bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alzheimer’s Disease mechanistic pathways were discovered through in silico experiments in causal AI based digital twins
Authors: Sanjay Apoorva Bharthur , Shokeen Deepanshi , Shen Xinyu , Shin So‐Youn , Latourelle Jeanne 
Published: December 2023

AbstractBackgroundBeyond a single‐gene‐based approach, pathway‐based approaches have become important in drug development paradigm. Several pathways are known for the pathogenesis of Alzheimer’s disease (AD), but these may be from animal studies or observational human subject studies. Here, we focus on identification of gene pathways with direct causal relationships to AD through Gemini Digital Twins of AD patients.MethodTwo independent and complementary AD Digital Twins were built using an A.I. platform REFSTM [aitiabio.com], based on Bayesian network models of ADNI and ANMerge consortium data which reverse‐engineered the connectivity of ∼59K and ∼35K multi‐modal variables and a wide range of AD‐related outcomes (cognitive, imaging and biomarker) profiled from 317 subjects (Control:MCI:Dementia = 97:191:29) and 199 subjects (Control:MCI:Dementia = 65:63:71), respectively [Fig1]. The average causal effect of each gene (at the blood gene expression level) on each outcome was estimated through in silico counterfactual experiments. Pathway enrichment analyses were performed on metascape.org.ResultWe identified a total of 573 and 300 AD‐driver‐genes from ADNI‐ and ANMerge‐based Digital Twins, of which 41 overlapped (significance‐of‐overlap = 6e‐15). These 41 robustly validated genes, of which 61% were identified by the network as causal mediators of APOE4 genotype, were enriched in several biological processes known for AD such as ‘regulation of RNA splicing’ and ‘macrophage activation’ [Fig2]. The AD‐driver‐genes were also enriched in other interesting pathways in both Digital Twins, such as ‘immune response’ and ‘oxidative stress’. Furthermore, the ADNI‐specific AD‐driver‐genes, representing a sample population with a higher proportion of MCI patients, were related to additional processes such as ‘mitochondrial respiration’ and ‘ribosomal sub‐complexes pathways’, previously known to be involved specifically in early stage AD.ConclusionWe prioritized several AD‐related pathways for potential drug development identified from causal driver genes discovered and validated in two independent Digital Twins. Some of these pathways are more related to proteopathic biochemical phase of AD, rather than cellular phase, suggesting an area of a potential early intervention. Investigating causal genes from two complementary consortium studies with a different proportion of early vs. late stage AD patients may be a promising approach to identify disease‐stage‐specific and disease‐stage‐common signatures in the pathway‐based drug discovery efforts.
Development of FKBP5 ASOs to mitigate tau pathology
Authors: Gebru Niat T , Hill Shannon E. , Blair Laura J. 
Published: December 2023

AbstractBackgroundAlzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by the accumulation of abnormal protein aggregates, including tau tangles, in the brain. FKBP51 (encoded by FKBP5 gene) is a chaperone protein that regulates tau and has been implicated in AD pathology. FKBP51 overexpression in the brains of tau transgenic mice correlates with increased tau oligomers and neuronal toxicity, whereas siRNA mediated knockdown of FKBP5 decreased tau levels in cell culture models. In this study, we developed antisense oligonucleotides (ASOs) to target FKBP5, in an effort to lower tau levels. We hypothesize that ASOs targeting FKBP5 will reduce FKBP51, which will decrease tau levels and improve tau‐associated deficits.MethodWe designed and synthesized vivo‐morpholino ASOs that specifically bind to and target FKBP5 mRNA degradation. We tested three ASOs in vitro using human neuroglioma and mouse hippocampal neuronal cultures but encountered tissue toxicity when using direct injections into the brains of wild‐type mice. To overcome this, we designed and synthesized locked‐nucleic acid (LNA) GapmeR ASOs targeting regions conserved between human and mouse FKBP5. These have been tested in human neuroglioma and mouse hippocampal neuroblastoma cells lines for their ability to decrease dexamethasone induced FKBP5 upregulation and assessed for toxicity.ResultInitial screening of vivo morpholino ASOs resulted in 50% ‐ 80% reduction in dexamethasone induced FKBP51 levels at 10 µM. This was further corroborated in mouse primary cortico‐hippocampal neurons where FKBP51 levels were reduced by 50% ‐ 75%, which correlated with significant reduction in total tau levels. However, in vivo pilot studies showed tissue toxicity for our control construct. LNA GapmeR ASOs reduced FKBP51 levels at much lower concentrations (<10 nM) with no apparent toxicity.Conclusion
Fkbp5 ASOs have shown promising results at decreasing FKBP51 and total tau levels. Future studies will include further testing in vivo for efficacy and safety, followed by studies in tau transgenic mice.
The AI‐based AlphaFold 2 algorithm predicts an open structure for tauC3
Authors: Chain Daniel G , Margolin Richard A 
Published: December 2023

