bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aberrant XIST beyond the inactivated X chromosome modulates the intracellular dysregulation in Alzheimer’s disease
Authors: Sen Somenath , Mukhopadhyay Debashis 
Published: January 2025

AbstractBackgroundRecent advances in understanding the regulatory networks implicated in Alzheimer’s Disease (AD) evinces the involvement of long non‐coding RNAs (lncRNAs) as crucial regulatory players. The present study explores the role played by maternally imprinted lncRNA XIST in regulating the sex‐biased prevalence of AD.MethodWith whole transcriptomic sequencing data from the hippocampal RNA of post‐mortem AD brains from humans and APP/PS1 mice, the altered expression of XIST in AD was studied. The data was further validated in an in vitro AD cell model. RNA FISH and subcellular fractionation‐qPCR studies were then performed to trace and quantitate the distribution of XIST in nuclear and cytoplasmic compartments. The nuclear XIST in AD was studied for its altered dynamics with H3K27me3 levels using RNA Immunoprecipitation (RIP)‐qPCR. The fate of the cytosolic XIST was further explored using RIP and miRNA‐lncRNA pull‐down experiments using antibody against RBPMS and biotinylated mimic of miR‐186‐5p.ResultXIST was found to be significantly upregulated in AD. RNA FISH experiments revealed that XIST from the inactivated X chromosome (Xi) was getting translocated to the cytoplasmic compartment in AD. Upon quantification of the transcript by subcellular fractionation/qPCR, it was found that the heightened XIST expression in AD was due to the ectopic upregulation of the lncRNA in cytoplasm relative to the nucleus. Nuclear XIST on the other hand showed downregulation in AD compared to the control sets. ICC+FISH and RIP studies showed altered dynamics between H3K27me3 levels and XIST in the nucleus in AD. The ectopic XIST was found to be interacting with RBPMS and miR‐186 and knocking down XIST showed opposing effects in the expression levels of RBPMS and miR‐186 in AD. Moreover, RBPMS mRNA was found to be regulated by miR‐186 forming a competitive endogenous RNA (ceRNA) triad modulated by the lncRNA XIST in AD.ConclusionThis study reports the presence of XIST in cytoplasm in AD for the first time and sheds light on its downstream mechanisms mediated by this aberrant translocation. Studying XIST from the context of AD further allows us to establish the role of this imprinted lncRNA on the gender specific prevalence of AD.
Whole genome methylation sequencing identifies sex‐specific DNA methylation levels in late onset dementia due to Alzheimer’s disease
Authors: Bergmann Phillip E , Madrid Andy , Papale Ligia A , Breen Coleman , Clark Lindsay R. , Asthana Sanjay , Johnson Sterling C. , Keles Sündüz , Hogan Kirk J. , Alisch Reid S 
Published: January 2025

AbstractBackgroundLate onset dementia due to Alzheimer’s disease (AD) has a sex‐biased incidence with females comprising nearly two thirds of all cases. Females have a more rapid progression in cognitive decline and higher levels of known AD biomarker pathology compared to men. Genetic sequence variation does not account for the sex‐biased incidence of AD, directing attention to the emerging role of epigenetics in AD. Using whole genome methylation sequencing (WGMS), we previously reported 28,038 differentially methylated position (DMPs) within 2,707 genes between persons with and without AD. Here we report sex‐specific DNA methylation levels in AD.MethodWGMS data quantified DNA methylation levels at 25,406,945 CpG loci in 281 blood samples from 109 AD (47 female, 62 male) and 174 cognitively unimpaired (CU) individuals (90 female, 84 male) in the Wisconsin Alzheimer’s Disease Research Center and the Wisconsin Registry for Alzheimer’s Prevention cohorts. Beta‐binomial regression models were developed to test for significant sex‐specific DNA methylation levels between CU and AD accounting for batch effects, estimated white blood cell proportions, BMI, and age. P‐values were corrected and local false discovery rates (lFDRs) were calculated.Result13,293 DMPs were identified in females and 20,719 DMPs were identified in males (Figure 1) when comparing CU and AD (lFDR < 0.05; mean methylation difference > 2.5%). Approximately 2% (280) of the DMPs overlap between sexes with 87 having opposite mean methylation differences. The majority of DMPs annotate to introns (55.9% females; 54.8% males) with most of the remainder intergenic (37.0% females; 37.9% males). Annotation of DMPs to genes identified 1,498 genes that are only differentially methylated in females, and 2,183 genes that are only differentially methylated in males, with 1,365 differentially methylated genes shared between females and males (Figure 2). Gene ontological analyses identified significant enrichment of pathways related to glutamate receptor and ion channel activity in shared gene sets (Figure 3).Conclusion33,732 unique, sex‐specific DMPs in AD were identified with more than 60% annotated to one of 5,067 genes. DMP‐associated genes have sex‐specific DNA methylation levels suggesting that these DMPs may play a role in the biased pathogenesis of AD.
