Alzheimer's Disease Susceptibility Research Articles

Transcriptomic analysis reveals sex-specific patterns in the hippocampus in Alzheimer's disease.

The hippocampus, vital for memory and learning, is among the first brain regions affected in Alzheimer's Disease (AD) and exhibits adult neurogenesis. Women face twice the risk of developing AD compare to men, making it crucial to understand sex differences in hippocampal function for comprehending AD susceptibility. We conducted a comprehensive analysis of bulk mRNA postmortem samples from the whole hippocampus (GSE48350, GSE5281) and its CA1 and CA3 subfields (GSE29378). Our aim was to perform a comparative molecular signatures analysis, investigating sex-specific differences and similarities in the hippocampus and its subfields in AD. This involved comparing the gene expression profiles among: (a) male controls (M-controls) vs. female controls (F-controls), (b) females with AD (F-AD) vs. F-controls, (c) males with AD (M-AD) vs. M-controls, and (d) M-AD vs. F-AD. Furthermore, we identified AD susceptibility genes interacting with key targets of menopause hormone replacement drugs, specifically the ESR1 and ESR2 genes, along with GPER1. The hippocampal analysis revealed contrasting patterns between M-AD vs. M-controls and F-AD vs. F-controls, as well as M-controls vs. F-controls. Notably, BACE1, a key enzyme linked to amyloid-beta production in AD pathology, was found to be upregulated in M-controls compared to F-controls in both CA1 and CA3 hippocampal subfields. In M-AD vs. M-controls, the GABAergic synapse was downregulated, and the Estrogen signaling pathway was upregulated in both subfields, unlike in F-AD vs. F-controls. Analysis of the whole hippocampus also revealed upregulation of the GABAergic synapse in F-AD vs. F-controls. While direct comparison of M-AD vs. F-AD, revealed a small upregulation of the ESR1 gene in the CA1 subfield of males. Conversely, F-AD vs. F-controls exhibited downregulation of the Dopaminergic synapse in both subfields, while the Calcium signaling pathway showed mixed regulation, being upregulated in CA1 but downregulated in CA3, unlike in M-AD vs. M-controls. The upregulated Estrogen signaling pathway in M-AD, suggests a compensatory response to neurodegenerative specifically in males with AD. Our results also identified potential susceptibility genes interacting with ESR1 and ESR2, including MAPK1, IGF1, AKT1, TP53 and CD44. These findings underscore the importance of sex-specific disease mechanisms in AD pathogenesis. Region-specific analysis offers a more detailed examination of localized changes in the hippocampus, enabling to capture sex-specific molecular patterns in AD susceptibility and progression.

Interpretation of 10years of Alzheimer's disease genetic findings in the perspective of statistical heterogeneity.

Common genetic variants and susceptibility loci associated with Alzheimer's disease (AD) have been discovered through large-scale genome-wide association studies (GWAS), GWAS by proxy (GWAX) and meta-analysis of GWAS and GWAX (GWAS+GWAX). However, due to the very low repeatability of AD susceptibility loci and the low heritability of AD, these AD genetic findings have been questioned. We summarize AD genetic findings from the past 10years and provide a new interpretation of these findings in the context of statistical heterogeneity. We discovered that only 17% of AD risk loci demonstrated reproducibility with a genome-wide significance of P < 5.00E-08 across all AD GWAS and GWAS+GWAX datasets. We highlighted that the AD GWAS+GWAX with the largest sample size failed to identify the most significant signals, the maximum number of genome-wide significant genetic variants or maximum heritability. Additionally, we identified widespread statistical heterogeneity in AD GWAS+GWAX datasets, but not in AD GWAS datasets. We consider that statistical heterogeneity may have attenuated the statistical power in AD GWAS+GWAX and may contribute to explaining the low repeatability (17%) of genome-wide significant AD susceptibility loci and the decreased AD heritability (40-2%) as the sample size increased. Importantly, evidence supports the idea that a decrease in statistical heterogeneity facilitates the identification of genome-wide significant genetic loci and contributes to an increase in AD heritability. Collectively, current AD GWAX and GWAS+GWAX findings should be meticulously assessed and warrant additional investigation, and AD GWAS+GWAX should employ multiple meta-analysis methods, such as random-effects inverse variance-weighted meta-analysis, which is designed specifically for statistical heterogeneity.

