1
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Zhang J, Ma Z, Yang Y, Guo L, Du L. Modeling genotype-protein interaction and correlation for Alzheimer's disease: a multi-omics imaging genetics study. Brief Bioinform 2024; 25:bbae038. [PMID: 38348747 PMCID: PMC10939371 DOI: 10.1093/bib/bbae038] [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: 10/11/2023] [Revised: 11/23/2023] [Accepted: 01/14/2024] [Indexed: 02/15/2024] Open
Abstract
Integrating and analyzing multiple omics data sets, including genomics, proteomics and radiomics, can significantly advance researchers' comprehensive understanding of Alzheimer's disease (AD). However, current methodologies primarily focus on the main effects of genetic variation and protein, overlooking non-additive effects such as genotype-protein interaction (GPI) and correlation patterns in brain imaging genetics studies. Importantly, these non-additive effects could contribute to intermediate imaging phenotypes, finally leading to disease occurrence. In general, the interaction between genetic variations and proteins, and their correlations are two distinct biological effects, and thus disentangling the two effects for heritable imaging phenotypes is of great interest and need. Unfortunately, this issue has been largely unexploited. In this paper, to fill this gap, we propose $\textbf{M}$ulti-$\textbf{T}$ask $\textbf{G}$enotype-$\textbf{P}$rotein $\textbf{I}$nteraction and $\textbf{C}$orrelation disentangling method ($\textbf{MT-GPIC}$) to identify GPI and extract correlation patterns between them. To ensure stability and interpretability, we use novel and off-the-shelf penalties to identify meaningful genetic risk factors, as well as exploit the interconnectedness of different brain regions. Additionally, since computing GPI poses a high computational burden, we develop a fast optimization strategy for solving MT-GPIC, which is guaranteed to converge. Experimental results on the Alzheimer's Disease Neuroimaging Initiative data set show that MT-GPIC achieves higher correlation coefficients and classification accuracy than state-of-the-art methods. Moreover, our approach could effectively identify interpretable phenotype-related GPI and correlation patterns in high-dimensional omics data sets. These findings not only enhance the diagnostic accuracy but also contribute valuable insights into the underlying pathogenic mechanisms of AD.
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Affiliation(s)
- Jin Zhang
- Department of Intelligent Science and Technology, Northwestern Polytechnical University School of Automation, 127 Youyi Road, 710072 Shaanxi, China
| | - Zikang Ma
- Department of Intelligent Science and Technology, Northwestern Polytechnical University School of Automation, 127 Youyi Road, 710072 Shaanxi, China
| | - Yan Yang
- Department of Intelligent Science and Technology, Northwestern Polytechnical University School of Automation, 127 Youyi Road, 710072 Shaanxi, China
| | - Lei Guo
- Department of Intelligent Science and Technology, Northwestern Polytechnical University School of Automation, 127 Youyi Road, 710072 Shaanxi, China
| | - Lei Du
- Department of Intelligent Science and Technology, Northwestern Polytechnical University School of Automation, 127 Youyi Road, 710072 Shaanxi, China
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2
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Sanders OD. Virus-Like Cytosolic and Cell-Free Oxidatively Damaged Nucleic Acids Likely Drive Inflammation, Synapse Degeneration, and Neuron Death in Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:1-19. [PMID: 36761106 PMCID: PMC9881037 DOI: 10.3233/adr-220047] [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: 07/25/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Oxidative stress, inflammation, and amyloid-β are Alzheimer's disease (AD) hallmarks that cause each other and other AD hallmarks. Most amyloid-β-lowering, antioxidant, anti-inflammatory, and antimicrobial AD clinical trials