A Novel platform for precision quantitative analyses of neuropathology in Alzheimer’s disease
Authors: Keene C Dirk 
Published: January 2025

AbstractBackgroundThe BRAIN Initiative has stimulated development of novel single cell and spatial molecular approaches to understand human brain structure and function. However, traditional methods for human brain specimen collection, including retrospective archival tissues, have not been optimized for these latest methods. A modernized approach that optimizes tissue quality, anatomical precision, and comprehensive, quantitative neuropathological assessments is needed to maximize the impact of the tremendous investment and remarkable technological advances in human neuroscience research.MethodWe developed a modernized methodology that incorporates rapid neuroimaging, hemibrain embedding in dental alginate, consistently thin (4mm) coronal slicing, and alternating fixation or freezing in supercooled isopentane. Fixed tissues are comprehensively sampled using functionally‐informed, network‐based approach. Traditional neuropathological examination is combined with quantitative neuropathological analysis of digital images of pathologic peptides and markers of neurons, glia, and neuroinflammation. We developed a temporally‐based case series (all donor brains collected during a certain time frame, excluding frontotemporal lobar degeneration) from participants in the UW ADRC Clinical Core and the Kaiser Adult Changes in Thought (ACT) study. Brain regions for examination were chosen to model the temporal progression of AD neuropathology; samples for molecular studies we from adjacent frozen slices.ResultEighty‐four brains were included in this study from donors (∼60% female) ranging from no cognitive impairment to dementia. Tissue quality metrics (RIN, pH, PMI) were high, nuclear yields for single cell omics were robust (with rare exceptions), and spatial transcriptomics performed well, with minimal tissue freezing artifact. Traditional neuropathological examination confirmed a spectrum of not to high AD neuropathologic change (ADNC), with a subset of the cohort exhibiting some level of one or more age‐related comorbid pathologies. HALO‐based analysis of digital pathology of beta amyloid, pTau, pTDP‐43, alpha‐synuclein, NeuN, GFAP, and Iba‐1 across cortical layers resulted in an array of quantitative variables which were used to generate continuous pseudo progression scores for the cohort that informed molecular omics analyses.ConclusionDevelopment and implementation of improved methods for tissue collection, characterization, and preservation, combined with enhanced sampling and integrated neuropathology, resulted in a robust tissue and data resource to support modern molecular cell‐types and pathway‐based analyses.
