bims-proned 2023-11-12 papers

bims-proned

Biomed News

on Proteostasis in neurodegeneration

Issue of 2023–11–12
twelve papers selected by
Verena Kohler, Umeå University

Single-Molecule Detection of α-Synuclein Oligomers in Parkinson's Disease Patients Using Nanopores.
Antagonizing pathological α-synuclein-mediated neurodegeneration by J24335 via the activation of immunoproteasome.
Conformational dynamics of α-synuclein and study of its intramolecular forces in the presence of selected compounds.
Effective Inhibition of TDP-43 Aggregation by Native State Stabilization.
Aggregation of alpha-synuclein disrupts mitochondrial metabolism and induce mitophagy via cardiolipin externalization.
Syrosingopine Enhances 20S Proteasome Activity and Degradation of α-Synuclein.
Peptide-based approaches to directly target alpha-synuclein in Parkinson's disease.
Cholestanol accelerates α-synuclein aggregation and spreading by activating asparagine endopeptidase.
Structural insights into the co-aggregation of Aβ and tau amyloid core peptides: Revealing potential pathological heterooligomers by simulations.
Unveiling the structural and functional consequences of the p.D109G pathogenic mutation in human αB-Crystallin responsible for restrictive cardiomyopathy and skeletal myopathy.
Simple model systems reveal conserved mechanisms of Alzheimer's disease and related tauopathies.
Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging.

ACS Nano. 2023 Nov 10.

Single-Molecule Detection of α-Synuclein Oligomers in Parkinson's Disease Patients Using Nanopores.

Yaxian Liu, Xiaoyi Wang, Giulia Campolo, Xiangyu Teng, Liming Ying, Joshua B Edel, Aleksandar P Ivanov.

  α-Synuclein (α-Syn) is an intrinsically disordered protein whose aggregation in the brain has been significantly implicated in Parkinson's disease (PD). Beyond the brain, oligomers of α-Synuclein are also found in cerebrospinal fluid (CSF) and blood, where the analysis of these aggregates may provide diagnostic routes and enable a better understanding of disease mechanisms. However, detecting α-Syn in CSF and blood is challenging due to its heterogeneous protein size and shape, and low abundance in clinical samples. Nanopore technology offers a promising route for the detection of single proteins in solution; however, the method often lacks the necessary selectivity in complex biofluids, where multiple background biomolecules are present. We address these limitations by developing a strategy that combines nanopore-based sensing with molecular carriers that can specifically capture α-Syn oligomers with sizes of less than 20 nm. We demonstrate that α-Synuclein oligomers can be detected directly in clinical samples, with minimal sample processing, by their ion current characteristics and successfully utilize this technology to differentiate cohorts of PD patients from healthy controls. The measurements indicate that detecting α-Syn oligomers present in CSF may potentially provide valuable insights into the progression and monitoring of Parkinson's disease.

Keywords:  Parkinson’s disease; carrier; cerebrospinal fluid; nanopore; neurodegeneration; protein aggregation; single-molecule; α-Synuclein oligomers

DOI:  https://doi.org/10.1021/acsnano.3c08456
Toxicol Appl Pharmacol. 2023 Nov 04. pii: S0041-008X(23)00384-8. [Epub ahead of print]480 116745

Antagonizing pathological α-synuclein-mediated neurodegeneration by J24335 via the activation of immunoproteasome.

Zhijian Pan, Chao-Wu Yu, Chen Zhao, Min Shao, Xuanjun Yang, Xiaonan Liang, Haitao Li, Yucong Lu, Qingqing Ye, Ji-Wang Chern, Jiahong Lu, Hefeng Zhou, Simon Ming-Yuen Lee.

