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Cóppola-Segovia V, Reggiori F. Molecular Insights into Aggrephagy: Their Cellular Functions in the Context of Neurodegenerative Diseases. J Mol Biol 2024; 436:168493. [PMID: 38360089 DOI: 10.1016/j.jmb.2024.168493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Protein homeostasis or proteostasis is an equilibrium of biosynthetic production, folding and transport of proteins, and their timely and efficient degradation. Proteostasis is guaranteed by a network of protein quality control systems aimed at maintaining the proteome function and avoiding accumulation of potentially cytotoxic proteins. Terminal unfolded and dysfunctional proteins can be directly turned over by the ubiquitin-proteasome system (UPS) or first amassed into aggregates prior to degradation. Aggregates can also be disposed into lysosomes by a selective type of autophagy known as aggrephagy, which relies on a set of so-called selective autophagy receptors (SARs) and adaptor proteins. Failure in eliminating aggregates, also due to defects in aggrephagy, can have devastating effects as underscored by several neurodegenerative diseases or proteinopathies, which are characterized by the accumulation of aggregates mostly formed by a specific disease-associated, aggregate-prone protein depending on the clinical pathology. Despite its medical relevance, however, the process of aggrephagy is far from being understood. Here we review the findings that have helped in assigning a possible function to specific SARs and adaptor proteins in aggrephagy in the context of proteinopathies, and also highlight the interplay between aggrephagy and the pathogenesis of proteinopathies.
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Affiliation(s)
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, 8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark.
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2
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Aboalroub AA, Al Azzam KM. Protein S-Nitrosylation: A Chemical Modification with Ubiquitous Biological Activities. Protein J 2024; 43:639-655. [PMID: 39068633 DOI: 10.1007/s10930-024-10223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2024] [Indexed: 07/30/2024]
Abstract
Nitric oxide (NO) induces protein posttranslational modification (PTM), known as S-nitrosylation, which has started to gain attention as a critical regulator of thousands of substrate proteins. However, our understanding of the biological consequences of this emerging PTM is incomplete because of the limited number of identified S-nitrosylated proteins (S-NO proteins). Recent advances in detection methods have effectively contributed to broadening the spectrum of discovered S-NO proteins. This article briefly reviews the progress in S-NO protein detection methods and discusses how these methods are involved in characterizing the biological consequences of this PTM. Additionally, we provide insight into S-NO protein-related diseases, focusing on the role of these proteins in mitigating the severity of infectious diseases.
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Affiliation(s)
- Adam A Aboalroub
- Pharmacological and Diagnostic Research Center (PDRC), Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, 19328, Jordan.
| | - Khaldun M Al Azzam
- Department of Chemistry, School of Science, The University of Jordan, Amman, 11942, Jordan
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3
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Zhu YF, Yu RH, Zhou S, Tang PP, Zhang R, Wu YX, Xu R, Wei JM, Wang YY, Zhang JL, Li MK, Shi XJ, Zhang YW, Liu GZ, Thorne RF, Zhang XD, Wu M, Chen S. TAX1BP1 and FIP200 orchestrate non-canonical autophagy of p62 aggregates for mouse neural stem cell maintenance. Zool Res 2024; 45:937-950. [PMID: 39021082 PMCID: PMC11298671 DOI: 10.24272/j.issn.2095-8137.2024.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/30/2024] [Indexed: 07/20/2024] Open
Abstract
Autophagy plays a pivotal role in diverse biological processes, including the maintenance and differentiation of neural stem cells (NSCs). Interestingly, while complete deletion of Fip200 severely impairs NSC maintenance and differentiation, inhibiting canonical autophagy via deletion of core genes, such as Atg5, Atg16l1, and Atg7, or blockade of canonical interactions between FIP200 and ATG13 (designated as FIP200-4A mutant or FIP200 KI) does not produce comparable detrimental effects. This highlights the likely critical involvement of the non-canonical functions of FIP200, the mechanisms of which have remained elusive. Here, utilizing genetic mouse models, we demonstrated that FIP200 mediates non-canonical autophagic degradation of p62/sequestome1, primarily via TAX1BP1 in NSCs. Conditional deletion of Tax1bp1 in fip200 hGFAP conditional knock-in (cKI) mice led to NSC deficiency, resembling the fip200 hGFAP conditional knockout (cKO) mouse phenotype. Notably, reintroducing wild-type TAX1BP1 not only restored the maintenance of NSCs derived from tax1bp1-knockout fip200 hGFAP cKI mice but also led to a marked reduction in p62 aggregate accumulation. Conversely, a TAX1BP1 mutant incapable of binding to FIP200 or NBR1/p62 failed to achieve this restoration. Furthermore, conditional deletion of Tax1bp1 in fip200 hGFAP cKO mice exacerbated NSC deficiency and p62 aggregate accumulation compared to fip200 hGFAP cKO mice. Collectively, these findings illustrate the essential role of the FIP200-TAX1BP1 axis in mediating the non-canonical autophagic degradation of p62 aggregates towards NSC maintenance and function, presenting novel therapeutic targets for neurodegenerative diseases.