Creating an Unprotected Class: Addressing Legal Risks in the Era of Biologically-Defined Alzheimer's Disease.

Documentation of preclinical biomarker tests for Alzheimer's disease (AD) in the medical record may expose patients to employment and insurance discrimination risks. There is a gap in research describing clinicians' approaches to documenting biomarker results. To evaluate discrimination risks faced by patients undergoing biomarker testing for AD through a qualitative analysis of clinician documentation practices. Semi-structured interviews using hypothetical patient scenarios. The qualitative analysis focused on interviewees' responses related to documentation and disclosure of results. We collected and analyzed 17 interviews with dementia experts; and identified three approaches to documenting biomarkers as: an association with active AD, noninformative, and an increased susceptibility for AD. Those who associated biomarkers with active disease were more likely to favor disclosure to employers and insurers, which could increase discrimination risks. This study demonstrates the variety of documentation and disclosure practices likely to emerge for preclinical AD biomarker tests and highlights a need for guidelines in this area.

Evaluation of the Protective Bioactivity and Molecular Mechanism Verification of Lactoferrin in an Alzheimer's Mouse Model with Ulcerative Enteritis

The development of new drug therapies for Alzheimer's disease (AD) is an important research topic today, but the pathogenesis of AD has not been thoroughly studied, and there are still several shortcomings in existing drug therapies. Therefore, this study aims to explore the molecular mechanism of lactoferrin in the treatments of AD and ulcerative colitis (UC) which are susceptible to AD, starting from the principle of "one drug, two diseases, and the same treatment." This study used pathological staining and specific indicators staining to preliminarily evaluate the interventions of lactoferrin on UC injury and AD progression. And 16s RNA full-length sequencing was used to investigate the effect of lactoferrin on the abundance of intestinal microbiota in AD mice. Then, intestinal tissue and brain tissue metabolomics analysis were used to screen specific metabolic pathways and preliminarily verify the metabolic mechanism of lactoferrin in alleviating 2 diseases by regulating certain specific metabolites. Moreover, lactoferrin significantly changed the types and abundance of gut microbiota in AD mice complicated by UC. To conclude, this study proved the clinical phenomenon of AD susceptibility to UC, and verified the therapeutic effect of lactoferrin on 2 diseases. More importantly, we revealed the possible molecular mechanism of LF, not only does it enrich the cognitive level of lactoferrin in alleviating AD by regulating the gut microbiota through the brain gut axis from the perspective of the theory of "food nutrition promoting human health," but it also provides a practical basis for the subsequent research and development of lactoferrin and drug validation from the perspective of "drug food homology."

New candidate SNPs for genetic association with Alzheimer's disease: a linkage disequilibrium analysis for the FCGRIIB and PILRA genes.

Two new SNPs have been recently associated to Alzheimer's disease in African American populations: FCGRIIB rs1050501 C/T, and PILRA rs1859788 A/G. The risk of Alzheimer's disease in FCGRIIB C and PILRA A allele carriers is three times higher than in non-carriers. However, the association between these and other single nucleotide polymorphisms (SNPs) has not been assessed. Linkage disequilibrium analysis, with r= 0.8 as a threshold value, was used to impute new candidate SNPs, on genomic data from both genes in 26 populations worldwide (n= 2504) from the 1000Genomes database. Four SNPs (rs13376485, rs3767640, rs3767639 and rs3767641) were linked to rs1050501 and one (rs2405442) to rs1859788 in the whole sample. Five novel SNPs could be associated with Alzheimer's disease susceptibility and play a causal role, even if none of them are exon variants since their potential roles in the regulation of gene expression.

RPTOR Is an Alzheimer's Disease Susceptibility Gene Associated with the Risk Factors Body Mass Index and Infectious Encephalitis.