  The aggregation of misfolded proteins, such as α-synuclein in Parkinson's disease (PD), occurs intracellularly or extracellularly in the majority of neurodegenerative diseases. The immunoproteasome has more potent chymotrypsin-like activity than normal proteasome. Thus, degradation of α-synuclein aggregation via immunoproteasome is an attractive approach for PD drug development. Herein, we aimed to determine if novel compound, 11-Hydroxy-1-(8-methoxy-5-(trifluoromethyl)quinolin-2-yl)undecan-1-one oxime (named as J24335), is a promising candidate for disease-modifying therapy to prevent the pathological progression of neurodegenerative diseases, such as PD. The effects of J24335 on inducible PC12/A53T-α-syn cell viability and cytotoxicity were evaluated by MTT assay and LDH assay, respectively. Evaluation of various proteasome activities was done by measuring the luminescence of enzymatic activity after the addition of different amounts of aminoluciferin. Immunoblotting and real-time PCR were employed to detect the expression of various proteins and genes, respectively. We also used a transgenic mouse model for behavioral testing and immunochemical analysis, to assess the neuroprotective effects of J24335. J24335 inhibited wild-type and mutant α-synuclein aggregation without affecting the growth or death of neuronal cells. The inhibition of α-synuclein aggregation by J24335 was caused by activation of immunoproteasome, as mediated by upregulation of LMP7, and increased cellular chymotrypsin-like activity in 20S proteasome. J24335-enhanced immunoproteasome activity was mediated by PKA/Akt/mTOR pathway activation. Moreover, animal studies revealed that J24335 treatment markedly mitigated both the loss of tyrosine hydroxylase-positive (TH-) neurons and impaired motor skill development. This is the first report to use J24335 as an immunoproteasome enhancing agent to antagonize pathological α-synuclein-mediated neurodegeneration.

Keywords:  Immunoproteasome; J24335; LMP7; Parkinson's disease; Protein degradation; α-Synuclein

DOI:  https://doi.org/10.1016/j.taap.2023.116745
Sci Rep. 2023 11 03. 13(1): 19020

Conformational dynamics of α-synuclein and study of its intramolecular forces in the presence of selected compounds.

Zahed Khatooni, Keivan Akhtari, Heather L Wilson.

Protein misfolding and aggregation play crucial roles in amyloidogenic diseases through the self-assembly of intrinsically disordered proteins (IDPs) in type II diabetes (T2D), Alzheimer's disease (AD) and Parkinson's disease (PD). PD is the most common neurodegenerative disorder after AD, and is associated with the loss of dopaminergic signaling, which causes motor and nonmotor signs and symptoms. Lewy bodies and Lewy neurites are common pathological hallmarks of PD that are mainly composed of aggregates of disordered α-synuclein (α-Syn). There have been many efforts to develop chemical compounds to prevent aggregation or facilitate disruption of the aggregates. Furthermore, the roles and interactions of many compounds have yet to be revealed at the atomistic level, especially their impacts on the dynamics and chain-chain interactions of the oligomers, which are of interest in this study. The conformational diversity and detailed interactions among homo-oligomer chains of α-Syn are not fully discovered; identifying these might help uncover a practical approach to developing a potent therapy. In this study, we used an in-silico investigation to address the conformational diversity of α-Syn oligomer. The roles of several point mutations in protein aggregation in PD are known; we take this further by evaluating the interaction energies and contributions of all residues in stability and residue-chain interactions. In this study, we docked chemical derivatives of three compounds with high drug-likeness properties to evaluate the roles of our ligands in the conformational dynamicity of the oligomers, with emphasis on intramolecular forces. Free energy evaluation of the modeled inter and intramolecular interactions through MD simulation shows effective interaction and binding between α-Syn and our compounds. However, we find that they do not significantly disrupt the chain-chain interactions, compared to unliganded simulation.

DOI: https://doi.org/10.1038/s41598-023-46181-1
Angew Chem Int Ed Engl. 2023 Nov 10. e202314587

Effective Inhibition of TDP-43 Aggregation by Native State Stabilization.

Lixin Yang, Yllza Jasiqi, Agnès Zettor, Oscar Vadas, Jeanne Chiaravalli, Fabrice Agou, Hilal A Lashuel.

  Preventing the misfolding or aggregation of transactive response DNA binding protein with 43 kDa (TDP-43) is the most actively pursued disease-modifying strategy to treat amyotrophic lateral sclerosis and other neurodegenerative diseases. In this work, we provide proof of concept that native state stabilization of TDP-43 is a viable and effective strategy for treating TDP-43 proteinopathies. Firstly, we leveraged the Cryo-EM structures of TDP-43 fibrils to design C-terminal substitutions that disrupt TDP-43 aggregation. Secondly, we showed that these substitutions (S333D/S342D) stabilize monomeric TDP-43 without altering its physiological properties. Thirdly, we demonstrated that binding native oligonucleotide ligands stabilized monomeric TDP-43 and prevented its fibrillization and phase separation in the absence of direct binding to the aggregation-prone C-terminal domain. Fourthly, we showed that the monomeric TDP-43 variant could be induced to aggregate in a controlled manner, which enabled the design and implementation of a high-throughput screening assay to identify native state stabilizers of TDP-43. Altogether, our findings demonstrate that different structural domains in TDP-43 could be exploited and targeted to develop drugs that stabilize the native state of TDP-43 and provide a platform to discover novel drugs to treat TDP-43 proteinopathies.

