Browsing by Subject "Alzheimer’s Disease"
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Item A human induced pluripotent stem cell model of Alzheimer’s Disease‐associated fractalkine receptor polymorphism to assess AD‐related microglial dysfunction(Wiley, 2025-01-03) Tutrow, Kaylee; Harkin, Jade; Hernandez, Melody; Huang, Kang-Chieh S.; Bissel, Stephanie J.; Puntambekar, Shweta S.; Lamb, Bruce T.; Meyer, Jason S.; Medical and Molecular Genetics, School of MedicineBackground: Dysfunctional microglial activity has recently been identified as a potential mechanism leading to accumulation of amyloid beta and pTau and subsequent neurodegeneration in Alzheimer’s Disease. The CX3CR1/fractalkine axis serves as a mechanism for bi‐directional communication between microglia and neurons, respectively, to promote a resting, anti‐inflammatory state in microglia. Previous studies have demonstrated that deficiency in CX3CR1 signaling leads microglia to a more pro‐inflammatory phenotype, phagocytic deficits, and increased susceptibility of neurons to cell death. Additionally, the CX3CR1‐V249I polymorphism was recently identified as a potential risk allele for Alzheimer’s Disease with worsened Braak staging in post‐mortem Alzheimer’s patients. However, the role of fractalkine dysfunction in human cells and the mechanisms by which microglia with the CX3CR1‐V249I SNP contribute to neurodegeneration remain unclear. Method: To address this shortcoming, we utilized human induced pluripotent stem cells and CRISPR/Cas9 gene editing technology to elucidate the effects of the CX3CR1‐V249I polymorphism on human microglia‐like cells (hMGLs) compared to an isogenic control cell line. Isogenic control cells alongside both heterozygous and homozygous CX3CR1 V249I cell lines were differentiated in parallel to yield enriched populations of hMGLs. Resulting hMGLs were then assessed for uptake of amyloid beta 1‐42 using flow cytometry, cell death in response to cytokine starvation, changes in proliferation, and finally alterations to migratory behavior using a microfluidic chamber. Result: We demonstrate the effective differentiation of hMGLS from both isogenic control and CX3CR1‐V249I backgrounds, which express characteristic microglial markers and are functionally phagocytic. Microglia bearing the homozygous CX3CR1‐V249I allele, but not heterozygous cells, demonstrated decreased uptake of amyloid beta in vitro compared to isogenic controls. Additionally, homozygous V249I microglia demonstrated increased stress‐induced cell death, as well as altered proliferation and decreased migratory capability. Conclusion: These findings suggest that the CX3CR1‐V249I polymorphism may cause a dysfunctional microglia phenotype that may contribute to neuronal dysfunction and death. Ongoing work will expand upon the transcriptome and secretome profile of CX3CR1‐V249I microglia and elucidate how this gene variant contributes to Alzheimer’s Disease‐related neurodegeneration.Item Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer's disease patients(Biomed Central, 2018-12-31) Xiang, Shunian; Huang, Zhi; Wang, Tianfu; Han, Zhi; Yu, Christina Y.; Ni, Dong; Huang, Kun; Zhang, Jie; Medicine, School of MedicineBACKGROUND: Gene co-expression network (GCN) mining is a systematic approach to efficiently identify novel disease pathways, predict novel gene functions and search for potential disease biomarkers. However, few studies have systematically identified GCNs in multiple brain transcriptomic data of Alzheimer's disease (AD) patients and looked for their specific functions. METHODS: In this study, we first mined GCN modules from AD and normal brain samples in multiple datasets respectively; then identified gene modules that are specific to AD or normal samples; lastly, condition-specific modules with similar functional enrichments were merged and enriched differentially expressed upstream transcription factors were further examined for the AD/normal-specific modules. RESULTS: We obtained 30 AD-specific modules which showed gain of correlation in AD samples and 31 normal-specific modules with loss of correlation in AD samples compared to normal ones, using the network mining tool lmQCM. Functional and pathway enrichment analysis not only confirmed known gene functional categories related to AD, but also identified novel regulatory factors and pathways. Remarkably, pathway analysis suggested that a variety of viral, bacteria, and parasitic infection pathways are activated in AD samples. Furthermore, upstream transcription factor analysis