In comparison to persons who did not have viral encephalitis, people with viral encephalitis had a later-life risk of Alzheimer's disease (AD) that was 31 times higher. In a previous study, we were able to confirm the association of viral encephalitis with AD and suggest that West Nile Virus infection is a significant AD risk factor. A genome wide association study (GWAS) with UK Biobank data revealed that the gene RAR Related Orphan Receptor B (RORB) is significantly associated with viral encephalitis. To use data from the 8 PheWeb datasets to try to identify genes other than RORB that might be involved in both infectious encephalitis and AD. PheWeb includes data from UKBB and 5 other databanks. We used UK Biobank data to examine gene expression and phenotypic expression. PheWeb identified additional genes associated with both infectious encephalitis and AD. RPTOR, a gene associated with the mTOR pathway, emerges as significant. Analyses of UK Biobank data reveal the impact of RPTOR on AD risk, with carriers of the minor allele A exhibiting decreased prevalence in subjects under age 55. Further analysis demonstrates that RPTOR genotypes influence body mass index (BMI) in subjects of all ages, with carriers of the minor allele A having lower BMI. Logistic regression analyses confirm the association between reduced BMI and increased AD risk, along with the established factor of age. RPTOR may represent an AD gene, though mTOR's role in AD and BMI is complex. Nevertheless, RPTOR and mTOR could represent potential therapeutic targets for AD.

Alzheimer’s disease susceptibility in African American elders: a classification and regression tree (CART) analysis approach

Alzheimer's disease (AD) is increasingly prevalent, especially among African American older adults. Despite its widespread nature, accurate and timely diagnosis of AD remains challenging. Addressing the research gap in sociodemographic and cardiovascular risk factor research associated with AD in African American older adults, this study aimed to identify and analyze distinct subgroups within this population that are particularly vulnerable to AD, thereby contributing to the development of targeted interventions and healthcare strategies. This study employs a rigorous methodology utilizing classification and regression tree (CART) analysis to examine data from the 2017 Uniform Data Set (UDS). This approach enables a nuanced analysis of AD susceptibility among African American older adults. The CART analysis revealed significant associations between the studied sociodemographic and cardiovascular risk factors and AD susceptibility among African American older adults. The results indicate the presence of specific subgroups with increased vulnerability to AD, shaped by varying levels of education [relative importance (RI): 100%], antidepressant usage (RI: 83.1%), BMI (RI: 71.2%), use of antipsychotic agents (RI: 35.5%), and age of smoking cessation (RI: 21.5%). These findings underscore the importance of culturally specific research and interventions for addressing AD among African Americans. This study's findings, revealing significant associations between sociodemographic and cardiovascular risk factors and AD susceptibility among African American older adults, underscore the necessity of developing healthcare policies and interventions specifically tailored to address these risks.

The cytoskeletal protein Plectin regulates Tau‐induced neurotoxicity in Alzheimer’s Disease

AbstractBackgroundThe genetic causes for most cases of Alzheimer’s disease (AD) and the underlying biology of pathogenesis remain unknown. Recent large scale proteomics studies on AD patient brains have identified novel protein networks and targets that are highly correlated with AD diagnosis and neuropathology. The most significantly AD‐correlated protein network identified contains the cytoskeletal protein Plectin (PLEC) as a network hub. PLEC functions to crosslink different cytoskeletal components and plays a role in axonal transport of synaptic proteins. Considering that microtubule associated protein‐Tau (MAPT) dysfunction is an AD hallmark, we hypothesize that PLEC dysfunction increases AD susceptibility by disrupting cytoskeletal homeostasis and synaptic function.MethodUtilizing a combination of genetic and proteomic analyses, we validate Plectin as a potential AD risk factor. We assessed the role of PLEC in Tau‐induced neurotoxicity in the animal model Drosophila melanogaster and human neuronal cell culture. Furthermore, we have also elucidated PLEC mutant neurodegenerative phenotypes independent of Tau overexpression in the fly. Immunoprecipitation‐mass spectrometry (IP‐MS) analysis was performed to define a Drosophila Plectin protein‐protein interaction network in adult brains. This network will serve as the basis for cross‐species analysis of protein networks.ResultThe Drosophila homolog of Plectin (dPLEC) is ubiquitously expressed within the adult brain with strong enrichment in neuronal rich tissues. Using Drosophila models of human tauopathy, dPLEC regulates age dependent Tau‐induced neurotoxicity and locomotor dysfunction. Plus, altering levels dPLEC regulates Tau‐phosphorylation in both adult Drosophila brains and human neurons. In the absence of Tau overexpression, dPLEC functions in light‐induced neuronal transmission confirming its role in normal neuronal function. Continued mechanistic analysis in both Drosophila and human neuronal cultures will determine PLEC’s role in AD neuropathogenesis and elucidate the underlying role of the cytoskeleton in AD susceptibility. To that end, we generated an endogenous GFP‐tagged dPLEC (dPLEC‐GFP) and performed immunoprecipitation‐mass spectrometry (IP‐MS) analysis to identify dPLEC protein interactors. Several cytoskeletal and synaptic proteins were identified and are currently being tested for their role in Tau‐induced neurodegeneration and synaptic dysfunction.ConclusionWe functionally validate the AD target PLEC as a regulator of Tau‐induced neurodegeneration and identify PLEC as a regulator of Tau dynamics and neuronal function.