failed; none stopped or reversed AD. Although signs suggest an infectious etiology, no pathogen accumulated consistently in AD patients. Neuropathology, neuronal cell culture, rodent, genome-wide association, epidemiological, biomarker, and clinical studies, plus analysis using Hill causality criteria and revised Koch's postulates, indicate that the virus-like oxidative damage-associated molecular-pattern (DAMP) cytosolic and cell-free nucleic acids accumulated in AD patients' brains likely drive neuroinflammation, synaptotoxicity, and neurotoxicity. Cytosolic oxidatively-damaged mitochondrial DNA accumulated outside mitochondria dose-dependently in preclinical AD and AD patients' hippocampal neurons, and in AD patients' neocortical neurons but not cerebellar neurons or glia. In oxidatively-stressed neural cells and rodents' brains, cytosolic oxidatively-damaged mitochondrial DNA accumulated and increased antiviral and inflammatory proteins, including cleaved caspase-1, interleukin-1β, and interferon-β. Cytosolic double-stranded RNA and DNA are DAMPs that induce antiviral interferons and/or inflammatory proteins by oligomerizing with various innate-immune pattern-recognition receptors, e.g., cyclic GMP-AMP synthase and the nucleotide-binding-oligomerization-domain-like-receptor-pyrin-domain-containing-3 inflammasome. In oxidatively-stressed neural cells, cytosolic oxidatively-damaged mitochondrial DNA caused synaptotoxicity and neurotoxicity. Depleting mitochondrial DNA prevented these effects. Additionally, cell-free nucleic acids accumulated in AD patients' blood, extracellular vesicles, and senile plaques. Injecting cell-free nucleic acids bound to albumin oligomers into wild-type mice's hippocampi triggered antiviral interferon-β secretion; interferon-β injection caused synapse degeneration. Deoxyribonuclease-I treatment appeared to improve a severe-AD patient's Mini-Mental Status Exam by 15 points. Preclinical and clinical studies of deoxyribonuclease-I and a ribonuclease for AD should be prioritized.
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Affiliation(s)
- Owen Davis Sanders
- Nebraska Medical Center, Omaha, NE, USA,Correspondence to: Owen Davis Sanders, 210 S 16th St. Apt. 215, Omaha, NE 68102, USA. E-mails: and
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3
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Sanders OD, Rajagopal L, Rajagopal JA. The oxidatively damaged DNA and amyloid-β oligomer hypothesis of Alzheimer's disease. Free Radic Biol Med 2022; 179:403-412. [PMID: 34506904 DOI: 10.1016/j.freeradbiomed.2021.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/15/2021] [Accepted: 08/19/2021] [Indexed: 01/13/2023]
Abstract
The amyloid-β (Aβ) oligomer hypothesis of Alzheimer's disease (AD) still dominates the field, yet the clinical trial evidence does not robustly support it. A falsifiable prediction of the hypothesis is that Aβ oligomer levels should be elevated in the brain regions and at the disease stages where and when neuron death and synaptic protein loss begin and are the most severe, but we review previous evidence to demonstrate that this is not consistently the case. To rescue the Aβ oligomer hypothesis from falsification, we propose the novel ad-hoc hypothesis that the exceptionally vulnerable hippocampus may normally produce Aβ peptides even in healthily aging individuals, and hippocampal oxidatively damaged DNA, pathogen DNA, and metal ions such as zinc may initiate and drive Aβ peptide aggregation into oligomers and spreading, neuron death, synaptic dysfunction, and other aspects of AD neurodegeneration. We highlight additional evidence consistent with the underwhelming efficacy of Aβ oligomer-lowering agents, such as aducanumab, and of antioxidants, such as vitamin E, versus the so far isolated case report that DNase-I treatment for 2 months resulted in a severe AD patient's Mini-Mental State Exam score increasing from 3 to 18, reversing his diagnosis to moderate AD, according to the Mini-Mental State Exam.