The Potential of Non‐invasive Neurostimulation, tDCS for Cognitive Decline in Alzheimer’s Disease: Through the Lens of an Ongoing Clinical Trial
Authors: Vanzyl Jordan , Zhen Ivan , Ha Kevin , Flores Itzel , Taranto Melany , Melecio‐Vazquez Mairim , Ayers Emmeline , Weiss Erica , Zwerling Jessica L , Blumen Helena M , Verghese Joe , Knotkova Helena 
Published: January 2025

AbstractBackgroundTranscranial direct current stimulation (tDCS) is a non‐invasive neuromodulation method. Short‐term tDCS protocols have shown positive effects on cognitive outcomes in Alzheimer’s Disease (AD) populations1‐5. Less is known about the long‐term benefits of tDCS on cognition in AD. Here, we discuss the evidence on efficacy of tDCS in AD and the potential of this novel technique applied in home settings6‐8 through the lens of our ongoing long‐term, large‐scale (N = 100) randomized controlled clinical trial in patients with mild‐to‐moderate AD. This RCT aims to determine the effects of tDCS on cognition, mood, quality of life and functional/structural brain connectivity, and to explore the durability of these effects after 9‐months.MethodParticipants age ≥60 years with mild‐to‐moderate stage AD and the ability to provide informed consent are eligible. Participants receiving/have received monoclonal antibody treatment for AD or have history or head trauma or seizures are excluded. Participants are randomized to receive active tDCS at 2mA or sham delivered with two saline‐soaked electrodes placed over the dorsolateral prefrontal cortex for 30 minutes/day, 5 days/week for 6‐months at home.ResultThe study protocol has been developed and approved by the IRB. It includes 6 study visits (V1‐6) over 9 months. Eligible participants undergo in‐person tDCS training (V2), followed by a refresh training and the first tDCS session under supervision of study personnel (V3). Daily tDCS sessions proceed at home for 6 months, with a daily remote supervision via phone/video. Outcome assessments post‐intervention occur at 6, 7 and 9‐months (V4‐6). Our team developed and implemented an enhanced remote monitoring procedure (ERMP) that promotes safety and protocol adherence by monitoring skin condition and allowing for quality checks of electrode placement. The study protocol has been successfully implemented and is ongoing. To date, 101 participants have been consented/screened; of those, 62 were eligible and randomized to apply tDCS at‐home for 6‐months. Enrollment will continue until 2025.ConclusionThere is preliminary evidence on the potential of tDCS for symptom management in AD. Our study will expand the understanding of the long‐term benefits of tDCS in AD. If effective, this non‐pharmacological intervention could become an important strategy for symptom management in AD patients.
Cellular and molecular changes in a unified and integrated single cell atlas of Alzheimer’s disease across community datasets
Authors: Travaglini Kyle J 
Published: January 2025

AbstractBackgroundNumerous studies have identified AD‐associated molecular and cellular changes to the cortex using single nucleus RNA sequencing (snRNA‐seq) and, to a lesser extent, single nucleus ATAC‐seq (snATAC‐seq), applied to millions of cells across hundreds of donors. It has proven challenging, however, to determine whether changes are consistent because of differences in cohort selection, reported clinical metadata, data pre‐processing, cellular taxonomy construction/mapping, and analytical strategies across studies.MethodWe uniformly re‐processed 10 publicly available datasets (Table 1) that had applied snRNA‐seq to 4.3 million cells from the dorsolateral pre‐frontal cortex (DLPFC) of 780 donors. We integrated each of them with SEA‐AD’s multi‐modal, single cell atlas of AD, which contains 4.5 million cells from the middle temporal gyrus (MTG) and DLPFC that were profiled with snRNA‐seq, snATAC‐seq, snMulitome or spatial transcriptomics (MERFISH). We then harmonized clinical data across donors and mapped all cells to the same 139 fine‐grained cell supertypes in SEA‐AD’s shared MTG and DLPFC cellular taxonomy. With common clinical data and cellular labels, we then compared cohorts and data quality across studies as well as identified cellular changes consistently associated with AD.ResultCohorts from nearly every study sampled across the spectrum of plaque and tangle pathology, even in those that performed case‐control analyses. With rare exception, the fraction of donors in each cohort with an APOE4 allele, clinically diagnosed dementia, and severe co‐morbidities were also similar. Comparing datasets, SEA‐AD was uniquely successful in profiling both many donors and many nuclei per donor, while deeply sequencing libraries to drive high gene detection. Most importantly though, of the 34 supertypes that were significantly changed in the DLPFC in SEA‐AD, 8 were also significantly changed across external studies with large enough cohorts to power discovery. This included 5 selectively vulnerable Sst interneuron supertypes and 1 Microglia supertype that were changed early in AD in SEA‐AD.ConclusionConsistent and early selective loss of Sst interneurons and increase in disease associated Microglia underscore their importance to AD progression. Our integrated dataset provides a valuable common starting point for future comparative analyses from the community and, we hope, will accelerate discovery of novel therapeutic targets.
