bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alzheimer’s Disease patient stratification using iPSC‐derived hindbrain organoids as a novel pre‐clinical tool for drug testing
Authors: Zivko Cristina , Sagar Ram , Xydia Ariadni , Lyketsos Constantine G. , Machairaki Vasiliki 
Published: January 2025

AbstractBackgroundBy 2050 the number of Alzheimer’s Disease (AD) patients is projected to exceed 150 million worldwide. AD is an incurable, insufficiently understood, and devastating neurodegenerative disease, with high patient heterogeneity in terms of progression, clinical manifestation (including neuropsychiatric symptoms, NPS) and, importantly, responsiveness to treatment options.[1] In the last 20 years, 98% of clinical trials for AD have failed, highlighting the urgent need to drastically change pre‐clinical research to develop better predictors of drug safety and effectiveness.[2]This is where our precision medicine approach of organoid in vitro models can be a game changer.MethodHuman peripheral blood mononuclear cells from healthy volunteers (n = 6) and AD patient with (n = 12) and without NPS (n = 12) were reprogrammed into induced pluripotent stem cells (iPSCs)[3] and subsequently differentiated into hindbrain organoids, containing serotonin (5‐HT) producing neurons.ResultExtensive characterization and validation experiments were conducted to assess the quality of the iPSCs and of the 5‐HT‐organoids. These include karyotyping, fluorescent microscopy and flow cytometry to reveal the presence of pluripotency (OCT4, NANOG, TRA‐1‐60) and neuronal markers (TUJ1, TPH2, 5‐HT), real time qPCR, ELISA measurement of 5‐HT levels, size and circularity over 6 weeks of differentiation, for which we developed an in‐house algorithm in Python. The 5‐HT‐organoids were treated with a selective serotonin reuptake inhibitor acutely (1 h) and for 1 week, upon which we could stratify the 30 individuals according to drug responsiveness. Shotgun proteomics analysis was performed on the treated and non‐treated 5‐HT‐organoids from all 30 individuals by LC/MS to reveal distinctive relative abundance profiles. Experiments were run in biologically independent triplicates for 6 cell lines (3 healthy, 3 AD). The results from that training set were used to classify analytical results from the other 24 lines for AD biomarker discovery, as well as for drug responsiveness and effect.ConclusionHighly reproducible, people‐specific 5‐HT‐organoids were thus used to study inter‐patient phenotypical variability and drug response diversity in a powerful, novel pre‐clinical tool.References:[1] Kim CK et al (2022). J Alzheimers Dis. 2022;87(1):83‐100. https://doi.org/10.3233/JAD‐215699.[2] Lyketsos CG et al (2011). J. Alzheimers Assoc. 7(5):532‐539. https://doi.org/10.1016/j.jalz.2011.05.2410[3] Sagar R et al (2023). Cells. 12(15):1990. https://doi.org/10.3390/cells12151990.
