounding in observational studies and lack of human genetic evidence. Objective To address this, we conducted a Mendelian randomization (MR) analysis using genome-wide association data exclusively from individuals of European ancestry. Methods We obtained genome-wide association study (GWAS) summary statistics for EHMT2 expression, AD (n = 39,106), 211 gut microbiota taxa, and colorectal cancer (CRC; n = 6847) from the IEU OpenGWAS and FinnGen databases. MR was used to evaluate the causal effects, with CRC as a positive control. Five regression models were utilized to evaluate the causal effects, and two-step MR assessed the mediating role of gut microbiota. Sensitivity analyses tested result robustness. Results Inverse-variance weighted (IVW) analyses showed that EHMT2 inhibition was associated with reduced risks of CRC [odds ratio (OR) = 0.7850, 95% CI: 0.6782–0.9086, p = 0.0012], and AD (OR = 0.8585, 95% CI: 0.8056–0.9148, p < 0.0001). EHMT2 inhibition also influenced the abundance of 67 gut microbiota taxa. Among them, 17 taxa were linked to AD risk, with four showing shared causal associations. Notably, three of them (family Lactobacillaceae id.1836, genus Dialister id.2183, and unknown genus id.959) had positive mediating effects. Conclusions EHMT2 inhibition may play protective roles in AD via modulating specific gut microbiota, particularly three key taxa. These findings highlight a potential microbiota-mediated epigenetic mechanism in AD pathogenesis, warranting further mechanistic and translational studies.

Background Alzheimer's disease (AD) is a neurodegenerative disease causing memory and cognitive dysfunction, and it is well established that the gut microbiota has an important effect on AD. Objective In this study, we aimed to identify evidence in AD affecting the abundance of gut microbiota, analyzing age and post-disease, with the expectation of discovering new gut microbiota combinations for diagnostic purposes. Methods We initially retrieved 219 samples from five studies in the GMrepo, and after screening, 86 samples collected from the same location were retained, with 98 species of gut microbiota at the genus level. Results It was found that Clostridium, Ruminococcus, Roseburia, and Faecalibacterium were enriched in AD. We confirmed that AD altered the evenness of gut microbiota and validated the AD-induced significant changes in gut microbiota. For the impact of age on disease, we identified the most sensitive age group for AD detection by gut microbiota and the relevant species. When analyzing the association between AD and sex, we found that sex had no effect on the overall bacterial distribution, but in the subgroup analysis by sex, we identified significantly relevant species that could serve as diagnostic targets. Conclusions This study investigated the interaction between gut microbiota and AD utilizing an online free database and revealed a series of significant associations between the two. In the future, further emphasis should be placed on the identification of key bacteria and their associated genes to determine the relative causality of gut microbiota and AD.

Background Several recent studies have confirmed a causal relationship between gut microbiota and Alzheimer's disease (AD), but the potential mediators remain unclear. Objective This study aimed first to investigate the causal relationship between gut microbiota and AD, and second to explore potential mediators involved in this relationship. Methods We used a two-step Mendelian randomization study. Firstly, we mainly used inverse-variance weighted (IVW), weighted median, weighted mode, MR-Egger, and simple mode methods to assess the causal relationship between gut microbiota and AD. Secondly, we conducted mediation analysis to evaluate the roles of inflammatory factors, immune cells, and metabolites in this causal pathway. In addition, we performed sensitivity analysis, Steiger test, and linkage disequilibrium score regression (LDSC). Results Our results showed that ten types of gut microbiota were causally associated with AD, of which seven were associated with an increased risk of AD and three with a reduced risk. In addition, the mediation analysis showed that CD45 on Mo MDSC mediated 21.89% of the effect of class Actinobacteria on AD, while the cortisol to taurocholate ratio mediated 18.35% of the effect of genus Lactococcus on AD. Beta-hydroxyisovalerate and glycodeoxycholate levels respectively mediated 10.56% and 16.22% of the effects of class Betaproteobacteria on AD. Conclusions Our research not only supports modulating gut microbiota as a preventive measure for AD but also emphasizes the mediating roles of inflammatory factors, immune cells, and metabolites. These findings enhance our understanding of the gut-brain axis, providing new perspectives and potential targets for AD prevention.

Gut microbiota and their metabolites, particularly short‐chain fatty acids (SCFAs), play a vital role in the gut‐brain axis, and have been associated with neurodegenerative diseases like Alzheimer's disease (AD). However, the changes in gut microbiota composition and SCFA levels during the progression of AD are not yet well understood. This study seeks to investigate these variations to gain deeper insights into their potential role in disease development.

Background The association between gut microbes and Alzheimer's disease (AD) has not been entirely elucidated. Objective We aimed to demonstrate the association between gut microbes and AD and to further investigate the pathogenesis of microbes with a causal relationship to AD. Methods Mendelian randomization analyses were used to determine the significant causal relationship between gut microbes and AD. Protein-protein interaction (PPI) network was used to identify the hub genes. Functional enrichment analysis was used to reveal the pathogenesis theoretically between gut microbes and AD. Results In the present study, a total of 32 microbes were identified that were significantly associated with AD. Subsequently, DLGAP2, NRXN3, NEGR1, NTNAP2, MYH9, and SCN3A were identified as hub genes. The genes NRXN3, NEGR1, and NTNAP2 were enriched in the cell adhesion molecules (CAMs) signaling, and the taxons of gut microbes that corresponded to these were Bifidobacterium adolescentis, Actinomycetales, and Intestinimonas massiliensis. Conclusions Bifidobacterium adolescentis, Actinomycetales, and Intestinimonas massiliensis may promote the progression of AD through the regulation of the CAMs signaling pathway-mediated synaptic function. Hence, the in-depth study of gut microbes may increase the efficiency of screening and diagnosis of AD.

ABSTRACT The gut microbiota (GM) and its metabolites affect the host nervous system and are involved in the pathogeneses of various neurological diseases. However, the specific GM alterations under pathogenetic pressure and their contributions to the “microbiota – metabolite – brain axis” in Alzheimer’s disease (AD) remain unclear. Here, we investigated the GM and the fecal, serum, cortical metabolomes in APP/PS1 and wild-type (WT) mice, revealing distinct hub bacteria in AD mice within scale-free GM networks shared by both groups. Moreover, we identified diverse peripheral – central metabolic landscapes between AD and WT mice that featured bile acids (e.g. deoxycholic and isodeoxycholic acid) and unsaturated fatty acids (e.g. 11Z-eicosenoic and palmitoleic acid). Machine-learning models revealed the relationships between the differential/hub bacteria and these metabolic signatures from the periphery to the brain. Notably, AD-enriched Dubosiella affected AD occurrence via cortical palmitoleic acid and vice versa. Considering the transgenic background of the AD mice, we propose that Dubosiella enrichment impedes AD progression via the synthesis of palmitoleic acid, which has protective properties against inflammation and metabolic disorders. We identified another association involving fecal deoxycholic acid-mediated interactions between the AD hub bacteria Erysipelatoclostridium and AD occurrence, which was corroborated by the correlation between deoxycholate levels and cognitive scores in humans. Overall, this study elucidated the GM network alterations, contributions of the GM to peripheral – central metabolic landscapes, and mediatory roles of metabolites between the GM and AD occurrence, thus revealing the critical roles of bacteria in AD pathogenesis and gut – brain communications under pathogenetic pressure.

Recently, the importance of the role of the gut microbiota in our organism has been highlighted, intervening mainly in immune activity and in the regulation of various metabolic pathways. Different studies have shown that both the gut microbiota of patients with T2DM and that of patients with AD present moderate dysbiosis, so we sought to characterize the gut microbiota of people with both pathologies.

Neuroinflammation contributes to the pathology and progression of Alzheimer's disease (AD), and it can be observed even with mild cognitive impairment (MCI), a prodromal phase of AD. Free water (FW) imaging estimates the extracellular water content and has been used to study neuroinflammation across several neurological diseases including AD. Recently, the role of gut microbiota has been implicated in the pathogenesis of AD. The relationship between FW imaging and gut microbiota was examined in patients with AD and MCI. Fifty-six participants underwent neuropsychological assessments, FW imaging, and gut microbiota analysis targeting the bacterial 16S rRNA gene. They were categorized into the cognitively normal control (NC) (n = 19), MCI (n = 19), and AD (n = 18) groups according to the neuropsychological assessments. The correlations of FW values, neuropsychological assessment scores, and the relative abundance of gut microbiota were analyzed. FW was higher in several white matter tracts and in gray matter regions, predominantly the frontal, temporal, limbic and paralimbic regions in the AD/MCI group than in the NC group. In the AD/MCI group, higher FW values in the temporal (superior temporal and temporal pole), limbic and paralimbic (insula, hippocampus and amygdala) regions were the most associated with worse neuropsychological assessment scores. In the AD/MCI group, FW values in these regions were negatively correlated with the relative abundances of butyrate-producing genera Anaerostipes, Lachnospiraceae UCG-004, and [Ruminococcus] gnavus group, which showed a significant decreasing trend in the order of the NC, MCI, and AD groups. The present study showed that increased FW in the gray matter regions related to cognitive impairment was associated with low abundances of butyrate producers in the AD/MCI group. These findings suggest an association between neuroinflammation and decreased levels of the short-chain fatty acid butyrate that is one of the major gut microbial metabolites having a potentially beneficial role in brain homeostasis.

Gender is a significant risk factor for late-onset Alzheimer’s disease (AD), often attributed to the decline of estrogen. The plant estrogen secoisolariciresinol diglucoside (SDG) has demonstrated anti-inflammatory and neuroprotective effects. However, the protective effects and mechanisms of SDG in female AD remain unclear. Ten-month-old female APPswe/PSEN1dE9 (APP/PS1) transgenic mice were treated with SDG to assess its potential ameliorative effects on cognitive impairments in a female AD model through a series of behavioral and biochemical experiments. Serum levels of gut microbial metabolites enterodiol (END) and enterolactone (ENL) were quantified using HPLC-MS. Correlation analysis and broad-spectrum antibiotic cocktail (ABx) treatment were employed to demonstrate the involvement of END and ENL in SDG’s cognitive improvement effects in female APP/PS1 mice. Additionally, an acute neuroinflammation model was constructed in three-month-old C57BL/6J mice treated with lipopolysaccharide (LPS) and subjected to i.c.v. injection of G15, an inhibitor of G protein-coupled estrogen receptor (GPER), to investigate the mediating role of the estrogen receptor GPER in the cognitive benefits conferred by SDG. SDG administration resulted in significant improvements in spatial, recognition, and working memory in female APP/PS1 mice. Neuroprotective effects were observed, including enhanced expression of CREB/BDNF and PSD-95, reduced β-amyloid (Aβ) deposition, and decreased levels of TNF-α, IL-6, and IL-10. SDG also altered gut microbiota composition, increasing serum levels of END and ENL. Correlation analysis indicated significant associations between END, ENL, cognitive performance, hippocampal Aβ-related protein mRNA expression, and cortical neuroinflammatory cytokine levels. The removal of gut microbiota inhibited END and ENL production and eliminated the neuroprotective effects of SDG. Furthermore, GPER was found to mediate the inhibitory effects of SDG on neuroinflammatory responses. These findings suggest that SDG promotes the production of gut microbial metabolites END and ENL, which inhibit cerebral β-amyloid deposition, activate GPER to enhance CREB/BDNF signaling pathways, and suppress neuroinflammatory responses. Consequently, SDG exerts neuroprotective effects and ameliorates cognitive impairments associated with AD in female mice.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterised by neuroinflammation, for which gut dysbiosis may be implicated. Our previous study showed that treatment with Pseudostellaria heterophylla aqueous extract and one of its cyclopeptides, heterophyllin B, attenuate memory deficits via immunomodulation and neurite regeneration. However, whether Pseudostellaria heterophylla polysaccharide (PH-PS) exerts neuroprotective effects against AD and its underlying mechanisms remain unclear. The infrared spectrum, molecular weight, and carbohydrate composition of the PH-PS were determined. The results showed that PH-PS (Mw 8.771 kDa) was composed of glucose (57.78 %), galactose (41.52 %), and arabinose (0.70 %). PH-PS treatment ameliorated learning and spatial memory deficits, reduced amyloid β build-up, and suppressed reactive glia and astrocytes in 5 × FAD mice. 16S rRNA sequencing further showed that PH-PS remodelled the intestinal flora composition by promoting probiotic microbiota, such as Lactobacillus, Muribaculum, Monoglobus, and [Eubacterium]_siraeum_group, and suppressing inflammation-related UCG-009 and Blautia. Additionally, PH-PS restored intestinal barrier function; ameliorated peripheral inflammation by reducing the secretion of inflammatory cytokines, thereby converting M1 microglia and A1 astrocyte toward beneficial M2 and A2 phenotypes; and contributed to Aβ plaques clearance by upregulation of insulin degradation enzyme and neprilysin. Collectively, our findings demonstrate that PH-PS may prevent the progression of AD via modulation of the gut microbiota and regulation of glial polarisation, which could provide evidence to design a potential diet therapy for preventing or curing AD.

