Role of Deubiquitinases in Parkinson's Disease-Therapeutic Perspectives

Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape

Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.

Status and role of the ubiquitin-proteasome system in renal fibrosis

The ubiquitin-proteasome system (UPS) is a basic regulatory mechanism in cells that is essential for maintaining cell homeostasis, stimulating signal transduction, and determining cell fate. These biological processes require coordinated signaling cascades across members of the UPS to achieve substrate ubiquitination and deubiquitination. The role of the UPS in fibrotic diseases has attracted widespread attention, and the aberrant expression of UPS members affects the fibrosis process. In this review, we provide an overview of the UPS and its relevance for fibrotic diseases. Moreover, for the first time, we explore in detail how the UPS promotes or inhibits renal fibrosis by regulating biological processes such as signaling pathways, inflammation, oxidative stress, and the cell cycle, emphasizing the status and role of the UPS in renal fibrosis. Further research on this system may reveal new strategies for preventing renal fibrosis.

Single-cell spatial transcriptomics reveals molecular patterns of selective neuronal vulnerability to α-synuclein pathology in a transgenic mouse model of Lewy body disease

One of the unifying pathological hallmarks of Parkinson's disease (PD) and dementia with Lewy bodies (DLB) is the presence of misfolded, aggregated, and often phosphorylated forms of the protein α-synuclein in neurons. α-Synuclein pathology appears in select populations of neurons throughout various cortical and subcortical regions, and little is currently known about why some neurons develop pathology while others are spared. Here, we utilized subcellular-resolution imaging-based spatial transcriptomics (IST) in a transgenic mouse model that overexpresses wild-type human α-synuclein (α-syn-tg) to evaluate patterns of selective neuronal vulnerability to α-synuclein pathology. By performing post-IST immunofluorescence for α-synuclein phosphorylated at Ser129 (pSyn), we identified cell types in the cortex and hippocampus that were vulnerable or resistant to developing pSyn pathology. Next, we investigated the transcriptional underpinnings of the observed selective vulnerability using a set of custom probes to detect genes involved in α-synuclein processing and toxicity. We identified expression of the kinase:substrate pair Plk2, which phosphorylates α-synuclein at Ser129, and human SNCA (hSNCA), as underlying the selective vulnerability to pSyn pathology. Finally, we performed differential gene expression analysis, comparing non-transgenic cells to pSyn- and pSyn+ α-syn-tg cells to reveal gene expression changes downstream of hSNCA overexpression and pSyn pathology, which included pSyn-dependent alterations in mitochondrial and endolysosomal genes. This study provides a comprehensive use case of IST, yielding new biological insights into the formation of α-synuclein pathology and its downstream effects in a PD/DLB mouse model.

Ubiquitin Carboxyl-Terminal Hydrolase L1 and Its Role in Parkinson's Disease

Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson's disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin-proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. Being the smallest member of the UCH family of DUBs, it catalyzes the reaction of ubiquitin precursor processing and the cleavage of ubiquitinated protein remnants, thus maintaining the level of ubiquitin monomers in the brain cells. UCHL1 mutants, containing amino acid substitutions, influence catalytic activity and its aggregability. Some of them protect cells and transgenic mice in toxin-induced Parkinson's disease (PD) models. Studies of putative protein partners of UCHL1 revealed about sixty individual proteins located in all major compartments of the cell: nucleus, cytoplasm, endoplasmic reticulum, plasma membrane, mitochondria, and peroxisomes. These include proteins related to the development of PD, such as alpha-synuclein, amyloid-beta precursor protein, ubiquitin-protein ligase parkin, and heat shock proteins. In the context of the catalytic paradigm, the importance of these interactions is not clear. However, there is increasing understanding that UCHL1 exhibits various effects in a catalytically independent manner through protein-protein interactions. Since this protein represents up to 5% of the soluble protein in the brain, PD-related changes in its structure will have profound effects on the proteomes/interactomes in which it is involved. Growing evidence is accumulating that the role of UCHL1 in PD is obviously determined by a balance of canonic catalytic activity and numerous activity-independent protein-protein interactions, which still need better characterization.

Targeting the Ubiquitin-Proteasome System and Recent Advances in Cancer Therapy

Ubiquitination is a reversible post-translational modification based on the chemical addition of ubiquitin to proteins with regulatory effects on various signaling pathways. Ubiquitination can alter the molecular functions of tagged substrates with respect to protein turnover, biological activity, subcellular localization or protein-protein interaction. As a result, a wide variety of cellular processes are under ubiquitination-mediated control, contributing to the maintenance of cellular homeostasis. It follows that the dysregulation of ubiquitination reactions plays a relevant role in the pathogenic states of human diseases such as neurodegenerative diseases, immune-related pathologies and cancer. In recent decades, the enzymes of the ubiquitin-proteasome system (UPS), including E3 ubiquitin ligases and deubiquitinases (DUBs), have attracted attention as novel druggable targets for the development of new anticancer therapeutic approaches. This perspective article summarizes the peculiarities shared by the enzymes involved in the ubiquitination reaction which, when deregulated, can lead to tumorigenesis. Accordingly, an overview of the main pharmacological interventions based on targeting the UPS that are in clinical use or still in clinical trials is provided, also highlighting the limitations of the therapeutic efficacy of these approaches. Therefore, various attempts to circumvent drug resistance and side effects as well as UPS-related emerging technologies in anticancer therapeutics are discussed.

Shuangshen Ningxin capsule alleviates myocardial ischemia-reperfusion injury in miniature pigs by modulating mitophagy: network pharmacology and experiments in vivo

BACKGROUND

Myocardial ischemia/reperfusion injury (MI/RI) is involved in a variety of pathological states for which there is no effective treatment exists. Shuangshen Ningxin (SSNX) capsule which is developed by Xiyuan Hospital, Chinese Academy of Traditional Chinese Medicine has been demonstrated to alleviate MI/RI, but its mechanism remains to be further elucidated.

METHODS

The MI/RI miniature pigs model was constructed to assess the pharmacodynamics of SSNX by blocking the proximal blood flow of the left anterior descending branch of the cardiac coronary artery through an interventional balloon. The principal chemical compounds and potential targets of SSNX were screened by HPLC-MS and SwissTargetPrediction. The targets of MI/RI were identified based on Online Mendelian Inheritance in Man (OMIM) and GeneCards. Cytoscape 3.9.0 was applied to construct a protein-protein interaction (PPI) network, and Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using metascape. To further validate the mechanism of SSNX, Molecular docking, Transmission electron microscopy, and Western blot analysis were used to test the effectiveness of targets in related pathways.

RESULTS

Our results indicated that SSNX significantly improved cardiac function, attenuated myocardial I/R injury. Through network analysis, a total of 15 active components and 201 targets were obtained from SSNX, 75 of which are potential targets for the treatment of MI/RI. KEGG and MCODE analysis showed that SSNX is involved in the mitophagy signaling pathway, and ginsenoside Rg1, ginsenoside Rb1 and ginsenoside Rb2 are key components associated with the mitophagy. Further experimental results proved that SSNX protected mitochondrial structure and function, and significantly reduced the expression of mitophagy-related proteins PTEN-induced putative kinase 1 (PINK1), Parkin, FUN14 domain containing 1 (FUNDC1) and Bcl-2/E1B-19 kDa interacting protein 3 (BNIP3) in MI/RI miniature pigs.

CONCLUSION

In our study, the integration of network pharmacology and experiments in vivo demonstrated that SSNX interfered with MI/RI by inhibiting mitophagy.