Dissociable influences of maternal vs paternal Alzheimer’s risk on neurocognitive and cardiovascular health in men and women

AbstractBackgroundParental history of sporadic Alzheimer’s disease (AD) is considered a prime risk factor since at least the late 1980s. Routinely used clinical samples of at‐risk individuals (8‐16 subjects) may conceal weaker population‐based effects, especially those of paternal inheritance. We performed a phenome‐wide examination of the dissociable influences of maternal vs. paternal AD risk on male vs. female probands in the largest single‐site family‐based at‐risk AD cohort: PREVENT‐AD.MethodWe built sex‐specific PLS‐regression models in which the APOE genotypes (e.g., ɛ3/3, ɛ3/4, ɛ3/2) were estimated based on ∼1,000 patient visits, each covering ∼260 risk indicators, to derive three APOE‐driven intermediate phenotypes (IPs). We examined how much the three IPs vary with regard to sex and maternal vs. paternal AD lineage across the phenome. We assessed the sex‐specific and lineage‐specific variation of the IPs over a 4‐year follow‐up period. Lastly, we examined how matri‐ vs. patrilinear AD risk captured by the IPs were expressed in AD‐vulnerable brain structures.ResultAcross IPs, we linked patrilinear AD risk to verbal‐numerical cognition and cardiovascular health in males. In contrast, we linked matrilinear AD risk to memory performance in both sexes. Over time, the mean difference in cognitive performance decreases with regard to sex but increases with regard to AD lineage. Cis‐ and trans‐generational sex effects in neocortex subregions (e.g., mPFC, PCu) were captured by the first and second IPs, respectively. The third IP mainly captured trans‐generational sex effects in hippocampus subregions (e.g., CA1, CA4).ConclusionWe uncovered IPs of AD susceptibility differently expressed in male and female probands and affected by the diagnosed parent’s sex. Maternal inheritance highlighted memory performance in both sexes, whereas paternal inheritance was particularly linked to cardiovascular health in males. The inheritance of the IPs was reflected in the brain structure at both superficial and deeper layers of the cortex. As the first study of its kind, our cross‐generational analysis of matri‐ vs. patrilinear AD risk bridges the epidemiological and clinical literature by leveraging the power of ∼1,000 patient visits. Our completely data‐driven framework ultimately dissociated phenotypes of maternal and paternal AD risk single‐handedly expressed in male and female probands.