Noninvasive monitoring of Alzheimer's disease (AD) biomarkers is essential for early diagnosis and treatment efficacy. However, noninvasive monitoring of tau protein secretion, a key biomarker of AD, across developmental stages, age‐related variations, and the interaction between apolipoprotein E (APOE) and the tau protein axis is not yet accomplished. Here, the label‐free and non‐invasive detection of multiple tau variants dynamics across developmental stages, age‐related variants, and various APOE isogenic genotyes is presented to investigate the APOE–tau axis using human cerebral organoids (hCOs) combined with surface‐enhanced Raman spectroscopy (SERS). Principal component analysis (PCA) of SERS signals successfully identifies four developmental stages of hCOs: embryonic body, neuronal differentiation, maturation, and maintenance phases. Temporal dynamics of age‐related tau protein secretion are observed, reflecting characteristics associated with AD, which are diminished by astrocyte expression. PCA‐based dimensionality reduction of SERS signals further reveals distinct clustering for different APOE isogenic genotypes, with tau protein secretion increasing from APOE2/E2 to APOE4/E4, providing direct insight into the APOE–tau axis in AD. This study introduces a novel method for the non‐invasive clinical assessments of disease conditions, dynamics, and the relationship between APOE and tau in AD.

Introduction Neuroinflammation is a key contributor to the pathogenesis of Alzheimer's disease (AD), and impaired clearance of amyloid-β (Aβ) by microglia is closely associated with disease progression. Oxytocin (OXT), a hypothalamic neuropeptide, has recently been reported to exert anti-inflammatory effects on microglia; however, its therapeutic potential in the human brain remains unclear. Methods We generated human cerebral organoids (hCOs) from induced pluripotent stem cells (iPSCs) to model early AD-like pathology. Aβ toxicity was induced by applying 3 μM Aβ1–42 for 48 h. The protective effects of OXT were evaluated through immunohistochemistry, RT-qPCR, calcium imaging, and multielectrode array (MEA) recordings. The involvement of microglia in Aβ clearance was assessed by immunostaining and gene expression analysis of TREM2. Results Aβ exposure led to significant deposition of Aβ in the outer layers of hCOs, accompanied by suppressed neural activity and increased apoptotic signaling. Pretreatment with OXT attenuated Aβ deposition and caspase-3-mediated apoptosis in a concentration-dependent manner. OXT also restored calcium oscillations and neuronal network activity as measured by MEA. Notably, OXT enhanced the recruitment of microglia to Aβ deposits and upregulated the expression of TREM2, a key regulator of microglial phagocytosis. Co-expression of oxytocin receptors (OXTR) on Iba1-positive microglia suggests that OXT directly modulates microglial activation and Aβ clearance. Conclusions OXT has neuroprotective effects on human cortical organoids by preserving their neuronal activity and promoting microglial-mediated Aβ clearance. This study provides novel insights into the therapeutic potential of OXT for targeting neuroinflammation and Aβ pathology in patients with AD.

Per- and polyfluoroalkyl substances (PFASs), a class of ubiquitous synthetic organic chemicals, are widely utilized across various industrial applications. However, the long-term neurological health effects of PFAS mixture exposure in humans remain poorly understood. To address this gap, we have designed a comprehensive study to predict and validate cell-type-specific neurotoxicity of PFASs using single-cell RNA sequencing (scRNA-seq) and cerebral organoids. Cerebral organoids were exposed to a PFAS mixture at concentrations of 1× (10 ng/ml PFOS and PFOA, and 1 ng/ml PFHxS), 30×, and 900× over 35 days, with a follow-up analysis at day 70. Pathological alterations and lipidomic profiles were analyzed to identify disrupted molecular pathways and mechanisms. The scRNA-seq data revealed a significant impact of PFASs on neurons, suggesting a potential role in Alzheimer's Disease (AD) pathology, as well as intellectual and cognitive impairments. PFAS-treated cerebral organoids exhibited Aβ accumulation and tau phosphorylation. Lipidomic analyses further revealed lipid disturbances in response to PFAS mixture exposure, linking PFAS-induced AD-like neuropathology to sphingolipid metabolism disruption. Collectively, our findings provide novel insights into the PFAS-induced neurotoxicity, highlighting the significance of sphingolipid metabolism in the development of AD-like neuropathology. The use of cerebral organoids and scRNA-seq offers a powerful methodology for evaluating the health risks associated with environmental contaminants, particularly those with neurotoxic potential.

Polygenic risk score (PRS) identifies individuals at high genetic risk for Alzheimer's disease (AD), but its utility in predicting cognitive trajectories and AD pathologies remains unclear. We optimized PRS (optPRS) for AD, investigated its association with cognitive trajectories and AD phenotypes of cerebral organoids.

No abstract available

A patient with the PSEN1 E280A mutation and homozygous for APOE3 Christchurch (APOE3Ch) displayed extreme resistance to Alzheimer’s disease (AD) cognitive decline and tauopathy, despite having a high amyloid burden. To further investigate the differences in biological processes attributed to APOE3Ch, we generated induced pluripotent stem (iPS) cell-derived cerebral organoids from this resistant case and a non-protected control, using CRISPR/Cas9 gene editing to modulate APOE3Ch expression. In the APOE3Ch cerebral organoids, we observed a protective pattern from early tau phosphorylation. ScRNA sequencing revealed regulation of Cadherin and Wnt signaling pathways by APOE3Ch, with immunostaining indicating elevated β-catenin protein levels. Further in vitro reporter assays unexpectedly demonstrated that ApoE3Ch functions as a Wnt3a signaling enhancer. This work uncovered a neomorphic molecular mechanism of protection of ApoE3 Christchurch, which may serve as the foundation for the future development of protected case-inspired therapeutics targeting AD and tauopathies.

A population of more than six million people worldwide at high risk of Alzheimer’s disease (AD) are those with Down Syndrome (DS, caused by trisomy 21 (T21)), 70% of whom develop dementia during lifetime, caused by an extra copy of β-amyloid-(Aβ)-precursor-protein gene. We report AD-like pathology in cerebral organoids grown in vitro from non-invasively sampled strands of hair from 71% of DS donors. The pathology consisted of extracellular diffuse and fibrillar Aβ deposits, hyperphosphorylated/pathologically conformed Tau, and premature neuronal loss. Presence/absence of AD-like pathology was donor-specific (reproducible between individual organoids/iPSC lines/experiments). Pathology could be triggered in pathology-negative T21 organoids by CRISPR/Cas9-mediated elimination of the third copy of chromosome 21 gene BACE2 , but prevented by combined chemical β and γ-secretase inhibition. We found that T21 organoids secrete increased proportions of Aβ-preventing (Aβ1–19) and Aβ-degradation products (Aβ1–20 and Aβ1–34). We show these profiles mirror in cerebrospinal fluid of people with DS. We demonstrate that this protective mechanism is mediated by BACE2 -trisomy and cross-inhibited by clinically trialled BACE1 inhibitors. Combined, our data prove the physiological role of BACE2 as a dose-sensitive AD-suppressor gene, potentially explaining the dementia delay in ~30% of people with DS. We also show that DS cerebral organoids could be explored as pre-morbid AD-risk population detector and a system for hypothesis-free drug screens as well as identification of natural suppressor genes for neurodegenerative diseases.

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No abstract available

The APOE ε4 allele (APOE4) is the strongest genetic risk factor for Alzheimer's disease (AD) in the typical population and increases the risk for AD in people with Down syndrome (DS‐AD) in comparison to the most common allele, APOE3. Data support the hypothesis that microglial‐apoE interactions drive neuroinflammation and contribute to DS‐AD progression, highlighting a valuable potential therapeutic target for improving cognition and longevity in people with DS‐AD. However, little is known about the mechanisms underlying microglial‐apoE interactions and their contributions to neuroinflammation and neurodegeneration.

Human cerebral organoids (hCOs) offer the possibility of deepening the knowledge of human brain development, as well as the pathologies that affect it. The method developed here describes the efficient generation of hCOs by going directly from two-dimensional (2D) pluripotent stem cell (PSC) cultures to three-dimensional (3D) neuroepithelial tissue, avoiding dissociation and aggregation steps. This has been achieved by subjecting 2D cultures, from the beginning of the neural induction step, to dual-SMAD inhibition in combination with CHIR99021. This is a simple and reproducible protocol in which the hCOs generated develop properly presenting proliferative ventricular zones (VZs) formed by neural precursor and radial glia (RG) that differentiate to give rise to mature neurons and glial cells. The hCOs present additional cell types such as oligodendrocyte precursors, astrocytes, microglia-like cells, and endothelial-like cells. This new approach could help to overcome some of the existing limitations in the field of organoid biotechnology, facilitating its execution in any laboratory setting.

Herpes simplex virus 1 (HSV‐1) has been associated with pathogenesis of Alzheimer’s Disease (AD) through several landmark studies. We explored the transcriptomics landscape of HSV‐1 infection and anti‐viral treatment using acyclovir on AD‐associated genes using large‐scale bulk RNA sequencing to identify biomarkers, cell types and cell type specific interactions.

The gene encoding sorting nexin SNX19 is highly expressed in neurons. SNX19 modulates synaptic functions that have been implicated in Aβ formation and tau phosphorylation. In our recent postmortem brain transcriptomic study (n = 409), we found an association of SNX19 gene expression with increased schizophrenia risk. To date, this gene has not been studied in AD. In this project, we will define AD risk single nucleotide variants (SNVs) at this locus, linking the SNVs to SNX19 gene expression and DNA methylation sites in human postmortem brains. we will test the hypothesis that SNX19 induces neuronal dysfunction and Alzheimer’s disease (AD)‐related pathologies in hiPSCs derived cerebral organoids.

During the past two decades, induced pluripotent stem cells (iPSCs) have been widely used to study human neural development and disease. Especially in the field of Alzheimer's disease (AD), remarkable effort has been put into investigating molecular mechanisms behind this disease. Then, with the advent of 3D neuronal cultures and cerebral organoids (COs), several studies have demonstrated that this model can adequately mimic familial and sporadic AD. Therefore, we created an AD-CO model using iPSCs derived from patients with familial AD forms and explored early events and the progression of AD pathogenesis. Our study demonstrated that COs derived from three AD-iPSC lines with PSEN1(A246E) or PSEN2(N141I) mutations developed the AD-specific markers in vitro, yet they also uncover tissue patterning defects and altered development. These findings are complemented by single-cell sequencing data confirming this observation and uncovering that neurons in AD-COs likely differentiate prematurely.

Understanding the role of small, soluble aggregates of beta-amyloid (Aβ) and tau in Alzheimer’s disease (AD) is of great importance for the rational design of preventative therapies. Here we report a set of methods for the detection, quantification, and characterisation of soluble aggregates in conditioned media of cerebral organoids derived from human iPSCs with trisomy 21, thus containing an extra copy of the amyloid precursor protein (APP) gene. We detected soluble beta-amyloid (Aβ) and tau aggregates secreted by cerebral organoids from both control and the isogenic trisomy 21 (T21) genotype. We developed a novel method to normalise measurements to the number of live neurons within organoid-conditioned media based on glucose consumption. Thus normalised, T21 organoids produced 2.5-fold more Aβ aggregates with a higher proportion of larger (300–2000 nm2) and more fibrillary-shaped aggregates than controls, along with 1.3-fold more soluble phosphorylated tau (pTau) aggregates, increased inflammasome ASC-specks, and a higher level of oxidative stress inducing thioredoxin-interacting protein (TXNIP). Importantly, all this was detectable prior to the appearance of histological amyloid plaques or intraneuronal tau-pathology in organoid slices, demonstrating the feasibility to model the initial pathogenic mechanisms for AD in-vitro using cells from live genetically pre-disposed donors before the onset of clinical disease. Then, using different iPSC clones generated from the same donor at different times in two independent experiments, we tested the reproducibility of findings in organoids. While there were differences in rates of disease progression between the experiments, the disease mechanisms were conserved. Overall, our results show that it is possible to non-invasively follow the development of pathology in organoid models of AD over time, by monitoring changes in the aggregates and proteins in the conditioned media, and open possibilities to study the time-course of the key pathogenic processes taking place.

Neuroinflammation is a key process associated with Alzheimer’s disease (AD). There is interest in developing New Approach Methodologies (NAMs) by using human in-vitro complex systems such as brain organoids, combined with machine learning and computational approaches, to reproducibly and robustly evaluate monoclonal antibodies and other therapeutic modalities on these human-derived systems. Herpesviruses such as herpes simplex virus 1 (HSV-1) had been shown to be associated with AD risk and molecular pathology. Building on top of previously reported work, we used herpes simplex virus 1 (HSV-1) infection in 2D dissociated cells from human cerebral organoids (dcOrgs) to recapitulate AD-associated molecular readouts, such as high co-abundance of intracellular beta amyloid (Aβ) and phosphorylated tau (pTau) with HSV-1. Secreted Aβ42/40 ratios in conditioned media were lower from HSV-1-infected dcOrgs, compared to mock dcOrgs. Differentially expressed transcripts from bulk and single-cell RNA sequence data in HSV-1-infected dcOrgs were enriched for AD-associated GWAS genes. Our high-throughput, quantitative framework represents a comprehensive approach to harness on the strengths of 2D dcOrgs for high-throughput applications such as therapeutic screens and can complement the 3D brain organoids and animal models for neuroinflammation in AD.

No abstract available

Previous animal models of sporadic Alzheimer's disease (sAD), based on the β-amyloid (Aβ) cascade hypothesis and induced by Aβ1-42 oligomers (AβO), only recapitulated early AD pathological features. sAD cerebral organoids (COs) model employed Aβ coculture approach and found no typical features of AD pathology. Type 2 diabetes (T2DM) is one of the most important modifiable AD risk factors, so we hypothesize that T2DM could substantially exacerbate Aβ neurotoxicity and reproduce typical AD pathology. Human islet amyloid polypeptide (hIAPP) was used to mimic T2DM and was co-oligomerized with Aβ1-42 peptide, and delivered to the central of human iPSC-derived mature COs through intermittently repeated microinjections, so as to simulate the chronic exposure to Aβ within the brain. The Aβ42-hIAPP co-oligomers induced a pathological phenotype more closely resembling the pathological features of advanced AD, notably, neuronal density showed significant reduction, with 3.2 times more neuronal death. Dynamic metabolomic analysis revealed the metabolic pathways and differential metabolites that may be correlated to the primary mechanism underlying the enhanced neurotoxic effects and accelerated AD pathology. Furthermore, this study developed a sAD CO model more resembling the pathological features of advanced AD, which potentially provides a valuable platform for AD pathogenesis research and novel drug screening.