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Affiliation(s)
| | - Lekshmy Rajagopal
- Seven Hills Hospital, Marol Maroshi Rd, Shivaji Nagar JJC, Marol, Andheri East, Mumbai, Maharashtra, 400059, India
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4
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Wiatrak B, Mieszała P, Gąsiorowski K. Impact of NMDA receptor activation on DNA damage in PC12 neuron-like cell cultures in the presence of β-amyloid peptides. Mol Biol Rep 2022; 49:10443-10455. [PMID: 36107376 PMCID: PMC9618537 DOI: 10.1007/s11033-022-07856-6] [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: 01/24/2022] [Revised: 07/14/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVE This study aimed to investigate the effect of low nanomolar concentrations of Aβ1-40 and Aβ25-35 on DNA double-strand breaks following NMDA activation of cells. MATERIALS AND METHODS After incubating the differentiated PC12 cells with Aβ25-35, Aβ1-40 or Aβ1-42 for 24 h, the culture was washed and stimulated for 15 min with NMDA. Then, tests were performed at four-time intervals from stimulation to assess the viability of the culture, the level of oxygen free radicals, and the γH2AX and pATM kinase. NMDAR1 expression was also evaluated by performing immunocytochemical staining. RESULTS It was found that amyloid peptides in nanomolar concentrations reduce double-stranded DNA breaks after NMDA neuron activation. A slight antioxidant effect was also demonstrated when measured 120 min after NMDA cell activation. CONCLUSION The NMDA stimulation of PC12 cells led to a rapid increase in the number of double-stranded DNA breaks in the cells and is assumed to be the initial step in IEG activation and LTP induction. The effect of Aβ on the reduction of double-strand breaks after NMDA cell stimulation indicates that at concentrations similar to physiological amyloid peptides, it may reduce the mobilization of the neuronal response to stimuli, leading to inhibition of LTP induction and decreasing synaptic plasticity in the early stages of Alzheimer's disease.
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Affiliation(s)
- Benita Wiatrak
- Department of Basic Medical Sciences, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland ,Department of Pharmacology, Faculty of Medicine, Wroclaw Medical University, Mikulicza-Radeckiego 2, 50-345 Wrocław, Poland
| | - Przemysław Mieszała
- Department of Basic Medical Sciences, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Kazimierz Gąsiorowski
- Department of Basic Medical Sciences, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
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5
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Lee EY, Srinivasan Y, de Anda J, Nicastro LK, Tükel Ç, Wong GCL. Functional Reciprocity of Amyloids and Antimicrobial Peptides: Rethinking the Role of Supramolecular Assembly in Host Defense, Immune Activation, and Inflammation. Front Immunol 2020; 11:1629. [PMID: 32849553 PMCID: PMC7412598 DOI: 10.3389/fimmu.2020.01629] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Pathological self-assembly is a concept that is classically associated with amyloids, such as amyloid-β (Aβ) in Alzheimer's disease and α-synuclein in Parkinson's disease. In prokaryotic organisms, amyloids are assembled extracellularly in a similar fashion to human amyloids. Pathogenicity of amyloids is attributed to their ability to transform into several distinct structural states that reflect their downstream biological consequences. While the oligomeric forms of amyloids are thought to be responsible for their cytotoxicity via membrane permeation, their fibrillar conformations are known to interact with the innate immune system to induce inflammation. Furthermore, both eukaryotic and prokaryotic amyloids can self-assemble into molecular chaperones to bind nucleic acids, enabling amplification of Toll-like receptor (TLR) signaling. Recent work has shown that antimicrobial peptides (AMPs) follow a strikingly similar paradigm. Previously, AMPs were thought of as peptides with the primary function of permeating microbial membranes. Consistent with this, many AMPs are facially amphiphilic and can facilitate membrane remodeling processes such as pore formation and fusion. We show that various AMPs and chemokines can also chaperone and organize immune ligands into amyloid-like ordered supramolecular structures that are geometrically optimized for binding to TLRs, thereby amplifying immune signaling. The ability of amphiphilic AMPs to self-assemble cooperatively into superhelical protofibrils that form structural scaffolds for the ordered presentation of immune ligands like DNA and dsRNA is central to inflammation. It is interesting to explore the notion that the assembly of AMP protofibrils may be analogous to that of amyloid aggregates. Coming full circle, recent work has suggested that Aβ and other amyloids also have AMP-like antimicrobial functions. The emerging perspective is one in which assembly affords a more finely calibrated system of recognition and response: the detection of single immune ligands, immune ligands bound to AMPs, and immune ligands spatially organized to varying degrees by AMPs, result in different immunologic outcomes. In this framework, not all ordered structures generated during multi-stepped AMP (or amyloid) assembly are pathological in origin. Supramolecular structures formed during this process serve as signatures to the innate immune system to orchestrate immune amplification in a proportional, situation-dependent manner.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yashes Srinivasan
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lauren K Nicastro
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Çagla Tükel
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States.,California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, United States
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6
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Lathe R, Darlix JL. Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy. Arch Virol 2020; 165:535-556. [PMID: 32025859 PMCID: PMC7024060 DOI: 10.1007/s00705-020-04529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022]
Abstract
The existence of more than 30 strains of transmissible spongiform encephalopathy (TSE) and the paucity of infectivity of purified PrPSc, as well as considerations of PrP structure, are inconsistent with the protein-only (prion) theory of TSE. Nucleic acid is a strong contender as a second component. We juxtapose two key findings: (i) PrP is a nucleic-acid-binding antimicrobial protein that is similar to retroviral Gag proteins in its ability to trigger reverse transcription. (ii) Retroelement mobilization is widely seen in TSE disease. Given further evidence that PrP also mediates nucleic acid transport into and out of the cell, a strong case is to be made that a second element – retroelement nucleic acid – bound to PrP constitutes the second component necessary to explain the multiple strains of TSE.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh School of Medicine, Edinburgh, UK. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Moscow Region, Russia.
