1
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Role of Microglia and Astrocytes in Alzheimer’s Disease: From Neuroinflammation to Ca2+ Homeostasis Dysregulation. Cells 2022; 11:cells11172728. [PMID: 36078138 PMCID: PMC9454513 DOI: 10.3390/cells11172728] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 12/12/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia worldwide, with a complex, poorly understood pathogenesis. Cerebral atrophy, amyloid-β (Aβ) plaques, and neurofibrillary tangles represent the main pathological hallmarks of the AD brain. Recently, neuroinflammation has been recognized as a prominent feature of the AD brain and substantial evidence suggests that the inflammatory response modulates disease progression. Additionally, dysregulation of calcium (Ca2+) homeostasis represents another early factor involved in the AD pathogenesis, as intracellular Ca2+ concentration is essential to ensure proper cellular and neuronal functions. Although growing evidence supports the involvement of Ca2+ in the mechanisms of neurodegeneration-related inflammatory processes, scant data are available on its contribution in microglia and astrocytes functioning, both in health and throughout the AD continuum. Nevertheless, AD-related aberrant Ca2+ signalling in astrocytes and microglia is crucially involved in the mechanisms underpinning neuroinflammatory processes that, in turn, impact neuronal Ca2+ homeostasis and brain function. In this light, we attempted to provide an overview of the current understanding of the interactions between the glia cells-mediated inflammatory responses and the molecular mechanisms involved in Ca2+ homeostasis dysregulation in AD.
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2
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Prista von Bonhorst F, Gall D, Dupont G. Impact of β-Amyloids Induced Disruption of Ca2+ Homeostasis in a Simple Model of Neuronal Activity. Cells 2022; 11:cells11040615. [PMID: 35203266 PMCID: PMC8869902 DOI: 10.3390/cells11040615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 01/25/2023] Open
Abstract
Alzheimer’s disease is characterized by a marked dysregulation of intracellular Ca2+ homeostasis. In particular, toxic β-amyloids (Aβ) perturb the activities of numerous Ca2+ transporters or channels. Because of the tight coupling between Ca2+ dynamics and the membrane electrical activity, such perturbations are also expected to affect neuronal excitability. We used mathematical modeling to systematically investigate the effects of changing the activities of the various targets of Aβ peptides reported in the literature on calcium dynamics and neuronal excitability. We found that the evolution of Ca2+ concentration just below the plasma membrane is regulated by the exchanges with the extracellular medium, and is practically independent from the Ca2+ exchanges with the endoplasmic reticulum. Thus, disruptions of Ca2+ homeostasis interfering with signaling do not affect the electrical properties of the neurons at the single cell level. In contrast, the model predicts that by affecting the activities of L-type Ca2+ channels or Ca2+-activated K+ channels, Aβ peptides promote neuronal hyperexcitability. On the contrary, they induce hypo-excitability when acting on the plasma membrane Ca2+ ATPases. Finally, the presence of pores of amyloids in the plasma membrane can induce hypo- or hyperexcitability, depending on the conditions. These modeling conclusions should help with analyzing experimental observations in which Aβ peptides interfere at several levels with Ca2+ signaling and neuronal activity.
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Affiliation(s)
- Francisco Prista von Bonhorst
- Unit of Theoretical Chronobiology, Faculté des Sciences (CP231), Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium;
| | - David Gall
- Research Laboratory in Human Reproduction, Faculté de Médecine (CP636), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium;
| | - Geneviève Dupont
- Unit of Theoretical Chronobiology, Faculté des Sciences (CP231), Université Libre de Bruxelles (ULB), 1050 Brussels, Belgium;
- Correspondence:
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3
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Exner CRT, Willsey HR. Xenopus leads the way: Frogs as a pioneering model to understand the human brain. Genesis 2021; 59:e23405. [PMID: 33369095 PMCID: PMC8130472 DOI: 10.1002/dvg.23405] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022]
Abstract
From its long history in the field of embryology to its recent advances in genetics, Xenopus has been an indispensable model for understanding the human brain. Foundational studies that gave us our first insights into major embryonic patterning events serve as a crucial backdrop for newer avenues of investigation into organogenesis and organ function. The vast array of tools available in Xenopus laevis and Xenopus tropicalis allows interrogation of developmental phenomena at all levels, from the molecular to the behavioral, and the application of CRISPR technology has enabled the investigation of human disorder risk genes in a higher-throughput manner. As the only major tetrapod model in which all developmental stages are easily manipulated and observed, frogs provide the unique opportunity to study organ development from the earliest stages. All of these features make Xenopus a premier model for studying the development of the brain, a notoriously complex process that demands an understanding of all stages from fertilization to organogenesis and beyond. Importantly, core processes of brain development are conserved between Xenopus and human, underlining the advantages of this model. This review begins by summarizing discoveries made in amphibians that form the cornerstones of vertebrate neurodevelopmental biology and goes on to discuss recent advances that have catapulted our understanding of brain development in Xenopus and in relation to human development and disease. As we engage in a new era of patient-driven gene discovery, Xenopus offers exceptional potential to uncover conserved biology underlying human brain disorders and move towards rational drug design.