Down syndrome (DS) is among the most common forms of familial Alzheimer’s disease (AD), resulting from triplication of the amyloid precursor protein (APP) gene on chromosome 21 which leads to increased amyloid beta (Aβ) peptide accumulation in the brain. As a result, all people with DS will develop Aβ plaques and tau tangles by the age of 40, and the majority will eventually develop AD‐related cognitive decline. Carrying the e4 allele of the apolipoprotein E gene (APOE), APOE4, because it catalyzes the formation of neurotoxic Aβ oligimers. The combination of APOE4 and trisomy 21 results in a very high risk for DS associated AD. APOE4 has also been shown to drive altered microglial activity in the AD brain, leading to increased neuroinflammation, neurodegeneration and cognitive decline. Studying mechanisms underlying APOE4‐microglial interactions could lead to identification of new therapeutic targets for DS‐AD treatments. Microglia‐containing cerebral organoids (MCOs) derived from human induced pluripotent stem cells (hiPSCs) with both trisomy 21 and APOE4 would offer a distinct advantage over prior models.

The apolipoprotein E4 (APOE4) genotype is one of the strongest genetic risk factors for Alzheimer’s disease (AD), and is generally believed to cause widespread pathological alterations in various types of brain cells. Here, we developed a novel engineering method of creating the chimeric human cerebral organoids (chCOs) to assess the differential roles of APOE4 in neurons and astrocytes. First, the astrogenic factors NFIB and SOX9 were introduced into induced pluripotent stem cells (iPSCs) to accelerate the induction of astrocytes. Then the above induced iPSCs were mixed and cocultured with noninfected iPSCs under the standard culturing condition of cerebral organoids. As anticipated, the functional astrocytes were detected as early as 45 days, and it helped more neurons matured in chCOs in comparation of the control human cerebral organoids (hCOs). More interestingly, this method enabled us to generate chCOs containing neurons and astrocytes with different genotypes, namely APOE3 or APOE4. Then, it was found in chCOs that astrocytic APOE4 already significantly promoted lipid droplet formation and cholesterol accumulation in neurons while both astrocytic and neuronal APOE4 contributed to the maximum effect. Most notably, we observed that the co-occurrence of astrocytic and neuronal APOE4 were required to elevate neuronal phosphorylated tau levels in chCOs while Aβ levels were increased in chCOs with neuronal APOE4. Altogether, our results not only revealed the essence of both neuronal and astrocytic APOE4 for tau pathology, but also suggested chCOs as a valuable pathological model for AD research and drug discovery.

By leveraging advances in 3D stem cell culture techniques, the authors describe, characterize and validate a novel platform to efficiently generate morphologically consistent human forebrain cerebral organoids. Human cerebral organoid (hCO) models offer the opportunity to understand fundamental processes underlying human-specific cortical development and pathophysiology in an experimentally tractable system. Although diverse methods to generate brain organoids have been developed, a major challenge has been the production of organoids with reproducible cell type heterogeneity and macroscopic morphology. Here, we have directly addressed this problem by establishing a robust production pipeline to generate morphologically consistent hCOs and achieve a success rate of >80%. These hCOs include both a radial glial stem cell compartment and electrophysiologically competent mature neurons. Moreover, we show using immunofluorescence microscopy and single-cell profiling that individual organoids display reproducible cell type compositions that are conserved upon extended culture. We expect that application of this method will provide new insights into brain development and disease processes.

APOE4 is the strongest genetic risk factor associated with late-onset Alzheimer’s disease (AD). To address the underlying mechanism, we develop cerebral organoid models using induced pluripotent stem cells (iPSCs) with APOE ε3/ε3 or ε4/ε4 genotype from individuals with either normal cognition or AD dementia. Cerebral organoids from AD patients carrying APOE ε4/ε4 show greater apoptosis and decreased synaptic integrity. While AD patient-derived cerebral organoids have increased levels of Aβ and phosphorylated tau compared to healthy subject-derived cerebral organoids, APOE4 exacerbates tau pathology in both healthy subject-derived and AD patient-derived organoids. Transcriptomics analysis by RNA-sequencing reveals that cerebral organoids from AD patients are associated with an enhancement of stress granules and disrupted RNA metabolism. Importantly, isogenic conversion of APOE4 to APOE3 attenuates the APOE4-related phenotypes in cerebral organoids from AD patients. Together, our study using human iPSC-organoids recapitulates APOE4-related phenotypes and suggests APOE4-related degenerative pathways contributing to AD pathogenesis. APOE4 is a strong genetic risk factor for late-onset Alzheimer’s disease. Here, the authors show that APOE4 is associated with AD features in hiPSCs-derived cerebral organoids. Isogenic conversion of APOE4 to APOE3 attenuates the AD-associated phenotype.

No abstract available

Herpes simplex virus type I (HSV-1) infection is a potential risk factor involved in the Amyloid β (Aβ) associated neuropathology. However, further understanding of the neuropathological effects of the HSV-1 infection is hampered by the limitations of existing infection models due to the distinct differences between human brains and other mammalians’ brains. Here we generated cerebral organoid models derived from pluripotent stem cells to investigate the HSV-induced Aβ associated neuropathology and the role of antiviral drugs in the phenotypic rescue. Our results identified that the HSV-1-infected cerebral organoids recapitulated Aβ associated neuropathology including the multicellular Aβ deposition, dysregulated endogenous AD mediators, reactive gliosis, neuroinflammation, and neural loss, indicating that cerebral organoids offer an opportunity for modeling the interaction of HSV-1 with the complex phenotypes across the genetic, cellular, and tissue levels of the human Alzheimer’s disease (AD). Furthermore, we identified that two antiviral drugs, namely Ribavirin (RBV) and Valacyclovir (VCV), inhibited HSV-1 replication and rescued the neuropathological phenotypes associated with AD in the HSV-1-infected cerebral organoids, implying their therapeutic potential to slow down the progression of AD. Our study provides a high-fidelity human-relevant in-vitro HSV-1 infection model to reconstitute the multiscale neuropathological features associated with AD and discover therapeutic drug candidates relevant to the AD viral hypothesis.

Background The apolipoprotein E ( APOE ) gene is the strongest genetic risk factor for Alzheimer’s disease (AD); however, how it modulates brain homeostasis is not clear. The apoE protein is a major lipid carrier in the brain transporting lipids such as cholesterol among different brain cell types. Methods We generated three-dimensional (3-D) cerebral organoids from human parental iPSC lines and its isogenic APOE -deficient ( APOE ^ −/− ) iPSC line. To elucidate the cell-type-specific effects of APOE deficiency in the cerebral organoids, we performed scRNA-seq in the parental and APOE ^ −/− cerebral organoids at Day 90. Results We show that APOE deficiency in human iPSC-derived cerebral organoids impacts brain lipid homeostasis by modulating multiple cellular and molecular pathways. Molecular profiling through single-cell RNA sequencing revealed that APOE deficiency leads to changes in cellular composition of isogenic cerebral organoids likely by modulating the eukaryotic initiation factor 2 (EIF2) signaling pathway as these events were alleviated by the treatment of an integrated stress response inhibitor (ISRIB). APOE deletion also leads to activation of the Wnt/β-catenin signaling pathway with concomitant decrease of secreted frizzled-related protein 1 ( SFRP1 ) expression in glia cells. Importantly, the critical role of apoE in cell-type-specific lipid homeostasis was observed upon APOE deletion in cerebral organoids with a specific upregulation of cholesterol biosynthesis in excitatory neurons and excessive lipid accumulation in astrocytes. Relevant to human AD, APOE4 cerebral organoids show altered neurogenesis and cholesterol metabolism compared to those with APOE3 . Conclusions Our work demonstrates critical roles of apoE in brain homeostasis and offers critical insights into the APOE4 -related pathogenic mechanisms.

No abstract available

Recent advances in stem cell technology have allowed researchers to generate 3D cerebral organoids (COs) from human pluripotent stem cells (hPSCs). Indeed, COs have provided an unprecedented opportunity to model the developing human brain in a 3D context, and in turn, are suitable for addressing complex neurological questions by leveraging advancements in genetic engineering, high resolution microscopy, and tissue transcriptomics. However, the use of this model is limited by substantial variations in the overall morphology and cellular composition of organoids derived from the same pluripotent cell line. To address these limitations, we established a robust, high-efficiency protocol for the production of consistent COs by optimizing the initial phase of embryoid body (EB) formation and neural induction. Using this protocol, COs can be reproducibly generated with a uniform size, shape, and cellular composition across multiple batches. Furthermore, organoids that developed over extended periods of time (3-6 months) showed the establishment of relatively mature features, including electrophysiologically active neurons, and the emergence of oligodendrocyte progenitors. Thus, this platform provides a robust experimental model that can be used to study human brain development and associated disorders. Graphic abstract: Overview of cerebral organoid development from pluripotent stem cells.

Human Alzheimer’s disease (AD) brains and transgenic AD mouse models manifest hyperexcitability. This aberrant electrical activity is caused by synaptic dysfunction that represents the major pathophysiological correlate of cognitive decline. However, the underlying mechanism for this excessive excitability remains incompletely understood. To investigate the basis for the hyperactivity, we performed electrophysiological and immunofluorescence studies on hiPSC-derived cerebrocortical neuronal cultures and cerebral organoids bearing AD-related mutations in presenilin-1 or amyloid precursor protein vs. isogenic gene corrected controls. In the AD hiPSC-derived neurons/organoids, we found increased excitatory bursting activity, which could be explained in part by a decrease in neurite length. AD hiPSC-derived neurons also displayed increased sodium current density and increased excitatory and decreased inhibitory synaptic activity. Our findings establish hiPSC-derived AD neuronal cultures and organoids as a relevant model of early AD pathophysiology and provide mechanistic insight into the observed hyperexcitability.

Alzheimer’s disease (AD) is a complex neurodegenerative condition characterized by a multifaceted interplay of genetic, environmental, and pathological factors. Traditional diagnostic and research methods, including neuropsychological assessments, imaging, and cerebrospinal fluid (CSF) biomarkers, have advanced our understanding but remain limited by late-stage detection and challenges in modeling disease progression. The emergence of three-dimensional (3D) brain organoids (BOs) offers a transformative platform for bridging these gaps. BOs derived from patient-specific induced pluripotent stem cells (iPSCs) mimic the structural and functional complexities of the human brain. This advancement offers an alternative or complementary approach for studying AD pathology, including β-amyloid and tau protein aggregation, neuroinflammation, and aging processes. By integrating biological complexity with cutting-edge technological tools such as organ-on-a-chip systems, microelectrode arrays, and artificial intelligence-driven digital twins (DTs), it is hoped that BOs will facilitate real-time modeling of AD progression and response to interventions. These models capture central nervous system biomarkers and establish correlations with peripheral markers, fostering a holistic understanding of disease mechanisms. Furthermore, BOs provide a scalable and ethically sound alternative to animal models, advancing drug discovery and personalized therapeutic strategies. The convergence of BOs and DTs potentially represents a significant shift in AD research, enhancing predictive and preventive capacities through precise in vitro simulations of individual disease trajectories. This approach underscores the potential for personalized medicine, reducing the reliance on invasive diagnostics while promoting early intervention. As research progresses, integrating sporadic and familial AD models within this framework promises to refine our understanding of disease heterogeneity and drive innovations in treatment and care.

Increasing evidence strongly links neuroinflammation to Alzheimer’s disease (AD) pathogenesis. Peripheral monocytes are crucial components of the human immune system, but their contribution to AD pathogenesis is still largely understudied partially due to limited human models. Here, we introduce human cortical organoid microphysiological systems (hCO-MPSs) to study AD monocyte-mediated neuroinflammation. By culturing doughnut-shape organoids on 3D-printed devices within standard 96-well plates, we generate hCO-MPSs with reduced necrosis, minimized hypoxia, and improved viability. Using these models, we found that monocytes from AD patients exhibit increased infiltration ability, decreased amyloid-β clearance capacity, and stronger inflammatory response than monocytes from age-matched control donors. Moreover, we observed that AD monocytes induce pro-inflammatory effects such as elevated astrocyte activation and neuronal apoptosis. Furthermore, the marked increase in IL1B and CCL3 expression underscores their pivotal role in AD monocyte-mediated neuroinflammation. Our findings provide insight into understanding monocytes’ role in AD pathogenesis, and our lab-compatible MPS models may offer a promising way for studying various neuroinflammatory diseases.