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Affiliation(s)
- Yi-Fu Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Rong-Hua Yu
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
| | - Shuai Zhou
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
| | - Pei-Pei Tang
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, Jiangsu 223300, China
| | - Rui Zhang
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
| | - Yu-Xin Wu
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
| | - Ran Xu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
| | - Jia-Ming Wei
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, Jiangsu 223300, China
| | - Ying-Ying Wang
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
| | - Jia-Li Zhang
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
| | - Meng-Ke Li
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
| | - Xiao-Jing Shi
- Laboratory Animal Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yu-Wei Zhang
- Henan Key Laboratory of Stem cell Differentiation and Modification, Henan Provincial People's Hospital, Henan University, Zhengzhou, Henan 450053, China
| | - Guang-Zhi Liu
- Henan Key Laboratory of Stem cell Differentiation and Modification, Henan Provincial People's Hospital, Henan University, Zhengzhou, Henan 450053, China
| | - Rick F Thorne
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
| | - Xu Dong Zhang
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, NSW 2308, Australia
| | - Mian Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
- Henan Key Laboratory of Stem cell Differentiation and Modification, Henan Provincial People's Hospital, Henan University, Zhengzhou, Henan 450053, China. E-mail:
| | - Song Chen
- Translational Research Institute of Henan Provincial People's Hospital and People''s Hospital of Zhengzhou University, Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450053, China
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, Jiangsu 223300, China
- Henan Key Laboratory of Stem cell Differentiation and Modification, Henan Provincial People's Hospital, Henan University, Zhengzhou, Henan 450053, China. E-mail:
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Yang PF, Nie TL, Sun XN, Xu LX, Ma C, Wang F, Long LH, Chen JG. Wheel-Running Exercise Alleviates Anxiety-Like Behavior via Down-Regulating S-Nitrosylation of Gephyrin in the Basolateral Amygdala of Male Rats. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400205. [PMID: 38965798 DOI: 10.1002/advs.202400205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 06/06/2024] [Indexed: 07/06/2024]
Abstract
Physical exercise has beneficial effect on anxiety disorders, but the underlying molecular mechanism remains largely unknown. Here, it is demonstrated that physical exercise can downregulate the S-nitrosylation of gephyrin (SNO-gephyrin) in the basolateral amygdala (BLA) to exert anxiolytic effects. It is found that the level of SNO-gephyrin is significantly increased in the BLA of high-anxiety rats and a downregulation of SNO-gephyrin at cysteines 212 and 284 produced anxiolytic effect. Mechanistically, inhibition of SNO-gephyrin by either Cys212 or Cys284 mutations increased the surface expression of GABAAR γ2 and the subsequent GABAergic neurotransmission, exerting anxiolytic effect in male rats. On the other side, overexpression of neuronal nitric oxide synthase in the BLA abolished the anxiolytic-like effects of physical exercise. This study reveals a key role of downregulating SNO-gephyrin in the anxiolytic effects of physical exercise, providing a new explanation for protein post-translational modifications in the brain after exercise.