Keywords:  TDP-43 * Aggregation * Oligonucleotides * Native state stabilization

DOI:  https://doi.org/10.1002/anie.202314587
Cell Death Dis. 2023 Nov 10. 14(11): 729

Aggregation of alpha-synuclein disrupts mitochondrial metabolism and induce mitophagy via cardiolipin externalization.

Olivier Lurette, Rebeca Martín-Jiménez, Mehtab Khan, Razan Sheta, Stéphanie Jean, Mia Schofield, Maxime Teixeira, Raquel Rodriguez-Aller, Isabelle Perron, Abid Oueslati, Etienne Hebert-Chatelain.

Accumulation of α-synuclein aggregates in the substantia nigra pars compacta is central in the pathophysiology of Parkinson's disease, leading to the degeneration of dopaminergic neurons and the manifestation of motor symptoms. Although several PD models mimic the pathological accumulation of α-synuclein after overexpression, they do not allow for controlling and monitoring its aggregation. We recently generated a new optogenetic tool by which we can spatiotemporally control the aggregation of α-synuclein using a light-induced protein aggregation system. Using this innovative tool, we aimed to characterize the impact of α-synuclein clustering on mitochondria, whose activity is crucial to maintain neuronal survival. We observed that aggregates of α-synuclein transiently and dynamically interact with mitochondria, leading to mitochondrial depolarization, lower ATP production, mitochondrial fragmentation and degradation via cardiolipin externalization-dependent mitophagy. Aggregation of α-synuclein also leads to lower mitochondrial content in human dopaminergic neurons and in mouse midbrain. Interestingly, overexpression of α-synuclein alone did not induce mitochondrial degradation. This work is among the first to clearly discriminate between the impact of α-synuclein overexpression and aggregation on mitochondria. This study thus represents a new framework to characterize the role of mitochondria in PD.

DOI: https://doi.org/10.1038/s41419-023-06251-8
J Nat Prod. 2023 Nov 08.

Syrosingopine Enhances 20S Proteasome Activity and Degradation of α-Synuclein.

Yusaku Sadahiro, Soichiro Nishimura, Yuki Hitora, Sachiko Tsukamoto.

Cellular proteins are degraded by the 26S proteasome in the ubiquitin-proteasome system in an ATP-dependent manner, whereas intrinsically disordered proteins (IDPs) are degraded by the 20S proteasome independent of ATP and ubiquitin. The accumulation and aggregation of IDPs are considered to be the etiology of neurodegenerative diseases. Notably, the 20S proteasome has a cylindrical structure, and its gate on the α-ring is closed in the inactive form. The compounds that open the gate promote the degradation of IDPs and prevent their accumulation, and therefore, such compounds may be promising therapeutic agents for neurodegenerative diseases. After screening the Prestwick Phytochemical Library, several yohimbine-type and ergot alkaloids were identified that enhance the 20S proteasome activity. Among them, syrosingopine was the most potent activator of the 20S proteasome and enhanced the degradation of fluorogenic substrates and α-synuclein, an IDP. Furthermore, in HeLa cells, syrosingopine enabled the binding of a membrane-permeable fluorescent probe to the catalytic site of the 20S proteasome by opening the gate.

DOI: https://doi.org/10.1021/acs.jnatprod.3c00661
Mol Neurodegener. 2023 Nov 09. 18(1): 80

Peptide-based approaches to directly target alpha-synuclein in Parkinson's disease.

Scott G Allen, Richard M Meade, Lucy L White Stenner, Jody M Mason.

  Peptides and their mimetics are increasingly recognised as drug-like molecules, particularly for intracellular protein-protein interactions too large for inhibition by small molecules, and inaccessible to larger biologics. In the past two decades, evidence associating the misfolding and aggregation of alpha-synuclein strongly implicates this protein in disease onset and progression of Parkinson's disease and related synucleinopathies. The subsequent formation of toxic, intracellular, Lewy body deposits, in which alpha-synuclein is a major component, is a key diagnostic hallmark of the disease. To reach their therapeutic site of action, peptides must both cross the blood-brain barrier and enter dopaminergic neurons to prevent the formation of these intracellular inclusions. In this review, we describe and summarise the current efforts made in the development of peptides and their mimetics to directly engage with alpha-synuclein with the intention of modulating aggregation, and importantly, toxicity. This is a rapidly expanding field with great socioeconomic impact; these molecules harbour significant promise as therapeutics, or as early biomarkers during prodromal disease stages, or both. As these are age-dependent conditions, an increasing global life expectancy means disease prevalence is rising. No current treatments exist to either prevent or slow disease progression. It is therefore crucial that drugs are developed for these conditions before health care and social care capacities become overrun.