APP‐dependent cell adhesion is regulated by GWAS genes

AbstractBackgroundThanks to Genome‐Wide Association Studies (GWAS), 75 susceptibility loci for Alzheimer’s disease (AD) have been identified (Bellenguez et al, Nat genetics. 2022). However, one of the greatest challenges resides in the understanding of the functional consequences of these genetic determinants. One of the main hypothesis would be that some of these genetic factors could be involved in APP metabolism and Aβ production. Indeed, even if numerous players of the APP metabolism have been characterized over the last 20 years, a large part of the is still unknown. Moreover, with more than 200 genes localized in the AD susceptibility loci, the classical approach, i.e., studying genes one by one, cannot be done in a timely manner. Therefore, we took advantage of Genome‐Wide siRNA screening using a High Content Screening (HCS) approach allowing a systematic functional assessment of human genes on APP metabolism.MethodA HEK293 cell line stably over‐expressing a fluorescently‐tagged APP was transitory transfected in 384‐well plates with the human siGENOME siRNA library to silence every human gene. High content analysis was performed to automatically quantify (i) fluorescence intensities reflecting the intracellular accumulation of APP byproducts and (ii) cell‐cell interaction. Enrichment pathway analysis was performed to identify the pathways in which the modulators of APP are mainly involved.ResultExpected GWAS‐defined genes were identified among the genes showing the stronger effects on APP metabolism (APP, ADAM10, SORL1). Moreover, we observed that a large portion of the GWAS‐defined genes are modulators of APP metabolism and are involved in cell adhesion signaling, including the genetic risk factors FERMT2 and Cass4. In our model, silencing of these genes was also able to modulate cell‐cell interaction, suggesting that APP‐dependent cell adhesion is regulated by GWAS‐defined genes.ConclusionRemarkably, many genetic risk factors of AD are involved in cell adhesion pathway, such as APP which has been shown to be involved in synaptic formation and plasticity. Since synaptic dysfunction and loss is one of the very early hallmarks of AD, our data suggest that beyond Aβ production, APP could impact AD process through an impairment of cell adhesion at the synaptic level.

A new risk locus on chromosome 1 is suggested by genome‐wide association study in Peruvians for Alzheimer disease

AbstractBackgroundIncreasing ethnic/ancestral diversity in genetic studies is critical for defining the genetic architecture of Alzheimer disease (AD). Amerindian (AI) populations are substantially underrepresented in AD genetic studies. The Peruvian (PE) population, with up to ∼80% of AI ancestry, provides a unique opportunity to assess the role of AI ancestry in AD. We performed the first genome‐wide association study (GWAS) in the PE population to identify novel AD susceptibility loci and characterize known AD genetic risk loci.MethodThe PE dataset includes array‐genotype and phenotype data from 542 individuals (189 cases; 353 controls), imputed to the NHLBI TOPMedv5 haplotype reference panel. We used a generalized linear mixed‐model (SAIGE software) for the GWAS analysis. We analyzed two separate models; the first model accounted for sex, age, and population substructure, while the second model also included the dosage of APOEe4. In both models, we included a genetic relationship matrix as a random effect to account for any potential relatedness. To determine if the associations are specific to specific ancestries, we employed ancestry‐aware approaches using the RFMix software.ResultAPOE was significantly associated with AD with an effect size comparable to that found in non‐Hispanic white (NHW) populations (OR = 3.3(2.2‐4.8),pv = 8.0×10−10). Two additional known AD loci, TREML2 (pv = 0.008) and CLU (pv = 0.012), showed nominal significance Variants at three additional loci reached suggestive significance (pv&lt;1×10−6): NFASC (pv = 9.4×10−8;chromosome 1), STK32A (pv = 9.3×10−7; chromosome 5), and LOC100132830 (pv = 6.7×10−7;chromosome 6). The NFASC locus neared genome‐wide significance in the APOE adjusted model (pv = 6.7×10−8). The haplotypes associated with AD at the NFASC locus were found to be of European origin. Additionally, the STK32A locus was found to have a protective effect specifically among individuals of AI background. We did not observe significant heterogeneity of effect at the APOE and LOC100132830 loci across different ancestral backgrounds.ConclusionPE GWAS identified a novel, promising AD susceptibility locus in the NFASC gene of European origin. We also detected a potential protective effect in the STK32A locus on AI background, emphasizing the importance of incorporating ancestry‐aware approaches in gene discovery in admixed populations.

Early Life Stress Enhances Cognitive Decline and Alters Synapse Function and Interneuron Numbers in Young Male APP/PS1 Mice.

