bims-proned 2024-07-21 papers

bims-proned

Biomed News

on Proteostasis in neurodegeneration

Issue of 2024–07–21
twenty-one papers selected by
Verena Kohler, Umeå University

Interplay between Copper, Phosphatidylserine, and α-Synuclein Suggests a Link between Copper Homeostasis and Synaptic Vesicle Cycling.
Pro-inflammatory protein S100A9 targeted by a natural molecule to prevent neurodegeneration onset.
Cellular and pathological functions of tau.
Novel Insights into Parkin-Mediated Mitochondrial Dysfunction and "Mito-Inflammation" in α-Synuclein Toxicity. The Role of the cGAS-STING Signalling Pathway.
Why Is Arginine the Only Amino Acid That Inhibits Polyglutamine Monomers from Taking on Toxic Conformations?
Structurally targeted mutagenesis identifies key residues supporting α-synuclein misfolding in multiple system atrophy.
Beta-Site APP-Cleaving Enzyme-1 Inhibitory Role of Natural Flavonoids in the Treatment of Alzheimer's Disease.
Regulation of MicroRNA-4697-3p by Parkinson's disease-associated SNP rs329648 and its impact on SNCA112 mRNA.
The duality of amyloid-β: its role in normal and Alzheimer's disease states.
Exploring the Impact of C-Terminal Based Pentapeptides on the Disassembly of Aβ42 Fibrils.
TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms.
Macrocyclic peptides derived from AcPHF6* and AcPHF6 to selectively modulate the Tau aggregation.
In vivo CRISPR base editing for treatment of Huntington's disease.
Authentic hSAA related with AA amyloidosis: New method of purification, folding and amyloid polymorphism.
Enhancing amyloid beta inhibition and disintegration by natural compounds: A study utilizing spectroscopy, microscopy and cell biology.
Rotating magnetic field inhibits Aβ protein aggregation and alleviates cognitive impairment in Alzheimer's disease mice.
The reciprocal relationship between amyloid precursor protein and mitochondrial function.
An E3 ligase and autophagy adaptor regulates tau proteostasis through nested phase separation.
Diastolic dysfunction in Alzheimer's disease model mice is associated with Aβ-amyloid aggregate formation and mitochondrial dysfunction.
Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation.
The autophagy adaptor TRIAD3A promotes tau fibrillation by nested phase separation.

ACS Chem Neurosci. 2024 Jul 16.

Interplay between Copper, Phosphatidylserine, and α-Synuclein Suggests a Link between Copper Homeostasis and Synaptic Vesicle Cycling.

Xiangyu Teng, Ewelina Stefaniak, Keith R Willison, Liming Ying.

  Copper homeostasis is critical to the functioning of the brain, and its breakdown is linked with many brain diseases. Copper is also known to interact with the negatively charged lipid, phosphatidylserine (PS), as well as α-synuclein, an aggregation-prone protein enriched in the synapse, which plays a role in synaptic vesicle docking and fusion. However, the interplay between copper, PS lipid, and α-synuclein is not known. Herein, we report a detailed and predominantly kinetic study of the interactions among these three components pertinent to copper homeostasis and neurotransmission. We found that synaptic vesicle-mimicking small unilamellar vesicles (SUVs) can sequester any excess free Cu2+ within milliseconds, and bound Cu2+ on SUVs can be reduced to Cu+ by GSH at a nearly constant rate under physiological conditions. Moreover, we revealed that SUV-bound Cu2+ does not affect the binding between wild-type α-synuclein and SUVs but affect that between N-terminal acetylated α-synuclein and SUVs. In contrast, Cu2+ can effectively displace both types of α-synuclein from the vesicles. Our results suggest that synaptic vesicles may mediate copper transfer in the brain, while copper could participate in synaptic vesicle docking to the plasma membrane via its regulation of the interaction between α-synuclein and synaptic vesicle.

Keywords:  copper homeostasis; kinetics; phosphatidylserine; synaptic vesicle; α-synuclein

DOI:  https://doi.org/10.1021/acschemneuro.4c00280
Int J Biol Macromol. 2024 Jul 11. pii: S0141-8130(24)04643-9. [Epub ahead of print] 133838

Pro-inflammatory protein S100A9 targeted by a natural molecule to prevent neurodegeneration onset.

Manuela Leri, Dan Sun, Željko M Svedružic, Darius Šulskis, Vytautas Smirnovas, Massimo Stefani, Ludmilla Morozova-Roche, Monica Bucciantini.

