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Zu L, Wang X, Liu P, Xie J, Zhang X, Liu W, Li Z, Zhang S, Li K, Giannetti A, Bi W, Chiavaioli F, Shi L, Guo T. Ultrasensitive and Multiple Biomarker Discrimination for Alzheimer's Disease via Plasmonic & Microfluidic Sensing Technologies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308783. [PMID: 38509587 PMCID: PMC11200013 DOI: 10.1002/advs.202308783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/03/2024] [Indexed: 03/22/2024]
Abstract
As the population ages, the worldwide prevalence of Alzheimer's disease (AD) as the most common dementia in the elderly is increasing dramatically. However, a long-term challenge is to achieve rapid and accurate early diagnosis of AD by detecting hallmarks such as amyloid beta (Aβ42). Here, a multi-channel microfluidic-based plasmonic fiber-optic biosensing platform is established for simultaneous detection and differentiation of multiple AD biomarkers. The platform is based on a gold-coated, highly-tilted fiber Bragg grating (TFBG) and a custom-developed microfluidics. TFBG excites a high-density, narrow-cladding-mode spectral comb that overlaps with the broad absorption of surface plasmons for high-precision interrogation, enabling ultrasensitive monitoring of analytes. In situ detection and in-parallel discrimination of different forms of Aβ42 in cerebrospinal fluid (CSF) are successfully demonstrated with a detection of limit in the range of ≈30-170 pg mL-1, which is one order of magnitude below the clinical cut-off level in AD onset, providing high detection sensitivity for early diagnosis of AD. The integration of the TFBG sensor with multi-channel microfluidics enables simultaneous detection of multiple biomarkers using sub-µL sample volumes, as well as combining initial binding rate and real-time response time to differentiate between multiple biomarkers in terms of binding kinetics. With the advantages of multi-parameter, low consumption, and highly sensitive detection, the sensor represents an urgently needed potentials for large-scale diagnosis of diseases at early stage.
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Affiliation(s)
- Lijiao Zu
- Institute of Photonics TechnologyJinan UniversityGuangzhou510632China
| | - Xicheng Wang
- Institute of Photonics TechnologyJinan UniversityGuangzhou510632China
| | - Peng Liu
- State Key Laboratory of Bioactive Molecules and Druggability AssessmentJNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan UniversityGuangzhou510632China
| | - Jiwei Xie
- Institute of Photonics TechnologyJinan UniversityGuangzhou510632China
| | - Xuejun Zhang
- Center for Advanced Biomedical Imaging and Photonics, Division of Gastroenterology, Department of MedicineBeth Israel Deaconess Medical Center, Harvard UniversityBoston02215USA
| | - Weiru Liu
- Institute of Photonics TechnologyJinan UniversityGuangzhou510632China
| | - Zhencheng Li
- Institute of Photonics TechnologyJinan UniversityGuangzhou510632China
| | - Shiqing Zhang
- State Key Laboratory of Bioactive Molecules and Druggability AssessmentJNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan UniversityGuangzhou510632China
| | - Kaiwei Li
- Institute of Photonics TechnologyJinan UniversityGuangzhou510632China
| | - Ambra Giannetti
- National Research Council of Italy (CNR), Institute of Applied Physics “Nello Carrara” (IFAC)Sesto Fiorentino50019Italy
| | - Wei Bi
- Department of NeurologyThe First Affiliated Hospital of Jinan UniversityGuangzhou510632China
| | - Francesco Chiavaioli
- National Research Council of Italy (CNR), Institute of Applied Physics “Nello Carrara” (IFAC)Sesto Fiorentino50019Italy
| | - Lei Shi
- State Key Laboratory of Bioactive Molecules and Druggability AssessmentJNU‐HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan UniversityGuangzhou510632China
| | - Tuan Guo
- Institute of Photonics TechnologyJinan UniversityGuangzhou510632China
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2
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Ruttenberg SM, Nowick JS. A turn for the worse: Aβ β-hairpins in Alzheimer's disease. Bioorg Med Chem 2024; 105:117715. [PMID: 38615460 DOI: 10.1016/j.bmc.2024.117715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
Amyloid-β (Aβ) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aβ peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aβ oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aβ oligomers, many of which consist of molecules of Aβ in β-hairpin conformations. β-Hairpins are intramolecular antiparallel β-sheets composed of two β-strands connected by a loop or turn. Three decades of research suggests that Aβ peptides form several different β-hairpin conformations, some of which are building blocks of toxic Aβ oligomers. The insights from these studies are currently being used to design anti-Aβ antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aβ may be more successful at treating AD than antibodies designed to target linear epitopes of Aβ or fibrillar Aβ. Aβ β-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aβ. This review summarizes the research on β-hairpins in Aβ peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.