Exposure to stress early in life increases the susceptibility to Alzheimer's disease (AD) pathology in aged AD mouse models. So far, the underlying mechanisms have remained elusive. To investigate 1) effects of early life stress (ELS) on early functional signs that precede the advanced neuropathological changes, and 2) correlate synaptosomal protein content with cognition to identify neural correlates of AD. APPswe/PS1dE9 mice and littermates were subjected to ELS by housing dams and pups with limited bedding and nesting material from postnatal days 2-9. At 3 months of age, an age where no cognitive loss or amyloid-β (Aβ) pathology is typically reported in this model, we assessed hippocampal Aβ pathology, synaptic strength and synapse composition and interneuron populations. Moreover, cognitive flexibility was assessed and correlated with synaptosomal protein content. While ELS did not affect Aβ pathology, it increased synaptic strength and decreased the number of calretinin+ interneurons in the hippocampal dentate gyrus. Both genotype and condition further affected the level of postsynaptic glutamatergic protein content. Finally, APP/PS1 mice were significantly impaired in cognitive flexibility at 3 months of age, and ELS exacerbated this impairment, but only at relatively high learning criteria. ELS reduced cognitive flexibility in young APP/PS1 mice and altered markers for synapse and network function. These findings at an early disease stage provide novel insights in AD etiology and in how ELS could increase AD susceptibility.

Identification of circulating proteins associated with general cognitive function among middle-aged and older adults

Identifying circulating proteins associated with cognitive function may point to biomarkers and molecular process of cognitive impairment. Few studies have investigated the association between circulating proteins and cognitive function. We identify 246 protein measures quantified by the SomaScan assay as associated with cognitive function (p < 4.9E-5, n up to 7289). Of these, 45 were replicated using SomaScan data, and three were replicated using Olink data at Bonferroni-corrected significance. Enrichment analysis linked the proteins associated with general cognitive function to cell signaling pathways and synapse architecture. Mendelian randomization analysis implicated higher levels of NECTIN2, a protein mediating viral entry into neuronal cells, with higher Alzheimer’s disease (AD) risk (p = 2.5E-26). Levels of 14 other protein measures were implicated as consequences of AD susceptibility (p < 2.0E-4). Proteins implicated as causes or consequences of AD susceptibility may provide new insight into the potential relationship between immunity and AD susceptibility as well as potential therapeutic targets.

Genetic background influences the 5XFAD Alzheimer's disease mouse model brain proteome.

There is an urgent need to improve the translational validity of Alzheimer's disease (AD) mouse models. Introducing genetic background diversity in AD mouse models has been proposed as a way to increase validity and enable the discovery of previously uncharacterized genetic contributions to AD susceptibility or resilience. However, the extent to which genetic background influences the mouse brain proteome and its perturbation in AD mouse models is unknown. In this study, we crossed the 5XFAD AD mouse model on a C57BL/6J (B6) inbred background with the DBA/2J (D2) inbred background and analyzed the effects of genetic background variation on the brain proteome in F1 progeny. Both genetic background and 5XFAD transgene insertion strongly affected protein variance in the hippocampus and cortex (n = 3,368 proteins). Protein co-expression network analysis identified 16 modules of highly co-expressed proteins common across the hippocampus and cortex in 5XFAD and non-transgenic mice. Among the modules strongly influenced by genetic background were those related to small molecule metabolism and ion transport. Modules strongly influenced by the 5XFAD transgene were related to lysosome/stress responses and neuronal synapse/signaling. The modules with the strongest relationship to human disease-neuronal synapse/signaling and lysosome/stress response-were not significantly influenced by genetic background. However, other modules in 5XFAD that were related to human disease, such as GABA synaptic signaling and mitochondrial membrane modules, were influenced by genetic background. Most disease-related modules were more strongly correlated with AD genotype in the hippocampus compared with the cortex. Our findings suggest that the genetic diversity introduced by crossing B6 and D2 inbred backgrounds influences proteomic changes related to disease in the 5XFAD model, and that proteomic analysis of other genetic backgrounds in transgenic and knock-in AD mouse models is warranted to capture the full range of molecular heterogeneity in genetically diverse models of AD.

Exploration of acupuncture therapy in the treatment of MCI patients with the ApoE ε4 gene based on the brain-gut axis theory