ADSP Whole Genome Sequencing (WGS) Release 5 data update from Genome Center for Alzheimer’s Disease
Authors: Carter Luke , Leung Yuk Yee , Lee Wan‐Ping , Kuzma Amanda B , Gangadharan Prabhakaran , Nicaretta Heather Issen , Qu Liming , Ren Youli , Valladares Otto , Zhao Yi , Iqbal Taha , Schmidt Michael A. , Mena Pedro R. ,   The Alzheimer’s Disease Sequencing Project (ADSP), Dalgard Clifton L. , Kunkle Brian W. , Bush William S. , Martin Eden R. , Naj Adam C. , Haines Johnathan L , Pericak‐Vance Margaret A. A , Wang Li‐San , Schellenberg Gerald D. ,   Alzheimer’s Disease Sequencing Project
Published: January 2025

AbstractBackgroundThe Genome Center for Alzheimer’s Disease (GCAD) coordinates the integration and meta‐analysis of all available Alzheimer’s disease (AD) relevant whole genome sequencing (WGS) data to facilitate the goal of identifying AD risk or protective genetic variants and eventual therapeutic targets. The WGS datasets are generated via the collaboration of scientists from the Alzheimer’s Disease Sequencing Project (ADSP) and GCAD. To minimize data heterogeneity introduced by different sequencing protocols and machines, GCAD processes all samples using identical pipelines.MethodsThe raw sequencing data are first mapped to GRCh38/hg38 and variants (SNVs and indels) are called using GATK. Additionally, compact VCF and GDS formatted files are generated to facilitate researchers who want to use smaller pVCFs. SNVs and indels are annotated using the ADSP annotation pipeline. Lastly, structural variants (SV) are called using Smoove and Manta and joint genotyped using GraphTyper2.ResultsThe dataset (ADSP Release 5, R5, 2024) includes ∼60,000 genomes from >50 diverse cohorts with 4 major ancestries: 47% Non‐Hispanic White, 29% Hispanic or Latino, 16% Black or African American and 8% Asian. Data are deeply sequenced (average genome coverage: >30x). CRAMs, gVCFs from GATK, and SV VCFs of a subset of the R5 samples (n = 36,361) were deposited into NIAGADS Data Sharing Service (DSS) (https://dss.niagads.org/) for public distribution in 2022, and similarly, the new samples in R5 will be released after the joint call is complete. In addition, joint‐genotype VCFs on SNVs, indels, and SVs will be available. These will undergo full quality control and annotation process.ConclusionThe ADSP and GCAD generate high quality genotype and SV calls. Currently the project is processing ∼60,000 WGS samples sequenced primarily through the ADSP Follow‐Up Study, which will contain a more ancestrally diverse set of populations. We anticipate this 2024 release will continue to benefit the research community studying AD genetics.