AbstractBackgroundTauC3 is an especially noxious C‐terminal tau fragment produced by caspase‐3 cleavage at Asp421. Two decades of accumulating evidence support its importance in the pathogenesis of AD and other tauopathies, notably FTD and PSP. TauC3 promotes aggregation and filament formation, recruits full length tau (FLT) to incipient fibrils, and despite low concentration in AD brain tissue relative to total tau, has been reported to account for substantially all the seeding activity in AD brain extracts. TauC3 has also been shown to slow fast axonal transport (FAT), with deleterious consequences. Although tau’s largely disordered structure prevents analysis by X‐ray crystallography, FRET analysis suggested the existence of a hairpin conformation in which the N‐terminus folds over the C‐terminus close to the MTBR. In this model, Ser432 is the point of closest contact with Pro301. Opening of the hairpin has been hypothesized to 1) make FLT prone to aggregation by exposing the MTBR, and 2) impair FAT by overexposing the phosphatase activating domain near the N‐terminus. We postulated that tauC3 cannot form the hairpin because it lacks Ser432 and thus has an “open” conformation. This would explain tauC3’s substantially increased pathogenicity compared to FLT. The AI‐based tool AlphaFold 2 (AF2) is being used to predict the conformation of many proteins with great accuracy. Applying it to FLT and tauC3 could provide valuable data about the hairpin and whether caspase cleavage alters it.MethodWe tested AF2’s ability to predict the conformation of 4‐repeat FLT and tauC3 from FASTA sequences, aligning the models produced with the MTBR.ResultAF2 modeling revealed a dramatically different conformation for tauC3 compared to FLT, specifically, an open conformation with the MTBR and N‐terminus far apart (Figure). Interestingly, it also revealed that the entire C‐terminus region of FLT starting at Gln423 is composed of a single α‐helix.ConclusionAF2 predictions support the existence of the hairpin conformation for tau and underscore the critical importance of residue 432 in maintaining it. The extended C‐terminus α‐helix may have functional implications. TauC3’s open conformation is consistent with its slowing of FAT and its ability to seed aggregation even at low concentrations.
Relationship between norepinephrine metabolism and plasma markers of tau pathology
Authors: Beckers Elise , Riphagen Joost M. , Ashton Nicholas J. , Janelidze Shorena , Blennow Kaj , Hansson Oskar , Zetterberg Henrik , Jacobs Heidi I.L. , Van Egroo Maxime 
Published: December 2023