BackgroundMild cognitive impairment (MCI) is the predementia phase of Alzheimer’s disease (AD). The intestinal microbiome is altered in MCI and AD, and apolipoprotein E (ApoE) ε4 gene polymorphism is a risk factor for the progression of MCI to AD. This study aims to investigate the improvement in cognitive function of MCI patients with and without ApoE ε4 due to acupuncture and the changes in gut microbiota community composition and abundance in MCI.MethodsThis randomized assessor-blind controlled study will enrol MCI patients with and without the ApoE ε4 gene (n = 60/60). Sixty subjects with the ApoE ε4 gene and 60 subjects without the ApoE ε4 gene will be randomly allocated into treatment and control groups in a 1:1 ratio. Intestinal microbiome profiles will be evaluated by 16 S rRNA sequencing of faecal samples and compared between the groups.Results/conclusionsAcupuncture is an effective method to improve cognitive function in MCI. This study will provide data on the relationship between the gut microbiota and the effectiveness of acupuncture in patients with MCI from a new angle. This study will also provide data on the relationship between the gut microbiota and an AD susceptibility gene by integrating microbiologic and molecular approaches.Trial registrationwww.chictr.org.cn, ID: ChiCTR2100043017, recorded on 4 February 2021.

A splicing transcriptome-wide association study identifies novel altered splicing for Alzheimer's disease susceptibility

Alzheimer's disease (AD) is a common neurodegenerative disease in aging individuals. Alternative splicing is reported to be relevant to AD development while their roles in etiology of AD remain largely elusive. We performed a comprehensive splicing transcriptome-wide association study (spTWAS) using intronic excision expression genetic prediction models of 12 brain tissues developed through three modelling strategies, to identify candidate susceptibility splicing introns for AD risk. A total of 111,326 (46,828 proxy) cases and 677,663 controls of European ancestry were studied. We identified 343 associations of 233 splicing introns (143 genes) with AD risk after Bonferroni correction (0.05/136,884 = 3.65 × 10−7). Fine-mapping analyses supported 155 likely causal associations corresponding to 83 splicing introns of 55 genes. Eighteen causal splicing introns of 15 novel genes (EIF2D, WDR33, SAP130, BYSL, EPHB6, MRPL43, VEGFB, PPP1R13B, TLN2, CLUHP3, LRRC37A4P, CRHR1, LINC02210, ZNF45-AS1, and XPNPEP3) were identified for the first time to be related to AD susceptibility. Our study identified novel genes and splicing introns associated with AD risk, which can improve our understanding of the etiology of AD.

A history of repeated alcohol intoxication promotes cognitive impairment and gene expression signatures of disease progression in the 3xTg mouse model of Alzheimer's disease.

The impact of alcohol abuse on Alzheimer's disease (AD) is poorly understood. Here, we show that the onset of neurocognitive impairment in a mouse model of AD is hastened by repeated alcohol intoxication through exposure to alcohol vapor, and we provide a comprehensive gene expression dataset of the prefrontal cortex by the single-nucleus RNA sequencing of 113,242 cells. We observed a broad dysregulation of gene expression that involves neuronal excitability, neurodegeneration, and inflammation, including interferon genes. Several genes previously associated with AD in humans by genome-wide association studies were differentially regulated in specific neuronal populations. Gene expression patterns of AD mice with a history of alcohol intoxication were more similar to gene expression signatures of older AD mice with more advanced disease and cognitive impairment than those of younger AD mice with prodromic disease, suggesting that alcohol promotes transcriptional changes consistent with AD progression. Our gene expression dataset at the single-cell level provides a unique resource for investigations of the molecular bases of the detrimental role of excessive alcohol intake in AD.Significance statementAlzheimer's disease (AD) is the most common neurodegenerative disease worldwide. Many efforts have been geared toward the identification of environmental and genetic risk factors. However, alcohol has received limited attention as a potential risk factor for AD. We explored effects of the interaction of a history of alcohol intoxication with genetic AD susceptibility on cognitive performance and gene expression at the single-cell level. We found that a history of repeated alcohol intoxication promotes the emergence of spatial learning and memory impairments in pre-symptomatic triple transgenic AD (3xTg-AD) mice. We also show that a history of repeated alcohol intoxication induces prefrontal cortex transcriptional changes associated with AD progression.

TOMM40 Genetic Variants Cause Neuroinflammation in Alzheimer's Disease.