No abstract available

Alzheimer’s disease (AD), a prevalent neurodegenerative disorder in the elderly, poses significant humanistic and economic burdens worldwide. Previously, we identified Trp-Leu-Pro (WLP), a novel antioxidant peptide derived from the sea squirt (Halocynthia roretzi); however, its effects on AD remained unexplored. In this study, we developed a rapid and efficient method to generate AD cerebral organoids with consistent quality using okadaic acid (OKA) exposure. This study aimed to evaluate the protective effects of WLP on OKA-induced AD pathology in cerebral organoids and elucidate its underlying mechanisms. Our results demonstrated that cerebral organoids exposed to 25 nM OKA successfully recapitulated hallmark AD pathologies, including amyloid-beta (Aβ) plaque deposits, neurofibrillary tangles (NFTs) formed by hyperphosphorylated tau proteins, and neuronal loss. WLP treatment significantly enhanced cell viability, increased the proportion of neuronal progenitor cells, and reduced Aβ plaques and NFTs in OKA-induced cerebral organoids. Furthermore, transcriptomic analysis revealed that the neuroprotective effects of WLP are primarily mediated through the regulation of synapse-related and oxidative stress pathways. These findings highlight the potential of WLP as a promising nutraceutical candidate for AD prevention.

Cerebral organoids (COs) are the most advanced in vitro models that resemble the human brain. The use of COs as a model for Alzheimer’s disease (AD), as well as other brain diseases, has recently gained attention. This study aimed to develop a human AD CO model using normal human pluripotent stem cells (hPSCs) that recapitulates the pathological phenotypes of AD and to determine the usefulness of this model for drug screening. We established AD hPSC lines from normal hPSCs by introducing genes that harbor familial AD mutations, and the COs were generated using these hPSC lines. The pathological features of AD, including extensive amyloid-β (Aβ) accumulation, tauopathy, and neurodegeneration, were analyzed using enzyme-linked immunosorbent assay, Amylo-Glo staining, thioflavin-S staining, immunohistochemistry, Bielschowsky’s staining, and western blot analysis. The AD COs exhibited extensive Aβ accumulation. The levels of paired helical filament tau and neurofibrillary tangle-like silver deposits were highly increased in the AD COs. The number of cells immunoreactive for cleaved caspase-3 was significantly increased in the AD COs. In addition, treatment of AD COs with BACE1 inhibitor IV, a β-secretase inhibitor, and compound E, a γ-secretase inhibitor, significantly attenuated the AD pathological features. Our model effectively recapitulates AD pathology. Hence, it is a valuable platform for understanding the mechanisms underlying AD pathogenesis and can be used to test the efficacy of anti-AD drugs.

AIMS To investigate the therapeutic effects and mechanisms of Semaglutide in Alzheimer's disease (AD), and identify its potential targets. METHODS We systematically evaluated the effect of Semaglutide on Alzheimer's disease (AD), using both mice and human organoid models. RESULTS Behavioral analyses on APP/PS1 mice demonstrated that Semaglutide improved the cognitive capabilities, particularly in the learning and memory domains. Biochemical investigations further highlighted its role in reducing amyloid plaque deposition and down-regulating the expression of glial fibrillary acidic protein (GFAP) and ionized calcium binding adaptor molecule 1 (Iba1) expression in the mouse brain tissues. Meanwhile, oxytocin (OXT) was up-regulated after Semaglutide treatment. Subsequent studies using human AD-brain organoids (BOs) models revealed that, upon Semaglutide treatment, these AD-BO models also exhibited reduced levels of amyloid-beta (Aβ), phosphorylated Tau (p-Tau) and GFAP expression as well as increased OXT level. CONCLUSIONS Semaglutide can ameliorate Alzheimer's disease in pre-clinical models, suggesting the promising therapeutic potential in AD patients.

As a progressive neurodegenerative disorder, Alzheimer’s disease (AD) can result in significant memory loss and cognitive deterioration. Several recent studies show that herpes simplex virus type I (HSV-1) is closely related to AD pathology. Microglia, the primary immune cells in the central nervous system, are also shown to play an important role in AD. In this study, we developed a microglia-containing 3-dimensional (3D) human brain organoid from human-induced pluripotent stem cells (hiPSCs) to study the relationship between microglia and HSV-1-induced AD phenotypes. We found that microglia increased the generation of amyloid-β protein (Aβ) and neurofibrillary tangles (NFTs), contributed to neural loss, and enhanced gliosis and neuroinflammation. We also employed shRNA vectors to inhibit certain cytokines related to neuroinflammation and examined the impact on Aβ aggregation. This model can facilitate future research on the treatment of AD regarding microglia and HSV-1.

Viral infections leading to inflammation have been implicated in several common diseases, such as Alzheimer’s disease (AD) and type 1 diabetes (T1D). Of note, herpes simplex virus 1 (HSV-1) has been reported to be associated with AD. We sought to identify the transcriptomic changes due to HSV-1 infection and anti-viral drug (acyclovir, ACV) treatment of HSV-1 infection in dissociated cells from human cerebral organoids (dcOrgs) versus stem cell-derived pancreatic islets (sc-islets) to gain potential biological insights into the relevance of HSV-1-induced inflammation in AD and T1D. We observed that differentially expressed genes (DEGs) in HSV-1-infected sc-islets were enriched for genes associated with several autoimmune diseases, most significantly, T1D, but also rheumatoid arthritis, psoriasis, Crohn’s disease, and multiple sclerosis, whereas DEGs in HSV-1-infected dcOrgs were exclusively enriched for genes associated with AD. The ACV treatment of sc-islets was not as effective in rescuing transcript perturbations of autoimmune disease-associated genes. Finally, we identified gene ontology categories that were enriched for DEGs that were in common across, or unique to, viral treatment of dcOrgs and sc-islets, such as categories involved in the transferase complex, mitochondrial, and autophagy function. In addition, we compared transcriptomic signatures from HSV-1-infected sc-islets with sc-islets that were infected with the coxsackie B virus (CVB) that had been associated with T1D pathogenesis. Collectively, this study provides tissue-specific insights into the molecular effects of inflammation in AD and T1D.

No abstract available

Pathological progression in sporadic Alzheimer's disease (sAD) initiates with an early rise in soluble amyloid-β (Aβ), preceding plaque formation and neurodegeneration. However, the molecular event triggering this initial accumulation remains unknown. We report that phosphoglycerate dehydrogenase (PHGDH), a consistent biomarker of prodromal sAD, drives Aβ production through a previously unrecognized RNA-binding function. Specifically, PHGDH binds the 3'UTR of EIF2AK1 mRNA, enabling the physical interaction between PHGDH and the EIF2AK1 protein. By facilitating the recruitment of EIF2AK1 to its substrate EIF2α, this complex drives EIF2α phosphorylation, thereby selectively promoting the translation of BACE1, the rate-limiting enzyme for Aβ generation. We demonstrate that PHGDH overexpression elevates BACE1 protein and intracellular Aβ in neurons and astrocytes across mouse models and human brain organoids, independent of its canonical enzymatic or transcriptional roles. Mechanistically, this process requires a specific RNA-binding surface within PHGDH and the EIF2AK1 3'UTR. These findings define a PHGDH-EIF2AK1-EIF2α-BACE1 axis as a key driver of the earliest amyloid pathology in sAD.

Dysfunctional mitochondria and mitophagy are hallmarks of Alzheimer’s disease (AD). It is widely accepted that restoration of mitophagy helps to maintain cellular homeostasis and ameliorates the pathogenesis of AD. It is imperative to create appropriate preclinical models to study the role of mitophagy in AD and to assess potential mitophagy-targeting therapies. Here, by using a novel 3D human brain organoid culturing system, we found that amyloid-β (Aβ1-42,10 μM) decreased the growth level of organoids, indicating that the neurogenesis of organoids may be impaired. Moreover, Aβ treatment inhibited neural progenitor cell (NPC) growth and induced mitochondrial dysfunction. Further analysis revealed that mitophagy levels were reduced in the brain organoids and NPCs. Notably, galangin (10 μM) treatment restored mitophagy and organoid growth, which was inhibited by Aβ. The effect of galangin was blocked by the mitophagy inhibitor, suggesting that galangin possibly acted as a mitophagy enhancer to ameliorate Aβ-induced pathology. Together, these results supported the important role of mitophagy in AD pathogenesis and suggested that galangin may be used as a novel mitophagy enhancer to treat AD.

Alzheimer’s disease (AD) is one of the most well-known neurodegenerative diseases, with a substantial amount of advancements in the field of neuroscience and AD. Despite such progress, there has been no significant improvement in AD treatments. To improve in developing a research platform for AD treatment, AD patient-derived induced pluripotent stem cell (iPSC) was employed to generate cortical brain organoids, expressing AD phenotypes, with the accumulation of amyloid-beta (Aβ) and hyperphosphorylated tau (pTau). We have investigated the use of a medical grade mica nanoparticle, STB-MP, as a treatment to decrease the expression of AD’s major hallmarks. STB-MP treatment did not inhibit the expression of pTau; however, accumulated Aβ plaques were diminished in STB-MP treated AD organoids. STB-MP seemed to activate the autophagy pathway, by mTOR inhibition, and also decreased γ-secretase activity by decreasing pro-inflammatory cytokine levels. To sum up, the development of AD brain organoids successfully mimics AD phenotype expressions, and thus it could be used as a screening platform for novel AD treatment assessments.

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of Aβ plaques and neurofibrillary tangles, resulting in synaptic loss and neurodegeneration. The retina is an extension of the central nervous system within the eye, sharing many structural similarities with the brain, and previous studies have observed AD-related phenotypes within the retina. Three-dimensional retinal organoids differentiated from human pluripotent stem cells (hPSCs) can effectively model some of the earliest manifestations of disease states, yet early AD-associated phenotypes have not yet been examined. Thus, the current study focused upon the differentiation of hPSCs into retinal organoids for the analysis of early AD-associated alterations. Results demonstrated the robust differentiation of retinal organoids from both familial AD and unaffected control cell lines, with familial AD retinal organoids exhibiting a significant increase in the Aβ42:Aβ40 ratio as well as phosphorylated Tau protein, characteristic of AD pathology. Further, transcriptional analyses demonstrated the differential expression of many genes and cellular pathways, including those associated with synaptic dysfunction. Taken together, the current study demonstrates the ability of retinal organoids to serve as a powerful model for the identification of some of the earliest retinal alterations associated with AD.

Familial Alzheimer’s disease (fAD) is a autosomal dominant, early‐onset form of AD caused by genetic mutations such as duplication of the amyloid precursor protein gene (APP) on one chromosome (APPdup) or point mutations in APP such as the London mutation (APPV717I), both of which cause overproduction of the amyloid‐beta peptide (Aβ). People with Down syndrome (DS) also have a form of fAD due to triplication of APP which resides on chromosome 21. By age 40, all people with DS develop AD brain pathology, including Aβ plaques and neurofibrillary tangles of phosphorylated tau (pTau), and most go on to develop early‐onset dementia. We previously identified imipramine by high‐throughput screening for novel inhibitors of apolipoprotein E (apoE), which is the strongest risk factor for AD other than age itself. Here, we developed and characterized new cerebral organoid (CO) models of fAD and DS and used them to study common pathological mechanisms and to evaluate imipramine as a novel AD treatment.

Alzheimer’s disease (AD) is the most common condition in patients with dementia and affects a large population worldwide. The incidence of AD is expected to increase in future owing to the rapid expansion of the aged population globally. Researchers have shown that women are twice more likely to be affected by AD than men. This phenomenon has been attributed to the postmenopausal state, during which the level of estrogen declines significantly. Estrogen is known to alleviate neurotoxicity in the brain and protect neurons. While the effects of estrogen have been investigated in AD models, to our knowledge, they have not been investigated in a stem cell-based three-dimensional in vitro system. Here, we designed a new model for AD using induced pluripotent stem cells (iPSCs) in a three-dimensional, in vitro culture system. We used 5xFAD mice to confirm the potential of estrogen in alleviating the effects of AD pathogenesis. Next, we confirmed a similar trend in an AD model developed using iPSC-derived cerebral organoids, in which the key characteristics of AD were recapitulated. The findings emphasized the potential of estrogen as a treatment agent for AD and also showed the suitability of AD-recapitulating cerebral organoids as a reliable platform for disease modeling and drug screening.

The cerebral organoid (CO) model has been used in the study of various neurodegenerative diseases owing to its physiological implications. However, the CO model may only be representative of certain clinical findings in affected patients, while some features are not recapitulated. In this study, we found that neurons in the CO model from patients with Alzheimer’s disease were less responsive to depolarization, in contrast to previous reports. This difference may be partly attributed to the variations in brain spatial identity depending on the genetic background of the induced pluripotent stem cells. Our current observation raises concerns that the phenotypes observed in the CO model need to be carefully evaluated for their clinical implications.

The aim of this study was to validate the use of human brain organoids (hBOs) to investigate the therapeutic potential and mechanism of human-neural-crest-derived nasal turbinate stem cells (hNTSCs) in models of Alzheimer’s disease (AD). We generated hBOs from human induced pluripotent stem cells, investigated their characteristics according to neuronal markers and electrophysiological features, and then evaluated the protective effect of hNTSCs against amyloid-β peptide (Aβ1–42) neurotoxic activity in vitro in hBOs and in vivo in a mouse model of AD. Treatment of hBOs with Aβ1–42 induced neuronal cell death concomitant with decreased expression of neuronal markers, which was suppressed by hNTSCs cocultured under Aβ1–42 exposure. Cytokine array showed a significantly decreased level of osteopontin (OPN) in hBOs with hNTSC coculture compared with hBOs only in the presence of Aβ1–42. Silencing OPN via siRNA suppressed Aβ-induced neuronal cell death in cell culture. Notably, compared with PBS, hNTSC transplantation significantly enhanced performance on the Morris water maze, with reduced levels of OPN after transplantation in a mouse model of AD. These findings reveal that hBO models are useful to evaluate the therapeutic effect and mechanism of stem cells for application in treating AD.