AbstractBackgroundThe brainstem locus coeruleus (LC) constitutes the primary source of norepinephrine (NE) in the central nervous system and has been reported as one of the earliest accumulation sites of hyperphosphorylated tau protein in Alzheimer’s disease (AD). Autopsy and animal studies suggested that this aggregation of hyperphosphorylated tau in the LC is associated with hyperactivity in LC neurons and elevated concentrations of NE metabolites. Here, we investigated whether elevated concentrations of 3‐methoxy‐4‐hydrophenylglycol (MHPG), a NE metabolite measured in the plasma, is associated with plasma phosphorylated tau, a biomarker of AD pathology.MethodNinety‐eight cognitively unimpaired participants (age = 59.82 ± 13.13 [30‐84] y, 52 females, Table 1) underwent a blood draw. Plasma MHPG concentrations were measured and adjusted for NE. Levels of total tau, phosphorylated tau at threonine 181 (pTau181) and threonine 231 (pTau231) were quantified by single molecule array (Simoa), while phosphorylated tau at threonine 217 (pTau217) was quantified by the Meso Scale Discovery (MSD) platform. Multiple linear regression models tested for the relationship between MHPG concentrations and plasma levels of tau‐related measures, while controlling for age and sex.ResultPTau231 and MHPG concentrations were positively correlated (t = 2.26, p = .03, Figure 1). No significant relationships were found between MHPG and other phosphorylated tau biomarkers (all p > .23), but we observed a trend for a positive association with plasma total tau levels (t = 1.88, p = .06).ConclusionConsistent with previous CSF studies as well as animal studies, we found that elevated NE metabolism co‐occurs with the earliest events in the phosphorylation cascade of tau proteins, suggesting an important role of a dysregulated NE system early in the AD pathophysiologic cascade. Future work will need to determine the evolution of theses associations as the disease progresses, potential effect modifications by beta‐amyloid and the downstream effects of these processes on cognition and behavior.
U.S. Study to Protect Brain Health Through Lifestyle Intervention to Reduce Risk (U.S. POINTER): Baseline Characteristics of a Trial Cohort Enriched for Risk of Cognitive Decline
Authors: Whitmer Rachel A. 
Published: December 2023

AbstractBackgroundU.S. POINTER is a two‐year clinical trial to evaluate whether lifestyle interventions targeting multiple risk factors protect cognitive function in older adults at increased risk for cognitive decline. We describe the baseline characteristics of the U.S. POINTER clinical trial cohort overall, and before and after changes in risk factor enrichment inclusion criteria.MethodU.S. POINTER is a Phase 3, multicenter, randomized 2‐year clinical trial of two lifestyle interventions varying in intensity and format, in older adults at increased risk for cognitive decline and dementia. The study closed enrollment with 2111 individuals at 5 sites (North Carolina, Northern California, Chicagoland, Houston, Rhode Island). Eligible participants were sedentary and consumed a suboptimum diet and met other risk enrichment criteria that included first degree family history of memory impairment, and suboptimum cardiovascular health status (meeting specific cut‐points of systolic blood pressure, LDL cholesterol or hemoglobin A1c). 20 months into enrollment, risk enrichment criteria were revised to account for two other factors: older age (70‐79 years), and African American/Black or Native American race or Hispanic/Latine ethnicity.ResultMean age at baseline is 68.2 years, 31% represent communities of color, 69% are women, and 30% are not college graduates. 58% reported maternal memory loss, mean systolic blood pressure = 131 mmHg, mean total cholesterol = 193 mg/dl, mean HbA1C = 5.9%, and mean body mass index (BMI) = 29.9 kg/m2. Mean adjusted modified Telephone Interview for Cognitive Status (TICSm) score is = 37.6 (max = 50 pts), Geriatric Depression Score (GDS) is = 1.8, and Short Physical Performance Battery Chair Stand Score (SPBC) is = 3.3. Some baseline characteristics (BMI, total cholesterol, SBBP chair stand) vary by clinical site. The change to risk score enrichment criteria (Table 1) increased representation of participants from communities of color and number of males in the study cohort.ConclusionU.S. POINTER successfully enrolled 2111 participants across 5 sites who are at high risk for cognitive decline and dementia, with appropriate representation by groups typically underrepresented in clinical trials, individuals aged 75 or older, and men, with the expansion of risk score enrichment criteria.
Unsupervised Machine Learning Identify Cis‐Regulatory Network Involved in Neurodegeneration
Authors: Goncalves Tassia Mangetti , Xu Jason , Li Daofeng , Gabel Harrison , Wang Ting , Zhao Guoyan 
Published: December 2023