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Affiliation(s)
- Sarah M Ruttenberg
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States.
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Maity B, Kameyama S, Tian J, Pham TT, Abe S, Chatani E, Murata K, Ueno T. Fusion of amyloid beta with ferritin yields an isolated oligomeric beta-sheet-rich aggregate inside the ferritin cage. Biomater Sci 2024; 12:2408-2417. [PMID: 38511491 DOI: 10.1039/d4bm00173g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Alzheimer's disease is a severe brain condition caused by the formation of amyloid plaques composed of amyloid beta (Aβ) peptides. These peptides form oligomers, protofibrils, and fibrils before deposition into amyloid plaques. Among these intermediates, Aβ oligomers (AβOs) were found to be the most toxic and therefore an appealing target for drug development and understanding their role in the disease. However, precise isolation and characterization of AβOs have proven challenging because AβOs tend to aggregate and form heterogeneous mixtures in solution. As a solution, we genetically fused the Aβ peptide with a ferritin monomer. Such fusion allowed the encapsulation of precisely 24 Aβ peptides inside the 24-mer ferritin cage. Using high-speed atomic force microscopy (HS-AFM), we disassembled ferritin and directly visualized the Aβ core enclosed within the cage. The thioflavin-T assay (ThT) and attenuated total reflection infrared spectroscopy (ATR-IR) revealed the presence of a β-sheet structure in the encapsulated oligomeric aggregate. Gallic acid, an amyloid inhibitor, can inhibit the fluorescence of ThT bound AβOs. Our approach represents a significant advancement in the isolation and characterization of β-sheet rich AβOs and is expected to be useful for future studies of other disordered peptides such as α-synuclein and tau.
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Affiliation(s)
- Basudev Maity
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Shiori Kameyama
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Jiaxin Tian
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Thuc Toan Pham
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
| | - Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Hyogo 657-8501, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, 444-8585, Japan
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, 4259, Midori-ku, Yokohama 226 8501, Japan.
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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4
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Chen A, Shea D, Daggett V. Performance of SOBA-AD blood test in discriminating Alzheimer's disease patients from cognitively unimpaired controls in two independent cohorts. Sci Rep 2024; 14:7946. [PMID: 38575622 PMCID: PMC10995183 DOI: 10.1038/s41598-024-57107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024] Open
Abstract
Amyloid-beta (Aβ) toxic oligomers are critical early players in the molecular pathology of Alzheimer's disease (AD). We have developed a Soluble Oligomer Binding Assay (SOBA-AD) for detection of these Aβ oligomers that contain α-sheet secondary structure that discriminates plasma samples from patients on the AD continuum from non-AD controls. We tested 265 plasma samples from two independent cohorts to investigate the performance of SOBA-AD. Testing was performed at two different sites, with different personnel, reagents, and instrumentation. Across two cohorts, SOBA-AD discriminated AD patients from cognitively unimpaired (CU) subjects with 100% sensitivity, > 95% specificity, and > 98% area under the curve (AUC) (95% CI 0.95-1.00). A SOBA-AD positive readout, reflecting α-sheet toxic oligomer burden, was found in AD patients, and not in controls, providing separation of the two populations, aside from 5 SOBA-AD positive controls. Based on an earlier SOBA-AD study, the Aβ oligomers detected in these CU subjects may represent preclinical cases of AD. The results presented here support the value of SOBA-AD as a promising blood-based tool for the detection and confirmation of AD.