SUMMARY 5-hydroxymethylcytosine (5hmC) undergoes dynamic changes during mammalian brain development, and its dysregulation is associated with Alzheimer’s disease (AD). The dynamics of 5hmC during early human brain development and how they contribute to AD pathologies remain largely unexplored. We generate 5hmC and transcriptome profiles encompassing several developmental time points of healthy forebrain organoids and organoids derived from several familial AD patients. Stage-specific differentially hydroxymethylated regions demonstrate an acquisition or depletion of 5hmC modifications across developmental stages. Additionally, genes concomitantly increasing or decreasing in 5hmC and gene expression are enriched in neurobiological or early developmental processes, respectively. Importantly, our AD organoids corroborate cellular and molecular phenotypes previously observed in human AD brains. 5hmC is significantly altered in developmentally programmed 5hmC intragenic regions in defined fetal histone marks and enhancers in AD organoids. These data suggest a highly coordinated molecular system that may be dysregulated in these early developing AD organoids.

Alzheimer’s Disease (AD) is the most common cause of dementia, afflicting 55 million individuals worldwide, with limited treatment available. Current AD models mainly focus on familial AD (fAD), which is due to genetic mutations. However, models for studying sporadic AD (sAD), which represents over 95% of AD cases without specific genetic mutations, are severely limited. Moreover, the fundamental species differences between humans and animals might significantly contribute to clinical failures for AD therapeutics that have shown success in animal models, highlighting the urgency to develop more translational human models for studying AD, particularly sAD. In this study, we developed a complex human pluripotent stem cell (hPSC)-based vascularized neuroimmune organoid model, which contains multiple cell types affected in human AD brains, including human neurons, microglia, astrocytes, and blood vessels. Importantly, we demonstrated that brain extracts from individuals with sAD can effectively induce multiple AD pathologies in organoids four weeks post-exposure, including amyloid beta (Aβ) plaque-like aggregates, tau tangle-like aggregates, neuroinflammation, elevated microglial synaptic pruning, synapse/neuronal loss, and impaired neural network activity. Proteomics analysis also revealed disrupted AD-related pathways in our vascularized AD neuroimmune organoids. Furthermore, after treatment with Lecanemab, an FDA-approved antibody drug targeting Aβ, AD brain extracts exposed organoids showed a significant reduction of amyloid burden, along with an elevated vascular inflammation response. Thus, the vascularized neuroimmune organoid model provides a unique opportunity to study AD, particularly sAD, under a pathophysiological relevant three-dimensional (3D) human cell environment. It also holds great promise to facilitate AD drug development, particularly for immunotherapies.

Alzheimer's disease (AD) is an age‐related neurodegenerative disease. The most common pathological hallmarks are amyloid plaques and neurofibrillary tangles in the brain. In the brains of patients with AD, pathological tau is abnormally accumulated causing neuronal loss, synaptic dysfunction, and cognitive decline. We found a histone deacetylase 6 (HDAC6) inhibitor, CKD‐504, changed the tau interactome dramatically to degrade pathological tau not only in AD animal model (ADLPAPT) brains containing both amyloid plaques and neurofibrillary tangles but also in AD patient‐derived brain organoids. Acetylated tau recruited chaperone proteins such as Hsp40, Hsp70, and Hsp110, and this complex bound to novel tau E3 ligases including UBE2O and RNF14. This complex degraded pathological tau through proteasomal pathway. We also identified the responsible acetylation sites on tau. These dramatic tau‐interactome changes may result in tau degradation, leading to the recovery of synaptic pathology and cognitive decline in the ADLPAPT mice.

Advances in the development of three-dimensional (3D) brain organoids maintained in vitro have provided excellent opportunities to study brain development and neurodegenerative disorders, including Alzheimer’s disease (AD). However, there remains a need to generate AD organoids bearing patient-specific genomic backgrounds that can functionally recapitulate key features observed in the AD patient’s brain. To address this need, we successfully generated cerebral organoids from human pluripotent stem cells (hPSCs) derived from a familial AD patient with a mutation in presenilin 2 (PSEN2). An isogenic control hPSC line was generated using CRISPR-Cas9 technology. Both organoids were characterized by analysing their morphology, Aβ42/Aβ40 ratio and functional neuronal network activity. It was found that AD organoids had a higher Aβ42/Aβ40 ratio, asynchronous calcium transients and enhanced neuronal hyperactivity, successfully recapitulating some aspects of AD pathology. Therefore, our study presents a promising organoid-based biosystem for the study of the pathophysiology of AD and a platform for drug development for neurodegenerative disorders.

Alzheimer’s disease (AD) is the most common type of neurodegenerative diseases. There are over 44 million people living with the disease worldwide. While there are currently no effective treatments for AD, induced pluripotent stem cell-derived brain organoids have the potential to provide a better understanding of Alzheimer’s pathogenesis. Nevertheless, developing brain organoid models is expensive, time consuming and often does not reflect disease progression. Using accurate and inexpensive computer simulations of human brain organoids can overcome the current limitations. Induced whole brain organoids (aiWBO) will greatly expand our ability to model AD and can guide wet lab research. In this study, we have successfully developed and validated artificially induced a whole brain organoid platform (NEUBOrg) using our previously validated machine learning platform, DeepNEU (v6.1). Using NEUBorg platform, we have generated aiWBO simulations of AD and provided a novel approach to test genetic risk factors associated with AD progression and pathogenesis.

Alzheimer's disease (AD) is a progressive neurodegenerative disease, characterized by cognitive impairment. However, the pathogenesis of AD are very complicated, and the theories of Aβ and neurofibrillary tangles cannot explain all pathological alterations and clinical symptoms. Here, we used three-dimensional (3D) neural organoids culture derived from mouse induced pluripotent stem cells (iPSCs) to investigate the pathological mechanisms of AD. In this study, AD cerebral organoids were generated by overexpressing familial AD mutations (APP and PS1 genes) in mouse induced pluripotent stem cells, so that the early pathogenesis of AD could be investigated well with protein and cellular phenotype analyses. The results showed that AD cerebral organoids appeared some AD pathological alterations, and high levels of Aβ and p-Tau were induced as well. Furthermore, the number of GFAP-positive astrocytes and glutamatergic excitatory neurons increased significantly, but the number of GABAergic interneurons decreased. In conclusion, we suggest that cerebral organoids are a suitable AD model for scientific study, and that will provide us a novel insight into the understanding of the pathogenesis of AD.

Alzheimer's disease (AD) is a progressive and neurodegenerative disease, predominantly causing dementia. Despite increasing clinical evidence suggesting the involvement of peripheral immune cells such as monocytes in AD pathology, the dynamic penetration and infiltration of monocytes crossing blood-brain barrier (BBB) and inducing neuroinflammation is largely understudied in an AD brain. Herein, we engineer BBB-like microphysiological system (BBB-MPS) models for recapitulating the dynamic penetration and infiltration of monocytes in an AD patient's brain. Each BBB-MPS model can be engineered by integrating a functional BBB-like structure on a human cortical organoid using a 3D-printed device within a well of a plate. By coculturing these BBB-MPS models with monocytes from AD patients and age-matched healthy donors, we found that AD monocytes exhibit significantly greater BBB penetration and brain infiltration compared to age-matched control monocytes. Moreover, we also tested the interventions including Minocycline and Bindarit, and found they can effectively inhibit AD monocyte infiltration, subsequently reducing neuroinflammation and neuronal apoptosis. We believe these scalable and user-friendly BBB-MPS models may hold promising potential in modeling and advancing therapeutics for neurodegenerative and neuroinflammatory diseases.

Alzheimer’s disease (AD) is the most common form of dementia worldwide. Despite extensive progress, the cellular and molecular mechanisms of AD remain incompletely understood, partially due to inadequate disease models. To illuminate the earliest changes in hereditary (familial) Alzheimer’s disease, we developed an isogenic AD cerebrocortical organoid (CO) model. Our refined methodology produces COs containing excitatory and inhibitory neurons alongside glial cells, utilizing established isogenic wild-type and diseased human induced pluripotent stem cells (hiPSCs) carrying heterozygous familial AD mutations, namely PSEN1ΔE9/WT, PSEN1M146V/WT, or APPswe/WT. Our CO model reveals time-progressive accumulation of amyloid beta (Aβ) species, loss of monomeric Tau, and accumulation of aggregated high-molecular-weight (HMW) phospho(p)-Tau species. This is accompanied by neuronal hyperexcitability, as observed in early human AD cases on electroencephalography (EEG), and synapse loss. Single-cell RNA-sequencing analyses reveal significant differences in molecular abnormalities in excitatory vs. inhibitory neurons, helping explain AD clinical phenotypes. Finally, we show that chronic dosing with autophagy activators, including a novel CNS-penetrant mTOR inhibitor-independent drug candidate, normalizes pathologic accumulation of Aβ and HMW p-Tau, normalizes hyperexcitability, and rescues synaptic loss in COs. Collectively, our results demonstrate these COs are a useful human AD model suitable for assessing early features of familial AD etiology and for testing drug candidates that ameliorate or prevent molecular AD phenotypes.

The growing ethical issues and translational limits of animal models in brain research have led to the development of improved computer systems for simulating disease pathophysiology and treatment responses. This study proposes a novel integrative strategy that uses artificial intelligence (AI)-driven in silico models to replace and improve traditional animal experimentation in the preclinical evaluation of Alzheimer’s disease (AD) nanomedicines. Machine learning models were trained using multi-omics datasets, quantum chemical descriptors, and physicochemical parameters of polymer-encapsulated ursolic acid (UA) nanoformulations to predict neuroprotective efficacy, target binding affinity (AChE, amyloid-β, tau), and potential toxicity profiles. Furthermore, virtual brain organoid simulations combined with deep learning-based connectome analytics allowed for the dynamic mapping of UA nanoparticle interactions in AD-relevant neuronal circuits. A comparative investigation demonstrated significant connections between AI-predicted results and presumed in vivo data, supporting the computational workflow. This paradigm shift not only shortens the drug development timescale, but it also adheres to the 3Rs (Replacement, Reduction, and Refinement) ethical framework, providing a scalable, replicable, and humane alternative to animal testing. Our findings highlight AI’s transformational potential in developing precision nano-neurotherapeutics for neurodegenerative diseases.

Age-related neurodegenerative diseases, like Alzheimer’s disease (AD), are challenging diseases for those affected with no cure and limited treatment options. Functional, human derived brain tissues that represent the diverse genetic background and cellular subtypes contributing to sporadic AD (sAD) are limited. Human stem cell derived brain organoids recapitulate some features of human brain cytoarchitecture and AD-like pathology, providing a tool for illuminating the relationship between AD pathology and neural cell dysregulation leading to cognitive decline. In this review, we explore current strategies for implementing brain organoids in the study of AD as well as the challenges associated with investigating age-related brain diseases using organoid models.

Alzheimer’s disease (AD), characterized by memory loss and cognitive decline, affects nearly 50 million people worldwide. Amyloid beta (Aβ) plaques and intracellular neurofibrillary tangles (NFTs) of phosphorylated Tau protein (pTau) are key histopathological features of the disease in the brain, and recent advances have also identified AD histopathology in the retina. Thus, the retina represents a central nervous system (CNS) tissue highly amenable to non-invasive diagnostic imaging that shows promise as a biomarker for early AD. Given the devastating effects of AD on patients, their families, and society, new treatment modalities that can significantly alter the disease course are urgently needed. In this study, we have developed and characterized a novel human retinal organoid (RO) model derived from induced pluripotent stem cells (iPSCs) from patients with familial AD due to mutations in the amyloid precursor protein gene (APP). Using immunofluorescence and histological staining, we evaluated the cellular composition and AD histopathological features of AD-ROs compared to control ROs from healthy individuals. We found that AD-ROs largely resemble their healthy control counterparts in cellular composition but display increased levels of Aβ and pTau. We also present proof of principle of an assay to quantify amyloid levels in whole ROs. This in vitro model of the human AD retina constitutes a new tool for drug screening, biomarker discovery, and pathophysiological studies.

Brain organoid models were generated from healthy control or Alzheimer’s disease patient iPSCs to facilitate our understanding of AD pathogenesis.

Alzheimer´s disease is a neurodegenerative disease with high global prevalence and no cure available. It is known that the microbiota-gut-brain-axis plays a role in the pathogenesis, but the pathways are not fully understood yet. To elucidate the role of dietary fibre supplementation on this axis in a 5xFAD mouse model of Alzheimer´s disease, a feeding trial with an inulin supplement was conducted. At the start (Basis, n = 11) and after 7 weeks with (AD + F; n = 15) and without (AD; n = 15) supplementation, the mice were sacrificed and the following samples were taken: ingesta for 16 S rRNA sequencing and short-chain fatty acid (SCFA) analysis, and brain tissue for amyloid-beta staining and proteome analysis. The microbiota patterns in stomach, small intestine, caecum and colon differed between AD and AD + F. SCFA concentrations were significantly higher in group AD + F as compared to AD and Basis. In the AD mice, plaque load was significantly increased as compared to Basis, while a reduction in AD + F as compared to AD was observed. The brain proteome also differed between AD + F and AD, indicating a beneficial effect of the inulin supplementation, possibly mediated in part by microbial acetate. Since prebiotic substances like inulin are also part of human diets, this should be investigated further in the translational context.