  Accumulation of the pro-inflammatory protein S100A9 has been implicated in neuroinflammatory cascades in neurodegenerative diseases (NDs) such as Alzheimer's disease (AD) and Parkinson's disease (PD). S100A9 co-aggregates with other proteins such as α-synuclein in PD and Aβ in AD, contributing to amyloid plaque formation and neurotoxicity. The amyloidogenic nature of this protein and its role in chronic neuroinflammation suggest that it may play a key role in the pathophysiology of these diseases. Research into molecules targeting S100A9 could be a potential therapeutic strategy to prevent its amyloidogenic self-assembly and to attenuate the neuroinflammatory response in affected brain tissue. This work suggests that bioactive natural molecules, such as those found in the Mediterranean diet, may have the potential to alleviate neuroinflammation associated with the accumulation of proteins such as S100A9 in neurodegenerative diseases. A major component of extra virgin olive oil (EVOO), hydroxytyrosol (HT), with its ability to interact with and modulate S100A9 amyloid self-assembly and expression, offers a compelling approach for the development of novel and effective interventions for the prevention and treatment of ND. The findings highlight the importance of exploring natural compounds, such as HT, as potential therapeutic options for these complex and challenging neurological conditions.

Keywords:  Amyloid aggregation; Natural polyphenols; Neuro-inflammation; S100A9 protein

DOI:  https://doi.org/10.1016/j.ijbiomac.2024.133838
Nat Rev Mol Cell Biol. 2024 Jul 16.

Cellular and pathological functions of tau.

Celeste Parra Bravo, Sarah A Naguib, Li Gan.

Tau protein is involved in various cellular processes, including having a canonical role in binding and stabilization of microtubules in neurons. Tauopathies are neurodegenerative diseases marked by the abnormal accumulation of tau protein aggregates in neurons, as seen, for example, in conditions such as frontotemporal dementia and Alzheimer disease. Mutations in tau coding regions or that disrupt tau mRNA splicing, tau post-translational modifications and cellular stress factors (such as oxidative stress and inflammation) increase the tendency of tau to aggregate and interfere with its clearance. Pathological tau is strongly implicated in the progression of neurodegenerative diseases, and the propagation of tau aggregates is associated with disease severity. Recent technological advancements, including cryo-electron microscopy and disease models derived from human induced pluripotent stem cells, have increased our understanding of tau-related pathology in neurodegenerative conditions. Substantial progress has been made in deciphering tau aggregate structures and the molecular mechanisms that underlie protein aggregation and toxicity. In this Review, we discuss recent insights into the diverse cellular functions of tau and the pathology of tau inclusions and explore the potential for therapeutic interventions.

DOI: https://doi.org/10.1038/s41580-024-00753-9
J Inflamm Res. 2024 ;17 4549-4574

Novel Insights into Parkin-Mediated Mitochondrial Dysfunction and "Mito-Inflammation" in α-Synuclein Toxicity. The Role of the cGAS-STING Signalling Pathway.

Magdalena Gąssowska-Dobrowolska, Gabriela Olech-Kochańczyk, Carsten Culmsee, Agata Adamczyk.

  The prevalence of age-related neurodegenerative diseases, such as Parkinson's disease (PD) and related disorders continues to grow worldwide. Increasing evidence links intracellular inclusions of misfolded alpha-synuclein (α-syn) aggregates, so-called Lewy bodies (LB) and Lewy neuritis, to the progressive pathology of PD and other synucleinopathies. Our previous findings established that α-syn oligomers induce S-nitrosylation and deregulation of the E3-ubiquitin ligase Parkin, leading to mitochondrial disturbances in neuronal cells. The accumulation of damaged mitochondria as a consequence, together with the release of mitochondrial-derived damage-associated molecular patterns (mtDAMPs) could activate the innate immune response and induce neuroinflammation ("mito-inflammation"), eventually accelerating neurodegeneration. However, the molecular pathways that transmit pro-inflammatory signals from damaged mitochondria are not well understood. One of the proposed pathways could be the cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) (cGAS-STING) pathway, which plays a pivotal role in modulating the innate immune response. It has recently been suggested that cGAS-STING deregulation may contribute to the development of various pathological conditions. Especially, its excessive engagement may lead to neuroinflammation and appear to be essential for the development of neurodegenerative brain diseases, including PD. However, the precise molecular mechanisms underlying cGAS-STING pathway activation in PD and other synucleinopathies are not fully understood. This review focuses on linking mitochondrial dysfunction to neuroinflammation in these disorders, particularly emphasizing the role of the cGAS-STING signaling. We propose the cGAS-STING pathway as a critical driver of inflammation in α-syn-dependent neurodegeneration and hypothesize that cGAS-STING-driven "mito-inflammation" may be one of the key mechanisms promoting the neurodegeneration in PD. Understanding the molecular mechanisms of α-syn-induced cGAS-STING-associated "mito-inflammation" in PD and related synucleinopathies may contribute to the identification of new targets for the treatment of these disorders.

Keywords:  Parkin; cGAS–STING pathway; mito-inflammation; mtDAMPs; sterile inflammation; α-synuclein

DOI:  https://doi.org/10.2147/JIR.S468609
ACS Chem Neurosci. 2024 Jul 15.