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Affiliation(s)
- Amy Chen
- AltPep Corporation, 1150 Eastlake Avenue N, Suite 800, Seattle, WA, 98109, USA
| | - Dylan Shea
- AltPep Corporation, 1150 Eastlake Avenue N, Suite 800, Seattle, WA, 98109, USA
- University of Washington, Box 355610, Seattle, WA, 98195-5610, USA
| | - Valerie Daggett
- AltPep Corporation, 1150 Eastlake Avenue N, Suite 800, Seattle, WA, 98109, USA.
- University of Washington, Box 355610, Seattle, WA, 98195-5610, USA.
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Liu P, Lapcinski IP, Hlynialuk CJ, Steuer EL, Loude TJ, Shapiro SL, Kemper LJ, Ashe KH. Aβ∗56 is a stable oligomer that impairs memory function in mice. iScience 2024; 27:109239. [PMID: 38433923 PMCID: PMC10905009 DOI: 10.1016/j.isci.2024.109239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 12/12/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024] Open
Abstract
Amyloid-β (Aβ) oligomers consist of fibrillar and non-fibrillar soluble assemblies of the Aβ peptide. Aβ∗56 is a non-fibrillar Aβ assembly that is linked to memory deficits. Previous studies did not decipher specific forms of Aβ present in Aβ∗56. Here, we confirmed the memory-impairing characteristics of Aβ∗56 and extended its biochemical characterization. We used anti-Aβ(1-x), anti-Aβ(x-40), anti-Aβ(x-42), and A11 anti-oligomer antibodies in conjunction with western blotting, immunoaffinity purification, and size-exclusion chromatography to probe aqueous brain extracts from Tg2576, 5xFAD, and APP/TTA mice. In Tg2576, Aβ∗56 is a ∼56-kDa, SDS-stable, A11-reactive, non-plaque-dependent, water-soluble, brain-derived oligomer containing canonical Aβ(1-40). In 5xFAD, Aβ∗56 is composed of Aβ(1-42), whereas in APP/TTA, it contains both Aβ(1-40) and Aβ(1-42). When injected into the hippocampus of wild-type mice, Aβ∗56 derived from Tg2576 mice impairs memory. The unusual stability of this oligomer renders it an attractive candidate for studying relationships between molecular structure and effects on brain function.
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Affiliation(s)
- Peng Liu
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ian P. Lapcinski
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chris J.W. Hlynialuk
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Elizabeth L. Steuer
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Thomas J. Loude
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha L. Shapiro
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lisa J. Kemper
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Karen H. Ashe
- N. Bud Grossman Center for Memory Research and Care, Minneapolis, MN 55455, USA
- Department of Neurology, University of Minnesota, Minneapolis, MN 55455, USA
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6
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Teppang KL, Zhao Q, Yang J. Development of fluorophores for the detection of oligomeric aggregates of amyloidogenic proteins found in neurodegenerative diseases. Front Chem 2023; 11:1343118. [PMID: 38188930 PMCID: PMC10766704 DOI: 10.3389/fchem.2023.1343118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Alzheimer's disease and Parkinson's disease are the two most common neurodegenerative diseases globally. These neurodegenerative diseases have characteristic late-stage symptoms allowing for differential diagnosis; however, they both share the presence of misfolded protein aggregates which appear years before clinical manifestation. Historically, research has focused on the detection of higher-ordered aggregates (or amyloids); however, recent evidence has shown that the oligomeric state of these protein aggregates plays a greater role in disease pathology, resulting in increased efforts to detect oligomers to aid in disease diagnosis. In this review, we summarize some of the exciting new developments towards the development of fluorescent probes that can detect oligomeric aggregates of amyloidogenic proteins present in Alzheimer's and Parkinson's disease patients.
