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Protein-DNA Interaction at the Origin of Neurological Diseases: A Hypothesis
Abstract
A number of neurodegenerative diseases, including Alzheimer's disease, tauopathies, Parkinson's disease, and synucleinopathies, polyglutamine diseases, including Huntington's disease, amyotrophic lateral sclerosis, and transmissible spongiform encephalopathy, are characterized by the existence of a protein or peptide prone to aggregation specific to the disease: amyloid-β, tau protein, α-synuclein, atrophin 1, androgen receptor, prion protein, copper-zinc superoxide dismutase, α 1A subunit of CaV2.1, TATA-box binding protein, huntingtin, and ataxins 1, 2, 3, and 7. Beside this common molecular feature, we have found three additional main properties related to the disease-connected protein or peptide, which are shared by all those neurological disorders: first, proneness to aggregation, which, in many cases, seems to be bound to the lack of a clearly defined secondary structure; second, reported presence of the disease-related protein inside the nucleus; and finally, an apparently unspecific interaction with DNA. These findings, together with the lack of clear details to explain the molecular origin of these neurodegenerative diseases, invite a hypothesis that, together with other plausible molecular explanations, may contribute to find the molecular basis of these diseases: I propose here the hypothesis that many neurological disorders may be the consequence, at least in part, of an aberrant interaction of the disease-related protein with nucleic acids, therefore affecting the normal DNA expression and giving place to a genetic stress which, in turn, alters the expression of proteins needed for the normal cellular function and regulation.
... Growing evidence indicates that AD may result from abnormal interactions between disease-related protein changes and genetic variations. This is because many important biological processes such as RNA transport and translation are controlled by interactions of these two kinds of biomacromolecules [3,4]. Therefore, investigating the underlying relationship between proteins and genetic variations is essential for comprehending the mechanisms of AD and facilitating diagnostics and therapeutics [4][5][6]. ...
... This is because many important biological processes such as RNA transport and translation are controlled by interactions of these two kinds of biomacromolecules [3,4]. Therefore, investigating the underlying relationship between proteins and genetic variations is essential for comprehending the mechanisms of AD and facilitating diagnostics and therapeutics [4][5][6]. ...
... The second kind is genotype-protein correlation (GPC), which denotes that diseaserelated imaging phenotypes might be associated with genes and proteins simultaneously because genes and proteins ref lect individual information from different perspectives, which could result in a relatively high correlation between them. GPI and GPC may implicate distinct biological mechanisms, and, finally, lead to imaging phenotypes with substantial differences [4,13]. Consequently, the identification of GPI and correlation associated with heritable phenotypes is an urgent need. ...
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.
... 9−13 Among these other molecules, nucleic acids (NAs) are believed to act as catalysts in this process (reviewed in refs 14 and 15). Aberrant interactions between proteins and nucleic acids have been implicated in other neurodegenerative diseases, 16,17 as well. On the other hand, synthetic modified oligonucleotides have been shown to reverse prion infectivity both in cell-based assays and in prion animal models. ...
... 51,52 Interestingly, nonspecific interactions of nucleic acids with other proteins that aggregate in the CNS, besides the PrP, have been reported. 16,17,53 A recent study has shown that intact amyloid fibrils of recombinant PrP are highly toxic to cells in culture. 7 This result indicates that different aggregates formed by rPrP under different conditions (in the presence or absence of ligands) might result in a toxic profile similar to that of cellular systems. ...
... Thus, it has been hypothesized that many neurodegenerative diseases occur partly due to an aberrant interaction of the disease-related protein with nucleic acids. 16 In an interesting article, it has been shown that the interaction of short dsDNAs with a bacterial protein domain led to amyloid spheroids and fibers. 54 This result indicates that DNA binding by a bacterial protein promotes amyloidogenesis in a fashion similar to that described for the mammalian prion protein, suggesting a common mechanism for DNA-induced protein aggregation. ...
A misfolded form of the prion protein (PrP) is the primary culprit in mammalian prion diseases. It has been shown that nucleic acids catalyze the misfolding of cellular PrP into a scrapie-like conformer. It has also been observed that the interaction of PrP with nucleic acids is nonspecific and that the complex can be toxic to cultured cells. No direct correlation has yet been drawn between changes in PrP structure and toxicity due to nucleic acid binding. Here we asked whether different aggregation, stability, and toxicity effects are detected when nonrelated DNA sequences interact with recombinant PrP. Using spectroscopic techniques to analyze PrP tertiary and secondary structure and cellular assays to assess toxicity, we found that rPrP-DNA interactions lead to different aggregated species, depending on the sequence and size of the oligonucleotide tested. A 21-mer DNA sequence (D67) induced higher levels of aggregation and also dissimilar structural changes in rPrP, compared to binding to oligonucleotides with the same length and different nucleotide sequences or different GC contents. The rPrP-D67 complex induced significant cell dysfunction, which appears to be correlated with the biophysical properties of the complex. Although sequence specificity is not apparent for PrP-nucleic acid interactions, we believe that particular nucleic acid patterns, possibly related to GC content, oligonucleotide length, and structure, govern PrP recognition. Understanding the structural and cellular effects observed for PrP-nucleic acid complexes may shed light on the still mysterious pathology of the prion protein.
... In AD brain, Aβ plaques are structurally and biochemically heterogeneous (12,13). Besides Aβ peptides, nonprotein constituents, such as lipids, glycosaminoglycans, and nucleic acids, have been detected inside plaques (14)(15)(16)(17)(18)(19)(20)(21)(22)(23). Previously, we have shown that soluble protein oligomers (i.e., amyloid precursors) have intrinsic affinity toward anionic cofactors, such as nucleic acids and glycosaminoglycans (GAGs), and that their interaction expedites the formation of amyloid fibrils (24). ...
... Our detailed examination using multiple NA-specific dyes indicates that both DNA and RNA are present within Aβ plaques in AD brain; however, the origin of plaque-sequestered nucleic acids is unclear. Interestingly, not only does Aβ naturally aggregate with DNA in vitro, Aβ species have also been located inside the nuclei of neurons in AD brains (20,22). DAPI + nuclear Aβ aggregates were shown to accumulate prior to the formation of extracellular DAPI + Aβ plaques in 5XFAD brain, lending to a notion that neuritic plaques derive from intracellular amyloid and have a neuronal origin (22). ...
Type I interferon (IFN) is a key cytokine that curbs viral infection and cell malignancy. Previously, we have demonstrated a potent IFN immunogenicity of nucleic acid (NA)-containing amyloid fibrils in the periphery. Here, we investigated whether IFN is associated with β-amyloidosis inside the brain and contributes to neuropathology. An IFN-stimulated gene (ISG) signature was detected in the brains of multiple murine Alzheimer disease (AD) models, a phenomenon also observed in wild-type mouse brain challenged with generic NA-containing amyloid fibrils. In vitro, microglia innately responded to NA-containing amyloid fibrils. In AD models, activated ISG-expressing microglia exclusively surrounded NA-positive amyloid β plaques, which accumulated in an age-dependent manner. Brain administration of rIFNβ resulted in microglial activation and complement C3-dependent synapse elimination in vivo. Conversely, selective IFN receptor blockade effectively diminished the ongoing microgliosis and synapse loss in AD models. Moreover, we detected activated ISG-expressing microglia enveloping NA-containing neuritic plaques in post-mortem brains of AD patients. Gene expression interrogation revealed that IFN pathway was grossly upregulated in clinical AD and significantly correlated with disease severity and complement activation. Therefore, IFN constitutes a pivotal element within the neuroinflammatory network of AD and critically contributes to neuropathogenic processes.
... Though the amyloid proteins themselves differ in primary amino acid sequence, all self-assemble into a conserved beta-sheet structure and associate with DNA. 23,29,[47][48][49] Recent work suggests that chronic systemic exposure to biofilms or to the amyloid/DNA complexes from Gramnegative or Gram-positive bacteria, curli/DNA and PSM/DNA, respectively, are associated with the generation of autoimmune responses both in mice and humans. 22,23,25,31,37,49,50 Curli is produced in the gastrointestinal tract by Gramnegative enteric bacteria 37 and serves as a major biofilm-associated PAMP. ...
The Salmonella biofilm-associated amyloid protein, curli, is a dominant instigator of systemic inflammation and autoimmune responses following Salmonella infection. Systemic curli injections or infection of mice with Salmonella Typhimurium induce the major features of reactive arthritis, an autoimmune disorder associated with Salmonella infection in humans. In this study, we investigated the link between inflammation and microbiota in exacerbating autoimmunity. We studied C57BL/6 mice from two sources, Taconic Farms and Jackson Labs. Mice from Taconic Farms have been reported to have higher basal levels of the inflammatory cytokine IL − 17 than do mice from Jackson Labs due to the differences in their microbiota. When we systemically injected mice with purified curli, we observed a significant increase in diversity in the microbiota of Jackson Labs mice but not in that of the Taconic mice. In Jackson Labs, mice, the most striking effect was the expansion of Prevotellaceae. Furthermore, there were increases in the relative abundance of the family Akkermansiaceae and decreases in families Clostridiaceae and Muribaculaceae in Jackson Labs mice. Curli treatment led to significantly aggravated immune responses in the Taconic mice compared to Jackson Labs counterparts. Expression and production of IL − 1β, a cytokine known to promote IL − 17 production, as well as expression of Tnfa increased in the gut mucosa of Taconic mice in the first 24 hours after curli injections, which correlated with significant increases in the number of neutrophils and macrophages in the mesenteric lymph nodes. A significant increase in the expression of Ccl3 in colon and cecum of Taconic mice injected with curli was detected. Taconic mice injected with curli also had elevated levels of inflammation in their knees. Overall, our data suggest that autoimmune responses to bacterial ligands, such as curli, are amplified in individuals with a microbiome that promote inflammation.
... For instance, they could play a role in the toxicity of human amyloids responsible for neurological disorders, such as Alzheimer's Aβ disease. Indeed, these amyloids bind to DNA, have been found inside the nucleus, and may strongly affect genetic expression [41,42]. ...
... For instance, they could play a role in the toxicity of human amyloids responsible for neurological disorders, such as Alzheimer's Aβ disease. Indeed, these amyloids bind to DNA, have been found inside the nucleus, and may strongly affect genetic expression [40,41]. ...
The mobility of protein is fundamental in the machinery of life. Here, we have investigated the effect of DNA binding in conjunction with DNA internal motion of the bacterial Hfq master regulator devoid of its amyloid C-terminus domain. Hfq is one of the most abundant nucleoid associated proteins that shape the bacterial chromosome and is involved in several aspects of nucleic acid metabolism. Fluorescence microscopy has been used to track a C-terminus domain lacking mutant form of Hfq on double stranded DNA, which is stretched by confinement to a rectangular nanofluidic channel. The mobility of the mutant is strongly accelerated with respect to the wild type variant. Furthermore, it shows a reverse dependence on the internal motion of DNA, in that slower motion results in slower protein diffusion. Results demonstrate the subtle role of DNA internal motion in controlling the mobility of a nucleoid associated protein, and, in particular, the importance of transient binding and moving DNA strands out of the way.
... It is well documented that DNA binds to amyloid- peptides, especially those capable of aggregating [41][42][43], and in turn, amyloid can alter the conformation of DNA itself [44][45][46][47]. Jiménez has hypothesized that protein-DNA interactions not only occur but are key to the origin of neurodegenerative diseases [48]. ...
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.
... Amyloid-beta (Aβ) peptides and prion proteins also have high DNA binding capacity, suggesting that DNA binding may be a common property of amyloidogenic proteins (Hegde et al., 2010). Binding of α-synuclein and other amyloidogenic proteins to DNA may affect normal DNA functions and cause genetic stress altering the normal pattern of gene expression (Jiménez, 2010). Results supporting this unifying hypothesis were obtained from the investigation which identified DNA aptamers that specifically bind to α-synuclein (Tsukakoshi et al., 2010(Tsukakoshi et al., , 2012. ...
Synuclein family consists of three members, α, β, and γ-synuclein. Due to their involvement in human diseases, they have been thoroughly investigated for the last 30 years. Since the first synuclein identification and description, members of this family are found in all vertebrates. Sequencing of their genes indicates high evolutionary conservation suggesting important function(s) of these proteins. They are small naturally unfolded proteins prone to aggregate, easily change their conformation, and bind to the membranes. The genes for α, β, and γ-synuclein have different chromosomal localization and a well preserved general organization composed of five coding exons of similar size. Three genes encoding synucleins are present in the majority of vertebrates, however, a variable number of synuclein genes are described in fishes of different species. An important question concerns their normal function in cells and tissues. α-Synuclein is implicated in the regulation of synaptic activity through regulation of synaptic vesicle release, while the physiological functions of two other members of the family is understood less clearly. Here we discuss recent results describing their role in the regulation of gene expression.
... AFM proved to be suitable for the study of these fine mechanical changes appearing in the quaternary protein structure. Such single molecule studies could hold the key to early detection of conformational changes leading to neurodegenerative diseases, such as Parkinson's or Alzheimer's disease[150][151][152]. Due to its versatile functions in the body and the relative complexity of its structure, fibronectin is an interesting protein for research[153][154][155]. ...