AbstractBackgroundCis‐Regulatory Modules (CRMs) are crucial to ensure the precise spatiotemporal gene expression, but we still lack a complete catalog of mammalian CRMs.MethodsWe developed the Mammalian Regulatory Module Detector (MrMOD), that accurately predicts a comprehensive set of high‐resolution CRMs in mouse and human genomes including enhancers, promoters, silencers, locus control regions, and microRNA regulatory modules not limited to any tissue, cell type, developmental stage, or stimuli. We validated our predictions using 19 orthogonal experimental data sets, including thousands of experimental defined CRMs and millions of putative regulatory elements from multiple databases. Next, we used an unsupervised machine learning method to annotate CRM functions. We scanned the mouse genome for transcription factor binding sites (TFBS) using position weight matrices of known transcription factors (TF) from the CIS‐BP database and obtained TFBS abundance in each CRM for every TF. Unsupervised clustering was performed using Seurat on CRMs from chromosome 17. Each CRM cluster represents a set of CRMs with similar TFBS compositions. Cluster marker genes represent TFs whose binding sites are enriched in the CRM cluster. Genes associated with the CRMs in the cluster represent the putative target genes. Functional enrichment analyses of the TFs and CRM associated genes were performed using ClusterProfiler and disgenet2r.ResultsSeurat identified a total of 43 clusters. In particular, CRM cluster #17 is linked to neurodegeneration based on five supporting evidence: 1) TF marker genes of cluster #17 include TFs known to be involved in neurodegeneration such as Spi1, Yy1, Nr4a2, Nr4a3, and Tfeb. 2) TF marker genes of cluster #17 were significantly enriched for Alzheimer’s Disease, Parkinson’s Disease, Multiple Sclerosis, among others. 3) Genes associated with cluster #17 CRMs were significantly enriched for neurodegeneration: Multiple Sclerosis and neurodegenerative disorders. Gene Ontology Cellular Components terms significantly enriched for synapse, presynapse, axon, and synaptic membrane. 4) Genes associated with cluster #17 CRMs significantly overlap the known TF target genes in the ChIP‐Atlas database defined by human ChIP‐seq experiments. 5) Top TF marker genes of cluster #17 known to activate transcription in neurons cooperatively.ConclusionsWe developed a novel approach to elucidate mechanisms involved in neurodegeneration.
Human microglia, microglial LRRK2, and tau pathogenesis: a complex relationship
Authors: Karabova Maria Kreger , Santambrogio Alessia , Washer Sam J , Metrick Michael M , Caughey Byron , Vendruscolo Michele , James William S. , Cowley Sally A 
Published: December 2023

AbstractBackgroundEmerging evidence indicates leucine‐rich repeat kinase 2 (LRRK2) may be involved in tau uptake and spread throughout the brain. Microglia, the brain‐resident phagocytes, become one of the highest LRRK2 expressing cells under inflammatory conditions. Rodent microglia were also shown capable of secreting seeding‐competent tau into the extracellular space. We set out to examine the contribution of human microglia and microglial LRRK2 to tau pathogenesis.MethodIsogenic LRRK2 wild‐type (WT) and knockout (KO) induced pluripotent stem cell (iPSC) lines, together with Parkinson’s disease (PD) patient‐isolated LRRK2 G2019S‐mutated iPSC lines were differentiated into an in‐vitro model of human microglia, and incubated with in‐house purified, endotoxin‐free, human recombinant 2N4R tau in monomeric or in vitro aggregated form to examine the cellular response.ResultMicroglia internalise recombinant monomeric and aggregated tau by overlapping but distinct mechanisms. RNA‐seq analysis was performed to reveal changes in microglial gene expression upon tau internalisation. We further identified LRP1 as one of the major microglia receptors mediating soluble tau entry, and LRRK2 bona‐fide substrates, Rab8a and Rab10, as the Rab GTPases involved in the downstream LRP1‐tau complex trafficking. The internalised soluble tau is readily degraded but intracellular clearance of tau aggregates is concentration‐ and incubation‐length dependent, and inversely associated with microglial tau secretion. Following tau fibril incubation, the intracellular non‐cleared tau and tau secreted by microglia, shows seeding competency, supporting the role for microglia in tau prion‐like spreading. Finally, we describe the influence of microglial LRRK2 on tau processing. Compared to LRRK2 WT, tau uptake and clearance is accelerated in G2019S microglia. However, tau fibrils processed by G2019S microglia, though reduced in the amount, template pathogenic conformation faster and more consistently onto naive tau substrate.ConclusionCollectively, we provide detailed characterisation of the response of human iPSC‐microglia to tau protein in its native and pathogenic form, and show that microglial LRRK2 influences tau processing in a complex way that warrants further investigation.
Discordance in amyloid positivity defined by Visual Reads VR and Centiloids CL
Authors: Charil Arnaud , Nelson Todd , Devanarayan Viswanath , Reilhac Anthonin , Dhadda Shobha , Reyderman Larisa , Irizarry Michael C. 
Published: December 2023