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Affiliation(s)
| | | | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, CA, United States
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7
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Sharari S, Vaikath NN, Tsakou M, Ghanem SS, Vekrellis K. Screening for Novel Inhibitors of Amyloid Beta Aggregation and Toxicity as Potential Drugs for Alzheimer's Disease. Int J Mol Sci 2023; 24:11326. [PMID: 37511086 PMCID: PMC10379574 DOI: 10.3390/ijms241411326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/20/2023] [Accepted: 05/24/2023] [Indexed: 07/30/2023] Open
Abstract
AD is the most common neurodegenerative disorder characterized by progressive memory impairment and cognitive deficits. The pathology of AD is still unclear; however, several studies have shown that the aggregation of the Aβ peptide in the CNS is an exclusively pathological process involved in AD. Currently, there is no proven medication to cure or prevent the disease progression. Nevertheless, various therapeutic approaches for AD show only relief of symptoms and mostly work on cognitive recovery. However, one of the promising approaches for therapeutic intervention is to use inhibitors for blocking the Aβ peptide aggregation process. Recently, herbal phenolic compounds have been shown to have a therapeutic property for treatment of AD due to their multifaceted action. In this study, we investigated the effectiveness of SA, Gn Rb1, and DMyr on inhibiting the aggregation and toxicity of Aβ40 and Aβ42 using different biochemical and cell-based assays. Our results showed that SA and DMyr inhibit Aβ40 and Aβ42 fibrillation, seeded aggregation, and toxicity. Gn Rb1 did not have any effect on the aggregation or toxicity induced by Aβ40 and Aβ42. Moreover, SA and DMyr were able to disaggregate the preformed fibrils. Overall, these compounds may be used alone or synergistically and could be considered as a lead for designing new compounds that could be used as effective treatment of AD and related disorders.
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Affiliation(s)
- Sanaa Sharari
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Nishant N Vaikath
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Magdalini Tsakou
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Simona S Ghanem
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Kostas Vekrellis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
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8
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Schreiner TG, Schreiner OD, Adam M, Popescu BO. The Roles of the Amyloid Beta Monomers in Physiological and Pathological Conditions. Biomedicines 2023; 11:1411. [PMID: 37239082 PMCID: PMC10216198 DOI: 10.3390/biomedicines11051411] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/30/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Amyloid beta peptide is an important biomarker in Alzheimer's disease, with the amyloidogenic hypothesis as one of the central hypotheses trying to explain this type of dementia. Despite numerous studies, the etiology of Alzheimer's disease remains incompletely known, as the pathological accumulation of amyloid beta aggregates cannot fully explain the complex clinical picture of the disease. Or, for the development of effective therapies, it is mandatory to understand the roles of amyloid beta at the brain level, from its initial monomeric stage prior to aggregation in the form of senile plaques. In this sense, this review aims to bring new, clinically relevant data on a subject intensely debated in the literature in the last years. In the first part, the amyloidogenic cascade is reviewed and the possible subtypes of amyloid beta are differentiated. In the second part, the roles played by the amyloid beta monomers in physiological and pathological (neurodegenerative) conditions are illustrated based on the most relevant and recent studies published on this topic. Finally, considering the importance of amyloid beta monomers in the pathophysiology of Alzheimer's disease, new research directions with diagnostic and therapeutic impacts are suggested.