Translocase of outer mitochondrial membrane 40 (TOMM40) is located in the outer membrane of mitochondria. TOMM40 is essential for protein import into mitochondria. TOMM40 genetic variants are believed to increase the risk of Alzheimer's disease (AD) in different populations. In this study, three exonic variants (rs772262361, rs157581, and rs11556505) and three intronic variants (rs157582, rs184017, and rs2075650) of the TOMM40 gene were identified from Taiwanese AD patients using next-generation sequencing. Associations between the three TOMM40 exonic variants and AD susceptibility were further evaluated in another AD cohort. Our results showed that rs157581 (c.339T > C, p.Phe113Leu, F113L) and rs11556505 (c.393C > T, p.Phe131Leu, F131L) were associated with an increased risk of AD. We further utilized cell models to examine the role of TOMM40 variation in mitochondrial dysfunction that causes microglial activation and neuroinflammation. When expressed in BV2 microglial cells, the AD-associated mutant (F113L) or (F131L) TOMM40 induced mitochondrial dysfunction and oxidative stress-induced activation of microglia and NLRP3 inflammasome. Pro-inflammatory TNF-α, IL-1β, and IL-6 released by mutant (F113L) or (F131L) TOMM40-activated BV2 microglial cells caused cell death of hippocampal neurons. Taiwanese AD patients carrying TOMM40 missense (F113L) or (F131L) variants displayed an increased plasma level of inflammatory cytokines IL-6, IL-18, IL-33, and COX-2. Our results provide evidence that TOMM40 exonic variants, including rs157581 (F113L) and rs11556505 (F131L), increase the AD risk of the Taiwanese population. Further studies suggest that AD-associated mutant (F113L) or (F131L) TOMM40 cause the neurotoxicity of hippocampal neurons by inducing the activation of microglia and NLRP3 inflammasome and the release of pro-inflammatory cytokines.

A Comparison of the Various Methods for Selecting Features for Single-Cell RNA Sequencing Data in Alzheimer's Disease.

The high-throughput sequencing method known as RNA-Seq records the whole transcriptome of individual cells. Single-cell RNA sequencing, also known as scRNA-Seq, is widely utilized in the field of biomedical research and has resulted in the generation of huge quantities and types of data. The noise and artifacts that are present in the raw data require extensive cleaning before they can be used. When applied to applications for machine learning or pattern recognition, feature selection methods offer a method to reduce the amount of time spent on calculation while simultaneously improving predictions and offering a better knowledge of the data. The process of discovering biomarkers is analogous to feature selection methods used in machine learning and is especially helpful for applications in the medical field. An attempt is made by a feature selection algorithm to cut down on the total number of features by eliminating those that are unnecessary or redundant while retaining those that are the most helpful.We apply FS algorithms designed for scRNA-Seq to Alzheimer's disease, which is the most prevalent neurodegenerative disease in the western world and causes cognitive and behavioral impairment. AD is clinically and pathologically varied, and genetic studies imply a diversity of biological mechanisms and pathways. Over 20 new Alzheimer's disease susceptibility loci have been discovered through linkage, genome-wide association, and next-generation sequencing (Tosto G, Reitz C, Mol Cell Probes 30:397-403, 2016). In this study, we focus on the performance of three different approaches to marker gene selection methods and compare them using the support vector machine (SVM), k-nearest neighbors' algorithm (k-NN), and linear discriminant analysis (LDA), which are mainly supervised classification algorithms.

Disclosure of Genetic Risk Factors for Alzheimer's Disease to Cognitively Healthy Individuals-From Current Practice towards a Personalised Medicine Scenario.

Alzheimer's disease (AD) is a genetically complex disorder. In addition to the relatively small number of pathogenic variants causing autosomal dominant AD, many others have been associated with the much more common sporadic form. The E4 allele of the Apolipoprotein E (APOE) is the first discovered genetic risk factor for AD. In addition, more than 70 genetic risk loci contributing to AD have been identified. Current guidelines do not recommend AD susceptibility genetic testing in cognitively healthy adults because the implications for clinical care are limited. However, secondary prevention clinical trials of disease-modifying therapies enrol individuals based on genetic criteria, and participants are often informed of APOE testing results. Moreover, the availability of direct-to-consumer genetic testing allows individuals to learn their own AD genetic risk profile without medical supervision. A number of research protocols for AD susceptibility genetic testing have been proposed. In Italy, disclosure processes and protocols beyond those developed for inherited dementia have not been established yet. We reviewed the literature on the current practice and clinical issues related to disclosing AD genetic risk to cognitively healthy individuals and provide suggestions that may help to develop specific guidelines at the national level.