Spatial Transcriptomics Analysis Identifies Glial Signatures Spatially Associated with Neuritic Plaques in Human Post‐Mortem Brains
Authors: Karaahmet Berke , Duquesne Laurine , Sigalov Alina , Yung Christina J , Kroshilina Alexandra , Zhang Ya , Taga Mariko , Klein Hans‐Ulrich 
Published: January 2025

AbstractBackgroundGlial cells exhibit distinct transcriptional responses to β‐amyloid pathology in Alzheimer’s disease (AD). While sophisticated single‐cell based methods have revealed heterogeneous glial subpopulations in the human AD brain, the histological localization of these multicellular responses to AD pathology has not been fully characterized due to the loss of spatial information. Here, we combined spatial transcriptomics (ST) with immunohistochemistry to explore the molecular mechanisms in the neuritic plaque niche.Methods32 sections from the prefrontal cortices of 15 AD and 2 control cases were applied to ST arrays with spatially barcoded probes (spots) of 55µm diameter. Each of the 59,588 tissue‐covering spots in our dataset detected a median of 2,202 genes and included a median of 4 nuclei. Amyloid plaques were stained with Thioflavin S (ThioS) and astrocytes were stained using GFAP in the same ST tissue section. The immunohistochemistry data were then projected onto the ST profiles.ResultsClustering the spots reconstructed the cortical layer structure. We detected 263 ThioS+ amyloid plaques, and spots within 150µm of plaques were compared to distant spots (≥500µm), adjusted for cortical layer and donor. This approach identified 182 plaque‐associated genes and confirmed genes previously reported in mice, such as GFAP, CLU, MBP and MOBP. Interestingly, the AD‐related gene SERPINA3 was found to be upregulated at neuritic plaques. SERPINA3 is a marker of an inflammatory astrocyte subpopulation, resembling previously discovered disease‐associated astrocytes in mice. Indeed, computationally deconvoluting this astrocyte subpopulation from the ST data confirmed its enrichment at plaques. Further, we found a downregulation of metallothioneins, expressed by astrocytes, indicating a potential dysfunction of metal ion homeostasis. We validate these results using immunohistochemistry and in situ hybridization.ConclusionsHere, we demonstrate the heterogeneity in glial communities within the amyloid plaque microenvironment. We show evidence suggesting a spatial enrichment of SERPINA3+ astrocytes at neuritic plaques. Furthermore, the identification of the 182 plaque‐proximal genes suggests involvement of processes related to inflammation, and ion transport and homeostasis. The role of these subtypes and molecular signatures in AD pathophysiology remains to be elucidated.
Predisposition to Alzheimer’s Disease in First‐Degree Relatives: Cognitive Decline, Personality Traits, and Prodromal Neuropsychiatric Symptoms
Authors: Cezar Giovana Benassi , Dias Marcos Josué Costa , Costa Adriana Oliveira , Ferreira Diego Alves , Foss Maria Paula 
Published: January 2025

AbstractBackgroundFamilies with a history of Alzheimer’s Disease (AD) may have a genetic predisposition that raises the risk of developing the condition. However, not all members of these families can undergo genetic testing. Thus, this study aims to evaluate specific cognitive changes, neuropsychiatric symptoms (NPS), and personality traits that may act as early indicators of AD in family members compared to controls.MethodFifty participants were divided into two groups for this study: cognitively healthy controls (CG; n = 25) and individuals with first‐degree relatives of AD (GP; n = 25). The education was represented as primary education (PE) from 1 to 9 years, secondary education (SE) from 10 to 12 years, and higher education (HE) from more than 13 years. Both groups underwent a neuropsychological battery (Adapted Background Questionnaire, Subjective Memory Assessment Clinics questionnaire (MAC‐Q), Addeenbroke’s cognitive examination revised (ACE‐R), Personality Factor Battery (PFB) and Mild Behavioral Impairment Checklist (MBI‐C)). Subsequently, the collected data was subjected to statistical analysis using a t‐test, MANOVA, and chi‐square, with a significance level of p≤0.05.ResultNo significant differences between groups were found in age (p = 0.23), sex (p = 1.0), and education (p = 0.45) (Table 1). Except for alcohol consumption, there was no difference in medical history (Table 2). However, significant differences were encountered in ACE‐R (CG = 90.68±5.31; GP = 86±5.84; p = 0.005; d = 0.84) and MAC‐Q (GC = 23.4±3.52; GP = 26.68±3.29;p = 0.001;d = 0.96). In addition, no differences were demonstrated in MBI‐C (GC = 7.4±7.81; GP = 7.44±5.62;p = 0.984;d = 0.01) or the interaction between neuroticism (GC = 3.29±1.24;GP = 3.33±0.78) and conscientiousness (GC = 3.29±1.24;GP = 3.33±0.78;p = 0.94) in PFB (Table 3).ConclusionIndividuals who are first‐degree relatives of Alzheimer’s Disease patients tend to experience more cognitive complaints and show worse cognitive performance than controls. However, the two groups had no significant differences regarding NPS and personality traits. These findings were observed even after pairing the controls by sex, age, and education.