Why Is Arginine the Only Amino Acid That Inhibits Polyglutamine Monomers from Taking on Toxic Conformations?

Shoichi Tanimoto, Hisashi Okumura.

  Polyglutamine (polyQ) diseases are devastating neurodegenerative disorders characterized by abnormal expansion of glutamine repeats within specific proteins. The aggregation of polyQ proteins is a critical pathological hallmark of these diseases. Arginine was identified as a promising inhibitory compound because it prevents polyQ-protein monomers from forming intra- and intermolecular β-sheet structures and hinders polyQ proteins from aggregating to form oligomers. Such an aggregation inhibitory effect was not observed in other amino acids. However, the underlying molecular mechanism of the aggregation inhibition and the factors that differentiate arginine from other amino acids, in terms of the inhibition of the polyQ-protein aggregation, remain poorly understood. Here, we performed replica-permutation molecular dynamics simulations to elucidate the molecular mechanism by which arginine inhibits the formation of the intramolecular β-sheet structure of a polyQ monomer. We found that the intramolecular β-sheet structure with more than four β-bridges of the polyQ monomer with arginine is more unstable than without any ligand and with lysine. We also found that arginine has 1.6-2.1 times more contact with polyQ than lysine. In addition, we revealed that arginine forms more hydrogen bonds with the main chain of the polyQ monomer than lysine. More hydrogen bonds formed between arginine and polyQ inhibit polyQ from forming the long intramolecular β-sheet structure. It is known that intramolecular β-sheet structure enhances intermolecular β-sheet structure between proteins. These effects are thought to be the reason for the inhibition of polyQ aggregation. This study provides insights into the molecular events underlying arginine's inhibition of polyQ-protein aggregation.

Keywords:  amyloid; arginine; generalized-ensemble algorithm; molecular dynamics simulation; polyglutamine; protein-aggregation inhibition

DOI:  https://doi.org/10.1021/acschemneuro.4c00276
bioRxiv. 2024 Jul 08. pii: 2024.07.04.602104. [Epub ahead of print]

Structurally targeted mutagenesis identifies key residues supporting α-synuclein misfolding in multiple system atrophy.

Patricia M Reis, Sara A M Holec, Chimere Ezeiruaku, Matthew P Frost, Christine K Brown, Samantha L Liu, Steven H Olson, Amanda L Woerman.

Multiple system atrophy (MSA) and Parkinson's disease (PD) are caused by misfolded α-synuclein spreading throughout the central nervous system. While familial PD is linked to several point mutations in α-synuclein, there are no known mutations associated with MSA. Our previous work investigating differences in α-synuclein misfolding between the two disorders showed that the familial PD mutation E46K inhibits replication of MSA prions both in vitro and in vivo , providing key evidence to support the hypothesis that α-synuclein adopts unique strains in patients. Here, to further interrogate α-synuclein misfolding, we engineered a panel of cell lines harboring both PD-linked and novel mutations designed to identify key residues that facilitate α-synuclein misfolding in MSA. These data were paired with in silico analyses using Maestro software to predict the effect of each mutation on the ability of α-synuclein to misfold into one of the reported MSA cryo-electron microscopy conformations. In many cases, our modeling accurately identified mutations that facilitated or inhibited MSA replication. However, Maestro was occasionally unable to predict the effect of a mutation on MSA propagation in vitro , demonstrating the challenge of using computational tools to investigate intrinsically disordered proteins. Finally, we used our cellular models to determine the mechanism underlying the E46K-driven inhibition of MSA replication, finding that the E46/K80 salt bridge is necessary to support α-synuclein misfolding. Overall, our studies use a structure-based approach to investigate α-synuclein misfolding, resulting in the creation of a powerful panel of cell lines that can be used to interrogate MSA strain biology.

DOI: https://doi.org/10.1101/2024.07.04.602104
Cent Nerv Syst Agents Med Chem. 2024 Jul 12.

Beta-Site APP-Cleaving Enzyme-1 Inhibitory Role of Natural Flavonoids in the Treatment of Alzheimer's Disease.

Sandeep Singh, Virendra Kushwaha, Shriram Sisodia, Shivendra Kumar, Kantrol Kumar Sahu.

  Alzheimer's Disease (AD) is a devastating neurological condition characterized by a progressive decline in cognitive function, including memory loss, reasoning difficulties, and disorientation. Its hallmark features include the formation of neurofibrillary tangles and neuritic plaques in the brain, disrupting normal neuronal function. Neurofibrillary tangles, composed of phosphorylated tau protein and neuritic plaques, containing amyloid-β protein (Aβ) aggregates, contribute to the degenerative process. The discovery of the beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) in 1999 revolutionized our understanding of AD pathogenesis. BACE1 plays a crucial role in the production of Aβ, the toxic protein implicated in AD progression. Elevated levels of BACE1 have been observed in AD brains and bodily fluids, underscoring its significance in disease onset and progression. Despite setbacks in clinical trials of BACE1 inhibitors due to efficacy and safety concerns, targeting BACE1 remains a promising therapeutic strategy for early-stage AD. Natural flavonoids have emerged as potential BACE1 inhibitors, demonstrating the ability to reduce Aβ production in neuronal cells and inhibit BACE1 activity. In our review, we delve into the pathophysiology of AD, highlighting the central role of BACE1 in Aβ production and disease progression. We explore the therapeutic potential of BACE1 inhibitors, including natural flavonoids, in controlling AD symptoms. Additionally, we provide insights into ongoing clinical trials and available patents in this field, shedding light on future directions for AD treatment research.