identified differentially expressed upstream regulators such as ZFHX3 for several modules, which can be potential driver genes for AD etiology and pathology. CONCLUSIONS: Through our state-of-the-art network-based approach, AD/normal-specific GCN modules were identified using multiple transcriptomic datasets from multiple regions of the brain. Bacterial and viral infectious disease related pathways are the most frequently enriched in modules across datasets. Transcription factor ZFHX3 was identified as a potential driver regulator targeting the infectious diseases pathways in AD-specific modules. Our results provided new direction to the mechanism of AD as well as new candidates for drug targets.Item Deep trans-omic network fusion reveals altered synaptic network in Alzheimer’s Disease(CSH, 2023-02-21) Xie, Linhui; Raj, Yash; Varathan, Pradeep; He, Bing; Nho, Kwangsik; Risacher, Shannon L.; Salama, Paul; Saykin, Andrew J.; Yan, Jingwen; Electrical and Computer Engineering, School of Engineering and TechnologyMulti-omic data spanning from genotype, gene expression to protein expression have been increasingly explored to interpret findings from genome wide association studies of Alzheimer’s disease (AD) and to gain more insight of the disease mechanism. However, each -omics data type is usually examined individually and the functional interactions between genetic variations, genes and proteins are only used after discovery to interpret the findings, but not beforehand. In this case, multi-omic findings are likely not functionally related and therefore give rise to challenges in interpretation. To address this problem, we propose a new interpretable deep neural network model MoFNet to jointly model the prior knowledge of functional interactions and multi-omic data set. It aims to identify a subnetwork of functional interactions predictive of AD evidenced by multi-omic measures. Particularly, prior functional interaction network was embedded into the architecture of MoFNet in a way that it resembles the information flow from DNA to gene and protein. The proposed model MoFNet significantly outperformed all other state-of-art classifiers when evaluated using multi-omic data from the ROS/MAP cohort. Instead of individual markers, MoFNet yielded multi-omic sub-networks related to innate immune system, clearance of misfolded proteins, and neurotransmitter release respectively. Around 50% of these findings were replicated in another independent cohort. Our identified gene/proteins are highly related to synaptic vesicle function. Altered regulation or expression of these genes/proteins could cause disruption in neuron-neuron or neuron-glia cross talk and further lead to neuronal and synapse loss in AD. Further investigation of these identified genes/proteins could possibly help decipher the mechanisms underlying synaptic dysfunction in AD, and ultimately inform therapeutic strategies to modify AD progression in the early stage.Item Global neuropathologic severity of Alzheimer's disease and locus coeruleus vulnerability influences plasma phosphorylated tau levels(Springer, 2022-12-27) Murray, Melissa E.; Moloney, Christina M.; Kouri, Naomi; Syrjanen, Jeremy A.; Matchett, Billie J.; Rothberg, Darren M.; Tranovich, Jessica F.; Hicks Sirmans, Tiffany N.; Wiste, Heather J.; Boon, Baayla D. C.; Nguyen, Aivi T.; Reichard, R. Ross; Dickson, Dennis W.; Lowe, Val J.; Dage, Jeffrey L.; Petersen, Ronald C.; Jack, Clifford R., Jr.; Knopman , David S.; Vemuri, Prashanthi; Graff-Radford, Jonathan; Mielke, Michelle M.; Neurology, School of MedicineBackground Advances in ultrasensitive detection of phosphorylated tau (p-tau) in plasma has enabled the use of blood tests to measure Alzheimer’s disease (AD) biomarker changes. Examination of postmortem brains of participants with antemortem plasma p-tau levels remains critical to understanding comorbid and AD-specific contribution to these biomarker changes. Methods We analyzed 35 population-based Mayo Clinic Study of Aging participants with plasma p-tau at threonine 181 and threonine 217 (p-tau181, p-tau217) available within 3 years of death. Autopsied participants included cognitively unimpaired, mild cognitive impairment, AD dementia, and non-AD neurodegenerative disorders. Global neuropathologic scales of tau, amyloid-β, TDP-43, and cerebrovascular disease were examined. Regional digital pathology measures of tau (phosphorylated threonine 181 and 217 [pT181, pT217]) and amyloid-β (6F/3D) were quantified in hippocampus and parietal cortex. Neurotransmitter hubs