| | - Jean-Luc Darlix
- Faculté de Pharmacie, Centre Nationale de la Recherche Scientifique (CNRS) Laboratory of Bioimaging and Pathologies (Unité Mixte de Recherche 7021), Université de Strasbourg, Illkirch, France.
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7
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Smalheiser NR. Mining Clinical Case Reports to Identify New Lines of Investigation in Alzheimer's Disease: The Curious Case of DNase I. J Alzheimers Dis Rep 2019; 3:71-76. [PMID: 31025031 PMCID: PMC6481472 DOI: 10.3233/adr-190100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mining the case report literature identified an intriguing, yet neglected finding: Deoxyribonuclease I (DNase I) as a possible treatment for Alzheimer’s disease. This finding is speculative, both because it is based on one patient, and because the underlying mechanism(s) of action remain obscure. However, further literature review revealed that there are several plausible mechanisms by which DNase I might affect the course of Alzheimer’s disease. Given that DNase I is an FDA-approved drug, with extensive studies in both animals and man in the context of other diseases, I suggest that investigation of DNAse I in Alzheimer’s disease is worthwhile.
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Affiliation(s)
- Neil R Smalheiser
- Department of Psychiatry, University of Illinois College of Medicine, Chicago, IL, USA
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8
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Yang CF, Lin SP, Chiang CP, Wu YH, H'ng WS, Chang CP, Chen YT, Wu JY. Loss of GPNMB Causes Autosomal-Recessive Amyloidosis Cutis Dyschromica in Humans. Am J Hum Genet 2018; 102:219-232. [PMID: 29336782 DOI: 10.1016/j.ajhg.2017.12.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022] Open
Abstract
Amyloidosis cutis dyschromica (ACD) is a distinct form of primary cutaneous amyloidosis characterized by generalized hyperpigmentation mottled with small hypopigmented macules on the trunks and limbs. Affected families and sporadic case subjects have been reported predominantly in East and Southeast Asian ethnicities; however, the genetic cause has not been elucidated. We report here that the compound heterozygosity or homozygosity of GPNMB truncating alleles is the cause of autosomal-recessive ACD. Six nonsense or frameshift mutations were identified in nine individuals diagnosed with ACD. Immunofluorescence analysis of skin biopsies showed that GPNMB is expressed in all epidermal cells, with the highest staining observed in melanocytes. GPNMB staining is significantly reduced in the lesional skin of affected individuals. Hyperpigmented lesions exhibited significantly increased amounts of DNA/keratin-positive amyloid deposits in the papillary dermis and infiltrating macrophages compared with hypo- or depigmented macules. Depigmentation of the lesions was attributable to loss of melanocytes. Intracytoplasmic fibrillary aggregates were observed in keratinocytes scattered in the lesional epidermis. Thus, our analysis indicates that loss of GPNMB, which has been implicated in melanosome formation, autophagy, phagocytosis, tissue repair, and negative regulation of inflammation, underlies autosomal-recessive ACD and provides insights into the etiology of amyloidosis and pigment dyschromia.