Nickel oxide thin films were deposited on glass substrates as the main gas sensor for H2 by the DC sputtering
technique at various discharge voltages within the range of 1.8–2.5 kV. Their structural, optical and gas sensing
properties were investigated by XRD, AFM, SEM, ultraviolet visible spectroscopy and home-made gas sensing
measurement units. A diffraction peak in the direction of NiO (200) was observed for the sputtered films,
thereby indicating that these films were polycrystalline in nature. The optical band gap of the films decreased
from 3.8 to 3.5 eV when the thickness of the films was increased from 83.5 to 164.4 nm in relation to an
increase in the sputtering discharge voltage from 1.8 to 2.5 kV, respectively. The gas sensitivity performance of
the NiO films that were formed was studied and the electrical responses of the NiO-based sensors toward
different H2 concentrations were also considered. The sensitivity of the gas sensor increased with the working
temperature and H2 gas concentration. The thickness of the NiO thin films was also an important parameter in
determining the properties of the NiO films as H2 sensors. It was shown in this study that NiO films have the
capability to detect H2 concentrations below 3% in wet air, a feature that allows this material to be used directly
for the monitoring of the environment.
... AFM proved to be suitable for the study of these fine mechanical changes appearing in the quaternary protein structure. Such single molecule studies could hold the key to early detection of conformational changes leading to neurodegenerative diseases, such as Parkinson's or Alzheimer's disease [150][151][152]. ...
In recent years, a great deal of interest has been focused on the development of novel atomic force microscopy (AFM)-based methods. From first being an unstable method, AFM has emerged as the perfect tool for the study of phenomena at the nanoscale, which includes quantitative single molecule studies. Numerous novel AFM methods play a crucial role in the invention of novel drugs, their delivery systems, based on either polymers or inorganic/metallic matrices, and in the examination of disease-related tissue changes. Such contemporary progressive studies are a perfect example of interdisciplinary research, which results in exemplary findings and discoveries. This review focuses especially on the literature published in the last decade; however the most important earlier discoveries are also included.
... The AP of amyloidogenic proteins is only formed transiently in solution [38], which made it challenging to study their biochemical properties. However, we have recently generated a form of stabilized AP derived from HSA, referred to as AP-HSA, which displays partially misfolded structure and is capable of converting to amyloid [34]. ...
Objective:
Amyloid deposition is linked to multiple human ailments, including neurodegenerative diseases, type 2 diabetes, and systemic amyloidosis. The assembly of misfolded proteins into amyloid fibrils involves an intermediate form, i.e., soluble amyloid precursor (AP), which exerts cytotoxic function. Insoluble amyloid also stimulates innate immune cells to elicit cytokine response and inflammation. How any of these misfolded proteins are controlled by the host remains obscure. Serum amyloid-P component (SAP) is a universal constituent of amyloid deposits. Short-chain pentraxins, which include both SAP and C-reactive protein (CRP), are pattern recognition molecules that bind to diverse ligands and promote the clearance of microbes and cell debris. Whether these pentraxins interact with AP and cofactor-containing amyloid and subsequently impact their function is not known.
Methods and results:
To detect the interaction between SAP and different types of amyloids, we performed dot blot analysis. The results showed that SAP invariably bound to protein-only, nucleic acid-containing and glycosaminoglycan-containing amyloid fibrils. This interaction required the presence of calcium. By ELISA, both SAP and CRP bound to soluble AP in the absence of divalent cations. Further characterization, by gel filtration, implied that SAP decamer may recognize AP whereas aggregated SAP preferentially associates with amyloid fibril. Although SAP binding did not affect cytotoxic function of AP, SAP potently inhibited the production of interferon-α from human plasmacytoid dendritic cells triggered by DNA-containing amyloid.
Conclusions:
Our data suggest that short pentraxins differentially interact with various forms of misfolded proteins and, in particular, modulate the ability of nucleic acid-containing amyloid to stimulate aberrant type I interferon response. Hence, pentraxins may function as key players in modulating the pathogenesis of protein misfolding diseases as well as interferon-mediated autoimmune manifestation.
... More than two dozen aberrant polypeptides that deposit amyloid have been implicated in human pathological conditions, including Alzheimer disease, Parkinson disease, and type 2 diabetes (35)(36)(37)(38). In human tissues, amyloid often contains non-proteinaceous cofactors (34,39) because amyloid precursor proteins have an affinity for nucleic acids and glycosaminoglycans, and interactions with these molecules expedite the formation of amyloid (40). Intriguingly, nucleic acid-containing amyloid fibrils activate endosomal TLRs to induce the release of IFN-I from pDCs (41). ...
Plasmacytoid dendritic cells (pDCs), which are prominent type I interferon (IFN-I)-producing immune cells, have been extensively implicated in systemic lupus erythematosus (SLE). However, whether they participate critically in lupus pathogenesis remains unknown. Recent studies using various genetic and cell type-specific ablation strategies have demonstrated that pDCs play a pivotal role in the development of autoantibodies and the progression of lupus under diverse experimental conditions. The findings of several investigations highlight a notion that pDCs operate critically at the early stage of lupus development. In particular, pDCs have a profound effect on B-cell activation and humoral autoimmunity in vivo. This deeper understanding of the vital role of pDCs in lupus pathogenesis supports the therapeutic targeting of the pDC-IFN-I pathway in SLE.
... How ever, even in the absence of oxidative stress, Aβ can penetrate into the nucleus [15] and interact with DNA [13,14]. It is supposed that this interaction can cause unfavorable changes in DNA expression and, ulti mately, the death of neurons [16]. ...
Interaction of intranuclear β-amyloid with DNA is considered to be a plausible mechanism of Alzheimer’s disease pathogenesis. The interaction of single- and double-stranded DNA with synthetic peptides was analyzed using surface plasmon resonance. The peptides represent the metal-binding domain of β-amyloid (amino acids 1–16) and its variants with chemical modifications and point substitutions of amino acid residues which are associated with enhanced neurotoxicity of β-amyloid in cell tests. It has been shown that the presence of zinc ions is necessary for the interaction of the peptides with DNA in solution. H6R substitution has remarkably reduced the ability of domain 1–16 to bind DNA. This is in accordance with the supposition that the coordination of a zinc ion by amino acid residues His6, Glu11, His13, and His14 of the β-amyloid metal-binding domain results in the occurrence of an anion-binding site responsible for the interaction of the domain with DNA. Zinc-induced dimerization and oligomerization of domain 1–16 associated with phosphorylation of Ser8 and the presence of unblocked amino- and carboxy-terminal groups have resulted in a decrease of peptide concentrations required for detection of the peptide-DNA interaction. The presence of multiple anion-binding sites on the dimers and oligomers is responsible for the enhancement of the peptide-DNA interaction. A substitution of the negatively charged residue Asp7 for the neutral residue Asn in close proximity to the anion-binding site of the domain 1–16 of Aβ facilitates the electrostatic interaction between this site and phosphates of a polynucleotide chain, which enhances zinc-induced binding to DNA.
... In addition, many bacterial biofilms contain extracellular DNA (eDNA) which acts to stabilize the biofilm matrix (Whitchurch et al., 2002(Whitchurch et al., ). 2012bJimenez, 2010). Immunization with amyloid fibers complexed with nucleic acids, in the presence of the classic adjuvant CFA, can induce autoantibodies in non-autoimmune mice within 12 weeks (Di Domizio et al., 2012a). ...
Research on the human microbiome has established that commensal and pathogenic bacteria can influence obesity, cancer, and autoimmunity through mechanisms mostly unknown. We found that a component of bacterial biofilms, the amyloid protein curli, irreversibly formed fibers with bacterial DNA during biofilm formation. This interaction accelerated amyloid polymerization and created potent immunogenic complexes that activated immune cells, including dendritic cells, to produce cytokines such as type I interferons, which are pathogenic in systemic lupus erythematosus (SLE). When given systemically, curli-DNA composites triggered immune activation and production of autoantibodies in lupus-prone and wild-type mice. We also found that the infection of lupus-prone mice with curli-producing bacteria triggered higher autoantibody titers compared to curli-deficient bacteria. These data provide a mechanism by which the microbiome and biofilm-producing enteric infections may contribute to the progression of SLE and point to a potential molecular target for treatment of autoimmunity.
Copyright © 2015 Elsevier Inc. All rights reserved.
... Amyloid fibrils contain extensive β sheet structures and can be found extracellularly or intracellularly. Amyloid depositions in vivo are often heterogeneous and contain non-proteinaceous cofactors [141,143], which may be explained by the fact that amyloid precursor proteins display an intrinsic affinity towards nucleic acids and glycosaminoglycans, an interaction that promotes the rapid formation of amyloid [144]. We examined the innate immune properties of amyloid fibrils containing nucleic acids and found that these complexes are potent inducers of type I IFN from human pDCs [145] ( Figure 1). ...
Plasmacytoid dendritic cells (pDCs) were initially identified as the prominent natural type I interferon-producing cells during viral infection. Over the past decade, the aberrant production of interferon α/β by pDCs in response to self-derived molecular entities has been critically implicated in the pathogenesis of systemic lupus erythematosus and recognized as a general feature underlying other autoimmune diseases. On top of imperative studies on human pDCs, the functional involvement and mechanism by which the pDC-interferon α/β pathway facilitates the progression of autoimmunity have been unraveled recently from investigations with several experimental lupus models. This article reviews correlating information obtained from human in vitro characterization and murine in vivo studies and highlights the fundamental and multifaceted contribution of pDCs to the pathogenesis of systemic autoimmune manifestation.
... Several factors may contribute to the protein misfolding and aggregation in NDs. These mainly include genetic (gene mutations of specific neuronal proteins) and environmental factors (toxic agents, oxidative damage, alterations of clearing systems such as the autophagoproteasome cascade, and abnormal protein-DNA interaction) (Jiménez, 2010;Sarkar, 2013). Apart from motor symptoms, patients affected by several NDs also suffer from several non-motor disorders classified as autonomic, psychiatric and sensory. ...
Neurodegenerative diseases (NDs) include a large variety of disorders that affects specific areas of the centralnervous system, leading to psychiatric and movement pathologies. A common feature that characterizes thesedisorders is the neuronal formation and accumulation of misfolded protein aggregates that lead to cell death. Inparticular, different proteinaceous aggregates accumulate to trigger a variety of clinical manifestations: prionprotein (PrPSc) in prion diseases, β-amyloid (Aβ) in Alzheimer's disease (AD), α-synuclein in Parkinson's disease(PD), huntingtin in Huntington's disease (HD), superoxide dismutase and TDP-43 in amyotrophic lateral sclerosis(ALS), tau in tauopathies. Non-motor alterations also occur in several viscera, in particular the gastrointestinaltract. These often precede the onset of motor symptoms by several years. For this reason, dysautonomic changescan be predictive of NDs and their correct recognition is being assuming a remarkable importance. This peculiarfeature led more and more to the concept that neurodegeneration may initiate in the periphery and propagate retrogradelytowards the central nervous system in a prion-like manner. In recent years, a particular attention wasdedicated to the clinical assessment of autonomic disorders in patients affected by NDs. In this respect, experimentalanimal models have been developed to understand the neurobiology underlying these effects as well as toinvestigate autonomic changes in peripheral organs. This review summarizes experimental studies that have beencarried out to understand autonomic symptoms in NDs, with the purpose to provide appropriate tools for comprehensiveand integrated studies.
... We recently established a method to prepare stabilized soluble oligomers of native proteins, which readily form amyloid in the presence of various cofactors 16 . The resulting amyloid fibrils reflect the complex nature of the terminal protein misfolding aggregates 17,18 . Here we use the term protein-only amyloid to refer the protein fibrils without cofactors and hybrid amyloid for the fibrils containing nonproteinaceous components. ...
Proteins carry out crucial tasks in organisms by exerting functions elicited from their specific three dimensional folds. Although the native structures of polypeptides fulfill many purposes, it is now recognized that most proteins can adopt an alternative assembly of beta-sheet rich amyloid. Insoluble amyloid fibrils are initially associated with multiple human ailments, but they are increasingly shown as functional players participating in various important cellular processes. In addition, amyloid deposited in patient tissues contains nonproteinaceous components, such as nucleic acids and glycosaminoglycans (GAGs). These cofactors can facilitate the formation of amyloid, resulting in the generation of different types of insoluble precipitates. By taking advantage of our understanding how proteins misfold via an intermediate stage of soluble amyloid precursor, we have devised a method to convert native proteins to amyloid fibrils in vitro. This approach allows one to prepare amyloid in large quantities, examine the properties of amyloid generated from specific proteins, and evaluate the structural changes accompanying the conversion.
... Tau is a highly soluble protein devoid of any well-defined secondary or tertiary structure, as many other proteins prone to aggregation and fibrillation also involved in neurodegenerative diseases [1]. It is the main component of intracellular tangles, which form the paired helical filaments (PHFs), the aberrant proteinaceous aggregates found associated to Alzheimer's disease [2,3] together with the extracellular senile plaques containing amyloid-. ...
Tau protein has been proposed as a trigger of Alzheimer's disease once it is hyperphosphorylated. However, the role that native tau forms play inside the neuronal nucleus remains unclear. In this work we present results concerning the interaction of tau protein with double-stranded DNA, single-stranded DNA, and also with a histone-DNA complex. The tau-DNA interaction results in a structure resembling the beads-on-a-string form produced by the binding of histone to DNA. DNA retardation assays show that tau and histone induce similar DNA retardation. A surface plasmon resonance study of tau-DNA interaction also confirms the minor groove of DNA as a binding site for tau, similarly to the histone binding. A residual binding of tau to DNA in the presence of Distamycin A, a minor groove binder, suggests the possibility that additional structural domains on DNA may be involved in tau interaction. Finally, DNA melting experiments show that, according to the Zipper model of helix-coil transition, the binding of tau increases the possibility of opening the DNA double helix in isolated points along the chain, upon increasing temperature. This behavior is analogous to histones and supports the previously reported idea that tau could play a protective role in stress situations. Taken together, these results show a similar behavior of tau and histone concerning DNA binding, suggesting that post-translational modifications on tau might impair the role that, by modulating the DNA function, might be attributable to the DNA-tau interaction.