Keywords:  BACE-1 inhibitors; alzheimer's disease; flavonoids; isoflavonoids.; the amyloid-β protein (Aβ)

DOI:  https://doi.org/10.2174/0118715249315049240710063455
Mol Biol Rep. 2024 Jul 13. 51(1): 797

Regulation of MicroRNA-4697-3p by Parkinson's disease-associated SNP rs329648 and its impact on SNCA112 mRNA.

Myungsik Yoo, Klaudia Bunkowski, Andrew Lie, Eunsung Junn.

   BACKGROUND: Parkinson's disease (PD) is a common neurodegenerative disorder characterized by a multifaceted genetic foundation. Genome-Wide Association Studies (GWAS) have played a crucial role in pinpointing genetic variants linked to PD susceptibility. Current study aims to delve into the mechanistic aspects through which the PD-associated Single Nucleotide Polymorphism (SNP) rs329648, identified in prior GWAS, influences the pathogenesis of PD.
METHODS AND RESULTS: Employing the CRISPR/Cas9-mediated genome editing mechanism, we demonstrated the association of the disease-associated allele of rs329648 with increased expression of miR-4697-3p in differentiated SH-SY5Y cells. We revealed that miR-4697-3p contributes to the formation of high molecular weight complexes of α-Synuclein (α-Syn), indicative of α-Syn aggregate formation, as evidenced by Western blot analysis. Furthermore, our study unveiled that miR-4697-3p elevates SNCA112 mRNA levels. The resultant protein product, α-Syn 112, a variant of α-Syn with 112 amino acids, is recognized for augmenting α-Syn aggregation. Notably, this regulatory effect minimally impacts the levels of full-length SNCA140 mRNA, as evidenced by qRT-PCR. Additionally, we observed a correlation between the disease-associated allele and miR-4697-3p with increased cell death, substantiated by assessments including cell viability assays, alterations in cell morphology, and TUNEL assays.
CONCLUSION: Our research reveals that the disease-associated allele of rs329648 is linked to higher levels of miR-4697-3p. This increase in miR-4697-3p leads to elevated SNCA112 mRNA levels, consequently promoting the formation of α-Syn aggregates. Furthermore, miR-4697-3p appears to play a role in increased cell death, potentially contributing to the pathogenesis of PD.

Keywords:  Alpha-synuclein; Genome-wide association studies (GWAS); Parkinson’s disease; SNCA112 mRNA; miR-4697-3p; rs329638

DOI:  https://doi.org/10.1007/s11033-024-09725-w
Mol Brain. 2024 Jul 17. 17(1): 44

The duality of amyloid-β: its role in normal and Alzheimer's disease states.

Ali Azargoonjahromi.

  Alzheimer's disease (AD) is a degenerative neurological condition that gradually impairs cognitive abilities, disrupts memory retention, and impedes daily functioning by impacting the cells of the brain. A key characteristic of AD is the accumulation of amyloid-beta (Aβ) plaques, which play pivotal roles in disease progression. These plaques initiate a cascade of events including neuroinflammation, synaptic dysfunction, tau pathology, oxidative stress, impaired protein clearance, mitochondrial dysfunction, and disrupted calcium homeostasis. Aβ accumulation is also closely associated with other hallmark features of AD, underscoring its significance. Aβ is generated through cleavage of the amyloid precursor protein (APP) and plays a dual role depending on its processing pathway. The non-amyloidogenic pathway reduces Aβ production and has neuroprotective and anti-inflammatory effects, whereas the amyloidogenic pathway leads to the production of Aβ peptides, including Aβ40 and Aβ42, which contribute to neurodegeneration and toxic effects in AD. Understanding the multifaceted role of Aβ, particularly in AD, is crucial for developing effective therapeutic strategies that target Aβ metabolism, aggregation, and clearance with the aim of mitigating the detrimental consequences of the disease. This review aims to explore the mechanisms and functions of Aβ under normal and abnormal conditions, particularly in AD, by examining both its beneficial and detrimental effects.