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Affiliation(s)
- Thomas Gabriel Schreiner
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, 700115 Iași, Romania;
- Faculty of Electrical Engineering and Information Technology, Gheorghe Asachi Technical University of Iasi, 21–23 Professor Dimitrie Mangeron Blvd., 700050 Iasi, Romania;
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 020021 Bucharest, Romania;
| | - Oliver Daniel Schreiner
- Faculty of Medicine, University of Medicine and Pharmacy “Grigore T. Popa”, 700115 Iași, Romania;
- Medical Oncology Department, Regional Institute of Oncology, 700483 Iași, Romania
| | - Maricel Adam
- Faculty of Electrical Engineering and Information Technology, Gheorghe Asachi Technical University of Iasi, 21–23 Professor Dimitrie Mangeron Blvd., 700050 Iasi, Romania;
| | - Bogdan Ovidiu Popescu
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 020021 Bucharest, Romania;
- Neurology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
- Laboratory of Cell Biology, Neurosciences and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania
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Li X, Yang Z, Chen Y, Zhang S, Wei G, Zhang L. Dissecting the Molecular Mechanisms of the Co-Aggregation of Aβ40 and Aβ42 Peptides: A REMD Simulation Study. J Phys Chem B 2023; 127:4050-4060. [PMID: 37126408 DOI: 10.1021/acs.jpcb.3c01078] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The aggregation of amyloid-β protein (Aβ) into oligomers and amyloid fibrils is closely related to Alzheimer's disease (AD). Aβ40 and Aβ42, as two most prominent isoforms of Aβ peptides, can cross-interact with each other and form co-aggregates, which affect the progression of the disease. However, the molecular determinants underlying Aβ40 and Aβ42 cross-interaction and the structural details of their co-oligomers remain elusive. Herein, we performed all-atom explicit-solvent replica exchange molecular dynamics simulations on Aβ40-Aβ42 heterogeneous and Aβ40/Aβ42 homogeneous dimer systems to dissect the co-aggregation mechanisms of the two isoforms. Our results show that the interpeptide main-chain interaction of Aβ40-Aβ42 is stronger than that of Aβ40-Aβ40 and Aβ42-Aβ42. The positions of hotspot residues in heterodimers and homodimers display high similarity, implying similar molecular recognition sites for both cross-interaction and self-interaction. Contact maps of Aβ40-Aβ42 heterodimers reveal that residue pairs crucial for cross-interaction are mostly located in the C-terminal hydrophobic regions of Aβ40 and Aβ42 peptides. Conformational analysis shows that Aβ40 and Aβ42 monomers can co-assemble into β-sheet-rich heterodimers with shorter β-sheets than those in homodimers, which is decremental to monomer addition. Similar molecular recognition sites and β-sheet distribution of Aβ40 and Aβ42 peptides are observed in heterodimers and homodimers, which may provide the molecular basis for the two isoforms' co-aggregation and cross-seeding. Our work dissects the co-aggregation mechanisms of Aβ40 and Aβ42 peptides at the atomic level, which will help for in-depth understanding of the cross-talk between the two Aβ isoforms and the pathogenesis of AD.
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Affiliation(s)
- Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yujie Chen
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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10
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Kaumbekova S, Amouei Torkmahalleh M, Umezawa M, Wang Y, Shah D. Effect of carbonaceous ultrafine particles on the structure and oligomerization of Aβ 42 peptide. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121273. [PMID: 36780974 DOI: 10.1016/j.envpol.2023.121273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The impact of pervasive air pollutants on human health is a growing concern in scientific communities. Among different air pollutants, ultrafine particles (UFPs; with aerodynamic diameter <100 nm) might pass through biological barriers and have a severe impact on human health, including early progression of neurodegenerative diseases such as Alzheimer's disease (AD). A significant fraction of UFPs consists of carbonaceous compounds, composed of elemental and organic carbon (EC and OC). While in-vivo experimental studies showed the neurotoxicity of typical OC and polycyclic aromatic hydrocarbons (PAHs), the molecular interactions involved in the progression of AD remain unclear. In this study, molecular dynamics simulations were performed to investigate the impact of carbonaceous UFPs on the structure of the Aβ42 monomer and the oligomerization of four Aβ42 peptides, associated with the development of AD. For the simulations, a fullerene (C60) was used for the modeling of EC, while benzo [a]pyrene (B[a]P) was used for the modeling of OC. The results revealed that the presence of C60 accelerated the tetramerization of Aβ42 peptides by 2.5 times, while C60/B[a]P promoted the unfolding of the peptide monomer showing the strongest interactions with the Aβ42 monomer. Similarly, C60/4B[a]P decreased the number of helices in the secondary structure of the peptide monomer by 60%. The simplified UFP models in this study, promoted the early aggregation of peptides to dimers, suggesting the progression of AD.