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Affiliation(s)
- Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143, USA
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4
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Quantifying the dose-dependent impact of intracellular amyloid beta in a mathematical model of calcium regulation in xenopus oocyte. PLoS One 2021; 16:e0246116. [PMID: 33508037 PMCID: PMC7842920 DOI: 10.1371/journal.pone.0246116] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/13/2021] [Indexed: 12/04/2022] Open
Abstract
Alzheimer’s disease (AD) is a devastating illness affecting over 40 million people worldwide. Intraneuronal rise of amyloid beta in its oligomeric forms (iAβOs), has been linked to the pathogenesis of AD by disrupting cytosolic Ca2+ homeostasis. However, the specific mechanisms of action are still under debate and intense effort is ongoing to improve our understanding of the crucial steps involved in the mechanisms of AβOs toxicity. We report the development of a mathematical model describing a proposed mechanism by which stimulation of Phospholipase C (PLC) by iAβO, triggers production of IP3 with consequent abnormal release of Ca2+ from the endoplasmic reticulum (ER) through activation of IP3 receptor (IP3R) Ca2+ channels. After validating the model using experimental data, we quantify the effects of intracellular rise in iAβOs on model solutions. Our model validates a dose-dependent influence of iAβOs on IP3-mediated Ca2+ signaling. We investigate Ca2+ signaling patterns for small and large iAβOs doses and study the role of various parameters on Ca2+ signals. Uncertainty quantification and partial rank correlation coefficients are used to better understand how the model behaves under various parameter regimes. Our model predicts that iAβO alter IP3R sensitivity to IP3 for large doses. Our analysis also shows that the upstream production of IP3 can influence Aβ-driven solution patterns in a dose-dependent manner. Model results illustrate and confirm the detrimental impact of iAβOs on IP3 signaling.
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5
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Shah SI, Ong HL, Demuro A, Ullah G. PunctaSpecks: A tool for automated detection, tracking, and analysis of multiple types of fluorescently labeled biomolecules. Cell Calcium 2020; 89:102224. [PMID: 32502904 PMCID: PMC7343294 DOI: 10.1016/j.ceca.2020.102224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 01/21/2023]
Abstract
Recent advances in imaging technology and fluorescent probes have made it possible to gain information about the dynamics of subcellular processes at unprecedented spatiotemporal scales. Unfortunately, a lack of automated tools to efficiently process the resulting imaging data encoding fine details of the biological processes remains a major bottleneck in utilizing the full potential of these powerful experimental techniques. Here we present a computational tool, called PunctaSpecks, that can characterize fluorescence signals arising from a wide range of biological molecules under normal and pathological conditions. Among other things, the program can calculate the number, areas, life-times, and amplitudes of fluorescence signals arising from multiple sources, track diffusing fluorescence sources like moving mitochondria, and determine the overlap probability of two processes or organelles imaged using indicator dyes of different colors. We have tested PunctaSpecks on synthetic time-lapse movies containing mobile fluorescence objects of various sizes, mimicking the activity of biomolecules. The robustness of the software is tested by varying the level of noise along with random but known pattern of appearing, disappearing, and movement of these objects. Next, we use PunctaSpecks to characterize protein-protein interaction involved in store-operated Ca2+ entry through the formation and activation of plasma membrane-bound ORAI1 channel and endoplasmic reticulum membrane-bound stromal interaction molecule (STIM), the evolution of inositol 1,4,5-trisphosphate (IP3)-induced Ca2+ signals from sub-micrometer size local events into global waves in human cortical neurons, and the activity of Alzheimer's disease-associated β amyloid pores in the plasma membrane. The tool can also be used to study other dynamical processes imaged through fluorescence molecules. The open source algorithm allows for extending the program to analyze more than two types of biomolecules visualized using markers of different colors.
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Affiliation(s)
| | - Hwei Ling Ong
- Secretory Physiology Section, NIDCR, NIH, Bethesda, MD, 20892,USA
| | - Angelo Demuro
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33647, USA.