... Given the importance of DNA or RNA metabolism deregulation in many diseases, these new insights might contribute to the understanding of disease etiology or dynamics. For instance, we note that 6 Alzheimer-related proteins can bind nucleic acids which could provide additional links with stress granules in Alzheimer and other neuropathologies [1, 37, 38]. YB-1 affinity for methylated cytosines was an intriguing finding that we wanted to explore in more detail. ...
... Given the importance of DNA or RNA metabolism deregulation in many diseases, these new insights might contribute to the understanding of disease etiology or dynamics. For instance, we note that six Alzheimer's disease-related proteins can bind nucleic acids, which could provide additional links with stress granules in Alzheimer's disease and other neuropathologies [1,37,38]. ...
The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported.
We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 238 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function.
The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms.
... Several transcription factors were identified ,such as Stat1, Daxx, transcriptional activator Pur-α and Pur-β, Ilf-2, and Ilf-3 (also known as nuclear factors 45 and 90, respectively), and several members of the HDAC, heat shock proteins, DDX, MAPK, importin, dynein, and kinesin families, just to name a few (unpublished data). Proteins implicated in neurodegenerative diseases, including AD, Parkinson's disease, and Huntington's disease and known not only for their tendency to aggregate but also to bind DNA nonspecifically (for review, see [33]), were also purified. In particular, we detected microtubule-associated protein tau, amyloid-β (Aβ) A4, alpha-and beta-synuclein, superoxyde dismutase (Cu-Zn and Mn), Huntingtin, Huntingtininteracting protein K, Huntingtin-interacting protein-related-1, and ataxin-10 (unpublished data). ...
Apolipoprotein D (ApoD) gene expression is increased in several neurological disorders such as Alzheimer's disease (AD) and multiple sclerosis. We previously showed that transgenic mice that overexpress human ApoD show a better resistance against paraquat or OC43 coronavirus-induced neurodegeneration. Here, we identified several nuclear factors from the cortex of control and OC43-infected mice which bind a fragment of the proximal ApoD promoter in vitro. Of interest, we detected apolipoprotein E (ApoE). Human ApoE consists of three isoforms (E2, E3, and E4) with the E4 and E2 alleles representing a greater and a lower risk for developping AD, respectively. Our results show that ApoE is located in the nucleus and on the ApoD promoter in human hepatic and glioblastoma cells lines. Furthermore, overexpression of ApoE3 and ApoE4 isoforms but not ApoE2 significantly inhibited the ApoD promoter activity in U87 cells (E3/E3 genotype) cultured under normal or different stress conditions while ApoE knock-down by siRNA had a converse effect. Consistent with these results, we also demonstrated by ChIP assay that E3 and E4 isoforms, but not E2, bind the ApoD promoter. Moreover, using the Allen Brain Atlas in situ hybridization database, we observed an inverse correlation between ApoD and ApoE mRNA expression during development and in several regions of the mouse brain, notably in the cortex, hippocampus, plexus choroid, and cerebellum. This negative correlation was also observed for cortex layers IV-VI based on a new Transcriptomic Atlas of the Mouse Neocortical Layers. These findings reveal a new function for ApoE by regulating ApoD gene expression.
... One plausible hypothesis suggests that interaction of intracellular A with genomic DNA can contribute to AD pathogenesis through interference with the normal DNA expression [1]. Indeed the localization of the intracellular A was found in cell nuclei (e.g., [2] [3]) and binding of A to DNA was shown in vitro [4] [5] [6] [7] [8] [9] [10]. ...
The interaction of the 16-mer synthetic peptide (Aβ16), which represents the metal-binding domain of the amyloid-β with DNA, was studied employing the surface plasmon resonance technique. It has been shown that Aβ16 binds to the duplex DNA in the presence of zinc ions and thus the metal-binding domain can serve as a zinc-dependent DNA-binding site of the amyloid-β. The interaction of Aβ16 with DNA most probably depends on oligomerization of the peptide and is dominated by interaction with phosphates of the DNA backbone.
... Multiple aberrant polypeptides are implicated in multiple human pathological conditions exemplified by Alzheimer's disease [46], whereas an increasing list of functional amyloids participate in diverse cellular functions [47][48][49]. Amyloid dispositions in vivo are frequently heterogeneous and contain nonproteinaceous cofactors [45,50]. The authors first observed that amyloid precursor proteins rapidly convert to amyloid fibrils in the presence of nucleic acids or glycosaminoglycans [51]. ...
In recent years, active research using genomic, cellular and animal modeling approaches has revealed the fundamental forces driving the development of autoimmune diseases. Type I interferon imprints unique molecular signatures in a list of autoimmune diseases. Interferon is induced by diverse nucleic acid-containing complexes, which trigger innate immune activation of plasmacytoid dendritic cells. Interferon primes, activates or differentiates various leukocyte populations to promote autoimmunity. Accordingly, interferon signaling is essential for the initiation and/or progression of lupus in several experimental models. However, the heterogeneous nature of systemic lupus erythematosus requires better characterization on how interferon pathways are activated and subsequently promote the advancement of autoimmune diseases. Given the central role of type I interferon, various strategies are devised to target these cytokines or related pathways to curtail the progression of autoimmune diseases.
... Because human " amylome " constitutes approximately 15% of all coding polypeptides in the genome, many " self " proteins have the potential to form amyloid (28). Amyloid depositions are frequently heterogeneous containing nonproteinaceous cofactors(15,20,21). Our results suggest that only the type of amyloidcontaining nucleic acids is capable of inducing IFN-I through activating nucleic acid-sensing TLRs. ...
The immunopathophysiologic development of systemic autoimmunity involves numerous factors through complex mechanisms that
are not fully understood. In systemic lupus erythematosus, type I IFN (IFN-I) produced by plasmacytoid dendritic cells (pDCs)
critically promotes the autoimmunity through its pleiotropic effects on immune cells. However, the host-derived factors that
enable abnormal IFN-I production and initial immune tolerance breakdown are largely unknown. Previously, we found that amyloid
precursor proteins form amyloid fibrils in the presence of nucleic acids. Here we report that nucleic acid-containing amyloid
fibrils can potently activate pDCs and enable IFN-I production in response to self-DNA, self-RNA, and dead cell debris. pDCs
can take up DNA-containing amyloid fibrils, which are retained in the early endosomes to activate TLR9, leading to high IFNα/β
production. In mice treated with DNA-containing amyloid fibrils, a rapid IFN response correlated with pDC infiltration and
activation. Immunization of nonautoimmune mice with DNA-containing amyloid fibrils induced antinuclear serology against a
panel of self-antigens. The mice exhibited positive proteinuria and deposited antibodies in their kidneys. Intriguingly, pDC
depletion obstructed IFN-I response and selectively abolished autoantibody generation. Our study reveals an innate immune
function of nucleic acid-containing amyloid fibrils and provides a potential link between compromised protein homeostasis
and autoimmunity via a pDC-IFN axis.
... Aberrant protein-DNA interactions mediated by misfolded proteins have been proposed as a novel pathological mechanism common to a myriad of neurological disorders (53). The fact that we did not observed increased levels of p53 in cells accumulating ␣-syn led us to hypothesize that aggravated repression of Notch1 might be a result of the interaction of ␣-syn and p53, which we further demonstrated to occur in adult hippocampal neural progenitors. ...
Parkinson disease is characterized by the loss of dopaminergic neurons mainly in the substantia nigra. Accumulation of α-synuclein and cell loss has been also reported in many other brain regions including the hippocampus, where it might impair adult neurogenesis, contributing to nonmotor symptoms. However, the molecular mechanisms of these alterations are still unknown. In this report we show that α-synuclein-accumulating adult rat hippocampus neural progenitors present aberrant neuronal differentiation, with reduction of Notch1 expression and downstream signaling targets. We characterized a Notch1 proximal promoter that contains p53 canonical response elements. In vivo binding of p53 represses the transcription of Notch1 in neurons. Moreover, we demonstrated that α-synuclein directly binds to the DNA at Notch1 promoter vicinity and also interacts with p53 protein, facilitating or increasing Notch1 signaling repression, which interferes with maturation and survival of neural progenitors cells. This study provides a molecular basis for α-synuclein-mediated disruption of adult neurogenesis in Parkinson disease.
... Other proteins appear to act in a prion-like manner in the pathophysiology of diseases such as Parkinson's, 147 amyotrophic lateral sclerosis and even cancer involving p53 mutations, [148][149][150] and nucleic acids appear to interact with the proteins in causing some of these diseases. 151 Even in bacteria, the interaction with nucleic acids leading to amyloid aggregates has been found. 152 The replication initiator protein of Pseudomonas pPS10 plasmid (RepA) aggregates into amyloids. ...
Prion diseases remain a challenge to modern science in the 21st century because of their capacity for transmission without an encoding nucleic acid. PrPSc, the infectious and alternatively folded form of the PrP prion protein, is capable of self-replication, using PrPC, the properly folded form of PrP, as a template. This process is associated with neuronal death and the clinical manifestation of prion-based diseases. Unfortunately, little is known about the mechanisms that drive this process. Over the last decade, the theory that a nucleic acid, such as an RNA molecule, might be involved in the process of prion structural conversion has become more widely accepted; such a nucleic acid would act as a catalyst rather than encoding genetic information. Significant amounts of data regarding the interactions of PrP with nucleic acids have created a new foundation for understanding prion conversion and the transmission of prion diseases. Our knowledge has been enhanced by the characterization of a large group of RNA molecules known as non-coding RNAs, which execute a series of important cellular functions, from transcriptional regulation to the modulation of neuroplasticity. The RNA-binding properties of PrP along with the competition with other polyanions, such as glycosaminoglycans and nucleic acid aptamers, open new avenues for therapy. WIREs RNA 2012, 3:415–428. doi: 10.1002/wrna.118
For further resources related to this article, please visit the WIREs website.
Amyloid inhibitors, such as the green tea compound epigallocatechin gallate EGCG, apomorphine or curlicide, have antibacterial properties. Conversely, antibiotics such as tetracycline derivatives or rifampicin also affect eukaryotic amyloids formation and may be used to treat neurodegenerative diseases. This opens the possibility for existing drugs to be repurposed in view of new therapy, targeting amyloid-like proteins from eukaryotes to prokaryotes and conversely. Here we present how to evaluate the effect of these amyloid-forming inhibitors on bacterial amyloid self-assemblies in vitro and on bacterial survival. The different approaches possible are presented.
Nucleic acid amyloid proteins interactions have been observed in the past few years. These interactions often promote protein aggregation. Nevertheless, molecular basis and physiological consequences of these interactions are still poorly understood. Additionally, it is unknown whether the nucleic acid promotes the formation of self-assembly due to direct interactions or indirectly via sequences surrounding the amyloid region. Here we focus our attention on a bacterial amyloid, Hfq. This protein is a pleiotropic bacterial regulator that mediates many aspects of nucleic acids metabolism. The protein notably mediates mRNA stability and translation efficiency by using stress-related small non coding regulatory RNA. In addition, Hfq, thanks to its amyloid C-terminal region, binds and compacts DNA. A combination of experimental methodologies, including synchrotron radiation circular dichroism (SRCD), gel shift assay and infrared (FTIR) spectroscopy have been used to probe the interaction of Hfq C-terminal region with DNA. We clearly identify important amino acids in this region involved in DNA binding and polymerization properties. This allows to understand better how this bacterial amyloid interacts with DNA. Possible functional consequence to answer to stresses are discussed.
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.
Dr. Sergey A. Kozin is a Leading Research Scientist at the V. A. Engelhardt Institute of Molecular Biology (EIMB) of the Russian Academy of Sciences (Moscow, Russia) since 2011. He graduated from the Leningrad Lensovet Institute of Technology (St. Petersburg, Russia) in 1988. In 1988–1991 he worked in the Institute of Polymer Materials (Perm, Russia). He received Ph.D. in Biochemistry in 1995 at the Institute of Biomedical Chemistry (IBMC) of the Russian Academy of Medical Sciences (Moscow, Russia). In 1996 he joined the Institute of Physico-Chemical Biology (Paris, France) as a researcher. In 1997 he was a postdoc in the Brandeis University (Waltham, Mass, USA), and in 1998–2004 he worked first postdoc at the Institute of Physico-Chemical Biology and later as invited assistant professor at the National Museum of Natural History (Paris, France). In 2004 Sergey Kozin got a position at IBMC. His research interests are molecular mechanisms of prion and Alzheimer's diseases. He is an author of about 80 research papers in peer review journals and conference proceedings.
Demenzen können nach der Ätiologie eingeteilt werden in neurodegenerative, vaskuläre und andere Prozesse. Vor allem die Erkenntnisse über neurodegenerative Mechanismen sind in den letzten Jahren stark angewachsen. An der praktischen therapeutischen Umsetzung wird mit Nachdruck gearbeitet (Finder 2010; Ballard et al. 2011; Seelaar et al. 2011). Dass diese noch nicht von Erfolg gekrönt war, darf nicht zu einem Nachlassen der wissenschaft lichen Anstrengungen führen – und auch nicht zu einer Vernachlässigung der verfügbaren Methoden.