reported to influence development of tangles (nucleus basalis of Meynert) and amyloid-β plaques (locus coeruleus) were evaluated. Results The strongest regional associations were with parietal cortex for tau burden (p-tau181 R = 0.55, p = 0.003; p-tau217 R = 0.66, p < 0.001) and amyloid-β burden (p-tau181 R = 0.59, p < 0.001; p-tau217 R = 0.71, p < 0.001). Linear regression analysis of global neuropathologic scales explained 31% of variability in plasma p-tau181 (Adj. R2 = 0.31) and 59% in plasma p-tau217 (Adj. R2 = 0.59). Neither TDP-43 nor cerebrovascular disease global scales independently contributed to variability. Global scales of tau pathology (β-coefficient = 0.060, p = 0.016) and amyloid-β pathology (β-coefficient = 0.080, p < 0.001) independently predicted plasma p-tau217 when modeled together with co-pathologies, but only amyloid-β (β-coefficient = 0.33, p = 0.021) significantly predicted plasma p-tau181. While nucleus basalis of Meynert neuron count/mm2 was not associated with plasma p-tau levels, a lower locus coeruleus neuron count/mm2 was associated with higher plasma p-tau181 (R = -0.50, p = 0.007) and higher plasma p-tau217 (R = -0.55, p = 0.002). Cognitive scores (Adj. R2 = 0.25–0.32) were predicted by the global tau scale, but not by the global amyloid-β scale or plasma p-tau when modeled simultaneously. Conclusions Higher soluble plasma p-tau levels may be the result of an intersection between insoluble deposits of amyloid-β and tau accumulation in brain, and may be associated with locus coeruleus degeneration.Item Identifying highly heritable brain amyloid phenotypes through mining Alzheimer's imaging and sequencing biobank data(World Scientific, 2022) Bao, Jingxuan; Wen, Zixuan; Kim, Mansu; Zhao, Xiwen; Lee, Brian N.; Jung, Sang-Hyuk; Davatzikos, Christos; Saykin, Andrew J.; Thompson, Paul M.; Kim, Dokyoon; Zhao, Yize; Shen, Li; Alzheimer’s Disease Neuroimaging Initiative; Radiology and Imaging Sciences, School of MedicineBrain imaging genetics, an emerging and rapidly growing research field, studies the relationship between genetic variations and brain imaging quantitative traits (QTs) to gain new insights into the phenotypic characteristics and genetic mechanisms of the brain. Heritability is an important measurement to quantify the proportion of the observed variance in an imaging QT that is explained by genetic factors, and can often be used to prioritize brain QTs for subsequent imaging genetic association studies. Most existing studies define regional imaging QTs using predefined brain parcellation schemes such as the automated anatomical labeling (AAL) atlas. However, the power to dissect genetic underpinnings under QTs defined in such an unsupervised fashion could be negatively affected by heterogeneity within the regions in the partition. To bridge this gap, we propose a novel method to define highly heritable brain regions. Based on voxelwise heritability estimates, we extract brain regions containing spatially connected voxels with high heritability. We perform an empirical study on the amyloid imaging and whole genome sequencing data from a landmark Alzheimer’s disease biobank; and demonstrate the regions defined by our method have much higher estimated heritabilities than the regions defined by the AAL atlas. Our proposed method refines the imaging endophenotype constructions in light of their genetic dissection, and yields more powerful imaging QTs for subsequent detection of genetic risk factors along with better interpretability.Item Identifying imaging genetic associations via regional morphometricity estimation(World Scientific, 2022) Bao, Jingxuan; Wen, Zixuan; Kim, Mansu; Saykin, Andrew J.; Thompson, Paul M.; Zhao, Yize; Shen, Li; Alzheimer’s Disease Neuroimaging Initiative; Radiology and Imaging Sciences, School of MedicineBrain imaging genetics is an emerging research field aiming to reveal the genetic basis of brain traits captured by imaging data. Inspired by heritability analysis, the concept of morphometricity was recently introduced to assess trait association with whole brain morphology. In this study, we extend the concept of morphometricity from its original definition at the whole brain level to a more focal level based on a region of interest (ROI). We propose a novel framework to identify the SNP-ROI association via regional morphometricity estimation of each studied single nucleotide polymorphism (SNP). We perform an empirical study on the structural MRI and genotyping data from a landmark Alzheimer’s disease (AD) biobank; and yield