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6
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Lukiw WJ, Li W, Bond T, Zhao Y. Facilitation of Gastrointestinal (GI) Tract Microbiome-Derived Lipopolysaccharide (LPS) Entry Into Human Neurons by Amyloid Beta-42 (Aβ42) Peptide. Front Cell Neurosci 2019; 13:545. [PMID: 31866832 PMCID: PMC6908466 DOI: 10.3389/fncel.2019.00545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/22/2019] [Indexed: 01/01/2023] Open
Abstract
Human gastrointestinal (GI)-tract microbiome-derived lipopolysaccharide (LPS): (i) has been recently shown to target, accumulate within, and eventually encapsulate neuronal nuclei of the human central nervous system (CNS) in Alzheimer’s disease (AD) brain; and (ii) this action appears to impede and restrict the outward flow of genetic information from neuronal nuclei. It has previously been shown that in LPS-encased neuronal nuclei in AD brain there is a specific disruption in the output and expression of two AD-relevant, neuron-specific markers encoding the cytoskeletal neurofilament light (NF-L) chain protein and the synaptic phosphoprotein synapsin-1 (SYN1) involved in the regulation of neurotransmitter release. The biophysical mechanisms involved in the facilitation of the targeting of LPS to neuronal cells and nuclei and eventual nuclear envelopment and functional disruption are not entirely clear. In this “Perspectives article” we discuss current advances, and consider future directions in this research area, and provide novel evidence in human neuronal-glial (HNG) cells in primary culture that the co-incubation of LPS with amyloid-beta 42 (Aβ42) peptide facilitates the association of LPS with neuronal cells. These findings: (i) support a novel pathogenic role for Aβ42 peptides in neurons via the formation of pores across the nuclear membrane and/or a significant biophysical disruption of the neuronal nuclear envelope; and (ii) advance the concept that the Aβ42 peptide-facilitated entry of LPS into brain neurons, accession of neuronal nuclei, and down-regulation of neuron-specific components such as NF-L and SYN1 may contribute significantly to neuropathological deficits as are characteristically observed in AD-affected brain.
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Affiliation(s)
- Walter J Lukiw
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Ophthalmology, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Neurology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Wenhong Li
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Pharmacology, School of Pharmacy, Jiangxi University of Traditional Chinese Medicine (TCM), Nanchang, China
| | - Taylor Bond
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Yuhai Zhao
- LSU Neuroscience Center, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Department of Anatomy and Cell Biology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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7
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Shah SI, Demuro A, Mak DOD, Parker I, Pearson JE, Ullah G. TraceSpecks: A Software for Automated Idealization of Noisy Patch-Clamp and Imaging Data. Biophys J 2019; 115:9-21. [PMID: 29972815 DOI: 10.1016/j.bpj.2018.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/15/2018] [Accepted: 06/04/2018] [Indexed: 10/28/2022] Open
Abstract
Experimental records of single molecules or ion channels from fluorescence microscopy and patch-clamp electrophysiology often include high-frequency noise and baseline fluctuations that are not generated by the system under investigation and have to be removed. Moreover, multiple channels or conductance levels can be present at a time in the data that need to be quantified to accurately understand the behavior of the system. Manual procedures for removing these fluctuations and extracting conducting states or multiple channels are laborious, prone to subjective bias, and likely to hinder the processing of often very large data sets. We introduce a maximal likelihood formalism for separating signal from a noisy and drifting background such as fluorescence traces from imaging of elementary Ca2+ release events called puffs arising from clusters of channels, and patch-clamp recordings of ion channels. Parameters such as the number of open channels or conducting states, noise level, and background signal can all be optimized using the expectation-maximization algorithm. We implement our algorithm following the Baum-Welch approach to expectation-maximization in the portable Java language with a user-friendly graphical interface and test the algorithm on both synthetic and experimental data from the patch-clamp electrophysiology of Ca2+ channels and fluorescence microscopy of a cluster of Ca2+ channels and Ca2+ channels with multiple conductance levels. The resulting software is accurate, fast, and provides detailed information usually not available through manual analysis. Options for visual inspection of the raw and processed data with key parameters are provided, in addition to a range of statistics such as the mean open probabilities, mean open times, mean close times, dwell-time distributions for different number of channels open or conductance levels, amplitude distribution of all opening events, and number of transitions between different number of open channels or conducting levels in asci format with a single click.
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Affiliation(s)
| | - Angelo Demuro
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, California
| | - Don-On Daniel Mak
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ian Parker
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, California; Department of Physiology and Biophysics, University of California, Irvine, Irvine, California
| | - John E Pearson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, Florida.
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8
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Mesa-Herrera F, Taoro-González L, Valdés-Baizabal C, Diaz M, Marín R. Lipid and Lipid Raft Alteration in Aging and Neurodegenerative Diseases: A Window for the Development of New Biomarkers. Int J Mol Sci 2019; 20:E3810. [PMID: 31382686 PMCID: PMC6696273 DOI: 10.3390/ijms20153810] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/1970] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/13/2022] Open
Abstract
Lipids in the brain are major components playing structural functions as well as physiological roles in nerve cells, such as neural communication, neurogenesis, synaptic transmission, signal transduction, membrane compartmentalization, and regulation of gene expression. Determination of brain lipid composition may provide not only essential information about normal brain functioning, but also about changes with aging and diseases. Indeed, deregulations of specific lipid classes and lipid homeostasis have been demonstrated in neurodegenerative disorders such as Alzheimer's disease (AD) and Parkinson's disease (PD). Furthermore, recent studies have shown that membrane microdomains, named lipid rafts, may change their composition in correlation with neuronal impairment. Lipid rafts are key factors for signaling processes for cellular responses. Lipid alteration in these signaling platforms may correlate with abnormal protein distribution and aggregation, toxic cell signaling, and other neuropathological events related with these diseases. This review highlights the manner lipid changes in lipid rafts may participate in the modulation of neuropathological events related to AD and PD. Understanding and characterizing these changes may contribute to the development of novel and specific diagnostic and prognostic biomarkers in routinely clinical practice.