Tau protein consists of six different isoforms and each one has particular physiological roles. In order to analyze the specific function of each single isoforms, large quantity of highly purified tau isoforms is essential. Many studies have been done to purify tau isoforms by heat treatment, followed by perchloric acid and glycerol precipitation. We found out that 1N/4R tau is soluble in glycerol, that is why mentioned methods do not work for purifying this isoform. In this study, large amounts of active and highly purified (97 %) 1N/4R tau protein has been prepared by utilization of trichloroacetic acid as precipitating agent.
The toxic property thus far shared by both ALS-linked SOD1 variants and wild-type SOD1 is an increased propensity to aggregation. However, whether SOD1 oligomers or aggregates are toxic to cells remains to be well defined. Moreover, how the toxic SOD1 species are removed from intra- and extra-cellular environments also needs to be further explored. The DNA binding has been shown to be capable of accelerating the aggregation of wild-type and oxidized SOD1 forms under acidic and neutral conditions. Here, we explore the binding of DNA and heparin, two types of essential life polyanions, to A4V, an ALS-linked SOD1 mutant, under acidic conditions, and its consequences. The polyanion binding alters the A4V conformation, neutralizes its local positive charges, and increases its local concentrations along the polyanion chain, which are sufficient to lead to acceleration of the pH-dependent A4V aggregation. The accelerated aggregation, which is ascribed to the polyanion binding-mediated removal or shortening of the lag phase in aggregation, contributes to the formation of amorphous A4V nanoparticles. The prolonged incubation with polyanions not only results in the complete conversion of likely soluble toxic A4V oligomers into non- and low-toxic SDS-resistant aggregates, but also increases their stability. Although this is only an initial step toward reducing the toxicity of SOD1 mutants, the accelerating role of polyanions in protein aggregation might become one of the rapid pathways that remove toxic forms of SOD1 mutants from intra- and extra-cellular environments. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.
Protein misfolding disorders (PMDs) refer to a group of diseases related to the misfolding of particular pro-teins 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 under-stood. Increasing experimental evidence indicates that abnor-mal 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 ag-gregate 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 pep-tides, 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. Keywords Protein aggregation . Protein misfolding . Protein–nucleic acid interaction . Degenerative diseases . Conformational conversion Abbreviations AD Alzheimer's disease α-syn alpha-synuclein HD Huntington's disease Htt huntingtin PD Parkinson's disease PrP prion protein PK proteinase K rPrP recombinant prion protein TSE transmissible spongiform encephalopathy Introduction
Aggregation, nuclear location, and nucleic acid interaction are common features shared by a number of proteins related to neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, transmissible spongiform encephalopathy, Huntington's disease, spinobulbar muscular atrophy, dentatorubro-pallidoluysian atrophy, and several spinocerebellar ataxias. β-Amyloid peptides, tau protein, α-synuclein, superoxide dismutase1, prion protein, huntingtin, atrophin1, androgen receptor, and several ataxins are proteins prone to becoming aggregated, to translocate inside cell nucleus, and to bind DNA. In this chapter, we review those common features suggesting that neurological diseases too may share a transcriptional disorder, making it an important contribution to the origin of the disease.
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Anomalous protein aggregation is closely associated to age-related mental illness. Extraneuronal plaques, mainly composed of aggregated amyloid peptides, are considered as hallmarks of Alzheimer's Disease. According to the amyloid cascade hypothesis, this disease starts as a consequence of an abnormal processing of the amyloid precursor protein resulting in an excess of amyloid peptides. Nuclear localization of amyloid peptide aggregates together with amyloid-DNA interaction, have been repeatedly reported. In this paper we have used Surface Plasmon Resonance and Electron Microscopy to study the structure and behavior of different peptides and proteins, including β-lactoglobulin, bovine serum albumin, myoglobin, histone, casein and the amyloid-β peptides related to Alzheimer's disease Aβ(25-35) and Aβ(1-40). The main purpose of this study is to investigate whether proneness to DNA interaction is a general property displayed by aggregated forms of proteins, or it is an interaction specifically related to the aggregated forms of those particular proteins and peptides related to neurodegenerative diseases. Our results reveal that those aggregates formed by amyloid peptides show a particular proneness to interact with DNA. They are the only aggregated structures capable of binding DNA, and show more affinity for DNA than for other polyanions as heparin and polyglutamic acid, therefore strengthening the hypothesis that amyloid peptides may, by means of interaction with nuclear DNA, contribute to the onset of Alzheimer Disease.
Prion protein (PrP) is involved in lethal neurodegenerative diseases, and many issues remain unclear about its physio-pathological role. Quadruplex-forming nucleic acids (NAs) have been found to specifically bind to both PrP cellular and pathological isoforms. To clarify the relevance of these interactions, thermodynamic, kinetic and structural studies have been performed, using isothermal titration calorimetry, surface plasmon resonance and circular dichroism methodologies. Three quadruplex-forming sequences, d(TGGGGT), r(GGAGGAGGAGGA), d(GGAGGAGGAGGA), and various forms of PrP were selected for this study. Our results showed that these quadruplexes exhibit a high affinity and specificity toward PrP, with K(D) values within the range 62÷630 nM, and a weaker affinity toward a PrP-β oligomer, which mimics the pathological isoform. We demonstrated that the NA quadruplex architecture is the structural determinant for the recognition by both PrP isoforms. Furthermore, we spotted both PrP N-terminal and C-terminal domains as the binding regions involved in the interaction with DNA/RNAs, using several PrP truncated forms. Interestingly, a reciprocally induced structure loss was observed upon PrP-NA interaction. Our results allowed to surmise a quadruplex unwinding-activity of PrP, that may have a feedback in vivo.
Amino acids form the building blocks of all proteins. Naturally occurring amino acids are restricted to a few tens of sidechains,
even when considering post-translational modifications and rare amino acids such as selenocysteine and pyrrolysine. However,
the potential chemical diversity of amino acid sidechains is nearly infinite. Exploiting this diversity by using non-natural
sidechains to expand the building blocks of proteins and peptides has recently found widespread applications in biochemistry,
protein engineering and drug design. Despite these applications, there is currently no unified online bioinformatics resource
for non-natural sidechains. With the SwissSidechain database (http://www.swisssidechain.ch), we offer a central and curated platform about non-natural sidechains for researchers in biochemistry, medicinal chemistry,
protein engineering and molecular modeling. SwissSidechain provides biophysical, structural and molecular data for hundreds
of commercially available non-natural amino acid sidechains, both in l- and d-configurations. The database can be easily browsed by sidechain names, families or physico-chemical properties. We also provide
plugins to seamlessly insert non-natural sidechains into peptides and proteins using molecular visualization software, as
well as topologies and parameters compatible with molecular mechanics software.
According to the amyloid hypothesis, abnormal processing of the β-amyloid precursor protein in Alzheimer's disease patients increases the production of β-amyloid toxic peptides, which, after forming highly aggregated fibrillar structures, lead to extracellular plaques formation, neuronal loss and dementia. However, a great deal of evidence has point to intracellular small oligomers of amyloid peptides, probably transient intermediates in the process of fibrillar structures formation, as the most toxic species. In order to study the amyloid-DNA interaction, we have selected here three different forms of the amyloid peptide: Aβ1-40, Aβ25-35 and a scrambled form of Aβ25-35. Surface Plasmon Resonance was used together with UV-visible spectroscopy, Electrophoresis and Electronic Microscopy to carry out this study. Our results prove that, similarly to the full length Aβ1-42, all conformations of toxic amyloid peptides, Aβ1-40 and Aβ25-35, may bind DNA. In contrast, the scrambled form of Aβ25-35, a non-aggregating and nontoxic form of this peptide, could not bind DNA. We conclude that although the amyloid-DNA interaction is closely related to the amyloid aggregation proneness, this cannot be the only factor which determines the interaction, since small oligomers of amyloid peptides may also bind DNA if their predominant negatively charged amino acid residues are previously neutralized.
Ample evidence suggests that almost all polypeptides can either adopt a native structure (folded or intrinsically disordered) or form misfolded amyloid fibrils. Soluble protein oligomers exist as an intermediate between these two states, and their cytotoxicity has been implicated in the pathology of multiple human diseases. However, the mechanism by which soluble protein oligomers develop into insoluble amyloid fibrils is not clear, and investigation of this important issue is hindered by the unavailability of stable protein oligomers. Here, we have obtained stabilized protein oligomers generated from common native proteins. These oligomers exert strong cytotoxicity and display a common conformational structure shared with known protein oligomers. They are soluble and remain stable in solution. Intriguingly, the stabilized protein oligomers interact preferentially with both nucleic acids and glycosaminoglycans (GAG), which facilitates their rapid conversion into insoluble amyloid. Concomitantly, binding with nucleic acids or GAG strongly diminished the cytotoxicity of the protein oligomers. EGCG, a small molecule that was previously shown to directly bind to protein oligomers, effectively inhibits the conversion to amyloid. These results indicate that stabilized oligomers of common proteins display characteristics similar to those of disease-associated protein oligomers and represent immediate precursors of less toxic amyloid fibrils. Amyloid conversion is potently expedited by certain physiological factors, such as nucleic acids and GAGs. These findings concur with reports of cofactor involvement with disease-associated amyloid and shed light on potential means to interfere with the pathogenic properties of misfolded proteins.
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterised by progressive muscular paralysis reflecting degeneration of motor neurones in the primary motor cortex, corticospinal tracts, brainstem and spinal cord. Incidence (average 1.89 per 100,000/year) and prevalence (average 5.2 per 100,000) are relatively uniform in Western countries, although foci of higher frequency occur in the Western Pacific. The mean age of onset for sporadic ALS is about 60 years. Overall, there is a slight male prevalence (M:F ratio approximately 1.5:1). Approximately two thirds of patients with typical ALS have a spinal form of the disease (limb onset) and present with symptoms related to focal muscle weakness and wasting, where the symptoms may start either distally or proximally in the upper and lower limbs. Gradually, spasticity may develop in the weakened atrophic limbs, affecting manual dexterity and gait. Patients with bulbar onset ALS usually present with dysarthria and dysphagia for solid or liquids, and limbs symptoms can develop almost simultaneously with bulbar symptoms, and in the vast majority of cases will occur within 1-2 years. Paralysis is progressive and leads to death due to respiratory failure within 2-3 years for bulbar onset cases and 3-5 years for limb onset ALS cases. Most ALS cases are sporadic but 5-10% of cases are familial, and of these 20% have a mutation of the SOD1 gene and about 2-5% have mutations of the TARDBP (TDP-43) gene. Two percent of apparently sporadic patients have SOD1 mutations, and TARDBP mutations also occur in sporadic cases. The diagnosis is based on clinical history, examination, electromyography, and exclusion of 'ALS-mimics' (e.g. cervical spondylotic myelopathies, multifocal motor neuropathy, Kennedy's disease) by appropriate investigations. The pathological hallmarks comprise loss of motor neurones with intraneuronal ubiquitin-immunoreactive inclusions in upper motor neurones and TDP-43 immunoreactive inclusions in degenerating lower motor neurones. Signs of upper motor neurone and lower motor neurone damage not explained by any other disease process are suggestive of ALS. The management of ALS is supportive, palliative, and multidisciplinary. Non-invasive ventilation prolongs survival and improves quality of life. Riluzole is the only drug that has been shown to extend survival.
Filamentous inclusions made of -synuclein constitute the defining neuropathological characteristic of Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Rare familial cases of Parkinson's disease are associated with mutations A53T and A30P in -synuclein. We report here the assembly properties and secondary structure characteristics of recombinant -synuclein. Carboxy-terminally truncated human -synuclein (1-87) and (1-120) showed the fastest rates of assembly, followed by human A53T -synuclein,and rat and zebra finch alpha-synuclein. Wild-type human alpha-synuclein and the A30P mutant showed slower rates of assembly. Upon shaking, filaments formed within 48 h at 37°C. The related proteins beta- and gamma-synuclein only assembled after several weeks of incubation. Synthetic human alpha-synuclein filaments were decorated by an antibody directed against the carboxy-terminal 10 amino acids of alpha-synuclein, as were filaments extracted from dementia with Lewy bodies and multiple system atrophy brains. Circular dichroism spectroscopy indicated that alpha-synuclein undergoes a conformational change from random coil to beta-sheet structure during assembly. X-ray diffraction and electron diffraction of the alpha-synuclein assemblies showed a cross-beta conformation characteristic of amyloid.
Transcriptional dysregulation is a central pathogenic mechanism in Huntington's disease, a fatal neurodegenerative disorder associated with polyglutamine (polyQ) expansion in the huntingtin (Htt) protein. In this study, we show that mutant Htt alters the normal expression of specific mRNA species at least partly by disrupting the binding activities of many transcription factors which govern the expression of the dysregulated mRNA species. Chromatin immunoprecipitation (ChIP) demonstrates Htt occupation of gene promoters in vivo in a polyQ-dependent manner, and furthermore, ChIP-on-chip and ChIP subcloning reveal that wild-type and mutant Htt exhibit differential genomic distributions. Exon 1 Htt binds DNA directly in the absence of other proteins and alters DNA conformation. PolyQ expansion increases Htt–DNA interactions, with binding to recognition elements of transcription factors whose function is altered in HD. Together, these findings suggest mutant Htt modulates gene expression through abnormal interactions with genomic DNA, altering DNA confor-mation and transcription factor binding.