Mitochondrial DNA depletion induces AD like phenotypes in neuronal and glial cells
Authors: Molina Carmen Romero , Lysaker Colton R , Roberts Anysja , Gilmore Caleb , See Wen Yi , Liu Yiyuan , Pa Judy , Swerdlow Russell H , Goate Alison M. , Andrews Shea J , Wilkins Heather M 
Published: January 2025

AbstractBackgroundMitochondrial dysfunction is an early and prominent feature of Alzheimer’s disease (AD). We have recently published that lower brain mitochondrial DNA copy number (mtDNAcn) is associated with increased risk of AD neuropathological change and reduced cognitive performance. Here, we addressed how mtDNAcn affects cell‐type specific phenotypes.MethodiPSC derived neural progenitor cells were infected with a lentivirus encoding a mitochondrial targeted exonuclease under the control of a Tet promoter. mtDNA was depleted with doxycycline and cells were differentiated into neurons or astrocytes using established protocols (StemCell Technologies). iPSC derived astrocyte migration/chemotaxis was measured in the presence of ATP. Microglial BV2 cells were treated with ethidium bromide (etbr) to reduce mtDNAcn. Cells were characterized by RNAseq, ELISAs, Western Blotting, and Seahorse experiments. BV2 cells were challenged with latex beads and zymosan‐pHrodo to analyze phagocytosis. BV2 cells were stimulated with LPS to measure cytokine release. After BV2 stimulation, fresh media was conditioned for 6 hours and collected to treat neurons (SH‐SY5Y) and human primary astrocytes.ResultmtDNAcn reduction led to reduced oxidative phosphorylation and a mild reduction in proliferation for glial cell types. iPSC derived neurons and astrocytes with mtDNAcn reduction showed increased expression of STING and reduced oxidative phosphorylation. iPSC derived neurons with mtDNAcn reduction showed increased Aβ secretion and changes to tau homeostasis. iPSC derived astrocytes with mtDNAcn reductions had reduced migration/chemotaxis but increased TNFα production. RNAseq data from BV2 cells showed an increase in the hypoxia signature and cellular senescence, coupled with a reduction in biosynthetic process and response to interferon. No changes were observed in phagocytic capacity. However, after LPS stimulation, etbr‐treated cells showed a reduction in the production of IL1B and IL6 cytokines, suggesting an impairment in the response to challenge. Neurons exposed to media from etbr‐treated BV2 cells showed an increase in MAPT and APOE expression.ConclusionmtDNAcn reduction can lead to AD pathological hallmarks including changes in Aβ secretion, tau homeostasis, and glial cell phenotypes. mtDNAcn reduction impairs mitochondrial respiration in glial cells, which affects the production of cytokines and leads to cell senescence. Cytokines released by glial cells with reduced mtDNAcn affected neuronal expression of AD‐related genes.
A deep learning‐based deconvolution framework identifies human brain cell‐type specific expression quantitative trait loci (eQTLs) and pathobiology in Alzheimer’s disease
Authors: Dou Lijun , Xu Jielin , Hou Yuan , Cheng Feixiong 
Published: January 2025

AbstractBackgroundCell‐type specific expression quantitative trait loci (eQTLs) can help dissect cellular heterogeneity in the impact of genetic variation on gene expression for Alzheimer’s disease (AD) and AD‐related dementia (ADRD). However, due to the high cost and stringent sample collection criteria, it is challenging to obtain large single‐nuclei RNA sequencing (snRNA‐seq) data with sufficient cohort size to match genotyping data to systematically identify human brain‐specific eQTLs for AD/ADRD.MethodIn this study, we presented a deep learning‐based deconvolution framework on large‐scale bulk RNA sequencing (RNA‐seq) data to infer cell‐type specific eQTLs in the human brains with AD/ADRD. Specifically, we first predicted the brain cell‐type specific gene expression for the harmonized bulk RNA dataset (n = 1,092) from Religious Orders Study and Memory and Aging Project (ROS/MAP). We then incorporated the inferred cell‐type specific gene expression with matched whole genome sequencing (WGS) data from ROS/MAP to identify the brain cell‐type specific eQTLs. These cell‐type specific eQTLs were further colocalized with AD genome‐wide association study (GWAS) findings to discover potential risk genes and druggable targets for AD.ResultWe identified 44,504 genome‐wide significant cell‐type specific cis‐eQTLs (window size = 1Mb, p < 5 × 10‐8) from eight brain cell types, including excitatory neurons, inhibitory neurons, microglia, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelium. Approximate 2,732 eQTLs in astrocytes and 7,628 in excitatory neurons are identical to the results from a large existing snRNA‐seq data, associated with the regulation of multiple genes (eGenes, e.g., ARL17B, LRRC37A2, ERAP2, PILRB, ZNF266). We illustrated that the GWAS variant rs199456 (AD GWAS: p = 2.57 × 10‐9) co‐localized with its regulatory effect on LRRC37A2, LRRC37A and ARL17B gene expression in excitatory neurons.ConclusionIn summary, this study presented comprehensive brain cell type‐specific eQTL analysis and identified potential eQTL‐regulated likely causal genes from AD GWAS findings using a deep learning‐based deconvolution framework. It offers an opportunity to efficiently discover the effect of GWAS loci on gene expression at cell type‐specific manners using genotyping data and matched bulk RNA‐seq data instead of costly snRNA‐seq data. Functional validation of candidate eQTLs and associated genes are warranted in the future.