SUMMARY Shifts in the magnitude and nature of gut microbial metabolites have been implicated in Alzheimer’s disease (AD), but the host receptors that sense and respond to these metabolites are largely unknown. Here, we develop a systems biology framework that integrates machine learning and multi-omics to identify molecular relationships of gut microbial metabolites with non-olfactory G-protein-coupled receptors (termed the “GPCRome”). We evaluate 1.09 million metabolite-protein pairs connecting 408 human GPCRs and 335 gut microbial metabolites. Using genetics-derived Mendelian randomization and integrative analyses of human brain transcriptomic and proteomic profiles, we identify orphan GPCRs (i.e., GPR84) as potential drug targets in AD and that triacanthine experimentally activates GPR84. We demonstrate that phenethylamine and agmatine significantly reduce tau hyperphosphorylation (p-tau181 and p-tau205) in AD patient induced pluripotent stem cell-derived neurons. This study demonstrates a systems biology framework to uncover the GPCR targets of human gut microbiota in AD and other complex diseases if broadly applied.

Intimate metabolic host–microbiome crosstalk regulates immune, metabolic, and neuronal response in health and disease, yet remains untapped for biomarkers or intervention for disease. Our recent study identified an altered microbiome in patients with pre-onset amnestic mild cognitive impairment (aMCI) and dementia Alzheimer’s disease (AD). Thus, we aimed to characterize the gut microbial metabolites among AD, aMCI, and healthy controls (HC). Here, a cohort of 77 individuals (22 aMCI, 27 AD, and 28 HC) was recruited. With the use of liquid-chromatography/gas chromatography mass spectrometry metabolomics profiling, we identified significant differences between AD and HC for tryptophan metabolites, short-chain fatty acids (SCFAs), and lithocholic acid, the majority of which correlated with altered microbiota and cognitive impairment. Notably, tryptophan disorders presented in aMCI and SCFAs decreased progressively from aMCI to AD. Importantly, indole-3-pyruvic acid, a metabolite from tryptophan, was identified as a signature for discrimination and prediction of AD, and five SCFAs for pre-onset and progression of AD. This study showed fecal-based gut microbial signatures were associated with the presence and progression of AD, providing a potential target for microbiota or dietary intervention in AD prevention and support for the host–microbe crosstalk signals in AD pathophysiology.

Alzheimer’s disease (AD) is characterized by behavioral and cognitive impairments and its increasing prevalence imposes a healthcare burden on society. To date, most intervention studies have only focused on a single AD-related factor and have yielded modest cognitive improvements. Here, we show that environmental enrichment (EE) training combined with Bifidobacterium breve CCFM1025 intervention significantly alleviated amyloid-β (Aβ)-induced cognitive impairment and inhibited neuroinflammation in mice. Moreover, we found that EE combined with B. breve CCFM1025 treatment restored AD-associated gut microbiota dysbiosis and reversed microbial metabolites changes. By integrating behavioral and neurological data with metabolomic profiles, we corroborated the microbiota–metabolite–brain interactions, with acetate and tryptophan metabolism as potential drivers. Taken together, our results provide a promising multidomain intervention strategy to prevent cognitive decline and delay the progression of AD through a combination of dietary microbiome-based approaches and lifestyle interventions.

Intermittent fasting (IF) offers a potential strategy to counteract Alzheimer’s disease (AD) progression. In our 16-week study on AD transgenic mice, IF positively affected cognitive function and reduced amyloid-β (Aβ) accumulation, verifying the IF’s role in modulating neuroinflammation. Multiomics integration revealed strong links between IF-induced hippocampal gene expression, gut microbiota, and serum metabolites beneficial for cognition. Indole-3-propionic acid (IPA) emerged as a pivotal microbial metabolite. Blocking its neuronal receptor, pregnane X receptor (PXR), abolished IF’s effects. Human data paralleled these findings, showing lower IPA levels in patients with mild cognitive impairment and AD than in controls. IPA supplementation and IPA-producing Clostridium sporogenes reproduced IF’s cognitive benefits, whereas PXR blockade in neurons or disruption of IPA synthesis abrogated them. IPA crossed the blood-brain barrier, exhibited potent anti-inflammatory activity, and suppressed Aβ accumulation, essential for neuroprotection. These results underscore microbial metabolites regulated by IF, particularly IPA, as therapeutic candidates for AD, highlighting the critical role of the gut-brain axis in neurodegeneration.

Cistanche deserticola polysaccharides (CDPS) exhibit a range of pharmacological activities, most notably in immune modulation, anti-oxidation, and gut microbiota regulation. Emerging evidence suggests that restoring gut microbial and metabolic homeostasis may decelerate the progression of Alzheimer's disease (AD). However, the specific in vivo effects and underlying mechanisms of CDPS in the context of AD remain incompletely understood. In this study, we employed behavioral tests, 16S rRNA high-throughput sequencing, and time-resolved metabolomic analyses to comprehensively evaluate the therapeutic efficacy of CDPS. CDPS administration significantly ameliorated cognitive impairment, suppressed pro-inflammatory cytokine expression, and reduced A[Formula: see text] deposition and Tau hyperphosphorylation in the brains of APP/PS1 Tg mice. These effects were associated with CDPS-induced modulation of gut microbial composition - especially the Firmicutes/Bacteroidetes ratio - and regulation of D-Proline and Histidine metabolism. Further in vitro and in vivo validation confirmed that D-Proline and Histidine, key CDPS-associated metabolites, protected against A[Formula: see text]-induced apoptosis and oxidative stress. Notably, the cognitive benefits of CDPS were markedly weakened under conditions of gut microbiota disruption or immune suppression, which highlights the importance of microbial and immune system integrity in mediating its therapeutic effects. Collectively, these findings highlight gut microbial and metabolic disturbances as critical contributors to AD pathogenesis, and support CDPS as a promising multi-target therapeutic strategy. The integration of longitudinal microbiota and metabolomic profiling offers novel mechanistic insights into the neuroprotective actions of CDPS in AD.

BACKGROUND Microbial-derived metabolites play important roles in Alzheimer's disease (AD) pathology, yet how intestinal microbes influence AD progression remains uncertain. Xanthoceraside (XAN), a triterpenoid saponin with anti-AD activity, was extracted from the husks of Xanthoceras sorbifolia Bunge. However, it is still unclear that how XAN modulates the gut microbiota community to regulate AD progression through changing the levels of microbial-derived metabolites. PURPOSE In this study, we investigated the mechanism underlying the anti-AD effect of XAN. METHODS The current combination studies of multiple-targeted metabolomics, natural product chemistry and pharmacology revealed that oral XAN mediated intestinal microbiota to ameliorate Aβ1-42-induced learning and memory deficits in rats, which were confirmed through antibiotic treatments and fecal microbiota transplantation. RESULTS As a poor water solubility and low permeability compound that hardly be absorbed into blood-brain barrier, XAN significantly regulated Aβ1-42-induced metabolism disorders directly or indirectly in gut, including neurotransmitters, amino acids, bile acids and SCFAs metabolism that were detected by UHPLC-MS/MS and GC-MS/MS. In particularly, the in vitro evaluation of XAN on SCFAs production not only found a striking increase in the production of SCFAs after fermentation, but revealed the inner relationship among XAN, gut microbiota and SCFAs in vivo. All results demonstrated that XAN could improve AD rats' learning and memory deficits by modulating the community of gut microbiota which was connected through 16S rRNA sequencing and CCA analyses. CONCLUSIONS Our study provided a novel mechanism for developing XAN as a potential anti-AD drug and revealed that the gut microbiota might be a potential target for AD treatment .

Summary There has been increasing interest in the connection between AD, gut microbiota, and metabolites. Kai-Xin-San (KXS) has been commonly employed in ancient and modern Chinese clinical trials for the treatment of dementia; however, whether the protective effect of KXS in AD is related to the gut microbiota remains elusive. APP/PS1 mice were used as the model of AD. 43 key metabolites influenced by KXS were screened using untargeted metabolomics. At the genus level, Clostridium_IV, Eubacterium, Acetatifactor, etc., were identified to be impacted by KXS using 16S rRNA sequencing. Additionally, we identified 9 distinct intestinal floras at the genus level that were correlated with 13 pivotal differential metabolites related to cognitive impairment. KXS also inhibited the neuroinflammation, mostly via regulating the key metabolites. A potential relationship between gut microbiota, metabolites, and neuroinflammation is suggested as a protective mechanism of KXS in AD. These findings provide support for further development of KXS.

The intricacy and multifaceted nature of Alzheimer's disease (AD) necessitate therapies that target multiple aspects of the disease. Mesenchymal stromal cells (MSCs) emerge as potential agents to mitigate AD symptoms; however, whether their therapeutic efficacy involves modulation of gut microbiota and the microbiome-gut-brain axis (MGBA) remains unexplored. In this study, we evaluated the effects of three distinct MSCs types-derived from the umbilical cord (UCMSC), dental pulp (SHED), and adipose tissue (ADSC)-in an APP/PS1 mouse model of AD. In comparison to saline control, MSCs administration resulted in a significant reduction of behavioral disturbances, amyloid plaques, and phosphorylated tau in the hippocampus and frontal cortex, accompanied by an increase in neuronal count and Nissl body density across AD-afflicted brain regions. Through 16S rRNA gene sequencing, we identified partial restoration of gut microbial balance in AD mice post-MSCs treatment, evidenced by the elevation of neuroprotective Akkermansia and reduction of the AD-associated Sphingomonas. To examine whether gut microbiota involved in MSCs efficacy in treating AD, SHED with better anti-inflammatory and gut microbiota recovery effects among three MSCs, and another AD model 5 × FAD mice with earlier and more pathological proteins in brain than APP/PS1, were selected for further studies. Antibiotic-mediated gut microbial inactivation attenuated MSCs efficacy in 5 × FAD mice, implicating the involvement of gut microbiota in the therapeutic mechanism. Functional analysis of altered gut microbiota and targeted bile acid metabolism profiling revealed a significant enhancement in bile acid variety following MSCs therapy. A chief bile acid constituent, taurocholic acid (TCA), was orally administered to AD mice and similarly abated AD symptoms. Nonetheless, the disruption of intestinal neuronal integrity with enterotoxin abrogated the ameliorative impact of both MSCs and TCA treatments. Collectively, our findings substantiate that MSCs confer therapeutic benefits in AD within a paradigm that primarily involves regulation of gut microbiota and their metabolites through the MGBA.

Background This study explores how gut metabolites, produced through bacterial metabolism in the gut, influence neurological conditions like Alzheimer's disease (AD). Key metabolites such as succinate and short-chain fatty acids signal through the autonomic nervous system and can cross the blood-brain barrier, impacting central nervous system functions. Objective The aim is to examine the role of the gut microbiota in compensating for metabolic deficiencies in AD. By analyzing wild-type (WT) and APP/PS1 mice, the study investigates how the microbiome affects key metabolic processes and whether it can slow AD progression. Methods High-throughput sequencing data from the gut microbiomes of APP/PS1 transgenic AD model mice and age-matched WT C57BL/6 male mice were analyzed for microbial and metabolite profiles. Results Alpha and beta diversity analyses showed differences in microbial composition between groups. Partial least squares discriminant analysis and Anosim confirmed distinct microbiome profiles in WT and APP/PS1 mice. At the genus level, Vescimonas was more abundant in WT mice, while Odoribacter, Lacrimispora, Helicobacter, Bacteroides, and Alloprevotella were more prevalent in APP/PS1 mice. Conclusions While taxonomic differences did not directly link specific microorganisms to AD, functional analysis identified key metabolites—acetyl-CoA, glucose, succinate, lipids, choline, and acetylcholine—that may alleviate energy deficits and synaptic dysfunction. This study suggests that the microbiome may help compensate for AD-related impairments, opening avenues for microbiome-based therapies.

BackgroundEmerging evidence indicates that gut microbiome dysbiosis may be linked to Nicotinamide adenine dinucleotide (NAD+) deficiency during Alzheimer's disease (AD) progression, a condition potentially alleviated by nicotinamide mononucleotide (NMN) supplementation.ObjectiveTo explore the therapeutic potential of NMN supplementation in regulating AD pathology as well as gut microbiome dynamics, APP/PS1 transgenic mouse models were employed in the research.MethodsMetagenomic and metabolomics analysis were conducted to assess modifications in the intestinal microbiota and metabolites of AD mice post-NMN treatment. Moreover, immunohistochemistry, immunofluorescence, western blot, and Morris water maze were applied to evaluate NMN's ameliorative effects on AD.ResultsNMN administration significantly altered gut microbial composition and fecal metabolite profiles, leading to improvements in colon damage and AD-related neuropathology. Key findings include the restoration of gut microbial balance, particularly increasing Bacteroides abundance, and the modulation of metabolites involved in lipid metabolism. Furthermore, NMN was found to regulate ferroptosis, improving gut barrier function in AD mice, which were mediated through gut-brain communication pathways. NMN supplementation also enhanced ATP production, mitochondrial function, and synaptic density in the hippocampus while reducing oxidative stress and Aβ accumulation in the brain. Ultimately, these multi-faceted improvements collectively alleviated cognitive deficits in AD mice.ConclusionsIn summary, NMN supplementation effectively modulated gut microbiota and metabolites, thus mitigating AD pathology in APP/PS1 mice. Our study offers novel perspectives on the mechanisms underlying NMN's therapeutic effects in AD and underlines its potential as a promising intervention strategy.