Dentato-rubral and pallido-luysian atrophy (DRPLA) is one of the family of neurodegenerative diseases caused by expansion of a polyglutamine tract. The drpla gene product, atrophin-1, is widely expressed, has no known function or activity, and is found in both the nuclear and cytoplasmic compartments of neurons. Truncated fragments of atrophin-1 accumulate in neuronal nuclei in a transgenic mouse model of DRPLA, and may underlie the disease phenotype.
Using the yeast two-hybrid system, we identified ETO/MTG8, a component of nuclear receptor corepressor complexes, as an atrophin-1–interacting protein. When cotransfected into Neuro-2a cells, atrophin-1 and ETO/MTG8 colocalize in discrete nuclear structures that contain endogenous mSin3A and histone deacetylases. These structures are sodium dodecyl sulfate–soluble and associated with the nuclear matrix. Cotransfection of ETO/MTG8 with atrophin-1 recruits atrophin-1 to the nuclear matrix, while atrophin-1 and ETO/MTG8 cofractionate in nuclear matrix preparations from brains of DRPLA transgenic mice. Furthermore, in a cell transfection–based assay, atrophin-1 represses transcription. Together, these results suggest that atrophin-1 associates with nuclear receptor corepressor complexes and is involved in transcriptional regulation.
Emerging links between disease-associated polyglutamine proteins, nuclear receptors, translocation-leukemia proteins, and the nuclear matrix may have important repercussions for the pathobiology of this family of neurodegenerative disorders.
Amyloid -protein (A) is linked to neuronal injury and death in
Alzheimer's disease (AD). Of particular relevance for elucidating the
role of A in AD is new evidence that oligomeric forms of A are potent
neurotoxins that play a major role in neurodegeneration and the strong
association of the 42-residue form of A, A42, with the disease. Detailed
knowledge of the structure and assembly dynamics of A thus is important
for the development of properly targeted AD therapeutics. Recently, we
have shown that A oligomers can be cross-linked efficiently, and their
relative abundances quantified, by using the technique of photo-induced
cross-linking of unmodified proteins (PICUP). Here, PICUP,
size-exclusion chromatography, dynamic light scattering, circular
dichroism spectroscopy, and electron microscopy have been combined to
elucidate fundamental features of the early assembly of A40 and A42.
Carefully prepared aggregate-free A40 existed as monomers, dimers,
trimers, and tetramers, in rapid equilibrium. In contrast, A42
preferentially formed pentamer/hexamer units (paranuclei) that assembled
further to form beaded superstructures similar to early protofibrils.
Addition of Ile-41 to A40 was sufficient to induce formation of
paranuclei, but the presence of Ala-42 was required for their further
association. These data demonstrate that A42 assembly involves formation
of several distinct transient structures that gradually rearrange into
protofibrils. The strong etiologic association of A42 with AD may thus
be a result of assemblies formed at the earliest stages of peptide
oligomerization.
An amber mutation at codon 145 (Y145stop) of the prion protein gene results in a variant of an inherited human prion disease
named Gerstmann-Sträussler-Scheinker syndrome. The characteristic features of this disorder include amyloid deposits of prion
protein in cerebral parenchyma and vessels. We have studied the biosynthesis and processing of the prion protein containing
the Y145stop mutation (PrP145) in transfected human neuroblastoma cells in an attempt to clarify the effect of the mutation on the metabolism of PrP145 and to gain insight into the underlying pathogenetic mechanism. Our results demonstrate that 1) a significant proportion
of PrP145 is not processed post-translationally and retains the N-terminal signal peptide, 2) most PrP145 is degraded very rapidly by the proteasome-mediated pathway, 3) blockage of proteasomal degradation results in intracellular
accumulation of PrP145, 4) most of the accumulated PrP145 is detergent-insoluble, and both the detergent-soluble and -insoluble fractions are resistant to mild proteinase K (PK) treatment,
suggesting that PK resistance is not simply because of aggregation. The present study demonstrates for the first time that
a mutant prion protein is degraded through the proteasomal pathway and acquires PK-resistance if degradation is impaired.
The main hypothesis for prion diseases proposes that the cellular protein (PrPC) can be altered into a misfolded, β-sheet-rich isoform (PrPSc), which in most cases undergoes aggregation. In an organism infected with PrPSc, PrPC is converted into the β-sheet form, generating more PrPSc. We find that sequence-specific DNA binding to recombinant murine prion protein (mPrP-(23–231)) converts it from an α-helical
conformation (cellular isoform) into a soluble, β-sheet isoform similar to that found in the fibrillar state. The recombinant
murine prion protein and prion domains bind with high affinity to DNA sequences. Several double-stranded DNA sequences in
molar excess above 2:1 (pH 4.0) or 0.5:1 (pH 5.0) completely inhibit aggregation of prion peptides, as measured by light scattering,
fluorescence, and circular dichroism spectroscopy. However, at a high concentration, fibers (or peptide aggregates) can rescue
the peptide bound to the DNA, converting it to the aggregating form. Our results indicate that a macromolecular complex of
prion-DNA may act as an intermediate for the formation of the growing fiber. We propose that host nucleic acid may modulate
the delicate balance between the cellular and the misfolded conformations by reducing the protein mobility and by making the
protein-protein interactions more likely. In our model, the infectious material would act as a seed to rescue the protein
bound to nucleic acid. Accordingly, DNA would act on the one hand as a guardian of the Sc conformation, preventing its propagation,
but on the other hand may catalyze Sc conversion and aggregation if a threshold level is exceeded.
Transmissible spongiform encephalopathies are fatal neurodegenerative diseases associated with the accumulation of a protease-resistant
form of the prion protein (PrP). Although PrP is conserved in vertebrates, its function remains to be identified.In vitro PrP binds large nucleic acids causing the formation of nucleoprotein complexes resembling human immunodeficiency virus type
1 (HIV-1) nucleocapsid-RNA complexes and in vivoMuLV replication accelerates the scrapie infectious process, suggesting possible interactions between retroviruses and PrP.
Retroviruses, including HIV-1 encode a major nucleic acid binding protein (NC protein) found within the virus where 2000 NC
protein molecules coat the dimeric genome. NC is required in virus assembly and infection to chaperone RNA dimerization and
packaging and in proviral DNA synthesis by reverse transcriptase (RT). In HIV-1, 5′-leader RNA/NC interactions appear to control
these viral processes. This prompted us to compare and contrast the interactions of human and ovine PrP and HIV-1 NCp7 with
HIV-1 5′-leader RNA. Results show that PrP has properties characteristic of NCp7 with respect to viral RNA dimerization and
proviral DNA synthesis by RT. The NC-like properties of huPrP map to the N-terminal region of huPrP. Interestingly, PrP localizes
in the membrane and cytoplasm of PrP-expressing cells. These findings suggest that PrP is a multifunctional protein possibly
participating in nucleic acid metabolism.
Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder associ- ated with CAG/glutamine repeat expansion. While the DRPLA gene is ubiquitously expressed, neuron death occurs in specific anatomical areas of the brain. This predicts that the DRPLA protein interacts with other pro- teins and that these interactions may play a role in pathogenesis. Here, we describe a protein that binds to the DRPLA product. One of the clones isolated with a yeast two-hybrid system was identified as a human homolog of the insulin receptor tyrosine kinase substrate protein of 53 kDa (IRSp53). The gene produced two mRNA forms by differential splicing and encoded 552 and 521 amino acids, respectively. The longer form was mainly expressed in the brain and the shorter one in other tissues. The products were phosphorylated upon stimulation of cultured cells with insulin or insulin-like growth factor 1. Binding of the DRPLA protein to IRSp53 was ascertained by co-immunoprecipitation with antibodies and also by co-localization in perinuclear oval dots in cells expressing engineered constructs. A proline-rich region near the polyglutamine tract of the DRPLA protein and the SH3 domain of IRSp53 were involved in the binding. An extended polyglutamine tract significantly reduced binding ability in yeast cells, but not in in vitro binding assays. The identification of IRSp53 and other proteins detected by the yeast hybrid system predicts that DRPLA functions in a signal transduction pathway coupled with insulin/IGF-1.
The cognitive hallmark of early Alzheimer's disease (AD) is an extraordinary inability to form new memories. For many years, this dementia was attributed to nerve-cell death induced by deposits of fibrillar amyloid beta (Abeta). A newer hypothesis has emerged, however, in which early memory loss is considered a synapse failure caused by soluble Abeta oligomers. Such oligomers rapidly block long-term potentiation, a classic experimental paradigm for synaptic plasticity, and they are strikingly elevated in AD brain tissue and transgenic-mouse AD models. The current work characterizes the manner in which Abeta oligomers attack neurons. Antibodies raised against synthetic oligomers applied to AD brain sections were found to give diffuse stain around neuronal cell bodies, suggestive of a dendritic pattern, whereas soluble brain extracts showed robust AD-dependent reactivity in dot immunoblots. Antigens in unfractionated AD extracts attached with specificity to cultured rat hippocampal neurons, binding within dendritic arbors at discrete puncta. Crude fractionation showed ligand size to be between 10 and 100 kDa. Synthetic Abeta oligomers of the same size gave identical punctate binding, which was highly selective for particular neurons. Image analysis by confocal double-label immunofluorescence established that >90% of the punctate oligomer binding sites colocalized with the synaptic marker PSD-95 (postsynaptic density protein 95). Synaptic binding was accompanied by ectopic induction of Arc, a synaptic immediate-early gene, the overexpression of which has been linked to dysfunctional learning. Results suggest the hypothesis that targeting and functional disruption of particular synapses by Abeta oligomers may provide a molecular basis for the specific loss of memory function in early AD.
Tau is mainly distributed in cytoplasm and also found to be localized in the nucleus. There is limited data on DNA binding potential of Tau. We provide novel evidence on nicking of DNA by Tau. Tau nicks the supercoiled DNA leading to open circular and linear forms. The metal ion magnesium (a co-factor for endonuclease) enhanced the Tau DNA nicking ability, while an endonuclease specific inhibitor, aurinetricarboxylic acid (ATA) inhibited the Tau DNA nicking ability. Further, we also evidenced that Tau induces B-C-A mixed conformational transition in DNA and also changes DNA stability. Tau-scDNA complex is more sensitive to DNAse I digestion indicating stability changes in DNA caused by Tau. These findings indicate that Tau alters DNA helicity and integrity and also nicks the DNA. The relevance of these novel intriguing findings regarding the role Tau in neuronal dysfunction is discussed.
The presence of intracellular ubiquitylated inclusions in neurodegenerative disorders and the role of the ubiquitin/proteasome system (UPS) in degrading abnormal hazardous proteins have given rise to the hypothesis that UPS-impairment underlies neurodegenerative processes. However, this remains controversial for polyglutamine disorders such as Huntington disease (HD). Whereas studies in cellular models have provided evidence in favor of UPS-impairment attributable to expression of the N-terminal fragment of mutant huntingtin (N-mutHtt), similar studies on mouse models failed to do so. Furthermore, we have recently shown that the increase in polyubiquitin conjugates reported in the brain of N-mutHtt mice occurs in the absence of a general UPS-impairment. In the present study we aim to clarify the potential of N-mutHtt to impair UPS function in vivo as well as the mechanisms by which neurons may adapt after prolonged exposure to N-mutHtt in genetic models. By combining UPS reporter mice with an inducible mouse model of HD, we demonstrate for the first time polyglutamine-induced global UPS-impairment in vivo. UPS-impairment occurred transiently after acute N-mutHtt expression and restoration correlated with appearance of inclusion bodies (IBs). Consistently, UPS recovery did not take place when IB formation was prevented through administration of N-mutHtt aggregation-inhibitors in both cellular and animal models. Finally, no UPS-impairment was detected in old mice constitutively expressing N-mutHtt despite the age-associated decrease in brain proteasome activity. Therefore, our data reconcile previous contradictory reports by showing that N-mutHtt can indeed impair UPS function in vivo and that N-mutHtt aggregation leads to long lasting restoration of UPS function.
Expansion of a polymorphic polyglutamine segment is the common denominator of neurodegenerative polyglutamine diseases. The
expanded proteins typically accumulate in large intranuclear inclusions and induce neurodegeneration. However, the mechanisms
that determine the subcellular site and rate of inclusion formation are largely unknown. We found that the conserved putative
nuclear localization sequence Arg-Lys-Arg-Arg, which is retained in a highly aggregation-prone fragment of ataxin-3, did not
affect the site and degree of inclusion formation in a cell culture model of spinocerebellar ataxia type 3. Addition of synthetic
nuclear export or import signals led to the expected localization of ataxin-3 and determined the subcellular site of aggregate
formation. Triggering a cellular stress response by heat shock transcription factor ΔHSF1 coexpression abrogated aggregation
in the cytoplasm but not in the nucleus. These findings indicate that native aggregation-prone fragments derived from expanded
ataxin-3 may eventually escape the cytoplasmic quality control, resulting in aggregation in the nuclear compartment.