Repurposing drugs that slow down aging for the prevention of Alzheimer’s disease
Authors: Tambaro Simone , Solis Andrea Mosqueda , Tang Bowen , De Oliveira Thais Lopes , Qin Chenxi , Kavsek Alan , Sjölander Arvid , Johnell Kristina , Religa Dorota , Riedel Christian , Nilsson Per , Hägg Sara 
Published: January 2025

AbstractBackgroundHigh age is the biggest risk factor for Alzheimer’s disease (AD). Approved drugs that slow down the aging process have the potential to be repurposed for the primary prevention of AD. The aim of our project was to use a reverse translational approach to identify such drug candidates in epidemiological data followed by validation in cell‐based models and animal models of aging and AD.MethodLongitudinal samples from a Swedish twin cohort (N = 672) were used to assess the effects of commonly prescribed medications on biological aging. Mendelian Randomization was used to identify associations between genetic variations in the glucagon‐like peptide 1 (GLP‐1) analogues target and the risk of developing AD. The identified classes of compounds were next evaluated in a pipe line of cellular and animal models for their potency of increasing lifespan using C. elegans models expressing amyloidbeta (Aβ) and tau, and for lowering Aβ levels in neuroblastoma SH‐SY5Y cells and AD‐associated pathologies in AppNL‐F knock‐in mice as well as their anti‐aging effects in a novel mouse model of CNS aging.ResultWe found that initiation of calcium channel blockers (CCBs) was associated with about a two‐year decrease in multiple epigenetic clocks (DNA methylation ages) as well as in functional biological ages. Moreover, genetic variants in GLP‐1 targets were associated with lower risk of developing AD. Several of the clinically used CCBs significantly increased the life span in C. elegans Aβ model and decreased levels of secreted Aβ from SH‐SY5Y cells. Several GLP‐1 analogues, similar to the CCBs, demonstrated a positive effect in reducing Aβ42 levels in SH‐SY5Y cell media.ConclusionThese preliminary data, demonstrating an extension of lifespan and a reduction in Aβ42 production, support the potential repurposing strategy for CCBs and GLP‐1 analogs in slowing down aging and preventing/treating AD. The investigation of these compounds in mouse models of aging and AD will provide a more complete picture of the therapeutic potential and may eventually identify novel preventive measures for AD within CCB and GLP‐1 analogs.
Rare genetic variation in fibronectin 1 (FN1) protects against APOE ɛ4 in Alzheimer’s Disease
Authors: Bhattarai Prabesh , Gunasekaran Tamil Iniyan , Uzrek Bengisu Turgutalp , Reyes‐Dumeyer Dolly , Jülich Dörthe , Lee Annie J. , Yilmaz Elanur , Tayran Huseyin , Lantigua Rafael A. , Medrano Martin , Mejia Diones Rivera , Recio Patricia , Flaherty Delaney , Dalgard Clifton L. , Nuriel Tal , Ertekin‐Taner Nilüfer , Dickson Dennis W. , Teich Andrew F , Holley Scott , Mayeux Richard , Kizil Caghan , Vardarajan Badri N. 