‘Latent’ mild behavioral impairment as a potential diagnostic strategy for preclinical Alzheimer’s disease: an animal model study
Authors: Forlenza Orestes Vicente , Singulani Monique Patricio , Talib Leda Leme , Camarini Rosana , Britto Luiz Roberto 
Published: January 2025

AbstractBackgroundIn Alzheimer’s disease (AD) the fact that neuropsychiatric symptoms can predate the onset of cognitive symptoms suggests that greater focus on the non‐cognitive behavioral changes in earlier life could be an opportunity to investigate ‘latent’ mild behavioral impairment (MBI) as a possible diagnostic strategy for preclinical AD.MethodWe used 1‐ and 6‐month‐old 3xTg‐AD male mice and age‐matched wild‐type animals (CEUA‐ICB/USP: 127/2015). Two batteries of behavioral tests were performed: (1) open field test (OFT), novel object recognition test (NORT), and rotarod test; (2) elevated zero maze test (EZMT), forced swim test (FST), and sucrose preference test (SPT). The immunohistochemistry method was performed to analyze amyloid‐β (Aβ) accumulation (6E10) in areas of the brain. Statistical analysis was performed through two‐way ANOVA followed by a Bonferroni post‐hoc test and unpaired t‐test (IBM SPSS Statistics® software 23). We considered statistically significant p<0.05.ResultIn both OFT (F(3, 28) = 22.92, p<0.001) and EZMT (F(3, 28) = 41.72, p<0.001), a rise in anxiety‐related responses was detected in 3xTg‐AD versus Controls mice from an early age. We also detected depressive‐like behavior in 1‐ and 6‐month‐old 3xTg‐AD evaluated by FST (F(3, 28) = 40.88, p<0.001). In SPT, 6‐month‐old 3xTg‐AD presented a decrease in sucrose preference versus Controls of the same age and versus 1‐month‐old 3xTg‐AD (F(3, 28) = 8.77, p = 0.006), suggesting signs of anhedonia at a later age. NORT was applied to evaluate cognition, which showed 6‐month‐old 3xTg‐AD mice were not able to discriminate the novel from the familiar object in short‐ (F(3, 28) = 132.14, p<0.001) and long‐term memory (F(3, 28) = 275.86, p<0.001) versus Controls. The immunoreactivity analysis showed that 6‐month‐old 3xTg‐AD exhibited a significant increase in Aβ versus 1‐month‐old 3xTg‐AD (parietal cortex, p<0.001; hippocampal CA1, p<0.001; dentate gyrus, p<0.001), justifying occurrence of memory impairment at a late age. When analyzing the amygdala, 1‐ and 6‐month‐old 3xTg‐AD showed similar Aβ immunoreactivity (p = 0.2), suggesting that premature accumulation of Aβ in amygdala can be contributed to dysfunction in emotional responses.ConclusionTaken together, we propose that anxiety‐like and depressive‐like behaviors can be detected at an early age in 3xTg‐AD mice as a ‘latent’ MBI syndrome, positioning it as a possible diagnostic strategy for preclinical AD.