Keywords:  Alzheimer’s disease; Beta amyloid; Cognitive decline; Long-term potentiation; Neuroinflammation; Neuroprotection; Neurotoxicity

DOI:  https://doi.org/10.1186/s13041-024-01118-1
ChemMedChem. 2024 Jul 18. e202400486

Exploring the Impact of C-Terminal Based Pentapeptides on the Disassembly of Aβ42 Fibrils.

Apneet Kaur, Opinder Kaur Mankoo, Diksha Rani, Nitesh Priyadarshi, Deepti Goyal, Nitin Kumar Singhal, Bhupesh Goyal.

  An effective therapeutic strategy to suppress Alzheimer's disease (AD) progression is to disrupt β-sheet rich neurotoxic soluble amyloid-β (Aβ) aggregates. Previously, we identified new pentapeptides (RVVPI and RIAPA) with notably enhanced ability to block Aβ42 aggregation as compared to Aβ42 C-terminal derived peptide RIIGL using integrated computational protocol. In this work, the potential of RIIGL, RVVPI, and RIAPA for the structural destabilization of Aβ42 protofibril was assessed by molecular dynamics (MD) simulations and in vitro studies. The binding free energy analysis depicts that charged residues influence Aβ42 protofibril-pentapeptide interactions. Notably, RVVPI displays a more pronounced destabilization effect than other peptides due to higher conformational fluctuations, and disruption of salt bridge (K28-A42) interactions in Aβ42 protofibril. RVVPI exhibited highest inhibitory activity (Inhibition= 66.2%, IC50= 5.57 ± 0.83 µM) against Aβ42 aggregation consistent with computational results. Remarkably, RVVPI displayed ~4.5 fold lower IC50 value as compared to RIIGL. ThT and TEM studies highlighted the enhanced efficiency of RVVPI (62.4%) in the disassembly of pre-formed Aβ42 fibrils than RIIGL and RIAPA. The combined in silico and in vitro studies identified a new peptide, RVVPI, as an efficient inhibitor of Aβ42 fibrillation and disassembly of Aβ42 aggregates.

Keywords:  Alzheimer's disease; Aβ protofibril disaggregation; amyloid-β (Aβ) aggregation; molecular dynamics; peptide inhibitor

DOI:  https://doi.org/10.1002/cmdc.202400486
bioRxiv. 2024 Jul 04. pii: 2024.07.02.601776. [Epub ahead of print]

TDP43 autoregulation gives rise to shortened isoforms that are tightly controlled by both transcriptional and post-translational mechanisms.

Megan M Dykstra, Kaitlin Weskamp, Nicolás B Gómez, Jacob Waksmacki, Elizabeth Tank, M Rebecca Glineburg, Allison Snyder, Emile Pinarbasi, Michael Bekier, Xingli Li, Jen Bai, Shameena Shahzad, Juno Nedumaran, Clare Wieland, Corey Stewart, Sydney Willey, Nikolas Grotewold, Jonathon McBride, John J Moran, Aditya V Suryakumar, Michael Lucas, Peter Tessier, Michael Ward, Peter Todd, Sami J Barmada.

The nuclear RNA-binding protein TDP43 is integrally involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previous studies uncovered N-terminal TDP43 isoforms that are predominantly cytosolic in localization, highly prone to aggregation, and enriched in susceptible spinal motor neurons. In healthy cells, however, these shortened (s)TDP43 isoforms are difficult to detect in comparison to full-length (fl)TDP43, raising questions regarding their origin and selective regulation. Here, we show that sTDP43 is created as a byproduct of TDP43 autoregulation and cleared by nonsense mediated RNA decay (NMD). The sTDP43-encoding transcripts that escape NMD can lead to toxicity but are rapidly degraded post-translationally. Circumventing these regulatory mechanisms by overexpressing sTDP43 results in neurodegeneration in vitro and in vivo via N-terminal oligomerization and impairment of flTDP43 splicing activity, in addition to RNA binding-dependent gain-of-function toxicity. Collectively, these studies highlight endogenous mechanisms that tightly regulate sTDP43 expression and provide insight into the consequences of aberrant sTDP43 accumulation in disease.

DOI: https://doi.org/10.1101/2024.07.02.601776
Bioorg Chem. 2024 Jul 10. pii: S0045-2068(24)00530-3. [Epub ahead of print]151 107625

Macrocyclic peptides derived from AcPHF6* and AcPHF6 to selectively modulate the Tau aggregation.

Abha Dangi, Tazeen Qureshi, Subashchandrabose Chinnathambi, Udaya Kiran Marelli.