Published: January 2025

AbstractBackgroundAPOEε4 significantly increases the risk of developing Alzheimer’s disease (AD). Cognitively healthy APOEε4‐carriers exist, suggesting potential protective mechanisms against APOEε4. We hypothesized that some APOEε4‐carriers may have genetic variations protecting them from developing APOEε4‐mediated AD pathology. We aim to identify these protective genetic variants.MethodsWhole genome sequencing (WGS) and cerebrospinal fluid (CSF) proteomics were performed from human cohorts to identify potential protective variants segregating exclusively among APOEε4 carriers. Bioinformatic analyses were performed to select candidate target genes. Immunohistochemistry on postmortem human brain tissues and mouse models expressing human APOE variants were performed along with in‐vivo functional studies in adult zebrafish AD model.ResultWGS analyses revealed 510 potential gene variants segregating exclusively among APOEε4 carriers, which included rare and loss‐of‐function (LOF) variants. Pathway analysis of these genes showed significant enrichment in extracellular matrix (ECM)‐related processes, suggesting protective effects of LOF in ECM proteins. This was further validated by CSF proteome profiling and subsequent analyses in APOEε4 carriers and non‐carriers. Fibronectin‐1 (FN1) and Collagen‐6A2 (COL6A2) were prioritized as candidate target genes for postmortem validation and in‐vivo functional studies. FN1 protein was increased in APOEε4 carriers resulting in thickened ECM at the basement membrane around the blood vessels, potentially impairing pathology‐induced responses such as clearance and immune system activity. This observation is validated in human brains, mouse models and zebrafish model; therefore, the pathological association of FN1 to AD is evolutionarily conserved. Supporting this hypothesis, in‐vivo functional study in zebrafish model with LOF mutations in fn1b revealed that fibronectin LOF enhanced gliovascular remodeling and microglial activation while reducing astrogliosis, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF.ConclusionThe vascular deposition of the ECM components FN1 and COL6A2 are increased in APOEε4 carriers. Rare variant in FN1 protect against APOEε4‐mediated pathogenesis in AD. We propose a new disease mechanisms and potential therapeutic intervention targets for vascular contribution to dementia to mitigate the risk of developing AD.
Meningeal and infiltrating T‐cells are associated with neuroinflammation after head injury and with tau pathology in CTE
Authors: Calderazzo Samantha M , Stein Thor D. , Holtzman David M. , McKee Ann C. , Huber Bertrand Russell 
Published: January 2025

AbstractBackgroundT‐cell infiltration into the brain parenchyma is associated with hyperphosphorylated tau (p‐tau) accumulation in neurodegenerative diseases. Chronic traumatic encephalopathy (CTE) is a progressive tauopathy caused by exposure to repetitive head impacts (RHI). CTE is defined by the perivascular accumulation of p‐tau at the cortical sulcal depths and can be stratified into mild and severe pathological stages. RHI exposure and CTE are associated with progressive microglial inflammation, but the involvement of T cells is unknown.MethodThe dorsolateral frontal cortex from 76 brain donors in the UNITE/ BU ADRC brain bank was analyzed, all men (age 30‐80 yrs), including 19 with mild CTE (stage 1‐2), 24 with severe CTE (stage 3‐4),18 with RHI exposure without CTE, and 19 without RHI exposure or neurodegenerative disease (Table 1). Years of football served as a proxy for the duration of RHI. Multiplex immunofluorescence for T‐cells (CD8 1:20, CD4 1:100), endothelial cells (CD31 1:200), microglia (iba1 1:500, MHC2 1:500), and p‐tau (AT8 1:500) were used. Synaptic markers (PSD95 1:100, Gephyrin 1:200, VGlut 1:1200, VGat 1:1500) were used on adjacent tissue sections to assess synaptic loss. Four regions were annotated: leptomeninges, sulcus (gray matter (gm) in bottom third of gyrus), crest (gm in top third of gyrus), and white matter. Slides were digitally scanned, and HALO software was used to quantify T‐cell numbers and spatial relationships. ANCOVA with posthoc Bonferroni corrections were performed for between group analyses; multivariate linear correlations were utilized for associations between T‐cells and other markers or RHI exposure, all using age as a covariate.ResultInfiltrating T‐cells were significantly increased at the sulcus in RHI, mild, and severe CTE, with distinct subtypes predominating in RHI and CTE. In addition, T‐cells were correlated with the duration of RHI exposure and synaptic loss. Meningeal and infiltrating T‐cells were notably elevated in p‐tau positive sulci (Fig. 1). Finally, T‐cells were spatially related to CNS‐associated macrophages expressing MHC2, including cortical microglia and meningeal macrophages (Fig. 2).ConclusionThese data suggest an adaptive immune T‐cell response occurs with RHI exposure, which might be microglia mediated and contribute to tau neurodegeneration in CTE.