promising results. Our findings indicate that the AD-related SNPs have higher overall regional morphometricity estimates than the SNPs not yet related to AD. This observation suggests that the variance of AD SNPs can be explained more by regional morphometric features than non-AD SNPs, supporting the value of imaging traits as targets in studying AD genetics. Also, we identified 11 ROIs, where the AD/non-AD SNPs and significant/insignificant morphometricity estimation of the corresponding SNPs in these ROIs show strong dependency. Supplementary motor area (SMA) and dorsolateral prefrontal cortex (DPC) are enriched by these ROIs. Our results also demonstrate that using all the detailed voxel-level measures within the ROI to incorporate morphometric information outperforms using only a single average ROI measure, and thus provides improved power to detect imaging genetic associations.Item IL-34 exacerbates pathogenic features of Alzheimer’s disease and calvaria osteolysis in triple transgenic (3x-Tg) female mice(Elsevier, 2023) Ho, Anny; Ngala, Bidii; Yamada, Chiaki; Garcia, Christopher; Duarte, Carolina; Akkaoui, Juliet; Ciolac, Dumitru; Nusbaum, Amilia; Kochen, William; Efremova, Daniela; Groppa, Stanislav; Nathanson, Lubov; Bissel, Stephanie; Oblak, Adrian; Kacena, Melissa A.; Movila, Alexandru; Biomedical and Applied Sciences, School of DentistryHallmark features of Alzheimer’s disease (AD) include elevated accumulation of aggregated Aβ40 and Aβ42 peptides, hyperphosphorylated Tau (p-Tau), and neuroinflammation. Emerging evidence indicated that interleukin-34 (IL-34) contributes to AD and inflammatory osteolysis via the colony-stimulating factor-1 receptor (CSF-1r). In addition, CSF-1r is also activated by macrophage colony-stimulating factor-1 (M-CSF). While the role of M-CSF in bone physiology and pathology is well addressed, it remains controversial whether IL-34-mediated signaling promotes osteolysis, neurodegeneration, and neuroinflammation in relation to AD. In this study, we injected 3x-Tg mice with mouse recombinant IL-34 protein over the calvaria bone every other day for 42 days. Then, behavioral changes, brain pathology, and calvaria osteolysis were evaluated using various behavioral maze and histological assays. We demonstrated that IL-34 administration dramatically elevated AD-like anxiety and memory loss, pathogenic amyloidogenesis, p-Tau, and RAGE expression in female 3x-Tg mice. Furthermore, IL-34 delivery promoted calvaria inflammatory osteolysis compared to the control group. In addition, we also compared the effects of IL-34 and M-CSF on macrophages, microglia, and RANKL-mediated osteoclastogenesis in relation to AD pathology in vitro. We observed that IL-34-exposed SIM-A9 microglia and 3x-Tg bone marrow-derived macrophages released significantly elevated amounts of pro-inflammatory cytokines, TNF-α, IL-1β, and IL-6, compared to M-CSF treatment in vitro. Furthermore, IL-34, but not M-CSF, elevated RANKL-primed osteoclastogenesis in the presence of Aβ40 and Aβ42 peptides in bone marrow derived macrophages isolated from female 3x-Tg mice. Collectively, our data indicated that IL-34 elevates AD-like features, including behavioral changes and neuroinflammation, as well as osteoclastogenesis in female 3x-Tg mice.Item Normal-Tension Glaucoma and Potential Clinical Links to Alzheimer’s Disease(MDPI, 2024-03-27) Ho, Kathleen; Bodi, Nicole E.; Sharma, Tasneem P.; Ophthalmology, School of MedicineGlaucoma is a group of optic neuropathies and the world’s leading cause of irreversible blindness. Normal-tension glaucoma (NTG) is a subtype of glaucoma that is characterized by a typical pattern of peripheral retinal loss, in which the patient’s intraocular pressure (IOP) is considered within the normal range (<21 mmHg). Currently, the only targetable risk factor for glaucoma is lowering IOP, and patients with NTG continue to experience visual field loss after IOP-lowering treatments. This demonstrates the need for a better understanding of the pathogenesis of NTG and underlying mechanisms leading to neurodegeneration. Recent studies have found significant connections between NTG and cerebral manifestations, suggesting NTG as a neurodegenerative disease beyond the eye. Gaining a better understanding of NTG can potentially provide new Alzheimer’s Disease diagnostics capabilities. This review identifies the epidemiology, current biomarkers, altered fluid dynamics, and cerebral and ocular manifestations to examine connections and discrepancies between the mechanisms of NTG and Alzheimer’s