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Affiliation(s)
- Samal Kaumbekova
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kabanbay Batyr 53, Astana, 010000, Kazakhstan
| | - Mehdi Amouei Torkmahalleh
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Masakazu Umezawa
- Department of Materials Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo, 125-8585, Japan
| | - Yanwei Wang
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kabanbay Batyr 53, Astana, 010000, Kazakhstan
| | - Dhawal Shah
- Department of Chemical and Materials Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Kabanbay Batyr 53, Astana, 010000, Kazakhstan.
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Liu P, Lapcinski IP, Shapiro SL, Kemper LJ, Ashe KH. Aβ*56 is a stable oligomer that correlates with age-related memory loss in Tg2576 mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533414. [PMID: 36993768 PMCID: PMC10055265 DOI: 10.1101/2023.03.20.533414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Amyloid-β (Aβ) oligomers consist of fibrillar and non-fibrillar soluble assemblies of the Aβ peptide. Tg2576 human amyloid precursor protein (APP)-expressing transgenic mice modeling Alzheimer's disease produce Aβ*56, a non-fibrillar Aβ assembly that has been shown by several groups to relate more closely to memory deficits than plaques. Previous studies did not decipher specific forms of Aβ present in Aβ*56. Here, we confirm and extend the biochemical characterization of Aβ*56. We used anti-Aβ(1-x), anti-Aβ(x-40), and A11 anti-oligomer antibodies in conjunction with western blotting, immunoaffinity purification, and size-exclusion chromatography to probe aqueous brain extracts from Tg2576 mice of different ages. We found that Aβ*56 is a ∼56-kDa, SDS-stable, A11-reactive, non-plaque-related, water-soluble, brain-derived oligomer containing canonical Aβ(1-40) that correlates with age-related memory loss. The unusual stability of this high molecular-weight oligomer renders it an attractive candidate for studying relationships between molecular structure and effects on brain function.
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Arbez-Gindre C, Steele BR, Micha-Screttas M. Dendrimers in Alzheimer’s Disease: Recent Approaches in Multi-Targeting Strategies. Pharmaceutics 2023; 15:pharmaceutics15030898. [PMID: 36986759 PMCID: PMC10059864 DOI: 10.3390/pharmaceutics15030898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Nanomaterials play an increasingly important role in current medicinal practice. As one of the most significant causes of human mortality, and one that is increasing year by year, Alzheimer’s disease (AD) has been the subject of a very great body of research and is an area in which nanomedicinal approaches show great promise. Dendrimers are a class of multivalent nanomaterials which can accommodate a wide range of modifications that enable them to be used as drug delivery systems. By means of suitable design, they can incorporate multiple functionalities to enable transport across the blood–brain barrier and subsequently target the diseased areas of the brain. In addition, a number of dendrimers by themselves often display therapeutic potential for AD. In this review, the various hypotheses relating to the development of AD and the proposed therapeutic interventions involving dendrimer–base systems are outlined. Special attention is focused on more recent results and on the importance of aspects such as oxidative stress, neuroinflammation and mitochondrial dysfunction in approaches to the design of new treatments.
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Matthes D, de Groot BL. Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. J Biol Chem 2023; 299:103034. [PMID: 36806684 PMCID: PMC10033322 DOI: 10.1016/j.jbc.2023.103034] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Oligomeric aggregates of the amyloid-beta peptide(1-42) (Aβ42) are regarded as a primary cause of cytotoxicity related to membrane damage in Alzheimer's disease. However, a dynamical and structural characterization of pore-forming Aβ42 oligomers at atomic detail has not been feasible. Here, we used Aβ42 oligomer structures previously determined in a membrane-mimicking environment as putative model systems to study the pore formation process in phospholipid bilayers with all-atom molecular dynamics simulations. Multiple Aβ42 oligomer sizes, conformations, and N-terminally truncated isoforms were investigated on the multi-μs time scale. We found that pore formation and ion permeation occur via edge conductivity and exclusively for β-sandwich structures that feature exposed side-by-side β-strand pairs formed by residues 9 to 21 of Aβ42. The extent of pore formation and ion permeation depends on the insertion depth of hydrophilic residues 13 to 16 (HHQK domain) and thus on subtle differences in the overall stability, orientation, and conformation of the aggregates in the membrane. Additionally, we determined that backbone carbonyl and polar side-chain atoms from the edge strands directly contribute to the coordination sphere of the permeating ions. Furthermore, point mutations that alter the number of favorable side-chain contacts correlate with the ability of the Aβ42 oligomer models to facilitate ion permeation in the bilayer center. Our findings suggest that membrane-inserted, layered β-sheet edges are a key structural motif in pore-forming Aβ42 oligomers independent of their size and play a pivotal role in aggregate-induced membrane permeabilization.