The relationship between apoe ε4 and cognitive function and pulvinar medial volume in patients age between 60 to 70 Years
Authors: Wu Jiajing , Wang Jiayu , Li Linlin , Chen Lei , Feng Qiansen , Wang Feiyan , Wang Ziqi 
Published: January 2025

AbstractBackgroundTo study the morphological characteristics of the thalamus in cognitively normal people with apolipoprotein E epsilon 4 (APOE ε4), and to explore whether it is affected by neuropsychiatric symptoms in patients aged between 60 and 70 years, and to provide evidence for the early brain structural changes in Alzheimer’s disease.MethodClinical assessment, neuropsychological assessment, blood text and MRI examination were performed in 101 cognitively normal elderly patients in a tertiary psychiatric memory clinic in Chengdu. The cognitive function and thalamic volume of APOE ε4 carriers (n = 30) and APOE ε4 non‐carriers (n = 71) were compared using an independent sample T‐test. Multiple linear regression was used to analyze the association between thalamic and neuropsychiatric symptoms in APOE ε4 carriers.ResultThe left pulvinar medial and right pulvinar medial volumes were significantly lower in 60 to70 year old APOE ε4 carriers than in non‐carriers (left pulvinar medial P = 0.039, right pulvinar medial P = 0.037). Long delayed recall score was not associated with left pulvinar medial or right pulvinar medial volume in individuals with APOE ε4 carriers (P > 0.05).ConclusionThe morphological changes of the pulvinar medial structure were associated with APOE epsilon 4 carriers at 60 to 70 years of age. There was no association between neuropsychiatric symptoms and pulvinar medial volume in APOE ε4 carriers.
The effect of non‐pathological aging on behavior, genetics, and epigenetics in mice
Authors: Scheinman Sarah B. , McClarty Bryan , Rodriguez Guadalupe , Carvill Gemma L. , Dong Hongxin 
Published: January 2025

AbstractBackgroundAging is a time‐dependent deterioration of physiological functions that occurs in both humans and animals. Within the brain, aging cells gradually become dysfunctional through a complex interplay of intrinsic and extrinsic factors, ultimately leading to behavioral deficits and enhanced risk of neurodegenerative diseases such as Alzheimer’s disease (AD). The characteristics of normal aging are distinct from those associated with age‐related diseases and it is important to understand the processes that contribute to this pathological divergence. The identification of behavioral, genetic, and epigenetic biomarkers associated with normal aging is key in determining the mechanisms of underlying pathological aging and how these impact AD.MethodWe conducted a comprehensive behavioral assessment of young (3‐month‐old) and aged (18‐month‐old) C57/BL6 mice including locomotion, memory‐relevant, and anxiety‐like behavior to elucidate the cognitive and behavioral phenotypes of aging. We subsequently employed RT‐qPCR to determine synapse‐related gene expression in the prefrontal cortex of mice at both ages, and ChIP to assess age‐related differences in histone acetylation (H3K9ac) at the same genes. Finally, we conducted CUT&RUN sequencing to analyze the relative abundancy of H3K27ac, a histone marker that associates with promoters and enhancers of active genes to determine age‐related changes in epigenomic profiles.ResultCompared to young mice, aged mice displayed decreased locomotion in the open field (p<0.0001), enhanced anxiety in the elevated plus maze (p = 0.0003), and deficits in the novel object recognition task (p = 0.0011) and novel arm entry task (p = 0.0155). These age‐related behavioral changes occurred in tandem with lower abundancy of H3K9ac at synapse‐related gene promotors nr2a (p = 0.001), glur1 (p<0.0001), glur2 (p<0.0001), and PSD‐95 (p<0.0001), and lower mRNA expression levels of nr2a (p = 0.028), glur1 (p = 0.016), glur2 (p = 0.038), and PSD‐95 (p = 0.0037) in 18‐month‐old mice. CUT&RUN analysis also revealed significant age‐related differences in H3K27ac genome occupancy, including sites associated with synaptic plasticity and neuron function.ConclusionThese data suggest that non‐pathological aging induces a unique behavioral phenotype that’s associated with alterations in epigenetic markers and gene expression. Future studies will be focused on disentangling epigenetic and behavioral alterations that occur during normal aging from those that occur during pathological aging and aging‐related diseases such as AD.