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Affiliation(s)
- Ping-Fen Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China
| | - Tai-Lei Nie
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China
| | - Xia-Nan Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China
| | - Lan-Xin Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fang Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China
- Hubei Shizhen Laboratory, Wuhan, 430030, China
| | - Li-Hong Long
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China
- Hubei Shizhen Laboratory, Wuhan, 430030, China
| | - Jian-Guo Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- The Key Laboratory for Drug Target Researches and Pharmacodynamic Evaluation of Hubei Province, Wuhan, 430030, China
- Hubei Shizhen Laboratory, Wuhan, 430030, China
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5
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Wang H, Wang W, Xue Z, Gong H. SIRT3 MEDIATES THE CARDIOPROTECTIVE EFFECT OF THERAPEUTIC HYPOTHERMIA AFTER CARDIAC ARREST AND RESUSCITATION BY RESTORING AUTOPHAGIC FLUX VIA THE PI3K/AKT/MTOR PATHWAY. Shock 2024; 62:127-138. [PMID: 38526135 DOI: 10.1097/shk.0000000000002366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
ABSTRACT Background : Postresuscitation cardiac dysfunction is a significant contributor to early death following cardiopulmonary resuscitation (CPR). Therapeutic hypothermia (TH) mitigates myocardial dysfunction due to cardiac arrest (CA); however, the underlying mechanism remains unclear. Sirtuin 3 (Sirt3) was found to affect autophagic activity in recent research, motivating us to investigate its role in the cardioprotective effects of TH in the treatment of CA. Methods : Sprague-Dawley rats were used to establish an in vivo CA/CPR model and treated with a selective Sirt3 inhibitor or vehicle. Survival rate, myocardial function, autophagic flux, and Sirt3 expression and activity were evaluated. H9C2 cells were subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) injury in vitro . The cells were transfected with Sirt3-siRNA and treated with the autophagy inhibitor chloroquine or the PI3K inhibitor LY294002, and cell viability and autophagic flux were assessed. Results : Rats exhibited decreased survival and impaired cardiac function after CA/CPR, which were alleviated by TH. Mechanistically, TH restored Sirt3 expression and autophagic flux, which were impaired by CA/CPR. Sirt3 inactivation diminished the capacity of TH to restore autophagic flux and partially abolished the improvements in myocardial function and survival. An in vitro study further showed that TH-induced restoration of disrupted autophagic flux by OGD/R was attenuated by pretreatment with Sirt3-siRNA, and this attenuation was partially rescued by the inhibition of PI3K/Akt/mTOR signaling cascades. Conclusions : Sirt3 mediates the cardioprotective effect of TH by restoring autophagic flux via the PI3K/Akt/mTOR pathway. These findings suggest the potential of Sirt3 as a therapeutic target for CA.
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Affiliation(s)
- Hui Wang
- Department of Geriatric Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenwen Wang
- Department of Emergency, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhiwei Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
| | - Huiping Gong
- Department of Emergency, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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6
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Masato A, Andolfo A, Favetta G, Bellini EN, Cogo S, Dalla Valle L, Boassa D, Greggio E, Plotegher N, Bubacco L. Sequestosome-1 (SQSTM1/p62) as a target in dopamine catabolite-mediated cellular dyshomeostasis. Cell Death Dis 2024; 15:424. [PMID: 38890356 PMCID: PMC11189528 DOI: 10.1038/s41419-024-06763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024]
Abstract
Alterations in the dopamine catabolic pathway are known to contribute to the degeneration of nigrostriatal neurons in Parkinson's disease (PD). The progressive cellular buildup of the highly reactive intermediate 3,4-dihydroxyphenylacetaldehye (DOPAL) generates protein cross-linking, oligomerization of the PD-linked αSynuclein (αSyn) and imbalance in protein quality control. In this scenario, the autophagic cargo sequestome-1 (SQSTM1/p62) emerges as a target of DOPAL-dependent oligomerization and accumulation in cytosolic clusters. Although DOPAL-induced oxidative stress and activation of the Nrf2 pathway promote p62 expression, p62 oligomerization rather seems to be a consequence of direct DOPAL modification. DOPAL-induced p62 clusters are positive for ubiquitin and accumulate within lysosomal-related structures, likely affecting the autophagy-lysosomal functionality. Finally, p62 oligomerization and clustering is synergistically augmented by DOPAL-induced αSyn buildup. Hence, the substantial impact on p62 proteostasis caused by DOPAL appears of relevance for dopaminergic neurodegeneration, in which the progressive failure of degradative pathways and the deposition of proteins like αSyn, ubiquitin and p62 in inclusion bodies represent a major trait of PD pathology.