The microtubule-associated tau protein participates in the organization and integrity of the neuronal cytoskeleton. A nuclear form of tau has been described in neuronal and non-neuronal cells, which displays a nucleolar localization during interphase but is associated with nucleolar-organizing regions in mitotic cells. In the present study, based on immunofluorescence, immuno-FISH and confocal microscopy, we show that nuclear tau is mainly present at the internal periphery of nucleoli, partially colocalizing with the nucleolar protein nucleolin and human AT-rich alpha-satellite DNA sequences organized as constitutive heterochromatin. By using gel retardation, we demonstrate that tau not only colocalizes with, but also specifically binds to, AT-rich alpha-satellite DNA sequences apparently through the recognition of AT- rich DNA stretches. Here we propose a functional role for nuclear tau in relation to the nucleolar organization and/or heterochromatinization of a portion of RNA genes. Since nuclear tau has also been found in neurons from patients with Alzheimer's disease (AD), aberrant nuclear tau could affect the nucleolar organization during the course of AD. We discuss nucleolar tau associated with AT-rich alpha-satellite DNA sequences as a potential molecular link between trisomy 21 and AD.
Spinocerebellar ataxia type 6 (SCA6) is an autosomal dominant neurodegenerative disease caused by a small polyglutamine (polyQ) expansion (control: 4-20Q; SCA6: 20-33Q) in the carboxyl(C)-terminal cytoplasmic domain of the alpha(1A) voltage-dependent calcium channel (Ca(v)2.1). Although a 75-85-kDa Ca(v)2.1 C-terminal fragment (CTF) is toxic in cultured cells, its existence in human brains and its role in SCA6 pathogenesis remains unknown. Here, we investigated whether the small polyQ expansion alters the expression pattern and intracellular distribution of Ca(v)2.1 in human SCA6 brains. New antibodies against the Ca(v)2.1 C-terminus were used in immunoblotting and immunohistochemistry. In the cerebella of six control individuals, the CTF was detected in sucrose- and SDS-soluble cytosolic fractions; in the cerebella of two SCA6 patients, it was additionally detected in SDS-insoluble cytosolic and sucrose-soluble nuclear fractions. In contrast, however, the CTF was not detected either in the nuclear fraction or in the SDS-insoluble cytosolic fraction of SCA6 extracerebellar tissues, indicating that the CTF being insoluble in the cytoplasm or mislocalized to the nucleus only in the SCA6 cerebellum. Immunohistochemistry revealed abundant aggregates in cell bodies and dendrites of SCA6 Purkinje cells (seven patients) but not in controls (n = 6). Recombinant CTF with a small polyQ expansion (rCTF-Q28) aggregated in cultured PC12 cells, but neither rCTF-Q13 (normal-length polyQ) nor full-length Ca(v)2.1 with Q28 did. We conclude that SCA6 pathogenesis may be associated with the CTF, normally found in the cytoplasm, being aggregated in the cytoplasm and additionally distributed in the nucleus.
Polyglutamine (polyQ) expansion within the ataxin-7 protein, a member of the STAGA [SPT3-TAF(II)31-GCN5L acetylase] and TFTC (GCN5 and TRRAP) chromatin remodeling complexes, causes the neurodegenerative disease spinocerebellar ataxia type 7 (SCA7). Proteolytic processing of ataxin-7 by caspase-7 generates N-terminal toxic polyQ-containing fragments that accumulate with disease progression and play an important role in SCA7 pathogenesis. To elucidate the basis for the toxicity of these fragments, we evaluated which posttranslational modifications of the N-terminal fragment of ataxin-7 modulate turnover and toxicity. Here, we show that mutating lysine 257 (K257), an amino acid adjacent to the caspase-7 cleavage site of ataxin-7 regulates turnover of the truncation product in a repeat-dependent manner. Modification of ataxin-7 K257 by acetylation promotes accumulation of the fragment, while unmodified ataxin-7 is degraded. The degradation of the caspase-7 cleavage product is mediated by macroautophagy in cell culture and primary neuron models of SCA7. Consistent with this, the fragment colocalizes with autophagic vesicle markers, and enhanced fragment accumulation increases in these lysosomal structures. We suggest that the levels of fragment accumulation within the cell is a key event in SCA7 neurodegeneration, and enhancing clearance of polyQ-containing fragments may be an effective target to reduce neurotoxicity in SCA7.
TATA binding protein (TBP), a universal transcription factor, is broadly required by nuclear RNA polymerases for the initiation of transcription. TBP contains a polymorphic polyglutamine tract in its N-terminal region, and expansion of this tract leads to spinocerebellar ataxia type 17 (SCA17), one of nine dominantly inherited neurodegenerative diseases caused by polyglutamine expansion in the affected proteins. The expanded polyglutamine proteins are ubiquitously expressed, but cause selective and characteristic neurodegeneration in distinct brain regions in each disease. Unlike many other polyglutamine proteins, whose functions are not yet fully understood, TBP is a well-characterized transcription factor that is restricted to the nucleus. Thus, investigating how mutant TBP mediates neuropathology should help elucidate the mechanisms by which transcriptional dysregulation contributes to neuronal dysfunction and/or neurodegeneration in polyglutamine diseases. To this end, we characterized cellular and mouse models expressing polyQ-expanded TBP. The cell model exhibits characteristic features of neuronal dysfunction, including decreased cell viability and defective neurite outgrowth. We found that the high-affinity nerve growth factor receptor, TrkA, is down-regulated by mutant TBP in cells. Down-regulation of TrkA also occurs in the cerebellum of SCA17 transgenic mice prior to Purkinje cell degeneration. Mutant TBP binds more Sp1, reduces its occupancy of the TrkA promoter and inhibits the activity of the TrkA promoter. These findings suggest that the transcriptional down-regulation of TrkA by mutant TBP contributes to SCA17 pathogenesis.
Identification of genes expressed in response to prion infection may elucidate biomarkers for disease, identify factors involved in agent replication, mechanisms of neuropathology and therapeutic targets. Although several groups have sought to identify gene expression changes specific to prion disease, expression profiles rife with cell population changes have consistently been identified. Cuprizone, a neurotoxicant, qualitatively mimics the cell population changes observed in prion disease, resulting in both spongiform change and astrocytosis. The use of cuprizone-treated animals as an experimental control during comparative expression profiling allows for the identification of transcripts whose expression increases during prion disease and remains unchanged during cuprizone-triggered neuropathology. In this study, expression profiles from the brains of mice preclinically and clinically infected with Rocky Mountain Laboratory (RML) mouse-adapted scrapie agent and age-matched controls were profiled using Affymetrix gene arrays. In total, 164 genes were differentially regulated during prion infection. Eighty-three of these transcripts have been previously undescribed as differentially regulated during prion disease. A 0.4% cuprizone diet was utilized as a control for comparative expression profiling. Cuprizone treatment induced spongiosis and astrocyte proliferation as indicated by glial fibrillary acidic protein (Gfap) transcriptional activation and immunohistochemistry. Gene expression profiles from brain tissue obtained from cuprizone-treated mice identified 307 differentially regulated transcript changes. After comparative analysis, 17 transcripts unaffected by cuprizone treatment but increasing in expression from preclinical to clinical prion infection were identified. Here we describe the novel use of the prion disease mimetic, cuprizone, to control for cell population changes in the brain during prion infection.
The structural and dynamical properties of the metal-free form of WT human superoxide dismutase 1 (SOD1) and its familial amyotrophic lateral sclerosis (fALS)-related mutants, T54R and I113T, were characterized both in solution, through NMR, and in the crystal, through X-ray diffraction. We found that all 3 X-ray structures show significant structural disorder in 2 loop regions that are, at variance, well defined in the fully-metalated structures. Interestingly, the apo state crystallizes only at low temperatures, whereas all 3 proteins in the metalated form crystallize at any temperature, suggesting that crystallization selects one of the most stable conformations among the manifold adopted by the apo form in solution. Indeed, NMR experiments show that the protein in solution is highly disordered, sampling a large range of conformations. The large conformational variability of the apo state allows the free reduced cysteine Cys-6 to become highly solvent accessible in solution, whereas it is essentially buried in the metalated state and the crystal structures. Such solvent accessibility, together with that of Cys-111, accounts for the tendency to oligomerization of the metal-free state. The present results suggest that the investigation of the solution state coupled with that of the crystal state can provide major insights into SOD1 pathway toward oligomerization in relation to fALS.
Concerns over the potential for infectious prion proteins to contaminate human biologics and biotherapeutics have been raised from time to time. Transmission of the pathogenic form of prion protein (PrP(Sc)) through veterinary vaccines has been observed, yet no human case through the use of vaccine products has been reported. However, iatrogenic transmissions of PrP(Sc) in humans through blood components, tissues and growth hormone have been reported. These findings underscore the importance of reliable detection or diagnostic methods to prevent the transmission of prion diseases, given that the number of asymptomatic infected individuals remains unknown, the perceived incubation time for human prion diseases could be decades, and no cure of the diseases has been found yet. A variety of biochemical and molecular methods can selectively concentrate PrP(Sc) to facilitate its detection in tissues and cells. Furthermore, some methods routinely used in the manufacturing process of biological products have been found to be effective in reducing PrP(Sc) from the products. Questions remain unanswered as to the validation criteria of these methods, the minimal infectious dose of the PrP(Sc) required to cause infection and the susceptibility of cells used in gene therapy or the manufacturing process of biological products to PrP(Sc) infections. Here, we discuss some of these challenging issues.
This book classifies and groups dementias and movement disorders in terms of Molecular Pathology, a strategy that proved to be successful in the first edition in 2003. Since 2003 there have been so many significant advances in the field that a new edition is urgently required. Authors from the wide field of experts in the International Society of Neuropathology and related disciplines bring together the pathological features of all neurodegenerative diseases.
AMYOTROPHIC lateral sclerosis (ALS) is a degenerative disorder of motor neurons in the cortex, brainstem and spinal cord1,2. Its cause is unknown and it is uniformly fatal, typically within five years3. About 10% of cases are inherited as an autosomal dominant trait, with high penetrance after the sixth decade4,5. In most instances, sporadic and autosomal dominant familial ALS (FALS) are clinically similar4,6,7. We have previously shown that in some but not all FALS pedigrees the disease is linked to a genetic defect on chromosome 21q (refs 8, 9). Here we report tight genetic linkage between FALS and a gene that encodes a cytosolic, Cu/Zn-binding superoxide dismutase (SOD1), a homodimeric metalloenzyme that catalyzes the dismutation of the toxic superoxide anion O2.- to O2 and H2O2 (ref. 10). Given this linkage and the potential role of free radical toxicity in other neurodenegerative disorders11, we investigated SOD1 as a candidate gene in FALS. We identified 11 different SOD1 missense mutations in 13 different FALS families.
The distribution of CuZn superoxide dismutase (SOD) molecules in subcellular organelles in rat liver hepatocytes was studied using integrated biochemical, stereological, and quantitative immunocytochemical techniques. A known concentration of purified CuZn SOD in 10% gelatin was embedded alongside the liver tissue for the calculation of CuZn SOD concentrations in hepatocyte organelles and total CuZn SOD in the rat liver. Most of the CuZn SOD was located in the cytoplasmic matrix (73.1%) and in the nucleus (11.9%) with concentrations of 1.36 and 0.71 mg/cm3, respectively. Lysosomes contained the highest concentration (5.81 mg/cm3). Only low concentrations were measured in mitochondria (0.21 mg/cm3). Membrane-bound spaces of rough endoplasmic reticulum (ER), smooth ER, and the Golgi system did not contain significant concentrations of the enzyme. By adding up the concentrations in all subcellular compartments, a total liver content of CuZn SOD was established from the immunocytochemical measurements (0.386 +/- 0.028 mg/gm liver) that agreed closely with those obtained by biochemical assays (0.380 +/- 0.058 mg/gm liver). The average distances between two CuZn SOD molecules can be calculated from enzyme concentrations. It was determined that CuZn SOD molecules in the cytoplasmic matrix and nucleus were 34 and 42 nm apart, respectively. In peroxisomes and mitochondria, average intermolecular distance increased to approximately 60 nm and increased to 136 nm in smooth ER. CuZn SOD is a relatively abundant protein in the cytosol of hepatocytes and its distribution overlaps with major sites of O2- production. The efficiency of protection CuZn SOD can provide to cytosolic proteins from attacks by superoxide anion depends on the rate of O2- production, distribution of CuZn SOD relative to cytosolic proteins, and the relative reaction rates between O2- with both cytosolic proteins and CuZn SOD. Future studies of these substrate-enzyme relationships in vivo can lead to a greater understanding of how cells handle oxidant stress.
Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder associated with CAG/glutamine repeat expansion. While the DRPLA gene is ubiquitously expressed, neuron death occurs in specific anatomical areas of the brain. This predicts that the DRPLA protein interacts with other proteins and that these interactions may play a role in pathogenesis. Here, we describe a protein that binds to the DRPLA product. One of the clones isolated with a yeast two-hybrid system was identified as a human homolog of the insulin receptor tyrosine kinase substrate protein of 53 kDa (IRSp53). The gene produced two mRNA forms by differential splicing and encoded 552 and 521 amino acids, respectively. The longer form was mainly expressed in the brain and the shorter one in other tissues. The products were phosphorylated upon stimulation of cultured cells with insulin or insulin-like growth factor 1. Binding of the DRPLA protein to IRSp53 was ascertained by co-immunoprecipitation with antibodies and also by co-localization in perinuclear oval dots in cells expressing engineered constructs. A proline-rich region near the polyglutamine tract of the DRPLA protein and the SH3 domain of IRSp53 were involved in the binding. An extended polyglutamine tract significantly reduced binding ability in yeast cells, but not in in vitro binding assays. The identification of IRSp53 and other proteins detected by the yeast hybrid system predicts that DRPLA functions in a signal transduction pathway coupled with insulin/IGF-1.