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Affiliation(s)
- Fátima Mesa-Herrera
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, Edaphology and Geology
| | - Lucas Taoro-González
- Laboratory of Cellular Neurobiology, Department of Basic Medical Sciences, Section of Medicine, Faculty of Health Sciences, University of La Laguna, Sta. Cruz de Tenerife 38200, Spain
| | - Catalina Valdés-Baizabal
- Laboratory of Cellular Neurobiology, Department of Basic Medical Sciences, Section of Medicine, Faculty of Health Sciences, University of La Laguna, Sta. Cruz de Tenerife 38200, Spain
| | - Mario Diaz
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, Edaphology and Geology
- Associate Research Unit ULL-CSIC "Membrane Physiology and Biophysics in Neurodegenerative and Cancer Diseases", University of La Laguna, Sta. Cruz de Tenerife 38200, Spain
| | - Raquel Marín
- Laboratory of Cellular Neurobiology, Department of Basic Medical Sciences, Section of Medicine, Faculty of Health Sciences, University of La Laguna, Sta. Cruz de Tenerife 38200, Spain.
- Associate Research Unit ULL-CSIC "Membrane Physiology and Biophysics in Neurodegenerative and Cancer Diseases", University of La Laguna, Sta. Cruz de Tenerife 38200, Spain.
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9
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Arispe N, De Maio A. Memory Loss and the Onset of Alzheimer's Disease Could Be Under the Control of Extracellular Heat Shock Proteins. J Alzheimers Dis 2019; 63:927-934. [PMID: 29689729 DOI: 10.3233/jad-180161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Alzheimer's disease (AD) is a major contemporary and escalating malady in which amyloid-β (Aβ) peptides are the most likely causative agent. Aβ peptides spontaneously tend to aggregate in extracellular fluids following a progression from a monomeric state, through intermediate forms, ending in amyloid fibers and plaques. It is generally accepted now that the neurotoxic agents leading to cellular death, memory loss, and other AD characteristics are the Aβ intermediate aggregated states. However, Aβ peptides are continuously produced, released into the extracellular space, and rapidly cleared from healthy brains. Coincidentally, members of the heat shock proteins (hsp) family are present in the extracellular medium of healthy cells and body fluids, opening the possibility that hsps and Aβ could meet and interact in the extracellular milieu of the brain. In this perspective and reflection article, we place our investigation showing that the presence of Hsp70s mitigate the formation of low molecular weight Aβ peptide oligomers resulting in a reduction of cellular toxicity, in context of the current understanding of the disease. We propose that it may be an inverse relationship between the presence of Hsp70, the stage of Aβ oligomers, neurotoxicity, and the incidence of AD, particularly since the expression and circulating levels of hsp decrease with aging. Combining these observations, we propose that changes in the dynamics of Hsp70s and Aβ concentrations in the circulating brain fluids during aging defines the control of the formation of Aβ toxic aggregates, thus determining the conditions for neuron degeneration and the incidence of AD.
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Affiliation(s)
- Nelson Arispe
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Antonio De Maio
- Department of Surgery and Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA, USA
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10
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Tamano H, Oneta N, Shioya A, Adlard PA, Bush AI, Takeda A. In vivo synaptic activity-independent co-uptakes of amyloid β 1-42 and Zn 2+ into dentate granule cells in the normal brain. Sci Rep 2019; 9:6498. [PMID: 31019269 PMCID: PMC6482136 DOI: 10.1038/s41598-019-43012-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/10/2019] [Indexed: 02/07/2023] Open
Abstract
Neuronal amyloid β1–42 (Aβ1–42) accumulation is considered an upstream event in Alzheimer’s disease pathogenesis. Here we report the mechanism on synaptic activity-independent Aβ1–42 uptake in vivo. When Aβ1–42 uptake was compared in hippocampal slices after incubating with Aβ1–42, In vitro Aβ1–42 uptake was preferentially high in the dentate granule cell layer in the hippocampus. Because the rapid uptake of Aβ1–42 with extracellular Zn2+ is essential for Aβ1–42-induced cognitive decline in vivo, the uptake mechanism was tested in dentate granule cells in association with synaptic activity. In vivo rapid uptake of Aβ1–42 was not modified in the dentate granule cell layer after co-injection of Aβ1–42 and tetrodotoxin, a Na+ channel blocker, into the dentate gyrus. Both the rapid uptake of Aβ1–42 and Zn2+ into the dentate granule cell layer was not modified after co-injection of CNQX, an AMPA receptor antagonist, which blocks extracellular Zn2+ influx, Both the rapid uptake of Aβ1–42 and Zn2+ into the dentate granule cell layer was not also modified after either co-injection of chlorpromazine or genistein, an endocytic repressor. The present study suggests that Aβ1–42 and Zn2+ are synaptic activity-independently co-taken up into dentate granule cells in the normal brain and the co-uptake is preferential in dentate granule cells in the hippocampus. We propose a hypothesis that Zn-Aβ1–42 oligomers formed in the extracellular compartment are directly incorporated into neuronal plasma membranes and form Zn2+-permeable ion channels.