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Affiliation(s)
- Chi-Fan Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shuan-Pei Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei 104, Taiwan; Department of Pediatrics, MacKay Memorial Hospital, Taipei 104, Taiwan; Department of Medicine, MacKay Medical College, New Taipei City 252, Taiwan
| | - Chien-Ping Chiang
- Departments of Dermatology, Tri-Service General Hospital, Taipei 114, Taiwan; Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan
| | - Yu-Hung Wu
- Department of Medicine, MacKay Medical College, New Taipei City 252, Taiwan; Department of Dermatology, MacKay Memorial Hospital, Taipei 104, Taiwan
| | - Weng Siong H'ng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Chun-Ping Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
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9
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Khmeleva SA, Radko SP, Kozin SA, Kiseleva YY, Mezentsev YV, Mitkevich VA, Kurbatov LK, Ivanov AS, Makarov AA. Zinc-Mediated Binding of Nucleic Acids to Amyloid-β Aggregates: Role of Histidine Residues. J Alzheimers Dis 2018; 54:809-19. [PMID: 27567853 DOI: 10.3233/jad-160415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Amyloid-β peptide (Aβ) plays a central role in Alzheimer's disease (AD) pathogenesis. Besides extracellular Aβ, intraneuronal Aβ (iAβ) has been suggested to contribute to AD onset and development. Based on reported in vitro Aβ-DNA interactions and nuclear localization of iAβ, the interference of iAβ with the normal DNA expression has recently been proposed as a plausible pathway by which Aβ can exert neurotoxicity. Employing the sedimentation assay, thioflavin T fluorescence, and dynamic light scattering we have studied effects of zinc ions on binding of RNA and single- and double-stranded DNA molecules to Aβ42 aggregates. It has been found that zinc ions significantly enhance the binding of RNA and DNA molecules to pre-formed β-sheet rich Aβ42 aggregates. Another type of Aβ42 aggregates, the zinc-induced amorphous aggregates, was demonstrated to also bind all types of nucleic acids tested. To evaluate the role of the Aβ metal-binding domain's histidine residues in Aβ-nucleic acid interactions mediated by zinc, Aβ16 mutants with substitutions H6R and H6A-H13A and rat Aβ16 lacking histidine residue 13 were used. The zinc-induced interaction of Aβ16 with DNA was shown to critically depend on histidine residues 6 and 13. However, the inclusion of H6R mutation in Aβ42 peptide did not affect DNA binding to Aβ42 aggregates. Since oxidative and/or nitrosative stresses implicated in AD pathogenesis are known to release zinc ions from metallothioneins in cytoplasm and cell nuclei, our findings suggest that intracellular zinc can be an important player in iAβ-nucleic acid interactions.
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Affiliation(s)
- Svetlana A Khmeleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Sergey P Radko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yana Y Kiseleva
- Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | | | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alexis S Ivanov
- Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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10
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Lathe R, Darlix JL. Prion Protein PRNP: A New Player in Innate Immunity? The Aβ Connection. J Alzheimers Dis Rep 2017; 1:263-275. [PMID: 30480243 PMCID: PMC6159716 DOI: 10.3233/adr-170037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2017] [Indexed: 12/25/2022] Open
Abstract
The prion protein PRNP has been centrally implicated in the transmissible spongiform encephalopathies (TSEs), but its normal physiological role remains obscure. We highlight emerging evidence that PRNP displays antimicrobial activity, inhibiting the replication of multiple viruses, and also interacts directly with Alzheimer's disease (AD) amyloid-β (Aβ) peptide whose own antimicrobial role is now increasingly secure. PRNP and Aβ share share membrane-penetrating, nucleic acid binding, and antiviral properties with classical antimicrobial peptides such as LL-37. We discuss findings that binding of abnormal nucleic acids to PRNP leads to oligomerization of the protein, and suggest that this may be an entrapment and sequestration process that contributes to its antimicrobial activity. Some antimicrobial peptides are known to be exploited by infectious agents, and we cover evidence that PRNP is usurped by herpes simplex virus (HSV-1) that has evolved a virus-encoded 'anti-PRNP'.unction. These findings suggest that PRNP, like LL-37 and Aβ, is likely to be a component of the innate immune system, with implications for the pathoetiology of both AD and TSE.