  Ten macrocyclic peptides, each comprising 14 amino acids, were designed and synthesized based on the Tau aggregation model hexapeptides AcPHF6* and AcPHF6. The design took into account the aggregation tendencies of each residue in AcPHF6* and AcPHF6, their aggregation models, while employing peptide-based structural design principles including N-methylation to promote turns and to block hydrogen bond propagation and elongation of the aggregation chain. NMR analysis supported that all these peptides adopted an antiparallel β-sheet conformation. Self-aggregation studies characterized the aggregation properties of these peptides, identifying two peptides with the highest (P3) and lowest (P8) aggregation tendencies. In cross-aggregation studies with the parent peptides AcPHF6* and AcPHF6, P3 and P8 were found to promote and reduce aggregation, respectively. Furthermore, P3 and P8 demonstrated an enhancement and diminution effect on the aggregation of K18wt, indicating their capacity to modulate aggregation even at the macromolecular level. Thus, the two simple peptides, P3 and P8 selectively exhibit pro- or anti-aggregation effects on PHF peptides and Tau. This study, has thus developed structurally well-defined non-complex peptides, derived from AcPHF6* and AcPHF6, to modulate Tau aggregation as desired, offering applications in Tau model studies and the development of Tau aggregation inhibitors or promoters.

Keywords:  Cyclic peptides; PHF peptides; Peptide conformation; Peptide-based drug design (PBDD); Tau aggregation

DOI:  https://doi.org/10.1016/j.bioorg.2024.107625
bioRxiv. 2024 Jul 06. pii: 2024.07.05.602282. [Epub ahead of print]

In vivo CRISPR base editing for treatment of Huntington's disease.

Shraddha Shirguppe, Michael Gapinske, Devyani Swami, Nicholas Gosstola, Pankaj Acharya, Angelo Miskalis, Dana Joulani, Maddie G Szkwarek, Abhishek Bhattacharjee, Gianna Elias, Michelle Stilger, Jackson Winter, Wendy S Woods, Daphine Anand, Colin K W Lim, Thomas Gaj, Pablo Perez-Pinera.

Huntington's disease (HD) is an inherited and ultimately fatal neurodegenerative disorder caused by an expanded polyglutamine-encoding CAG repeat within exon 1 of the huntingtin (HTT) gene, which produces a mutant protein that destroys striatal and cortical neurons. Importantly, a critical event in the pathogenesis of HD is the proteolytic cleavage of the mutant HTT protein by caspase-6, which generates fragments of the N-terminal domain of the protein that form highly toxic aggregates. Given the role that proteolysis of the mutant HTT protein plays in HD, strategies for preventing this process hold potential for treating the disorder. By screening 141 CRISPR base editor variants targeting splice elements in the HTT gene, we identified platforms capable of producing HTT protein isoforms resistant to caspase-6-mediated proteolysis via editing of the splice acceptor sequence for exon 13. When delivered to the striatum of a rodent HD model, these base editors induced efficient exon skipping and decreased the formation of the N-terminal fragments, which in turn reduced HTT protein aggregation and attenuated striatal and cortical atrophy. Collectively, these results illustrate the potential for CRISPR base editing to decrease the toxicity of the mutant HTT protein for HD.

DOI: https://doi.org/10.1101/2024.07.05.602282
Biophys Chem. 2024 Jul 10. pii: S0301-4622(24)00122-4. [Epub ahead of print]313 107293

Authentic hSAA related with AA amyloidosis: New method of purification, folding and amyloid polymorphism.

Natalya Katina, Victor Marchenkov, Yulia Lapteva, Vitalii Balobanov, Nelly Ilyina, Natalya Ryabova, Stanislav Evdokimov, Mariya Suvorina, Alexey Surin, Anatoly Glukhov.

  The secondary amyloidosis of humans is caused by the formation of hSAA fibrils in different organs and tissues. Until now hSAA was thought to have low amyloidogenicity in vitro and the majority of SAA aggregation experiments were done using murine protein or hSAA non-pathogenic isoforms. In this work a novel purification method for recombinant hSAA was introduced, enabling to obtain monomeric protein capable of amyloid aggregation under physiological conditions. The stability and amyloid aggregation of hSAA have been examined using a wide range of biophysical methods. It was shown that the unfolding of monomeric protein occurs through the formation of molten globule-like intermediate state. Polymorphism of hSAA amyloids was discovered to depend on the solution pH. At pH 8.5, rapid protein aggregation occurs, which leads to the formation of twisted short fibrils. Even a slight decrease of the pH to 7.8 results in delayed aggregation with the formation of long straight amyloids composed of laterally associated protofilaments. Limited proteolysis experiments have shown that full-length hSAA is involved in the formation of intermolecular interactions in both amyloid polymorphs. The results obtained, and the experimental approach used in this study can serve as a basis for further research on the mechanism of authentic hSAA amyloid formation.

Keywords:  Aggregation kinetic; Amyloid; Fibril morphology; Human SAA; Limited proteolysis

DOI:  https://doi.org/10.1016/j.bpc.2024.107293
Biophys Chem. 2024 Jul 10. pii: S0301-4622(24)00120-0. [Epub ahead of print]313 107291

Enhancing amyloid beta inhibition and disintegration by natural compounds: A study utilizing spectroscopy, microscopy and cell biology.