Keywords:  Alpha-Synuclein; Parkinson’s Disease; Peptide therapeutics; Peptidomimetics; Synucleinopathies

DOI:  https://doi.org/10.1186/s13024-023-00675-8
JCI Insight. 2023 Nov 08. pii: e165841. [Epub ahead of print]8(21):

Cholestanol accelerates α-synuclein aggregation and spreading by activating asparagine endopeptidase.

Ting Yu, Shuke Nie, Lihong Bu, Miao Liu, Juanfeng He, Xuan Niu, Hongyan Feng, Jifeng Guo, Beisha Tang, Zhaohui Zhang, Keqiang Ye, Haiqiang Jiang, Liam Chen, Zhentao Zhang.

  Cerebrotendinous xanthomatosis (CTX), an autosomal recessive disorder characterized by high levels of cholestanol in the blood and accumulation of cholestanol in multiple tissues, especially the brain, often presents in parkinsonism. However, it remains unknown whether cholestanol plays a role in the pathogenesis of sporadic Parkinson's disease (PD). Here, we show that the levels of serum cholestanol in patients with sporadic PD are higher than those in control participants. Cholestanol activates the protease asparagine endopeptidase (AEP) and induces the fragmentation of α-synuclein (α-syn) and facilitates its aggregation. Furthermore, cholestanol promotes the spreading of α-syn pathology in a mouse model induced by intrastriatal injection of α-syn fibrils. KO of AEP or administration of an AEP inhibitor ameliorates α-syn pathology, degeneration of the nigrostriatal dopaminergic pathway, and PD-like motor symptoms. These results not only indicate that cholestanol contributes to the aggregation and spreading of α-syn by activating AEP but also reveal an opportunity for treating PD with AEP inhibitors.

Keywords:  Neuroscience; Parkinson disease

DOI:  https://doi.org/10.1172/jci.insight.165841
Int J Biol Macromol. 2023 Nov 02. pii: S0141-8130(23)04740-2. [Epub ahead of print] 127841

Structural insights into the co-aggregation of Aβ and tau amyloid core peptides: Revealing potential pathological heterooligomers by simulations.

Xuhua Li, Yujie Chen, Zhiwei Yang, Shengli Zhang, Guanghong Wei, Lei Zhang.

  The self-aggregation of amyloid-β (Aβ) and tau proteins are closely implicated in Alzheimer's disease (AD). Recent evidence indicates that Aβ and tau proteins can cross-interact to form co-aggregates, which aggravates the development of AD. However, their transient heterooligomer conformations and co-aggregation molecular mechanisms are largely unknown. Herein, we utilize replica exchange molecular dynamics simulations to investigate the conformational ensembles formed by the central hydrophobic core of Aβ (Aβ16-22) and each of two fibril-nucleating core segments of tau (PHF6* and PHF6). Both PHF6 and PHF6* are found to co-aggregate with Aβ16-22 into β-sheet-rich heterooligomers. Intriguingly, PHF6 and Aβ16-22 peptides formed closed β-barrels, while PHF6* and Aβ16-22 formed open β-barrels, implying their distinct co-aggregation property. Compared to Aβ16-22-PHF6*, Aβ16-22-PHF6 heterooligomers have higher β-sheet content, and contain longer β-strands and larger β-sheets, indicative of stronger co-aggregation ability of PHF6 with Aβ16-22. Further analyses reveal that hydrophobic and π-π stacking interactions between Y310 of PHF6 and Aβ16-22 are crucial for the closed β-barrel/larger β-sheet formation in Aβ16-22-PHF6 heterooligomers. These results highlight the paramount importance of PHF6 fragment, particularly Y310 residue, as a potential target for inhibiting Aβ-tau co-aggregation, which could help for effective therapeutic design in mitigating Aβ-tau co-aggregation related amyloidogenesis.

Keywords:  Co-aggregation; Replica exchange molecular dynamics simulation; β-Barrel

DOI:  https://doi.org/10.1016/j.ijbiomac.2023.127841
Int J Biol Macromol. 2023 Nov 06. pii: S0141-8130(23)04832-8. [Epub ahead of print] 127933

Unveiling the structural and functional consequences of the p.D109G pathogenic mutation in human αB-Crystallin responsible for restrictive cardiomyopathy and skeletal myopathy.