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Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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Yi Y, Lim MH. Current understanding of metal-dependent amyloid-β aggregation and toxicity. RSC Chem Biol 2023; 4:121-131. [PMID: 36794021 PMCID: PMC9906324 DOI: 10.1039/d2cb00208f] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022] Open
Abstract
The discovery of effective therapeutics targeting amyloid-β (Aβ) aggregates for Alzheimer's disease (AD) has been very challenging, which suggests its complicated etiology associated with multiple pathogenic elements. In AD-affected brains, highly concentrated metals, such as copper and zinc, are found in senile plaques mainly composed of Aβ aggregates. These metal ions are coordinated to Aβ and affect its aggregation and toxicity profiles. In this review, we illustrate the current view on molecular insights into the assembly of Aβ peptides in the absence and presence of metal ions as well as the effect of metal ions on their toxicity.
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Affiliation(s)
- Yelim Yi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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Kabir ER, Chowdhury NM, Yasmin H, Kabir MT, Akter R, Perveen A, Ashraf GM, Akter S, Rahman MH, Sweilam SH. Unveiling the Potential of Polyphenols as Anti-Amyloid Molecules in Alzheimer's Disease. Curr Neuropharmacol 2023; 21:787-807. [PMID: 36221865 PMCID: PMC10227919 DOI: 10.2174/1570159x20666221010113812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/03/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
Alzheimer's disease (AD) is a devastating neurodegenerative disease that mostly affects the elderly population. Mechanisms underlying AD pathogenesis are yet to be fully revealed, but there are several hypotheses regarding AD. Even though free radicals and inflammation are likely to be linked with AD pathogenesis, still amyloid-beta (Aβ) cascade is the dominant hypothesis. According to the Aβ hypothesis, a progressive buildup of extracellular and intracellular Aβ aggregates has a significant contribution to the AD-linked neurodegeneration process. Since Aβ plays an important role in the etiology of AD, therefore Aβ-linked pathways are mainly targeted in order to develop potential AD therapies. Accumulation of Aβ plaques in the brains of AD individuals is an important hallmark of AD. These plaques are mainly composed of Aβ (a peptide of 39-42 amino acids) aggregates produced via the proteolytic cleavage of the amyloid precursor protein. Numerous studies have demonstrated that various polyphenols (PPHs), including cyanidins, anthocyanins, curcumin, catechins and their gallate esters were found to markedly suppress Aβ aggregation and prevent the formation of Aβ oligomers and toxicity, which is further suggesting that these PPHs might be regarded as effective therapeutic agents for the AD treatment. This review summarizes the roles of Aβ in AD pathogenesis, the Aβ aggregation pathway, types of PPHs, and distribution of PPHs in dietary sources. Furthermore, we have predominantly focused on the potential of food-derived PPHs as putative anti-amyloid drugs.