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Affiliation(s)
- Haruna Tamano
- Department of Neurophysiology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Naoya Oneta
- Department of Neurophysiology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Aoi Shioya
- Department of Neurophysiology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Paul A Adlard
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ashley I Bush
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Atsushi Takeda
- Department of Neurophysiology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
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11
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Nenni MJ, Fisher ME, James-Zorn C, Pells TJ, Ponferrada V, Chu S, Fortriede JD, Burns KA, Wang Y, Lotay VS, Wang DZ, Segerdell E, Chaturvedi P, Karimi K, Vize PD, Zorn AM. Xenbase: Facilitating the Use of Xenopus to Model Human Disease. Front Physiol 2019; 10:154. [PMID: 30863320 PMCID: PMC6399412 DOI: 10.3389/fphys.2019.00154] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/08/2019] [Indexed: 01/02/2023] Open
Abstract
At a fundamental level most genes, signaling pathways, biological functions and organ systems are highly conserved between man and all vertebrate species. Leveraging this conservation, researchers are increasingly using the experimental advantages of the amphibian Xenopus to model human disease. The online Xenopus resource, Xenbase, enables human disease modeling by curating the Xenopus literature published in PubMed and integrating these Xenopus data with orthologous human genes, anatomy, and more recently with links to the Online Mendelian Inheritance in Man resource (OMIM) and the Human Disease Ontology (DO). Here we review how Xenbase supports disease modeling and report on a meta-analysis of the published Xenopus research providing an overview of the different types of diseases being modeled in Xenopus and the variety of experimental approaches being used. Text mining of over 50,000 Xenopus research articles imported into Xenbase from PubMed identified approximately 1,000 putative disease- modeling articles. These articles were manually assessed and annotated with disease ontologies, which were then used to classify papers based on disease type. We found that Xenopus is being used to study a diverse array of disease with three main experimental approaches: cell-free egg extracts to study fundamental aspects of cellular and molecular biology, oocytes to study ion transport and channel physiology and embryo experiments focused on congenital diseases. We integrated these data into Xenbase Disease Pages to allow easy navigation to disease information on external databases. Results of this analysis will equip Xenopus researchers with a suite of experimental approaches available to model or dissect a pathological process. Ideally clinicians and basic researchers will use this information to foster collaborations necessary to interrogate the development and treatment of human diseases.
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Affiliation(s)
- Mardi J Nenni
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Malcolm E Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Virgilio Ponferrada
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Stanley Chu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Joshua D Fortriede
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Kevin A Burns
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Ying Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Vaneet S Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Dong Zhou Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Erik Segerdell
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, United States
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12
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Shah SI, Smith M, Swaminathan D, Parker I, Ullah G, Demuro A. CellSpecks: A Software for Automated Detection and Analysis of Calcium Channels in Live Cells. Biophys J 2018; 115:2141-2151. [PMID: 30447989 DOI: 10.1016/j.bpj.2018.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/27/2018] [Accepted: 10/22/2018] [Indexed: 02/01/2023] Open
Abstract
To couple the fidelity of patch-clamp recording with a more high-throughput screening capability, we pioneered a, to our knowledge, novel approach to single-channel recording that we named "optical patch clamp." By using highly sensitive fluorescent Ca2+ indicator dyes in conjunction with total internal fluorescence microscopy techniques, we monitor Ca2+ flux through individual Ca2+-permeable channels. This approach provides information about channel gating analogous to patch-clamp recording at a time resolution of ∼2 ms with the additional advantage of being massively parallel, providing simultaneous and independent recording from thousands of channels in the native environment. However, manual analysis of the data generated by this technique presents severe challenges because a video recording can include many thousands of frames. To overcome this bottleneck, we developed an image processing and analysis framework called CellSpecks capable of detecting and fully analyzing the kinetics of ion channels within a video sequence. By using randomly generated synthetic data, we tested the ability of CellSpecks to rapidly and efficiently detect and analyze the activity of thousands of ion channels, including openings for a few milliseconds. Here, we report the use of CellSpecks for the analysis of experimental data acquired by imaging muscle nicotinic acetylcholine receptors and the Alzheimer's disease-associated amyloid β pores with multiconductance levels in the plasma membrane of Xenopus laevis oocytes. We show that CellSpecks can accurately and efficiently generate location maps and create raw and processed fluorescence time traces; histograms of mean open times, mean close times, open probabilities, durations, and maximal amplitudes; and a "channel chip" showing the activity of all channels as a function of time. Although we specifically illustrate the application of CellSpecks for analyzing data from Ca2+ channels, it can be easily customized to analyze other spatially and temporally localized signals.