Mehrnaz Hosseini Jafari, Mohammad Bagher Shahsavani, Masaru Hoshino, Jun Hong, Ali Akbar Saboury, Ali Akbar Moosavi-Movahedi, Reza Yousefi.

  αB-Crystallin (αB-Cry) is expressed in many tissues, and mutations in this protein are linked to various diseases, including cataracts, Alzheimer's disease, Parkinson's disease, and several types of myopathies and cardiomyopathies. The p.D109G mutation, which substitutes a conserved aspartate residue involved in the interchain salt bridges, with glycine leads to the development of both restrictive cardiomyopathy (RCM) and skeletal myopathy. In this study, we generated this mutation in the α-Cry domain (ACD) which is crucial for forming the active chaperone dimeric state, using site-directed mutagenesis. After inducing expression in the bacterial host, we purified the mutant and wild-type recombinant proteins using anion exchange chromatography. Various spectroscopic evaluations revealed significant changes in the secondary, tertiary, and quaternary structures of human αB-Cry caused by this mutation. Furthermore, this pathogenic mutation led to the formation of protein oligomers with larger sizes than those of the wild-type protein counterpart. The mutant protein also exhibited increased chaperone activity and decreased chemical, thermal, and proteolytic stability. Atomic force microscopy (AFM), transmission electron microscopy (TEM), and fluorescence microscopy (FM) demonstrated that p.D109G mutant protein is more prone to forming amyloid aggregates. The misfolding associated with the p.D109G mutation may result in abnormal interactions of human αB-Cry with its natural partners (e.g., desmin), leading to the formation of protein aggregates. These aggregates can interfere with normal cellular processes and may contribute to muscle cell dysfunction and damage, resulting in the pathogenic involvement of the p.D109G mutant protein in restrictive cardiomyopathy and skeletal myopathy.

Keywords:  Chaperone activity; Human αB-crystallin; Myopathy; Stability; Structure

DOI:  https://doi.org/10.1016/j.ijbiomac.2023.127933
Mol Neurodegener. 2023 Nov 10. 18(1): 82

Simple model systems reveal conserved mechanisms of Alzheimer's disease and related tauopathies.

Yuwei Jiang, Lesley T MacNeil.

  The lack of effective therapies that slow the progression of Alzheimer's disease (AD) and related tauopathies highlights the need for a more comprehensive understanding of the fundamental cellular mechanisms underlying these diseases. Model organisms, including yeast, worms, and flies, provide simple systems with which to investigate the mechanisms of disease. The evolutionary conservation of cellular pathways regulating proteostasis and stress response in these organisms facilitates the study of genetic factors that contribute to, or protect against, neurodegeneration. Here, we review genetic modifiers of neurodegeneration and related cellular pathways identified in the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit fly Drosophila melanogaster, focusing on models of AD and related tauopathies. We further address the potential of simple model systems to better understand the fundamental mechanisms that lead to AD and other neurodegenerative disorders.

Keywords:  Aggregation; Alzheimer’s disease; Amyloid-β; C. elegans; Cellular pathways; Drosophila; Genetic modifiers; Neurodegeneration; S. cerevisiae; Tau; Tauopathy

DOI:  https://doi.org/10.1186/s13024-023-00664-x
Nat Commun. 2023 Nov 03. 14(1): 7034

Integrative analysis reveals a conserved role for the amyloid precursor protein in proteostasis during aging.

Vanitha Nithianandam, Hassan Bukhari, Matthew J Leventhal, Rachel A Battaglia, Xianjun Dong, Ernest Fraenkel, Mel B Feany.

Aβ peptides derived from the amyloid precursor protein (APP) have been strongly implicated in the pathogenesis of Alzheimer's disease. However, the normal function of APP and the importance of that role in neurodegenerative disease is less clear. We recover the Drosophila ortholog of APP, Appl, in an unbiased forward genetic screen for neurodegeneration mutants. We perform comprehensive single cell transcriptional and proteomic studies of Appl mutant flies to investigate Appl function in the aging brain. We find an unexpected role for Appl in control of multiple cellular pathways, including translation, mitochondrial function, nucleic acid and lipid metabolism, cellular signaling and proteostasis. We mechanistically define a role for Appl in regulating autophagy through TGFβ signaling and document the broader relevance of our findings using mouse genetic, human iPSC and in vivo tauopathy models. Our results demonstrate a conserved role for APP in controlling age-dependent proteostasis with plausible relevance to Alzheimer's disease.

DOI: https://doi.org/10.1038/s41467-023-42822-1