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Affiliation(s)
- Richard Lathe
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh, UK
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Jean-Luc Darlix
- Faculté de Pharmacie, Centre Nationale de la Recherche Scientifique (CNRS) Unité 7213, Université de Strasbourg, Illkirch, France
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11
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Xie B, Zhang H, Li X, Dong X, Sun Y. Iminodiacetic Acid-Modified Human Serum Albumin: A Multifunctional Agent against Metal-Associated Amyloid β-Protein Aggregation and Cytotoxicity. ACS Chem Neurosci 2017; 8:2214-2224. [PMID: 28767224 DOI: 10.1021/acschemneuro.7b00128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Metal-induced amyloid β-protein (Aβ) aggregation plays a key role in the pathogenesis of Alzheimer's disease. Although several agents have been recognized to block metal-associated Aβ aggregation, their therapeutic potential is marred due to the high-concentration metal ions in the amyloid plaques. To overcome this problem, we have herein developed iminodiacetic acid-modified human serum albumin (I-HSA) to fight against the aggregation. The multifunctional nature of I-HSA was extensively characterized in inhibiting the Aβ42 aggregation associated with Zn2+ and Cu2+. The results revealed the following: (1) I-HSA significantly inhibited Aβ42 aggregation and alleviated its cytotoxicity. (2) I-HSA possessed a metal-chelate capacity as high as 31.2 mol/mol, and 25 μM I-HSA could effectively inhibit the influence of 250 μM Zn2+ on Aβ42 aggregation. (3) Equimolar I-HSA remarkably attenuated the reactive oxygen species damage caused by the Aβ42 and Cu2+-Aβ42 species. (4) I-HSA could remodel metal-Aβ42 fibrils into unstructured aggregates with less neurotoxicity. The cytotoxicity of mature Cu2+-Aβ42 aggregates was mitigated from 64.8% to 25.4% under the functioning of I-HSA. In conclusion, I-HSA showed prominent advantages for the high metal-chelate capacity. To our knowledge, I-HSA is the first multifunctional macromolecule for inhibiting high-concentration metal-induced Aβ42 aggregation and remodeling mature metal-induced Aβ42 species.
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Affiliation(s)
- Baolong Xie
- Department of Biochemical
Engineering and Key Laboratory of Systems Bioengineering of the Ministry
of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300354, China
| | - Huan Zhang
- Department of Biochemical
Engineering and Key Laboratory of Systems Bioengineering of the Ministry
of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300354, China
| | - Xi Li
- Department of Biochemical
Engineering and Key Laboratory of Systems Bioengineering of the Ministry
of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300354, China
| | - Xiaoyan Dong
- Department of Biochemical
Engineering and Key Laboratory of Systems Bioengineering of the Ministry
of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300354, China
| | - Yan Sun
- Department of Biochemical
Engineering and Key Laboratory of Systems Bioengineering of the Ministry
of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300354, China
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12
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Abstract
Aggregation of the amyloid-β (Aβ) peptide is strongly correlated with Alzheimer's disease (AD). Recent research has improved our understanding of the kinetics of amyloid fibril assembly and revealed new details regarding different stages in plaque formation. Presently, interest is turning toward studying this process in a holistic context, focusing on cellular components which interact with the Aβ peptide at various junctures during aggregation, from monomer to cross-β amyloid fibrils. However, even in isolation, a multitude of factors including protein purity, pH, salt content, and agitation affect Aβ fibril formation and deposition, often producing complicated and conflicting results. The failure of numerous inhibitors in clinical trials for AD suggests that a detailed examination of the complex interactions that occur during plaque formation, including binding of carbohydrates, lipids, nucleic acids, and metal ions, is important for understanding the diversity of manifestations of the disease. Unraveling how a variety of key macromolecular modulators interact with the Aβ peptide and change its aggregation properties may provide opportunities for developing therapies. Since no protein acts in isolation, the interplay of these diverse molecules may differentiate disease onset, progression, and severity, and thus are worth careful consideration.