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Affiliation(s)
| | | | - Divya Swaminathan
- Department of Neurobiology and Behavior,University of California Irvine, Irvine, California
| | - Ian Parker
- Department of Neurobiology and Behavior,University of California Irvine, Irvine, California; Department of Physiology and Biophysics, University of California Irvine, Irvine, California
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, Florida.
| | - Angelo Demuro
- Department of Neurobiology and Behavior,University of California Irvine, Irvine, California.
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13
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Toglia P, Demuro A, Mak DOD, Ullah G. Data-driven modeling of mitochondrial dysfunction in Alzheimer's disease. Cell Calcium 2018; 76:23-35. [PMID: 30248575 DOI: 10.1016/j.ceca.2018.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023]
Abstract
Intracellular accumulation of oligomeric forms of β amyloid (Aβ) are now believed to play a key role in the earliest phase of Alzheimer's disease (AD) as their rise correlates well with the early symptoms of the disease. Extensive evidence points to impaired neuronal Ca2+ homeostasis as a direct consequence of the intracellular Aβ oligomers. However, little is known about the downstream effects of the resulting Ca2+ rise on the many intracellular Ca2+-dependent pathways. Here we use multiscale modeling in conjunction with patch-clamp electrophysiology of single inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) and fluorescence imaging of whole-cell Ca2+ response, induced by exogenously applied intracellular Aβ42 oligomers to show that Aβ42 inflicts cytotoxicity by impairing mitochondrial function. Driven by patch-clamp experiments, we first model the kinetics of IP3R, which is then extended to build a model for the whole-cell Ca2+ signals. The whole-cell model is then fitted to fluorescence signals to quantify the overall Ca2+ release from the endoplasmic reticulum by intracellular Aβ42 oligomers through G-protein-mediated stimulation of IP3 production. The estimated IP3 concentration as a function of intracellular Aβ42 content together with the whole-cell model allows us to show that Aβ42 oligomers impair mitochondrial function through pathological Ca2+ uptake and the resulting reduced mitochondrial inner membrane potential, leading to an overall lower ATP and increased production of reactive oxygen species and H2O2. We further show that mitochondrial function can be restored by the addition of Ca2+ buffer EGTA, in accordance with the observed abrogation of Aβ42 cytotoxicity by EGTA in our live cells experiments.
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Affiliation(s)
- Patrick Toglia
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Angelo Demuro
- Department of Neurobiology and Behavior and Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Don-On Daniel Mak
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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14
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Latulippe J, Lotito D, Murby D. A mathematical model for the effects of amyloid beta on intracellular calcium. PLoS One 2018; 13:e0202503. [PMID: 30133494 PMCID: PMC6105003 DOI: 10.1371/journal.pone.0202503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 08/03/2018] [Indexed: 12/21/2022] Open
Abstract
The accumulation of Alzheimer's disease (AD) associated Amyloid beta (Aβ) oligomers can trigger aberrant intracellular calcium (Ca2+) levels by disrupting the intrinsic Ca2+ regulatory mechanism within cells. These disruptions can cause changes in homeostasis levels that can have detrimental effects on cell function and survival. Although studies have shown that Aβ can interfere with various Ca2+ fluxes, the complexity of these interactions remains elusive. We have constructed a mathematical model that simulates Ca2+ patterns under the influence of Aβ. Our simulations shows that Aβ can increase regions of mixed-mode oscillations leading to aberrant signals under various conditions. We investigate how Aβ affects individual flux contributions through inositol triphosphate (IP3) receptors, ryanodine receptors, and membrane pores. We demonstrate that controlling for the ryanodine receptor's maximal kinetic reaction rate may provide a biophysical way of managing aberrant Ca2+ signals. The influence of a dynamic model for IP3 production is also investigated under various conditions as well as the impact of changes in membrane potential. Our model is one of the first to investigate the effects of Aβ on a variety of cellular mechanisms providing a base modeling scheme from which further studies can draw on to better understand Ca2+ regulation in an AD environment.