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Affiliation(s)
- Eva Rahman Kabir
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | | | - Hasina Yasmin
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | - Md. Tanvir Kabir
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka 1212, Bangladesh
| | - Rokeya Akter
- Department of Pharmacy, Jagannath University, Dhaka, Bangladesh
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Shamima Akter
- Department of Bioinformatics and Computational Biology, George Mason University, Fairfax, Virginia 22030, USA
| | | | - Sherouk Hussein Sweilam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Cairo-Suez Road, Badr City 11829, Egypt
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Prosswimmer T, Daggett V. The role of α-sheet structure in amyloidogenesis: characterization and implications. Open Biol 2022; 12:220261. [PMID: 36416010 PMCID: PMC9682440 DOI: 10.1098/rsob.220261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Amyloid diseases are linked to protein misfolding whereby the amyloidogenic protein undergoes a conformational change, aggregates and eventually forms amyloid fibrils. While the amyloid fibrils and plaques are hallmarks of these diseases, they typically form late in the disease process and do not correlate with disease. Instead, there is growing evidence that smaller, soluble toxic oligomers form prior and appear to be early triggers of the molecular pathology underlying these diseases. Nearly 20 years ago, we proposed the α-sheet hypothesis after discovering that the early conformational changes observed during atomistic molecular dynamics simulations involve the formation of a non-standard protein structure, α-sheet. Furthermore, we proposed that toxic oligomers contain α-sheet structure and that preferentially targeting this structure could neutralize the toxicity, prevent further aggregation and serve as the basis for early detection of disease. Here, we present the origin of the α-sheet hypothesis and describe α-sheet structure and the corresponding mechanisms of conversion. We discuss experimental studies demonstrating that both mammalian and bacterial amyloid systems form α-sheet oligomers before converting to conventional β-sheet fibrils. Furthermore, we show that the process can be inhibited with de novo designed α-sheet peptides complementary to the structure in the toxic oligomers.
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Affiliation(s)
- Tatum Prosswimmer
- Molecular Engineering Program, University of Washington, Seattle, WA 98195-5013, USA
| | - Valerie Daggett
- Molecular Engineering Program, University of Washington, Seattle, WA 98195-5013, USA,Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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Coto-Vilcapoma MA, Castilla-Silgado J, Fernández-García B, Pinto-Hernández P, Cipriani R, Capetillo-Zarate E, Menéndez-González M, Álvarez-Vega M, Tomás-Zapico C. New, Fully Implantable Device for Selective Clearance of CSF-Target Molecules: Proof of Concept in a Murine Model of Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms23169256. [PMID: 36012525 PMCID: PMC9408974 DOI: 10.3390/ijms23169256] [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: 07/29/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
We have previously proposed a radical change in the current strategy to clear pathogenic proteins from the central nervous system (CNS) based on the cerebrospinal fluid (CSF)-sink therapeutic strategy, whereby pathogenic proteins can be removed directly from the CNS via CSF. To this aim, we designed and manufactured an implantable device for selective and continuous apheresis of CSF enabling, in combination with anti-amyloid-beta (Aβ) monoclonal antibodies (mAb), the clearance of Aβ from the CSF. Here, we provide the first proof of concept in the APP/PS1 mouse model of Alzheimer’s disease (AD). Devices were implanted in twenty-four mice (seventeen APP/PS1 and seven Wt) with low rates of complications. We confirmed that the apheresis module is permeable to the Aβ peptide and impermeable to mAb. Moreover, our results showed that continuous clearance of soluble Aβ from the CSF for a few weeks decreases cortical Aβ plaques. Thus, we conclude that this intervention is feasible and may provide important advantages in terms of safety and efficacy.
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Affiliation(s)
- María Almudena Coto-Vilcapoma
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain
| | - Juan Castilla-Silgado
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain
| | - Benjamín Fernández-García
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain
- Departamento de Morfología y Biología Celular, Área de Anatomía, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Paola Pinto-Hernández
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Raffaela Cipriani
- Achucarro Basque Center for Neuroscience, Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), 48940 Leioa, Spain
| | - Estibaliz Capetillo-Zarate
- Achucarro Basque Center for Neuroscience, Departamento de Neurociencias, Universidad del País Vasco (UPV/EHU), 48940 Leioa, Spain
- Centro de Investigación en Red de Enfermedades, Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Manuel Menéndez-González
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain
- Servicio de Neurología, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Departamento de Medicina Área de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
- Correspondence:
| | - Marco Álvarez-Vega
- Servicio de Neurocirugía, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
- Departamento de Cirugía, Área de Cirugía, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Cristina Tomás-Zapico
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain
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