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Affiliation(s)
- Katie L Stewart
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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13
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Schwartz K, Ganesan M, Payne DE, Solomon MJ, Boles BR. Extracellular DNA facilitates the formation of functional amyloids in Staphylococcus aureus biofilms. Mol Microbiol 2015; 99:123-34. [PMID: 26365835 DOI: 10.1111/mmi.13219] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/27/2022]
Abstract
Persistent staphylococcal infections often involve surface-associated communities called biofilms. Staphylococcus aureus biofilm development is mediated by the co-ordinated production of the biofilm matrix, which can be composed of polysaccharides, extracellular DNA (eDNA) and proteins including amyloid fibers. The nature of the interactions between matrix components, and how these interactions contribute to the formation of matrix, remain unclear. Here we show that the presence of eDNA in S. aureus biofilms promotes the formation of amyloid fibers. Conditions or mutants that do not generate eDNA result in lack of amyloids during biofilm growth despite the amyloidogeneic subunits, phenol soluble modulin peptides, being produced. In vitro studies revealed that the presence of DNA promotes amyloid formation by PSM peptides. Thus, this work exposes a previously unacknowledged interaction between biofilm matrix components that furthers our understanding of functional amyloid formation and S. aureus biofilm biology.
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Affiliation(s)
- Kelly Schwartz
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Mahesh Ganesan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - David E Payne
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Michael J Solomon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Blaise R Boles
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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Khmeleva SA, Mezentsev YV, Kozin SA, Mitkevich VA, Medvedev AE, Ivanov AS, Bodoev NV, Makarov AA, Radko SP. Effect of mutations and modifications of amino acid residues on zinc-induced interaction of the metal-binding domain of β-amyloid with DNA. Mol Biol 2015. [DOI: 10.1134/s0026893315020053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Wang J, Zhao C, Zhao A, Li M, Ren J, Qu X. New Insights in Amyloid Beta Interactions with Human Telomerase. J Am Chem Soc 2015; 137:1213-9. [DOI: 10.1021/ja511030s] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiasi Wang
- Laboratory
of Chemical Biology
and Division of Biological Inorganic Chemistry, State Key Laboratory
of Rare Earth Resource Utilization, Changchun Institute of Applied
Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Chuanqi Zhao
- Laboratory
of Chemical Biology
and Division of Biological Inorganic Chemistry, State Key Laboratory
of Rare Earth Resource Utilization, Changchun Institute of Applied
Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Andong Zhao
- Laboratory
of Chemical Biology
and Division of Biological Inorganic Chemistry, State Key Laboratory
of Rare Earth Resource Utilization, Changchun Institute of Applied
Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Meng Li
- Laboratory
of Chemical Biology
and Division of Biological Inorganic Chemistry, State Key Laboratory
of Rare Earth Resource Utilization, Changchun Institute of Applied
Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jinsong Ren
- Laboratory
of Chemical Biology
and Division of Biological Inorganic Chemistry, State Key Laboratory
of Rare Earth Resource Utilization, Changchun Institute of Applied
Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaogang Qu
- Laboratory
of Chemical Biology
and Division of Biological Inorganic Chemistry, State Key Laboratory
of Rare Earth Resource Utilization, Changchun Institute of Applied
Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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16
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Pathological implications of nucleic acid interactions with proteins associated with neurodegenerative diseases. Biophys Rev 2014; 6:97-110. [PMID: 28509960 DOI: 10.1007/s12551-013-0132-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 12/03/2013] [Indexed: 10/25/2022] Open
Abstract
Protein misfolding disorders (PMDs) refer to a group of diseases related to the misfolding of particular proteins that aggregate and deposit in the cells and tissues of humans and other mammals. The mechanisms that trigger protein misfolding and aggregation are still not fully understood. Increasing experimental evidence indicates that abnormal interactions between PMD-related proteins and nucleic acids (NAs) can induce conformational changes. Here, we discuss these protein-NA interactions and address the role of deoxyribonucleic (DNA) and ribonucleic (RNA) acid molecules in the conformational conversion of different proteins that aggregate in PMDs, such as Alzheimer's, Parkinson's, and prion diseases. Studies on the affinity, stability, and specificity of proteins involved in neurodegenerative diseases and NAs are specifically addressed. A landscape of reciprocal effects resulting from the binding of prion proteins, amyloid-β peptides, tau proteins, huntingtin, and α-synuclein are presented here to clarify the possible role of NAs, not only as encoders of genetic information but also in triggering PMDs.
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17
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Camero S, Benítez MJ, Jiménez JS. Anomalous Protein–DNA Interactions Behind Neurological Disorders. PROTEIN-NUCLEIC ACIDS INTERACTIONS 2013; 91:37-63. [DOI: 10.1016/b978-0-12-411637-5.00002-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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