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Affiliation(s)
- Joe Latulippe
- Mathematics Department, Norwich University, Northfield, Vermont, United States of America
- * E-mail:
| | - Derek Lotito
- Chemistry and Biochemistry Department, Norwich University, Northfield, Vermont, United States of America
| | - Donovan Murby
- Mathematics Department, Norwich University, Northfield, Vermont, United States of America
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15
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Toglia P, Ullah G, Pearson JE. Analyzing optical imaging of Ca 2+ signals via TIRF microscopy: The limits on resolution due to chemical rates and depth of the channels. Cell Calcium 2017; 67:65-73. [PMID: 29029792 DOI: 10.1016/j.ceca.2017.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 11/17/2022]
Abstract
High resolution total internal reflection (TIRF) microscopy (TIRFM) together with detailed computational modeling provides a powerful approach towards the understanding of a wide range of Ca2+ signals mediated by the ubiquitous inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) channel. Exploiting this fruitful collaboration further requires close agreement between the models and observations. However, elementary Ca2+ release events, puffs, imaged through TIRFM do not show the rapid single-channel openings and closings during and between puffs as are present in simulated puffs using data-driven single channel models. TIRFM also shows a rapid equilibration of 10ms after a channel opens or closes which is not achievable in simulation using standard Ca2+ diffusion coefficients and reaction rates between indicator dye and Ca2+. Furthermore, TIRFM imaging cannot decipher the depth of the channel with respect to the microscope, which will affect the change in fluorescence that the microscope detects, thereby affecting its sensitivity to fast single-channel activity. Using the widely used Ca2+ diffusion coefficients and reaction rates, our simulations show equilibration rates that are eight times slower than TIRFM imaging. We show that to get equilibrium rates consistent with observed values, the diffusion coefficients and reaction rates have to be significantly higher than the values reported in the literature, and predict the channel depth to be 200-250nm. Finally, we show that with the addition of noise, short events due to 1-2ms opening and closing of channels that are observed in computational models can be missed in TIRFM.
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Affiliation(s)
- Patrick Toglia
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - John E Pearson
- T-6 Theoretical Biology and Biophysics Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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16
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Sater AK, Moody SA. Using Xenopus to understand human disease and developmental disorders. Genesis 2017; 55. [PMID: 28095616 DOI: 10.1002/dvg.22997] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 11/14/2016] [Indexed: 02/03/2023]
Abstract
Model animals are crucial to biomedical research. Among the commonly used model animals, the amphibian, Xenopus, has had tremendous impact because of its unique experimental advantages, cost effectiveness, and close evolutionary relationship with mammals as a tetrapod. Over the past 50 years, the use of Xenopus has made possible many fundamental contributions to biomedicine, and it is a cornerstone of research in cell biology, developmental biology, evolutionary biology, immunology, molecular biology, neurobiology, and physiology. The prospects for Xenopus as an experimental system are excellent: Xenopus is uniquely well-suited for many contemporary approaches used to study fundamental biological and disease mechanisms. Moreover, recent advances in high throughput DNA sequencing, genome editing, proteomics, and pharmacological screening are easily applicable in Xenopus, enabling rapid functional genomics and human disease modeling at a systems level.
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Affiliation(s)
- Amy K Sater
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Sally A Moody
- Department of Anatomy and Regenerative Biology, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia
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17
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Anwar H. Capturing intracellular Ca 2+ dynamics in computational models of neurodegenerative diseases. ACTA ACUST UNITED AC 2017; 19:37-42. [PMID: 28983320 DOI: 10.1016/j.ddmod.2017.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many signaling pathways crucial for homeostatic regulation, synaptic plasticity, apoptosis and immune response depend on Ca2+. Ca2+ dysregulation disrupts normal function of neurons and neuronal networks. This causes severe motor and cognitive disabilities. Understanding how Ca2+ dysregulation triggers disease onset and progression, and affects downstream processes, can help identify targets for treatments. Because of intermingling of molecular pathways, dissecting the role of individual mechanisms and establishing causality is very challenging. Computational models provide a way to decipher these processes. I review some computational models with Ca2+ dynamics to illustrate their predictive power, and note where extending those models to capture multiscale interaction of Ca2+ dependent molecular pathways can be useful for therapeutic and drug discovery purposes.
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Affiliation(s)
- Haroon Anwar
- Department of Biological Sciences, New Jersey Institute of Technology, 100 Summit St, University Heights, Newark, NJ 07102, United States
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18
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Perez C, Ziburkus J, Ullah G. Analyzing and Modeling the Dysfunction of Inhibitory Neurons in Alzheimer's Disease. PLoS One 2016; 11:e0168800. [PMID: 28036398 PMCID: PMC5201300 DOI: 10.1371/journal.pone.0168800] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 12/05/2016] [Indexed: 12/15/2022] Open
Abstract
Alzheimer's disease (AD) is characterized by the abnormal proteolytic processing of amyloid precursor protein, resulting in increased production of a self-aggregating form of beta amyloid (Aβ). Several lines of work on AD patients and transgenic mice with high Aβ levels exhibit altered rhythmicity, aberrant neuronal network activity and hyperexcitability reflected in clusters of hyperactive neurons, and spontaneous epileptic activity. Recent studies highlight that abnormal accumulation of Aβ changes intrinsic properties of inhibitory neurons, which is one of the main reasons underlying the impaired network activity. However, specific cellular mechanisms leading to interneuronal dysfunction are not completely understood. Using extended Hodgkin-Huxley (HH) formalism in conjunction with patch-clamp experiments, we investigate the mechanisms leading to the impaired activity of interneurons. Our detailed analysis indicates that increased Na+ leak explains several observations in inhibitory neurons, including their failure to reliably produce action potentials, smaller action potential amplitude, increased resting membrane potential, and higher membrane depolarization in response to a range of stimuli in a model of APPSWE/PSEN1DeltaE9 (APdE9) AD mice as compared to age-matched control mice. While increasing the conductance of hyperpolarization activated cyclic nucleotide-gated (HCN) ion channel could account for most of the observations, the extent of increase required to reproduce these observations render such changes unrealistic. Furthermore, increasing the conductance of HCN does not account for the observed changes in depolarizability of interneurons from APdE9 mice as compared to those from NTG mice. None of the other pathways tested could lead to all observations about interneuronal dysfunction. Thus we conclude that upregulated sodium leak is the most likely source of impaired interneuronal function.