Amyloid β protein (AβP) is the 40–42 residue polypeptide implicated in the pathogenesis of Alzheimer's disease (AD). We have reconstituted this peptide into phosphatidylserine liposomes and then fused the liposomes with a planar lipid bilayer. When incorporated into this bilayer, the AβP forms cation selective channels capable of transporting calcium and some monovalent cations including cesium, lithium, potassium, and sodium. The channels behave in an ohmic fashion and single channels can be shown to exhibit multiple subconductance states. Hitherto, AβP has been presumed to be neurotoxic, although direct demonstration of toxicity has proved elusive. On the basis of the present data we suggest that the ion channel activity of the polypeptide may be the basis of its neurotoxic effects.
To investigate whether the expansion of CAG repeats of the TATA-binding protein (TBP) gene is involved in the pathogenesis of neurodegenerative diseases, we have screened 118 patients with various forms of neurological disease and identified a sporadic-onset patient with unique neurologic symptoms consisting of ataxia and intellectual deterioration associated with de novo expansion of the CAG repeat of the TBP gene. The mutant TBP with an expanded polyglutamine stretch (63 glutamines) was demonstrated to be expressed in lymphoblastoid cell lines at a level comparable with that of wild-type TBP. The CAG repeat of the TBP gene consists of impure CAG repeat and the de novo expansion involves partial duplication of the CAG repeat. The present study provides new insights into sporadic-onset trinucleotide repeat diseases that involve de novo CAG repeat expansion.
Proteinaceous aggregates rich in copper, zinc superoxide dismutase (SOD1) have been found in both in vivo and in vitro models. We have shown that double-stranded DNA that acts as a template accelerates the in vitro formation of wild-type SOD1 aggregates. Here, we examined the polymorphism of templated-SOD1 aggregates generated in vitro upon association with DNA under different conditions. Electron microscopy imaging indicates that this polymorphism is capable of being manipulated by the shapes, structures, and doses of the DNAs tested. The nanometer- and micrometer-scale aggregates formed under acidic conditions and under neutral conditions containing ascorbate fall into three classes: aggregate monomers, oligomeric aggregates, and macroaggregates. The aggregate monomers observed at given DNA doses exhibit a polymorphism that is markedly corresponded to the coiled shapes of linear DNA and structures of plasmid DNA. On the other hand, the regularly branched structures observed under both atomic force microscopy and optical microscope indicate that the DNAs tested are simultaneously condensed into a nanoparticle with a specific morphology during SOD1 aggregation, revealing that SOD1 aggregation and DNA condensation are two concurrent phenomena. The results might provide the basis of therapeutic approaches to suppress the formation of toxic protein oligomers or aggregates by screening the toxicity of the protein aggregates with various sizes and morphologies. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 1154–1169, 2008.
This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Prions are unprecedented infectious pathogens that cause a group of
invariably fatal neurodegenerative diseases by an entirely novel
mechanism. Prion diseases may present as genetic, infectious, or
sporadic disorders, all of which involve modification of the prion
protein (PrP). Bovine spongiform encephalopathy (BSE), scrapie of
sheep, and Creutzfeldt–Jakob disease (CJD) of humans are among the
most notable prion diseases. Prions are transmissible particles that
are devoid of nucleic acid and seem to be composed exclusively of a
modified protein (PrPSc). The normal, cellular PrP
(PrPC) is converted into PrPSc through a
posttranslational process during which it acquires a high β-sheet
content. The species of a particular prion is encoded by the sequence
of the chromosomal PrP gene of the mammals in which it last replicated.
In contrast to pathogens carrying a nucleic acid genome, prions appear
to encipher strain-specific properties in the tertiary structure of
PrPSc. Transgenetic studies argue that PrPSc
acts as a template upon which PrPC is refolded into a
nascent PrPSc molecule through a process facilitated by
another protein. Miniprions generated in transgenic mice expressing
PrP, in which nearly half of the residues were deleted, exhibit unique
biological properties and should facilitate structural studies of
PrPSc. While knowledge about prions has profound
implications for studies of the structural plasticity of proteins,
investigations of prion diseases suggest that new strategies for the
prevention and treatment of these disorders may also find application
in the more common degenerative diseases.
Lewy bodies, a defining pathological characteristic of Parkinson's disease and dementia with Lewy bodies (DLB)1, 2, 3, 4, constitute the second most common nerve cell pathology, after the neurofibrillary lesions of Alzheimer's disease. Their formation may cause neurodegeneration, but their biochemical composition is unknown. Neurofilaments and ubiquitin are present5, 6, 7, 8, but it is unclear whether they are major components of the filamentous material of the Lewy body9,10. Here we describe strong staining of Lewy bodies from idiopathic Parkinson's disease with antibodies for -synuclein, a presynaptic protein of unknown function which is mutated in some familial cases of the disease11. -Synuclein may be the main component of the Lewy body in Parkinson's disease. We also show staining for -synuclein of Lewy bodies from DLB, indicating that the Lewy bodies from these two diseases may have identical compositions.
Bovine brain tau protein was tagged with the fluorescent dye 5 (and 6)-carboxy-x-rhodamine-succinimidyl ester and the functional properties of the fluorescent analog were tested in vitro by kinetic measurement and SDS gel electrophoresis. X-rhodamine tau was competent to bind to microtubules and promote microtubule assembly in vitro. Labeled tau was further characterized by microinjection of cultured Chinese hamster ovary (CHO) cells to study its intracellular distribution and potential new functions. X-rhodamine tau incorporated rapidly into centrosomes within seconds after microinjection. It distinctly labeled the microtubule network as early as 5 to 10 minutes following microinjection. In addition, X-rhodamine tau was transported into the nucleus and labeled the nucleolus specifically. Double labeling of the injected cells with DiC6(3) indicated that in some cases, fluorescent tau may associate with the endoplasmic reticulum. The concentrations of injected X-rhodamine tau ranged from 1.7 to 5.0 mg/ml, yet distinct bundling of microtubules was not observed. Studies of nocodazole effects on the microtubules established that X-rhodamine tau stabilized microtubules against depolymerization conditions. We conclude that this fluorescent analog of tau is associated with microtubules, the nucleolus, and other microtubule-related structures in living cells, and is competent to stabilize microtubules against microtubule depolymerizing drug treatment. This approach provides a useful model system for the study of modified tau in neurodegenerative disease. © 1993 Wiley-Liss, Inc.
A common feature of many neurodegenerative disorders is an abundance of activated glial cells (astrocytes and microglia). In Alzheimer's disease (AD), activated astrocytes are in close apposition to and surrounding the amyloid plaques. The mechanisms by which the astrocytes become activated in AD and the consequences of reactive astrocytosis to disease progression are not known. We examined the possibility that the amyloid-β (Aβ) peptide, a major constituent of the amyloid plaque, could act as a stimulus leading to activation. We found that treatment of rat cortical astrocyte cultures with aggregated Aβ 1–42 peptide induces activation, as assessed by reactive morphological changes and upregulation of selective glial mRNA and proteins, such as the inflammatory cytokine interleukin-1β. Aβ also stimulates inducible nitric oxide synthase (iNOS) mRNA levels and nitric oxide (NO) release. Aβ 1–42, a major form of amyloid associated with neurotoxicity, activated astrocytes in a time- and dose-dependent manner, whereas a scrambled Aβ 1–42 sequence or Aβ 17–42 had little or no effect. We also determined that the Aβ activity can be found in a supernatant fraction containing soluble Aβ oligomers. Our data suggest that Aβ plays a role in the reactive astrocytosis of AD and that the inflammatory response induced upon glial activation is a critical component of the neurodegenerative process.
The Huntington's disease (HD) gene has been mapped in 4p16.3 but has eluded identification. We have used haplotype analysis of linkage disequilibrium to spotlight a small segment of 4p16.3 as the likely location of the defect. A new gene, IT15, isolated using cloned trapped exons from the target area contains a polymorphic trinucleotide repeat that is expanded and unstable on HD chromosomes. A (CAG)n repeat longer than the normal range was observed on HD chromosomes from all 75 disease families examined, comprising a variety of ethnic backgrounds and 4p16.3 haplotypes. The (CAG)n repeat appears to be located within the coding sequence of a predicted approximately 348 kd protein that is widely expressed but unrelated to any known gene. Thus, the HD mutation involves an unstable DNA segment, similar to those described in fragile X syndrome, spino-bulbar muscular atrophy, and myotonic dystrophy, acting in the context of a novel 4p16.3 gene to produce a dominant phenotype.
Superoxide is generated by the mitochondrial respiratory chain. The transformation of this superoxide into hydrogen peroxide and, under certain conditions, then into hydroxyl radicals is important in diseases where respiratory chain function is abnormal or where superoxide dismutase function is altered, as in amyotrophic lateral sclerosis. In additon, these reactive oxygen species can influence the ageing process through mechanisms involving mutagenesis of mtDNA or increased rates of shortening of telomeric DNA.
Parkinson's disease is a primarily sporadic occurring neurodegenerative disorder of advanced age. However, in the last few years several genes have been identified that lead to a hereditary parkinsonian disorder with autosomal dominant or autosomal recessive inheritance. This includes autosomal dominant mutations in the alpha-synuclein, ubiquitin-C-terminal hydrolase-L1 (UCH-L1) and the leucine-rich repeat kinase (LRRK)2 genes and autosomal recessively inherited mutations in Parkin, PINK1, DJ-1 and the ATP13A2 genes. By taking the biochemical function of these genes and mutations into account, three underlying pathogenetic pathways can be identified: (i) altered protein quality control, (ii) oxidative stress and mitochondrial dysfunction, and (iii) disturbed kinase activity. It remains an open question whether alterations of these pathways lead to different entities of Parkinson's disease or whether they finally converge at a point that is the common pathogenetic denominator of Parkinson's disease. Finally cell death is executed by excitotoxicity, apoptosis and autophagy and appears to be facilitated by neuroinflammatory processes.
Spinocerebellar ataxia type 6 (SCA6) is a neurodegenerative disorder caused by abnormal expansions of a trinucleotide CAG repeat in exon 47 of the CACNA1A gene, which encodes the alpha1A subunit of the P/Q-type voltage-gated calcium channel. The CAG repeat expansion is translated into an elongated polyglutamine tract in the carboxyl terminus of the alpha1A subunit. The alpha1A subunit is the main pore-forming subunit of the P/Q-type calcium channel. Patients with SCA6 suffer from a severe form of progressive ataxia and cerebellar dysfunction. Design of treatments for this disorder will depend on better definition of the mechanism of disease. As a disease arising from a mutation in an ion channel gene, SCA6 may behave as an ion channelopathy, and may respond to attempts to modulate or correct ion channel function. Alternatively, as a disease in which the mutant protein contains an expanded polyglutamine tract, SCA6 may respond to the targets of drug therapies developed for Huntington's disease and other polyglutamine disorders. In this review we will compare SCA6 to other polyglutamine diseases and channelopathies, and we will highlight recent advances in our understanding of alpha1A subunits and SCA6 pathology. We also propose a mechanism for how two seemingly divergent hypotheses can be combined into a cohesive model for disease progression.
Spinal and bulbar muscular atrophy (SBMA) is a neurodegenerative disease caused by the expansion of a polyglutamine repeat within the androgen receptor (AR). We have studied the mutant AR in an in vitro system, and find both aggregation and proteolytic processing of the AR protein to occur in a polyglutamine repeat length-dependent manner. In addition, we find the aberrant metabolism of expanded repeat AR to be coupled to cellular toxicity, indicating a likely molecular basis for the toxic gain of AR function that produces neuronal degeneration in SBMA.
Neuropathologically, Alzheimer disease (AD) is characterized by the presence of extracellular plaques enriched in beta-amyloid peptides; however, the mechanism by which it results in the neurotoxicity is uncertain. The purpose of this study was to investigate whether it would prompt the progress of Alzheimer disease via enhancement of aberrant phosphorylated tau that results from its increased kinase gene expression.
Twenty-four male rats were divided into three groups, and each group had 8 rats: control, sham-operated, and Abeta(25-35) injected AD model groups. AD rat models were created by unilateral injections of Abeta(25-35) into the amygdala. The hyperphosphorylated tau protein was estimated by immunohistochemistry with paired helical filament-1 (PHF-1) antibody and paired helical filament-tau (AT8) antibody. The expressions of glycogen synthase kinase-3beta (GSK-3beta) and p38 mitogen-activated protein kinase (P(38)MAPK) mRNA were observed by in situ hybridization.
Compared with the control and sham-operated groups, the evaluation of paired AT8 and paired helical filament-1 (PHF-1) in the cortexes and hippocampus of the AD model group showed the numbers of AT8 and PHF-1 positive cells, as well as the optical density (OD) values of the proteins were significantly higher (AT8: in CA2: 0.318 +/- 0.037 vs. 0.135 +/- 0.028, 0.136 +/- 0.031; in frontal cortex: 0.278 +/- 0.040 vs. 0.130 +/- 0.028, 0.190 +/- 0.037. PHF-1: in CA2: 0.386 +/- 0.034 vs. 0.139 +/- 0.010, 0.193 +/- 0.041; in frontal cortex: 0.395 +/- 0.050 vs. 0.159 +/- 0.030, 0.190 +/- 0.044, respectively, P < 0.01); the number of GSK-3beta mRNA and P(38)MAPK mRNA positive cells of the AD model group, as well as the OD values, also increased significantly in the cortexes, hippocampus (GSK-3beta-mRNA: in CA2: 0.384 +/- 0.012 vs. 0.190 +/- 0.015, 0.258 +/- 0.064; in frontal cortex: 0.398 +/- 0.018 vs. 0.184 +/- 0.031, 0.218 +/- 0.049. P(38)MAPK mRNA: in CA2: 0.409 +/- 0.038 vs. 0.161 +/- 0.041, 0.189 +/- 0.035; in frontal cortex: 0.423 +/- 0.070 vs. 0.160 +/- 0.032, 0.203 +/- 0.053, respectively, P < 0.01).