Alzheimer’s disease (AD) is a complex neurodegenerative disease. Numerous investigations have demonstrated that medications that regulate the “brain–gut” axis can ameliorate disease symptoms of AD. Studies have shown that Ginkgo biloba extract (EGb) is involved in intestinal metabolism to meet the goal of illness treatment. EGb is currently utilized extensively in the clinical prevention and treatment of cardiovascular and cerebrovascular diseases. However, the regulatory effect of EGb on intestinal flora and its metabolites in AD pathology remains largely speculative. In this study, the Morris water maze test showed a significant improvement of spatial memory in the AD mouse model (APP/PS1 mice) after EGb treatment. We next confirmed the positive effects of EGb on the gut flora and metabolites of APP/PS1 mice and further showed that EGb treatment reshaped the disturbed gut microbiome, in particular by reducing the Firmicutes/Bacteroides ratio and increasing the abundance of Bacteroidetes, Uroviricota, Streptophyta, and Spirochaetes. Meanwhile, a non-targeted metabolomics analysis showed that EGb treatment significantly reversed the dysfunction of the microbial metabolic phenotype by altering Limosilactobacillus and Parvibacte, with 300 differential metabolites modulated (131 up-regulated, 169 down-regulated). Our findings highlight the significant regulatory impact of EGb on intestinal microflora and microbial metabolism in AD mice models and provide a potential therapeutic strategy for AD.

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Background Gut microbiota (GMB) alteration has been reported to influence the Alzheimer’s disease (AD) pathogenesis through immune, endocrine, and metabolic pathways. This study aims to investigate metabolic output of the dysbiosis of GMB in AD pathogenesis. In this study, the fecal microbiota and metabolome from 21 AD participants and 44 cognitively normal control participants were measured. Untargeted GMB taxa was analyzed through 16S ribosomal RNA gene profiling based on next-generation sequencing and fecal metabolites were quantified by using ultrahigh performance liquid chromatography-mass spectrometry (UPLC-MS). Results Our analysis revealed that AD was characterized by 15 altered gut bacterial genera, of which 46.7% (7/15 general) was significantly associated with a series of metabolite markers. The predicted metabolic profile of altered gut microbial composition included steroid hormone biosynthesis, N-Acyl amino acid metabolism and piperidine metabolism. Moreover, a combination of 2 gut bacterial genera ( Faecalibacterium and Pseudomonas ) and 4 metabolites (N-Docosahexaenoyl GABA, 19-Oxoandrost-4-ene-3,17-dione, Trigofoenoside F and 22-Angeloylbarringtogenol C) was able to discriminate AD from NC with AUC of 0.955 in these 65 subjects. Conclusions These findings demonstrate that gut microbial alterations and related metabolic output changes may be associated with pathogenesis of AD, and suggest that fecal markers might be used as a non-invasive examination to assist screening and diagnosis of AD.

Microbial flora is investigated to be related with neuropathological conditions in Alzheimer’s disease (AD), and is attracting attention as a drug discovery resource. However, the relevance between the soil microbiota and the pathological condition has not been fully clarified due to the difficulty in isolation culture and the component complexity. In this study, we established a library of secondly metabolites produced in microorganism to investigate the potential effect of microorganisms on the production of amyloid β (Aβ), one of the most representative pathogens of AD. We conducted a library screening to quantify Aβ and neuronal toxicity by using cortical neurons from human induced pluripotent stem cells (iPSCs) of AD patients after adding secondary metabolites. Screening results and following assessment of dose-dependency identified Verrucarin A, produced in Myrothecium spp., showed 80% decrease in Aβ production. Furthermore, addition of Mer-A2026A, produced in Streptomyces pactum, showed increase in Aβ42/40 ratio at the low concentration, and decrease in Aβ production at the higher concentration. As a result, established library and iPSC-based phenotyping assay clarified a direct link between Aβ production and soil microorganisms. These results suggest that Aβ-microorganism interaction may provide insight into the AD pathophysiology with potential therapeutics.

Alzheimer's disease is the most common form of dementia in the western world, however there is no cure available for this devastating neurodegenerative disorder. Despite clinical and experimental evidence implicating the intestinal microbiota in a number of brain disorders, its impact on Alzheimer's disease is not known. We generated a germ-free mouse model of Alzheimer's disease and discovered a drastic reduction of cerebral Ab amyloid pathology when compared to control Alzheimer's disease animals with intestinal microbiota. Sequencing bacterial 16S rRNA from fecal samples revealed a remarkable shift in the gut microbiota of conventionally-raised Alzheimer's disease mice as compared to healthy, wild-type mice. Colonization of germ-free Alzheimer mice with harvested microbiota from conventionally-raised Alzheimer mice dramatically increased cerebral Ab pathology. In contrast, colonization with microbiota from control wild-type mice was ineffective in increasing cerebral Ab levels. Our results indicate a microbial involvement in the development of Alzheimer's disease pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.

Alzheimer's disease (AD) has emerged as a progressively pervasive neurodegenerative disorder worldwide. Bile acids, synthesized in the liver and modified by the gut microbiota, play pivotal roles in diverse physiological processes, and their dysregulation in individuals with AD has been well-documented. However, the protein targets associated with microbiota-derived bile acids in AD have received limited attention. To address this gap, we conducted comprehensive thermal proteomic analyses to unravel and comprehend the protein targets affected by microbiota-derived bile acids in AD. Our investigation identified sixty-five unique proteins as potential targets of deoxycholic acid (DCA), a primary component of the bile acid pool originating from the gut microbiota. Particularly noteworthy among these proteins were Nicastrin and Casein kinase 1 epsilon. We found that DCA, through its interaction with the Nicastrin subunit of γ-secretase, significantly contributed to the formation of amyloid beta, a key hallmark of AD pathology. Additionally, We observed substantial elevations in the urine levels of four bile acids (DCA, GHCA, GHDCA, and GUDCA) in AD patients compared to healthy controls. Moreover, the ratios of DCA to cholic acid (CA) and glycodeoxycholic acid (GDCA) to DCA were significantly increased in AD patients, indicating aberrations in the biosynthetic pathway responsible for bile acid dehydroxylation. The augmented levels of microbiota-derived bile acids and their altered ratios to primary bile acids exhibited notable associations with AD. Collectively, our findings provide crucial insights into the intricate interplay between microbiota-derived bile acids and the pathogenesis of AD, thereby shedding light on potential therapeutic targets for this debilitating disease.

A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ~570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently-produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut.

We develop a Fokker-Planck theory of tissue growth with three types of cells (symmetrically dividing, asymmetrically dividing and non-dividing) as main agents to study the growth dynamics of human cerebral organoids. Fitting the theory to lineage tracing data obtained in next generation sequencing experiments, we show that the growth of cerebral organoids is a critical process. We derive analytical expressions describing the time evolution of clonal lineage sizes and show how power-law distributions arise in the limit of long times due to the vanishing of a characteristic growth scale. We discuss that the independence of critical growth on initial conditions could be biologically advantageous.

Diffusion models are important in tissue engineering as they enable an understanding of molecular delivery to cells in tissue constructs. As three-dimensional (3D) tissue constructs become larger, more intricate, and more clinically applicable, it will be essential to understand internal dynamics and signaling molecule concentrations throughout the tissue. Diffusion characteristics present a significant limitation in many engineered tissues, particularly for avascular tissues and for cells whose viability, differentiation, or function are affected by concentrations of oxygen and nutrients. This paper seeks to provide novel analytic solutions for certain cases of steady-state and non-steady-state diffusion and metabolism in 3D construct designs (planar, cylindrical, and spherical forms), solutions that otherwise require mathematical approximations achieved through numerical methods. This model is applied to cerebral organoids, where it is shown that limitations in diffusion and organoid size can be partially overcome by localizing metabolically-active cells to an outer layer in a sphere, a regionalization process that is known to occur through neuroglial precursor migration both in organoids and in early brain development. The given prototypical solutions include a review of metabolic information for many cell types and can be broadly applied to many forms of tissue constructs. This work enables researchers to model oxygen and nutrient delivery to cells, predict cell viability, design constructs with improved diffusion capabilities, and accurately control molecular concentrations in tissue constructs that may be used in studying models of development and disease or for conditioning cells to enhance survival after insults like ischemia or implantation into the body, thereby providing a framework for better understanding and exploring the characteristics of engineered tissue constructs.

Recent advances in brain organoid technology are exciting new ways, which have the potential to change the way how doctors and researchers understand and treat cerebral diseases. Despite the remarkable use of brain organoids derived from human stem cells in new drug testing, disease modeling, and scientific research, it is still heavily time-consuming work to observe and analyze the internal structure, cells, and neural inside the organoid by humans, specifically no standard quantitative analysis method combined growing AI technology for brain organoid. In this paper, an automated computer-assisted analysis method is proposed for brain organoid slice channels tagged with different fluorescent. We applied the method on two channels of two group microscopy images and the experiment result shows an obvious difference between Wild Type and Mutant Type cerebral organoids.

In biological and medical research, scientists now routinely acquire microscopy images of hundreds of morphologically heterogeneous organoids and are then faced with the task of finding patterns in the image collection, i.e., subsets of organoids that appear similar and potentially represent the same morphological class. We adopt models and algorithms for correlating organoid images, i.e., for quantifying the similarity in appearance and geometry of the organoids they depict, and for clustering organoid images by consolidating conflicting correlations. For correlating organoid images, we adopt and compare two alternatives, a partial quadratic assignment problem and a twin network. For clustering organoid images, we employ the correlation clustering problem. Empirically, we learn the parameters of these models, infer a clustering of organoid images, and quantify the accuracy of the inferred clusters, with respect to a training set and a test set we contribute of state-of-the-art light microscopy images of organoids clustered manually by biologists.

Understanding the mechanics of brain embryogenesis can provide insights on pathologies related to brain development, such as lissencephaly, a genetic disease which cause a reduction of the number of cerebral sulci. Recent experiments on brain organoids have confirmed that gyrification, i.e. the formation of the folded structures of the brain, is triggered by the inhomo-geneous growth of the peripheral region. However, the rheology of these cellular aggregates and the mechanics of lissencephaly are still matter of debate. In this work, we develop a mathematical model of brain organoids based on the theory of morpho-elasticity. We describe them as non-linear elastic bodies, composed of a disk surrounded by a growing layer called cortex. The external boundary is subjected to a tissue surface tension due the intercellular adhesion forces. We show that the resulting surface energy is relevant at the small length scales of brain organoids and significantly affects the mechanics of cellular aggregates. We perform a linear stability analysis of the radially symmetric configuration and we study the post-buckling behaviour through finite element simulations. We find that the process of gyrification is triggered by the cortex growth and modulated by the competition between two length scales: the radius of the organoid and the capillary length due to surface tension. We show that a solid model can reproduce the results of the in-vitro experiments. Furthermore, we prove that the lack of brain sulci in lissencephaly is caused by a reduction of the cell stiffness: the softening of the organoid strengthens the role of surface tension, delaying or even inhibiting the onset of a mechanical instability at the free boundary.

We present an analytical and numerical investigation of the activity-induced hydrodynamic instabilities in model brain organoids. While several mechanisms have been introduced to explain the experimental observation of surface instabilities in brain organoids, the role of activity has been largely overlooked. Our results show that the active stress generated by the cells can be a, previously overlooked, contributor to the emergence of surface deformations in brain organoids.

Organoids are prototypes of human organs derived from cultured human stem cells. They provide a reliable and accurate experimental model to study the physical mechanisms underlying the early developmental stages of human organs morphogenesis and, in particular, the early morphogenesis of the cortex. Here, we propose a mathematical model to elucidate the role played by two mechanisms which have been experimentally proven to be crucial in shaping human brain organoids: the contraction of the inner core of the organoid and the microstructural remodeling of the outer cortex. Our results show that both mechanisms are crucial for the final shape of the organoid and can explain the origin of brain pathologies such as lissencephaly (smooth brain).

This study proposes a transferable encoding strategy that maps tactile sensor data to electrical stimulation patterns, enabling neural organoids to perform an open-loop artificial tactile Braille classification task. Human forebrain organoids cultured on a low-density microelectrode array (MEA) are systematically stimulated to characterize the relationship between electrical stimulation parameters (number of pulse, phase amplitude, phase duration, and trigger delay) and organoid responses, measured as spike activity and spatial displacement of the center of activity. Implemented on event-based tactile inputs recorded from the Evetac sensor, our system achieved an average Braille letter classification accuracy of 61% with a single organoid, which increased significantly to 83% when responses from a three-organoid ensemble were combined. Additionally, the multi-organoid configuration demonstrated enhanced robustness against various types of artificially introduced noise. This research demonstrates the potential of organoids as low-power, adaptive bio-hybrid computational elements and provides a foundational encoding framework for future scalable bio-hybrid computing architectures.

The intricate interplay between host organisms and their gut microbiota has catalyzed research into the microbiome's role in disease, shedding light on novel aspects of disease pathogenesis. However, the mechanisms through which the microbiome exerts its influence on disease remain largely unclear. In this study, we first introduce a structural equation model to delineate the pathways connecting the microbiome, metabolome, and disease processes, utilizing a target multiview microbiome data. To mitigate the challenges posed by hidden confounders, we further propose an integrative approach that incorporates data from an external microbiome cohort. This method also supports the identification of disease-specific and microbiome-associated metabolites that are missing in the target cohort. We provide theoretical underpinnings for the estimations derived from our integrative approach, demonstrating estimation consistency and asymptotic normality. The effectiveness of our methodologies is validated through comprehensive simulation studies and an empirical application to inflammatory bowel disease, highlighting their potential to unravel the complex relationships between the microbiome, metabolome, and disease.

Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity assessment. Recent microscopy techniques provide a potent tool to acquire organoid morphology features, but manual image analysis remains a labor and time-intensive process. Thus, this paper proposes a comprehensive pipeline for microscopy analysis that leverages the SegmentAnything to precisely demarcate individual organoids. Additionally, we introduce a set of morphological properties, including perimeter, area, radius, non-smoothness, and non-circularity, allowing researchers to analyze the organoid structures quantitatively and automatically. To validate the effectiveness of our approach, we conducted tests on bright-field images of human induced pluripotent stem cells (iPSCs) derived neural-epithelial (NE) organoids. The results obtained from our automatic pipeline closely align with manual organoid detection and measurement, showcasing the capability of our proposed method in accelerating organoids morphology analysis.

High-throughput image analysis in the biomedical domain has gained significant attention in recent years, driving advancements in drug discovery, disease prediction, and personalized medicine. Organoids, specifically, are an active area of research, providing excellent models for human organs and their functions. Automating the quantification of organoids in microscopy images would provide an effective solution to overcome substantial manual quantification bottlenecks, particularly in high-throughput image analysis. However, there is a notable lack of open biomedical datasets, in contrast to other domains, such as autonomous driving, and, notably, only few of them have attempted to quantify annotation uncertainty. In this work, we present MultiOrg a comprehensive organoid dataset tailored for object detection tasks with uncertainty quantification. This dataset comprises over 400 high-resolution 2d microscopy images and curated annotations of more than 60,000 organoids. Most importantly, it includes three label sets for the test data, independently annotated by two experts at distinct time points. We additionally provide a benchmark for organoid detection, and make the best model available through an easily installable, interactive plugin for the popular image visualization tool Napari, to perform organoid quantification.

There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with similar microbiome profiles. We propose a novel unsupervised clustering approach in the Bayesian framework that innovates over existing model-based clustering approaches, such as the Dirichlet multinomial mixture model, in three key respects: we incorporate feature selection, learn the appropriate number of clusters from the data, and integrate information on the tree structure relating the observed features. We compare the performance of our proposed method to existing methods on simulated data designed to mimic real microbiome data. We then illustrate results obtained for our motivating data set, a clinical study aimed at characterizing the tumor microbiome of pancreatic cancer patients.

Adenosine triphosphate (ATP) is a high-energy phosphate compound and the most direct energy source in organisms. ATP is an essential biomarker for evaluating cell viability in biology. Researchers often use ATP bioluminescence to measure the ATP of organoid after drug to evaluate the drug efficacy. However, ATP bioluminescence has some limitations, leading to unreliable drug screening results. Performing ATP bioluminescence causes cell lysis of organoids, so it is impossible to observe organoids' long-term viability changes after medication continually. To overcome the disadvantages of ATP bioluminescence, we propose Ins-ATP, a non-invasive strategy, the first organoid ATP estimation model based on the high-throughput microscopic image. Ins-ATP directly estimates the ATP of organoids from high-throughput microscopic images, so that it does not influence the drug reactions of organoids. Therefore, the ATP change of organoids can be observed for a long time to obtain more stable results. Experimental results show that the ATP estimation by Ins-ATP is in good agreement with those determined by ATP bioluminescence. Specifically, the predictions of Ins-ATP are consistent with the results measured by ATP bioluminescence in the efficacy evaluation experiments of different drugs.

Microbiota profiles measure the structure of microbial communities in a defined environment (known as microbiomes). In the past decade, microbiome research has focused on health applications as a result of which the gut microbiome has been implicated in the development of a broad range of diseases such as obesity, inflammatory bowel disease, and major depressive disorder. A key goal of many microbiome experiments is to characterise or describe the microbial community. High-throughput sequencing is used to generate microbiota profiles, but data gathered via this method are extremely challenging to analyse, as the data violate multiple strong assumptions of standard models. Rough Set Theory (RST) has weak assumptions that are less likely to be violated, and offers a range of attractive tools for extracting knowledge from complex data. In this paper we present the first application of RST for characterising microbiomes. We begin with a demonstrative benchmark microbiota profile and extend the approach to gut microbiomes gathered from depressed subjects to enable knowledge discovery. We find that RST is capable of excellent characterisation of the gut microbiomes in depressed subjects and identifying previously undescribed alterations to the microbiome-gut-brain axis. An important aspect of the application of RST is that it provides a possible solution to an open research question regarding the search for an optimal normalisation approach for microbiome census data, as one does not currently exist.

AI tools can greatly enhance the analysis of organoid microscopy images, from detection and segmentation to feature extraction and classification. However, their limited accessibility to biologists without programming experience remains a major barrier, resulting in labor-intensive and largely manual workflows. Although a few AI models for organoid analysis have been developed, most existing tools remain narrowly focused on specific tasks. In this work, we introduce the Napari Organoid Analyzer (NOA), a general purpose graphical user interface to simplify AI-based organoid analysis. NOA integrates modules for detection, segmentation, tracking, feature extraction, custom feature annotation and ML-based feature prediction. It interfaces multiple state-of-the-art algorithms and is implemented as an open-source napari plugin for maximal flexibility and extensibility. We demonstrate the versatility of NOA through three case studies, involving the quantification of morphological changes during organoid differentiation, assessment of phototoxicity effects, and prediction of organoid viability and differentiation state. Together, these examples illustrate how NOA enables comprehensive, AI-driven organoid image analysis within an accessible and extensible framework.

Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We seek a modeling strategy that can capture emergent behavior when built from sets of universal individual interactions. Our investigation reveals that species-metabolite interaction modeling is better able to capture emergent behavior in community composition dynamics than direct species-species modeling. Using publicly available data, we examine the ability of species-species models and species-metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species-species interaction models and quadratic species-metabolite interaction models, and conclude that only species-metabolite models have the necessary complexity to to explain a wide variety of interdependent growth outcomes. We also show that general species-species interaction models cannot match patterns observed in community growth dynamics, whereas species-metabolite models can. We conclude that species-metabolite modeling will be important in the development of accurate, clinically useful models of microbial communities.

Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. Results: To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads. Conclusions: Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and designing microbial communities. COMETS (Computation Of Microbial Ecosystems in Time and Space) was initially developed as an extension of dynamic flux balance analysis, which incorporates cellular and molecular diffusion, enabling simulations of multiple microbial species in spatially structured environments. Here we describe how to best use and apply the most recent version of this platform, COMETS 2, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, as well as several new biological simulation modules, including evolutionary dynamics and extracellular enzyme activity. COMETS 2 provides user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, and comprehensive documentation and tutorials, facilitating the use of COMETS for researchers at all levels of expertise with metabolic simulations. This protocol provides a detailed guideline for installing, testing and applying COMETS 2 to different scenarios, with broad applicability to microbial communities across biomes and scales.

The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired microbiome-metabolome studies (PM2S), provide valuable insights into gut metabolism as a key mediator of these interactions. Our preliminary data reveal strong correlations among certain gut metabolites, suggesting shared metabolic pathways and microbial co-metabolism. However, these findings are confounded by various factors, underscoring the need for a more rigorous statistical approach. Thus, we introduce microbial correlation, a novel metric that quantifies how two metabolites are co-regulated by the same gut microbes while accounting for confounders. Statistically, it is based on a partially linear model that isolates microbial-driven associations, and a consistent estimator is established based on semi-parametric theory. To improve efficiency, we develop a calibrated estimator with a parametric rate, maximizing the use of large external metagenomic datasets without paired metabolomic profiles. This calibrated estimator also enables efficient p-value calculation for identifying significant microbial co-metabolism signals. Through extensive numerical analysis, our method identifies important microbial co-metabolism patterns for healthy individuals, serving as a benchmark for future studies in diseased populations.

The intestinal barrier is essential in human health and constitutes the interface between the outside and the internal milieu of the body. A functional intestinal barrier allows absorption of nutrients and fluids but simultaneously prevents harmful substances like toxins and bacteria from crossing the intestinal epithelium and reaching the body. An altered intestinal permeability, a sign of a perturbed barrier function, has during the last decade been associated with several chronic conditions, including diseases originating in the gastrointestinal tract but also diseases such as Alzheimer and Parkinson disease. This has led to an intensified interest from researchers with diverse backgrounds to perform functional studies of the intestinal barrier in different conditions. Intestinal permeability is defined as the passage of a solute through a simple membrane and can be measured by recording the passage of permeability markers over the epithelium via the paracellular or the transcellular route. The methodological tools to investigate the gut barrier function are rapidly expanding and new methodological approaches are being developed. Here we outline and discuss, in vivo, in vitro and ex vivo techniques and how these methods can be utilized for thorough investigation of the intestinal barrier.

Inhibiting γ-secretase-mediated Notch signaling has been explored as a potential treatment for Alzheimer's disease and cancer. However, clinical trials have revealed that this approach can lead to side effects, such as gut inflammation. Notch signaling has been shown to be a key mediator of intestinal epithelial homeostasis. We aimed to investigate the molecular mechanisms of γ-secretase inhibition-associated colitis. Mice and small intestinal organoids were treated with γ-secretase inhibitors and analyzed for intestinal epithelial cell (IEC) differentiation and inflammation-associated markers using different molecular and histological approaches, along with transcriptomic and proteomic analyses. To evaluate the role of the microbiome in colitis development, mice undergoing pharmacological γ-secretase inhibition were treated with antibiotics. Additionally, inflammatory bowel disease (IBD) patient samples and control samples were analyzed to assess the expression of Notch signaling pathway components in IECs. This study shows that pharmacological γ-secretase inhibition induces inflammation in both the small and large intestine of mice, a phenotype that could be rescued upon microbiota depletion. Inhibiting the γ-secretase induced structural disruption of the epithelium and inflammatory cytokine release. On a molecular level, epithelial organoids exhibited disrupted IEC differentiation and impaired proliferation, associated with defective Notch signaling. Finally, analysis of IBD patients revealed deregulation of Notch pathway components within IECs. In conclusion, systemic use of γ-secretase inhibitors disrupts epithelial cell function by impairing IEC differentiation and triggering gut inflammation in mice. These findings should be considered when designing future therapeutic interventions involving γ-secretase inhibitors.

The antioxidant and anti-inflammatory effects of hormetic nutrition for enhancing stress resilience and overall human health have received much attention. Recently, the gut-brain axis has attracted prominent interest for preventing and therapeutically impacting neuropathologies and gastrointestinal diseases. Polyphenols and polyphenol-combined nanoparticles in synergy with probiotics have shown to improve gut bioavailability and blood-brain barrier (BBB) permeability, thus inhibiting the oxidative stress, metabolic dysfunction and inflammation linked to gut dysbiosis and ultimately the onset and progression of central nervous system (CNS) disorders. In accordance with hormesis, polyphenols display biphasic dose-response effects by activating at a low dose the Nrf2 pathway resulting in the upregulation of antioxidant

Alzheimer's disease (AD) is a complex neurodegenerative condition and the leading cause of dementia worldwide. Treatments that safely and effectively counteract disease progression are currently lacking. While the formation of amyloid plaques has long been considered the leading hypothesis of disease onset, growing evidence suggests that the emergence of AD could be driven by a combination of underlying factors that promote chronic neuroinflammation, including pathogenic infections, environmental toxicants, and disruptions along the gut-brain axis. Traditional nonclinical models of AD, such as monolayer cell cultures and transgenic mice, struggle to capture the complexity of the disease as it occurs in humans. Human-centered complex

The intestinal stem cells (ISCs) of old mice and humans exhibit a reduced capacity for regeneration and repair. Compromised intestinal function may play a key role in systemic aging-related changes: not only in the affected gut, but also in the nervous and cardiovascular systems. For example, progression of age-related neurodegenerative diseases such as Alzheimer's and Parkinson's has been linked to increased inflammation from gut microbiota in old mammals, which, in turn, may be linked bidirectionally with reduced ISC function. Intestinal organoid formation has been used to dissect the mechanisms of decline of ISC function. Alterations of the Wnt pathway, including downregulation of Wnt ligands in ISCs and upregulation of Wnt ligand inhibitor Notum in Paneth cells, and dysregulation of mTORC1 contribute to the observed age-related decline. Short-term fasting, caloric restriction, and peroxisome proliferator-activated receptor delta agonists have been reported to increase ISC function in adult mice. Moreover, the mTOR inhibitor rapamycin, NAD+ precursor nicotinamide riboside, and ABC99, a small molecule Notum inhibitor, have all been reported to rejuvenate ISC function in old mice and thus may have promise in humans. However, there is some controversy over the key mechanisms involved in loss of function of ISCs, which likely results, in part, from differences in how the

Advanced Glycation End products (AGEs) are a heterogeneous group of stable reaction products formed when amino acids, peptides, or proteins are glycated by the non-enzymatic Maillard Reaction. The formation and accumulation of these products in vivo are linked to many inflammation-based pathological outcomes and part of the pathophysiology of non-communicable diseases like eye cataracts and Alzheimer's disease. Since our diet contains high levels of the same compounds, it has been questioned whether their consumption is also detrimental to health. However, this is still under debate. In this context, the intestinal epithelium is an important target tissue since it is chronically exposed to relatively high concentrations of dietary AGEs. This review summarizes the current evidence on the impact of dietary AGEs on the intestinal epithelium and critically reflects on its methodology. In healthy rodent models, an inflammation-independent impaired intestinal barrier function is claimed; however, dietary AGEs showed anti-inflammatory activity in IBD models. In vitro studies could be a valuable tool to unravel the underlying mechanisms of these effects, however the available studies face some limitations, e.g. lack of the physicochemical characterization of the glycated proteins, the inclusion of the proper controls and the dose-dependency of the effect. In addition, studies using more advanced in vitro models like intestinal organoids and co-cultures with immune cells exposed to gut microbial metabolites derived from the fermentation of AGEs are still needed.