Disease.Item Numerical Modeling and Computer Simulation of a Meander Line Antenna for Alzheimer's Disease Treatment, a Feasibility Study(Scientific Research Publishing, 2023) Perez, Felipe P.; Rahmani, Maryam; Morisaki, Jorge; Amran, Farhan; Bakri, Syazwani; Halim, Akmal; Dsouza, Alston; Yusuf, Nurafifi Mohd; Farhan, Amran; Maulucci, James; Rizkalla, Maher; Medicine, School of MedicineAlzheimer’s disease (AD) is a brain disorder that eventually causes memory loss and the ability to perform simple cognitive functions; research efforts within pharmaceuticals and other medical treatments have minimal impact on the disease. Our preliminary biological studies showed that Repeated Electromagnetic Field Stimulation (REFMS) applying an EM frequency of 64 MHz and a specific absorption rate (SAR) of 0.4 – 0.9 W/kg decrease the level of amyloid-β peptides (Aβ), which is the most likely etiology of AD. This study emphasizes uniform E/H field and SAR distribution with adequate penetration depth penetration through multiple human head layers driven with low input power for safety treatments. In this work, we performed numerical modeling and computer simulations of a portable Meander Line antenna (MLA) to achieve the required EMF parameters to treat AD. The MLA device features a low cost, small size, wide bandwidth, and the ability to integrate into a portable system. This study utilized a High-Frequency Simulation System (HFSS) in the design of the MLA with the desired characteristics suited for AD treatment in humans. The team designed a 24-turn antenna with a 60 cm length and 25 cm width and achieved the required resonant frequency of 64 MHz. Here we used two numerical human head phantoms to test the antenna, the MIDA and spherical head phantom with six and seven tissue layers, respectively. The antenna was fed from a 50-Watt input source to obtain the SAR of 0.6 W/kg requirement in the center of the simulated brain tissue layer. We found that the E/H field and SAR distribution produced was not homogeneous; there were areas of high SAR values close to the antenna transmitter, also areas of low SAR value far away from the antenna. This paper details the antenna parameters, the scattering parameters response, the efficiency response, and the E and H field distribution; we presented the computer simulation results and discussed future work for a practical model.Item Regulation of Proteins Implicated in Alzheimer’s Disease by MicroRNAs(Office of the Vice Chancellor for Research, 2013-04-05) Chopra, Nipun; Long, Justin M.; Ray, Balmiki; Obukhov, Alexander G.; Lahiri, Debomoy K.Alzheimer’s Disease (AD) is a neurodegenerative disorder characterized by the deposition of Amyloid-Beta (Aβ) peptide in the brain. This toxic peptide is generated by the sequential cleavage of Amyloid Precursor Protein (APP) by Beta-site APP-cleaving enzyme-1 (BACE-1) and γ-secretase. The disorder is also characterized by the perturbation of calcium homeostasis in neurons. MicroRNAs are short, single-stranded RNAs that are able to influence protein expression by targeting the 3’ Untranslated region (UTR) or 5’ UTR of mRNAs. Previous work in our laboratory has shown that miR-101, miR-153 and miR-346 can regulate APP whereas miR-339-5p can lower BACE1 expression. Here, we aim to reduce APP, BACE1 and Aβ levels, in vitro, by the addition of microRNAs that target the 3’ UTR of APP and BACE1. We show that in a human astrocytoma-glioblastoma (U373) cell line, the expression of BACE1 protein is significantly reduced compared to the mock condition upon transfecting miR-298, miR-328 and miR-144. miR-298 also reduces Aβ levels in these cells. Similarly, in HeLa cells, we show that miR-520c, miR-20b and miR-144 produce a reduction in APP expression compared to both mock and a negative control microRNA mimic. Additionally, we observed that knocking down APP using siRNA, but not knocking down BACE1, lowers basal intracellular calcium levels as well as changes the kinetics of Potassium Chloride (KCl)-induced intracellular calcium influx in a human fetal brain (HFB) culture, when compared to control. miR-346 increases basal calcium levels, but does not affect KCl-induced calcium transients in our HFB culture. Taken together, these results show that miRNAs can influence both the protein expression as well as calcium homeostasis in different human cell culture models. By reducing levels of proteins implicated in AD pathology and by reversing calcium dysregulation, our results will benefit AD research and generate possibilities for novel therapeutics.