Elevated amyloid‐ß and tau burden is associated with accelerated cognitive decline on a digital clock drawing test in preclinical AD
Authors: Fu Jessie Fanglu , Robinson Talia L , Alonso Marina Rodriguez , Malave Adela Francis , Jutten Roos J , Healy Brian , Montenegro Grace A Del Carmen , Thibault Emma G , Penney Dana , Davis Randall , Sperling Reisa A , Johnson Keith A , Price Julie C , Rentz Dorene M 
Published: January 2025

AbstractBackgroundPET quantifies tau and amyloid‐ß (Aß) pathology in preclinical AD. A 2‐min digital clock‐drawing test (DCTclockTM
) captures clock‐drawing outcomes and processes, potentially more sensitive to cognitive deficits in preclinical AD than pencil‐and‐paper tests. The DCTclock summary score comprised subscores targeting multi‐domain cognitive performance (i.e., Drawing Efficiency, Information Processing, Spatial Reasoning, and Simple Motor). These subscores included unique features reflecting hesitation (pen‐stroke latencies) and speed during the drawing process (Table.1). Previous cross‐sectional study showed worse performance in the Spatial Reasoning domain was associated with high Aß and tau burden in older cognitive normal (CN) participants. This study evaluates whether longitudinal changes in DCTclock performance are associated with Aß and tau burden in preclinical AD, and explores DCTclock features that are most important for such associations.MethodsA total of 204 CN participants underwent baseline and follow‐up DCTclock assessments, Aß PET ([11C]PiB) and tau PET (Flortaucipir or [18F]MK‐6240, Table.2). Global Aß and regional tau burden were estimated as distribution volume ratios in neocortical aggregate regions and standardized uptake value ratios in entorhinal and inferior temporal using cerebellar gray reference, respectively. Separate linear mixed models examined associations between longitudinal DCTclock and 1) Aß, 2) tau, and 3) Aß and tau burden, adjusted for age, sex, and education. Separate models first examined DCTclock summary scores and domain‐specific subscores. Exploratory analyses then evaluated features within domains showing significant associations.ResultsElevated baseline Aß or tau is most strongly associated with accelerated decline in DCTclock performance in the Information Processing domain (Fig.1). Evaluating both Aß and tau in a single model, only tau showed significant associations with Information Processing subscores. The associations between DCTclock and Aß or tau were driven by latency features (Information Processing domain), including latency variability, longest latency, and average latency (Table.1). Notably, these features showed improved performance longitudinally in participants without Aß/tau burden, suggesting expected practice effects.ConclusionOur results suggest that longitudinal decline in DCTclock performance, especially in information processing or executive function, is related to early Aß/tau burden in older CN adults. Diminished longitudinal DCTclock performance, especially in latency features uniquely captured by digital tools, may reflect greater cognitive efforts in preclinical AD.