Ranit Pariary, Gourav Shome, Tista Dutta, Anuradha Roy, Anup Kumar Misra, Kuladip Jana, Sanjeev Rastogi, Dulal Senapati, Atin Kumar Mandal, Anirban Bhunia.

  Amyloid proteins and peptides play a pivotal role in the etiology of various neurodegenerative diseases, including Alzheimer's disease (AD). Synthetically designed small molecules/ peptides/ peptidomimetics show promise towards inhibition of various kinds of amyloidosis. However, exploration of compounds isolated from natural extracts having such potential is lacking. Herein, we have investigated the repurposing of a traditional Indian medicine Lasunadya Ghrita (LG) in AD. LG is traditionally used to treat gut dysregulation and mental illnesses. Various extracts of LG were obtained, characterized, and analyzed for inhibition of Aβ aggregation. Biophysical studies show that the water extract of LG (LGWE) is more potent in inhibiting Aβ peptide aggregation and defibrillation of Aβ40/Aβ42 aggregates. NMR studies showed that LGWE binds to the central hydrophobic area and C-terminal residues of Aβ40/Aβ42, thereby modulating the aggregation, and reducing cell membrane damage. Additionally, LGWE rescues Aβ toxicity in neuronal SH-SY5Y cells evident from decreases in ROS generation, membrane leakage, cellular apoptosis, and calcium dyshomeostasis. Notably, LGWE is non-toxic to neuronal cells and mouse models. Our study thus delves into the mechanistic insights of a repurposed drug LGWE with the potential to ameliorate Aβ induced neuroinflammation.

Keywords:  Alzheimer's disease; Amyloid β peptide inhibition; Fibril disaggregation; NMR; Natural extract; Neurotoxicity

DOI:  https://doi.org/10.1016/j.bpc.2024.107291
Zool Res. 2024 Jul 18. pii: 2095-8137(2024)04-0924-13. [Epub ahead of print]45(4): 924-936

Rotating magnetic field inhibits Aβ protein aggregation and alleviates cognitive impairment in Alzheimer's disease mice.

Ruo-Wen Guo, Wen-Jing Xie, Biao Yu, Chao Song, Xin-Miao Ji, Xin-Yu Wang, Mei Zhang, Xin Zhang.

  Amyloid beta (Aβ) monomers aggregate to form fibrils and amyloid plaques, which are critical mechanisms in the pathogenesis of Alzheimer's disease (AD). Given the important role of Aβ1-42 aggregation in plaque formation, leading to brain lesions and cognitive impairment, numerous studies have aimed to reduce Aβ aggregation and slow AD progression. The diphenylalanine (FF) sequence is critical for amyloid aggregation, and magnetic fields can affect peptide alignment due to the diamagnetic anisotropy of aromatic rings. In this study, we examined the effects of a moderate-intensity rotating magnetic field (RMF) on Aβ aggregation and AD pathogenesis. Results indicated that the RMF directly inhibited Aβ amyloid fibril formation and reduced Aβ-induced cytotoxicity in neural cells in vitro. Using the AD mouse model APP/PS1, RMF restored motor abilities to healthy control levels and significantly alleviated cognitive impairments, including exploration and spatial and non-spatial memory abilities. Tissue examinations demonstrated that RMF reduced amyloid plaque accumulation, attenuated microglial activation, and reduced oxidative stress in the APP/PS1 mouse brain. These findings suggest that RMF holds considerable potential as a non-invasive, high-penetration physical approach for AD treatment.

Keywords:  Alzheimer’s disease; Alzheimer’s disease animal models; Amyloid-β; Cognitive function; Rotating magnetic field

DOI:  https://doi.org/10.24272/j.issn.2095-8137.2024.034
J Neurochem. 2024 Jul 18.

The reciprocal relationship between amyloid precursor protein and mitochondrial function.

Taylor A Strope, Heather M Wilkins.

  Amyloid precursor protein (APP), secretase enzymes, and amyloid beta (Aβ) have been extensively studied in the context of Alzheimer's disease (AD). Despite this, the function of these proteins and their metabolism is not understood. APP, secretase enzymes, and APP processing products (Aβ and C-terminal fragments) localize to endosomes, mitochondria, endoplasmic reticulum (ER), and mitochondrial/ER contact sites. Studies implicate significant relationships between APP, secretase enzyme function, APP metabolism, and mitochondrial function. Mitochondrial dysfunction is a key pathological hallmark of AD and is intricately linked to proteostasis. Here, we review studies examining potential functions of APP, secretase enzymes, and APP metabolites in the context of mitochondrial function and bioenergetics. We discuss implications and limitations of studies and highlight knowledge gaps that remain in the field.

Keywords:  Alzheimer's disease; amyloid beta; amyloid precursor protein; mitochondria; γ‐Secretase

DOI:  https://doi.org/10.1111/jnc.16183
Nat Cell Biol. 2024 Jul 19.