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Affiliation(s)
- Carlos Perez
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
| | - Jokubas Ziburkus
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, United States of America
| | - Ghanim Ullah
- Department of Physics, University of South Florida, Tampa, FL 33620, United States of America
- * E-mail:
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19
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Briggs CA, Chakroborty S, Stutzmann GE. Emerging pathways driving early synaptic pathology in Alzheimer's disease. Biochem Biophys Res Commun 2016; 483:988-997. [PMID: 27659710 DOI: 10.1016/j.bbrc.2016.09.088] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/13/2016] [Accepted: 09/17/2016] [Indexed: 11/25/2022]
Abstract
The current state of the AD research field is highly dynamic is some respects, while seemingly stagnant in others. Regarding the former, our current lack of understanding of initiating disease mechanisms, the absence of effective treatment options, and the looming escalation of AD patients is energizing new research directions including a much-needed re-focusing on early pathogenic mechanisms, validating novel targets, and investigating relevant biomarkers, among other exciting new efforts to curb disease progression and foremost, preserve memory function. With regard to the latter, the recent disappointing series of failed Phase III clinical trials targeting Aβ and APP processing, in concert with poor association between brain Aβ levels and cognitive function, have led many to call for a re-evaluation of the primacy of the amyloid cascade hypothesis. In this review, we integrate new insights into one of the earliest described signaling abnormalities in AD pathogenesis, namely intracellular Ca2+ signaling disruptions, and focus on its role in driving synaptic deficits - which is the feature that does correlate with AD-associated memory loss. Excess Ca2+release from intracellular stores such as the endoplasmic reticulum (ER) has been well-described in cellular and animal models of AD, as well as human patients, and here we expand upon recent developments in ER-localized release channels such as the IP3R and RyR, and the recent emphasis on RyR2. Consistent with ER Ca2+ mishandling in AD are recent findings implicating aspects of SOCE, such as STIM2 function, and TRPC3 and TRPC6 levels. Other Ca2+-regulated organelles important in signaling and protein handling are brought into the discussion, with new perspectives on lysosomal regulation. These early signaling abnormalities are discussed in the context of synaptic pathophysiology and disruptions in synaptic plasticity with a particular emphasis on short-term plasticity deficits. Overall, we aim to update and expand the list of early neuronal signaling abnormalities implicated in AD pathogenesis, identify specific channels and organelles involved, and link these to proximal synaptic impairments driving the memory loss in AD. This is all within the broader goal of identifying novel therapeutic targets to preserve cognitive function in AD.
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Affiliation(s)
- Clark A Briggs
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Shreaya Chakroborty
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Grace E Stutzmann
- Department of Neuroscience, Rosalind Franklin University of Medicine and Science, The Chicago Medical School, North Chicago, IL 60064, USA.
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20
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Ultra rapid in vivo screening for anti-Alzheimer anti-amyloid drugs. Sci Rep 2016; 6:23349. [PMID: 27000658 PMCID: PMC4802339 DOI: 10.1038/srep23349] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
More than 46 million people worldwide suffer from Alzheimer’s disease. A
large number of potential treatments have been proposed; among these, the inhibition
of the aggregation of amyloid β-peptide (Aβ), considered one
of the main culprits in Alzheimer’s disease. Limitations in monitoring
the aggregation of Aβ in cells and tissues restrict the screening of
anti-amyloid drugs to in vitro studies in most cases. We have developed a
simple but powerful method to track Aβ aggregation in vivo in
real-time, using bacteria as in vivo amyloid reservoir. We use the specific
amyloid dye Thioflavin-S (Th-S) to stain bacterial inclusion bodies (IBs), in this
case mainly formed of Aβ in amyloid conformation. Th-S binding to
amyloids leads to an increment of fluorescence that can be monitored. The
quantification of the Th-S fluorescence along the time allows tracking
Aβ aggregation and the effect of potential anti-aggregating agents.
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