AbstractBackgroundAmyloid PET VR is the most common method to determine Aβ pathology in clinical practice. Amyloid positivity by VR or CL cut‐off generally shows a good concordance, however, it is possible to have discordant cases whereby the VR is positive, but CL is below the cut‐off of amyloid positivity, or vice versa. The objective of this analysis was to assess the rate and cause of discordance in defining amyloid pathology using VR and CL in Eisai’s Elenbecestat MissionAD Phase 3 program.MethodFlorbetaben, Florbetapir, and Flutemetamol amyloid PET scans from 3412 participants with MCI due to AD or mild AD dementia were visually read at screening by trained neuroradiologists and quantitated using CLs. VR classification of the amyloid status is based on the higher or equal grey matter (GM) uptake relative to uptake in the white matter (WM) in at least one area, as per manufacturer’s guidance. Quantitatively, amyloid negativity was defined as CL<30. The number of positive cortical regions (SUVR>1.17) was also calculated.ResultThe positivity concordance between VR and CL was 92%, while the negativity concordance was 94.6%. VR+/CL‐ discordance was 8% (n = 1814 VR+, n = 145 CL‐) whereas VR‐/CL+ discordance was 5.4% (n = 1598 VR‐, n = 86 CL+). VR+/CL‐ discordant cases had significantly fewer positive cortical regions than both VR+/CL+ and VR‐/CL+ cases (Figure 1). VR‐/CL+ had a significantly higher WM uptake than both VR‐/CL‐ and VR+/CL‐ cases (Figure 2).ConclusionVR+/CL‐ discordant cases show fewer amyloid positive cortical regions, computing CLs results in below cut‐off values due to a dilution effect. These cases are considered VR+ as per manufacturer’s guidelines as they show at least one area of amyloid accumulation. On the other hand, VR‐/CL+ discordant cases result from an increased WM uptake, reducing GM/WM contrast required to determine visual read positivity. VR represents a robust and validated method to determine the presence of amyloid deposition and enables enrolling patients with amyloid beta pathology, as visible on amyloid PET scans, while CLs are optimal for assessing longitudinal changes over time and are a more sensitive measure to assess disease progression.
Use of online therapy session data to develop behavioural markers for cognitive outcomes in non‐pharmacological intervention
Authors: Li Yong , Chan Antoni , Hsiao Janet , Choy Jacky Chak Pui , Ma Maggie , Wong Gloria HY 
Published: December 2023

AbstractBackgroundEvidence‐based non‐pharmacological interventions such as group‐based cognitive stimulation therapy (CST) involve complex interpersonal interactions based on the putative mechanism of person‐centred engagement. Empirical evidence of the hypothesised mechanism of action is lacking. Behavioural markers such as eye movement patterns can be used to predict cognitive ability. The rapid development of online interventions during the pandemic has made behavioural information such as eye movement patterns during therapy more readily available for hypothesis testing on mechanisms.MethodWe retrieve behavioural data using random time sampling of virtual CST session from people with mild to moderate dementia. Intervention characteristics of interest are frequency and relevance of self‐identity stimuli presented during the therapy session. Behavioural markers of interest are visual attention, language output, and facial expression. For visual attention, we compare subject‐independent and subject‐dependent protocols of automatic gaze estimation, using private and public (MPIIFaceGaze) dataset for pre‐training.ResultsPerson‐centredness of the intervention can be operationalised based on a pre‐intervention assessment of self‐identity roles and video annotation. For determination of eye movement pattern, pretraining findings using 45,000 public train images, 6,420 private train images, and 600 private test images showed an average angle error of 9.79 using subject‐independent protocol, versus 5.91 using subject‐dependent protocol.ConclusionBehaviours captured on computer cameras during online therapy sessions can be automatically estimated reliably, especially with subject‐dependent protocol for eye movement and gaze analyses. This is a proof of concept for further development of behavioural markers, with advantages of simultaneously observing multiple interacting participants without Hawthrone effect and distraction in the group therapy. Further protocol finetuning using a larger data set, and models incorporating hand‐coded markers of person‐centred engagement for outcome prediction will be the next steps.