Unilateral injection of Abeta(25-35) into the rat amygdala increases the generation of aberrant phosphorylated tau by increasing GSK-3beta and P(38)MAPK gene expression, that accelerates the process of Alzhemer's disease.
The brain responds to injury and infection by activating innate defense and tissue repair mechanisms. Working upon the hypothesis that the brain defense response involves common genes and pathways across diverse pathologies, we analysed global gene expression in brain from mouse models representing three major central nervous system disorders, cerebral stroke, multiple sclerosis and Alzheimer's disease compared to normal brain using DNA microarray expression profiling. A comparison of dysregulated genes across disease models revealed common genes and pathways including key components of estrogen and TGF-beta signaling pathways that have been associated with neuroprotection as well as a neurodegeneration mediator, TRPM7. Further, for each disease model, we discovered collections of differentially expressed genes that provide novel insight into the individual pathology and its associated mechanisms. Our data provide a resource for exploring the complex molecular mechanisms that underlie brain neurodegeneration and a new approach for identifying generic and disease-specific targets for therapy.
Expanded polyglutamine tracts cause neurodegeneration through a toxic gain-of-function mechanism. Generation of inclusions is a common feature of polyglutamine diseases and other protein misfolding disorders. Inclusion formation is likely to be a defensive response of the cell to the presence of unfolded protein. Recently, the compound B2 has been shown to increase inclusion formation and decrease toxicity of polyglutamine-expanded huntingtin in cultured cells. We explored the effect of B2 on spinal and bulbar muscular atrophy (SBMA). SBMA is caused by expansion of polyglutamine in the androgen receptor (AR) and is characterized by the loss of motor neurons in the brainstem and spinal cord. We found that B2 increases the deposition of mutant AR into nuclear inclusions, without altering the ligand-induced aggregation, expression, or subcellular distribution of the mutant protein. The effect of B2 on inclusions was associated with a decrease in AR transactivation function. We show that B2 reduces mutant AR toxicity in cell and fly models of SBMA, further supporting the idea that accumulation of polyglutamine-expanded protein into inclusions is protective. Our findings suggest B2 as a novel approach to therapy for SBMA.
Mice bearing mutations of copper-zinc-superoxide dismutase recapitulate spinal cord motor neuron degeneration and disease progression occurring in human amyotrophic lateral sclerosis. We have investigated the relationship between disease progression and altered gene expression by comparing the transcriptional profiles in lumbar spinal cord, fronto-parietal cortex and hippocampus of mutant G93A-SOD1, wild-type SOD1 transgenic and non-transgenic mice. Gene expression was evaluated at 55 and 110 days of age, representing pre-symptomatic and advanced disease stages of G93A mice, respectively. Whereas no significant variations were detectable in cortical and hippocampal areas, several mutation-related changes were detected in the lumbar spinal cord at the symptomatic stage, consistent with a condition of neuronal distress. Also, at both ages, we found a number of transgene-related changes, i.e. variations occurring in both transgenic groups independently of the G93A mutation, with wild-type SOD1- and G93A-SOD1-overexpressing mice displaying global transcriptional similarity at 110 days of age. Some of the changes in common between the two transgenic groups involve genes implicated in oxidative stress, inflammation, spinocerebellar degeneration and other neurodegenerative disorders. The finding that gene expressional alterations potentially associated to cellular distress are shared by wild-type and mutant human SOD1-overexpressing mice raises the possibility that mutated (in familial ALS) or otherwise dysregulated (in sporadic ALS) SOD1 expression is a common pathogenetic substrate of the disease.
Alzheimer's disease (AD) is characterized by a complex neurodegenerative process affecting multiple genes and proteins in the neocortex, many of which have not been well-studied. In this study, we investigated genome-wide gene alterations in the temporal cortex of a well-characterized cohort of AD patients using a recently developed microarray platform, and compared some of the transcript changes with immunoblotting. Of the 5485 genes found to be significantly altered in AD, there were consistent patterns of changes which show that the AD transcriptome in neocortex is characterized by changes indicative of synaptic dysfunction, perturbed neurotransmission and activation of neuroinflammation. We also highlighted several genes of potential pathogenic significance which have not been well studied in AD. The current study aims to add to the growing body of knowledge relating to gene changes in AD and provide further insights into pathogenic mechanisms and potential targets of pharmacotherapy.
Neuronal protein aggregates are considered as pathological hallmarks of various human neurodegenerative diseases, including the so-called CAG-repeat disorders, such as spinocerebellar ataxia Type 6 (SCA6). Since the immunocytochemical findings of an initial post-mortem study using a specific antibody against the disease protein of SCA6 (i.e., pathologically altered alpha-1A subunit of the P/Q type voltage-dependent calcium channel, CACNA1A) have not been confirmed so far, the occurrence and central nervous system distribution of neuronal protein aggregates in SCA6 is still a matter of debate. Owing to the fact that the antibody against the pathologically altered CACNA1A is not commercially available, we decided to apply a recently generated p62 antibody on brain tissue from two clinically diagnosed and genetically confirmed SCA6 patients. Application of this p62 antibody revealed numerous cytoplasmic neuronal inclusions in the degenerated cerebellar dentate nucleus and inferior olive of both SCA6 patients studied, whereby a subset of these aggregates were also ubiquitin-immunopositive. In view of the known role of p62 in protein degradation as well as aggresome/sequestosome formation, the p62 aggregate formation observed in the present study suggests that SCA6 not only is associated with an impairment of the calcium channel function and an elongated polyglutamine stretch in CACNA1A, but also with a defective protein handling by the protein quality control system.
The mechanisms underlying selective motor neuron degeneration in amyotrophic lateral sclerosis (ALS) remain unknown. There have been several important clinical trials on the treatment of ALS and treatment efficacy studies using mouse (SOD1) models of ALS. The latter revealed that diminished mutant SOD1 expression in the astrocytes delayed microglial activation and slowed disease progression. Dyslipidemia has been reported to have a protective effect in ALS patients. Current evidence has implicated a 43-kDa TAR DNA-binding protein (TDP-43) in the pathologenesis of ALS. Several mutations in TDP-43 were discovered in families with inherited motor neuron disease. Although phase III trials revealed that creatine monohydrate and IGF-1 was not beneficial for patients with ALS, favorable outcomes in SOD1 mice were reported with lithium, NADPH oxidase inhibitor, free-radical scavenger, and ammonium tetrathiomolybdate. Spinal and bulbar muscular atrophy (SBMA) is an adult-onset motor neuron disease affecting only males. Animal studies have revealed that the pathogenesis of SBMA depends on the serum testosterone level and that androgen deprivation mitigates neurodegeneration through inhibition of nuclear accumulation of the pathogenic androgen receptor (AR). Our studies have also identified several candidates for the treatment of SBMA. Selective inhibition of heat shock protein (HSP) facilitates the proteasomal degradation of pathogenic AR, leading to improvements in the signs and symptoms of SBMA mice. Oral administration of sodium butyrate--a histone deacetylase inhibitor--resulted in the improvement of neurological dysfunction in the SBMA mouse model, although its therapeutic dose range is narrow.
Spinal and bulbar muscular atrophy (SBMA) is an hereditary, adult-onset, lower motor neuron disease caused by an aberrant elongation of a trinucleotide CAG repeat, which encodes the polyglutamine tract, in the first exon of the androgen receptor (AR) gene. The main symptoms are slowly progressive muscle weakness and atrophy of bulbar, facial and limb muscles. The cardinal histopathological findings of SBMA are an extensive loss of lower motor neurons in the anterior horn of the spinal cord as well as in brainstem motor nuclei and intranuclear accumulations of mutant AR protein in the residual motor neurons. Androgen deprivation therapy rescues neuronal dysfunction in animal models of SBMA, suggesting that the molecular basis for motor neuron degeneration in this disorder is testosterone-dependent nuclear accumulation of the mutant AR. Suppression of disease progression by leuprorelin acetate has also been demonstrated in a phase 2 clinical trial. In addition, the clarification of pathophysiology leads to appearance of candidate drugs to treat this devastating disease: heat shock protein (HSP) inducer, Hsp90 inhibitor, and histone deacetylase inhibitor. Advances in basic and clinical research on SBMA are now paving the way for clinical application of pathogenesis-targeting therapeutics.
Inclusions of TAR DNA-binding protein-43 (TDP-43), a nuclear protein that regulates transcription and RNA splicing, are the defining histopathological feature of frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-Us) and sporadic and familial forms of amyotrophic lateral sclerosis (ALS). In ALS and FTLD-U, aggregated, ubiquitinated, and N-terminally truncated TDP-43 can be isolated from brain tissue rich in neuronal and glial cytoplasmic inclusions. The loss of TDP-43 function resulting from inappropriate cleavage, translocation from the nucleus, or its sequestration into inclusions could play important roles in neurodegeneration. However, it is not known whether TDP-43 fragments directly mediate toxicity and, more specifically, whether their abnormal aggregation is a cause or consequence of pathogenesis. We report that the ectopic expression of a approximately 25-kDa TDP-43 fragment corresponding to the C-terminal truncation product of caspase-cleaved TDP-43 leads to the formation of toxic, insoluble, and ubiquitin- and phospho-positive cytoplasmic inclusions within cells. The 25-kDa C-terminal fragment is more prone to phosphorylation at S409/S410 than full-length TDP-43, but phosphorylation at these sites is not required for inclusion formation or toxicity. Although this fragment shows no biological activity, its exogenous expression neither inhibits the function nor causes the sequestration of full-length nuclear TDP-43, suggesting that the 25-kDa fragment can induce cell death through a toxic gain-of-function. Finally, by generating a conformation-dependent antibody that detects C-terminal fragments, we show that this toxic cleavage product is specific for pathologic inclusions in human TDP-43 proteinopathies.
Previous evidence demonstrates that TAR DNA binding protein (TDP-43) mislocalization is a key pathological feature of amyotrophic lateral sclerosis (ALS). TDP-43 normally shows nuclear localization, but in CNS tissue from patients who died with ALS this protein mislocalizes to the cytoplasm. Disease specific TDP-43 species have also been reported to include hyperphosphorylated TDP-43, as well as a C-terminal fragment. Whether these abnormal TDP-43 features are present in patients with SOD1-related familial ALS (fALS), or in mutant SOD1 over-expressing transgenic mouse models of ALS remains controversial. Here we investigate TDP-43 pathology in transgenic mice expressing the G93A mutant form of SOD1. In contrast to previous reports we observe redistribution of TDP-43 to the cytoplasm of motor neurons in mutant SOD1 transgenic mice, but this is seen only in mice having advanced disease. Furthermore, we also observe rounded TDP-43 immunoreactive inclusions associated with intense ubiquitin immunoreactivity in lumbar spinal cord at end stage disease in mSOD mice. These data indicate that TDP-43 mislocalization and ubiquitination are present in end stage mSOD mice. However, we do not observe C-terminal TDP-43 fragments nor TDP-43 hyperphosphorylated species in these end stage mSOD mice. Our findings indicate that G93A mutant SOD1 transgenic mice recapitulate some key pathological, but not all biochemical hallmarks, of TDP-43 pathology previously observed in human ALS. These studies suggest motor neuron degeneration in the mutant SOD1 transgenic mice is associated with TDP-43 histopathology.
The spinocerebellar ataxias (SCAs) are diseases characterized by neurodegeneration of the spinocerebellum. To date, 28 autosomal dominant SCAs have been described and seventeen causative genes identified. These genes play a role in a broad range of cellular processes. Recent studies focused on the wild type and pathogenic functions of these genes implicate both gene expression and glutamate-dependent and calcium-dependent neuronal signaling as important pathways leading to cerebellar dysfunction. Understanding how these genes cause disease will allow a deeper understanding of the cerebellum in particular as well as neurodegenerative disease in general.
The nucleus is the primary site of protein aggregation in many polyglutamine diseases, suggesting a central role in pathogenesis. In SBMA, the nucleus is further implicated by the critical role for disease of androgens, which promote the nuclear translocation of the mutant androgen receptor (AR). To clarify the importance of the nucleus in SBMA, we genetically manipulated the nuclear localization signal of the polyglutamine-expanded AR. Transgenic mice expressing this mutant AR displayed inefficient nuclear translocation and substantially improved motor function compared with SBMA mice. While we found that nuclear localization of polyglutamine-expanded AR is required for SBMA, we also discovered, using cell models of SBMA, that it is insufficient for both aggregation and toxicity and requires androgens for these disease features. Through our studies of cultured motor neurons, we further found that the autophagic pathway was able to degrade cytoplasmically retained expanded AR and represents an endogenous neuroprotective mechanism. Moreover, pharmacologic induction of autophagy rescued motor neurons from the toxic effects of even nuclear-residing mutant AR, suggesting a therapeutic role for autophagy in this nucleus-centric disease. Thus, our studies firmly establish that polyglutamine-expanded AR must reside within nuclei in the presence of its ligand to cause SBMA. They also highlight a mechanistic basis for the requirement for nuclear localization in SBMA neurotoxicity, namely the lack of mutant AR removal by the autophagic protein degradation pathway.