An E3 ligase and autophagy adaptor regulates tau proteostasis through nested phase separation.

DOI: https://doi.org/10.1038/s41556-024-01466-z
Sci Rep. 2024 Jul 19. 14(1): 16715

Diastolic dysfunction in Alzheimer's disease model mice is associated with Aβ-amyloid aggregate formation and mitochondrial dysfunction.

Richa Aishwarya, Chowdhury S Abdullah, Naznin Sultana Remex, Mohammad Alfrad Nobel Bhuiyan, Xiao-Hong Lu, Nirav Dhanesha, Karen Y Stokes, A Wayne Orr, Christopher G Kevil, Md Shenuarin Bhuiyan.

  Alzheimer's Disease (AD) is a progressive neurodegenerative disease caused by the deposition of Aβ aggregates or neurofibrillary tangles. AD patients are primarily diagnosed with the concurrent development of several cardiovascular dysfunctions. While few studies have indicated the presence of intramyocardial Aβ aggregates, none of the studies have performed detailed analyses for pathomechanism of cardiac dysfunction in AD patients. This manuscript used aged APPSWE/PS1 Tg and littermate age-matched wildtype (Wt) mice to characterize cardiac dysfunction and analyze associated pathophysiology. Detailed assessment of cardiac functional parameters demonstrated the development of diastolic dysfunction in APPSWE/PS1 Tg hearts compared to Wt hearts. Muscle function evaluation showed functional impairment (decreased exercise tolerance and muscle strength) in APPSWE/PS1 Tg mice. Biochemical and histochemical analysis revealed Aβ aggregate accumulation in APPSWE/PS1 Tg mice myocardium. APPSWE/PS1 Tg mice hearts also demonstrated histopathological remodeling (increased collagen deposition and myocyte cross-sectional area). Additionally, APPSWE/PS1 Tg hearts showed altered mitochondrial dynamics, reduced antioxidant protein levels, and impaired mitochondrial proteostasis compared to Wt mice. APPSWE/PS1 Tg hearts also developed mitochondrial dysfunction with decreased OXPHOS and PDH protein complex expressions, altered ETC complex dynamics, decreased complex activities, and reduced mitochondrial respiration. Our results indicated that Aβ aggregates in APPSWE/PS1 Tg hearts are associated with defects in mitochondrial respiration and complex activities, which may collectively lead to cardiac diastolic dysfunction and myocardial pathological remodeling.

Keywords:  Alzheimer’s disease; Diastolic dysfunction; Fibrosis; Mitochondrial dysfunction

DOI:  https://doi.org/10.1038/s41598-024-67638-x
Nat Commun. 2024 Jul 13. 15(1): 5890

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation.

Meera Gupta, Alex N T Johnson, Edward R Cruz, Eli J Costa, Randi L Guest, Sophia Hsin-Jung Li, Elizabeth M Hart, Thao Nguyen, Michael Stadlmeier, Benjamin P Bratton, Thomas J Silhavy, Ned S Wingreen, Zemer Gitai, Martin Wühr.

Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.

DOI: https://doi.org/10.1038/s41467-024-49920-8
Nat Cell Biol. 2024 Jul 15.

The autophagy adaptor TRIAD3A promotes tau fibrillation by nested phase separation.

Jiechao Zhou, Yang 'an Chuang, Javier Redding-Ochoa, Rongzhen Zhang, Alexander J Platero, Alexander H Barrett, Juan C Troncoso, Paul F Worley, Wenchi Zhang.

Multiple neurodegenerative diseases are characterized by aberrant proteinaceous accumulations of tau. Here, we report a RING-in-between-RING-type E3 ligase, TRIAD3A, that functions as an autophagy adaptor for tau. TRIAD3A(RNF216) is an essential gene with mutations causing age-progressive neurodegeneration. Our studies reveal that TRIAD3A E3 ligase catalyses mixed K11/K63 polyubiquitin chains and self-assembles into liquid-liquid phase separated (LLPS) droplets. Tau is ubiquitinated and accumulates within TRIAD3A LLPS droplets and, via LC3 interacting regions, targets tau for autophagic degradation. Unexpectedly, tau sequestered within TRIAD3A droplets rapidly converts to fibrillar aggregates without the transitional liquid phase of tau. In vivo studies show that TRIAD3A decreases the accumulation of phosphorylated tau in a tauopathy mouse model, and a disease-associated mutation of TRIAD3A increases accumulation of phosphorylated tau, exacerbates gliosis and increases pathological tau spreading. In human Alzheimer disease brain, TRIAD3A co-localizes with tau amyloid in multiple histological forms, suggesting a role in tau proteostasis. TRIAD3A is an autophagic adaptor that utilizes E3 ligase and LLPS as a mechanism to capture cargo and appears especially relevant to neurodegenerative diseases.

DOI: https://doi.org/10.1038/s41556-024-01461-4