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Affiliation(s)
- Anna Masato
- Department of Biology, University of Padova, Padova, Italy
- UK Dementia Research Institute at University College London, London, UK
| | - Annapaola Andolfo
- Proteomics and Metabolomics Facility (ProMeFa), Center for Omics Sciences (COSR), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulia Favetta
- Department of Biology, University of Padova, Padova, Italy
| | - Edoardo Niccolò Bellini
- Proteomics and Metabolomics Facility (ProMeFa), Center for Omics Sciences (COSR), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Susanna Cogo
- Department of Biology, University of Padova, Padova, Italy
- School of Biological Sciences, University of Reading, Reading, UK
| | | | - Daniela Boassa
- Department of Neurosciences and National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Elisa Greggio
- Department of Biology, University of Padova, Padova, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
| | - Nicoletta Plotegher
- Department of Biology, University of Padova, Padova, Italy
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy.
- Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy.
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Cucinotta L, Mannino D, Filippone A, Romano A, Esposito E, Paterniti I. The role of autophagy in Parkinson's disease: a gender difference overview. Front Pharmacol 2024; 15:1408152. [PMID: 38933683 PMCID: PMC11199695 DOI: 10.3389/fphar.2024.1408152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Recent studies have demonstrated dysregulation of the autophagy pathway in patients with Parkinson's disease (PD) and in animal models of PD, highlighting its emerging role in disease. In particular, several studies indicate that autophagy, which is an essential degradative process for the damaged protein homeostasis and the management of cell balance, can manifest significant variations according to gender. While some evidence suggests increased autophagic activation in men with PD, women may have distinct regulatory patterns. In this review, we examined the existing literature on gender differences in PD-associated autophagic processes, focusing on the autophagy related proteins (ATGs) and leucine rich repeat kinase 2 (LRRK2) genes. Also, this review would suggest that an in-depth understanding of these gender differences in autophagic processes could open new perspectives for personalized therapeutic strategies, promoting more effective and targeted management of PD.
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Affiliation(s)
- Laura Cucinotta
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Deborah Mannino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Alessia Filippone
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Adele Romano
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, Rome, Italy
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Irene Paterniti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
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8
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Morey A, Ng M, Spanos M, Zhang P, Xu T, Cheung W, Chatterjee E, Gokulnath P, Carnel-Amar N, Soares Chiaretti AL, Nelson C, George J, Luo M, Chakraborty A, Perucci L, Jones JC, Hoff PD, Franklin JL, Raffai RL, Das S, Routenberg DA, Nolan JP, Charest A, Laurent LC, Alexander RP. The EV antibody database: An interactive database of curated antibodies for extracellular vesicle and nanoparticle research. EXTRACELLULAR VESICLE 2024; 3:100040. [PMID: 38872853 PMCID: PMC11175471 DOI: 10.1016/j.vesic.2024.100040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Antibodies are critical tools for research into extracellular vesicles (EVs) and other extracellular nanoparticles (ENPs), where they can be used for their identification, characterization, and isolation. However, the lack of a centralized antibody platform where researchers can share validation results thus minimizing wasted personnel time and reagents, has been a significant obstacle. Moreover, because the performance of antibodies varies among assay types and conditions, detailed information on assay variables and protocols is also of value. To facilitate sharing of results on antibodies that are relevant to EV/ENP research, the EV Antibody Database has been developed by the investigators of the Extracellular RNA Communication Consortium (ERCC). Hosted by the ExRNA Portal (https://exrna.org/resources/evabdb/), this interactive database aggregates and shares results from antibodies that have been tested by research groups in the EV/ENP field. Currently, the EV Antibody Database includes modules for antibodies tested for western Blot, EV Flow Cytometry, and EV Sandwich Assays, and holds 110 records contributed by 6 laboratories from the ERCC. Detailed information on antibody sources, assay conditions, and results is provided, including negative results. We encourage ongoing expert input and community feedback to enhance the database's utility, making it a valuable resource for comprehensive validation data on antibodies and protocols in EV biology.
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Affiliation(s)
- Amber Morey
- University of California San Diego, Department of Obstetrics, Gynecology, and Reproductive Medicine, La Jolla, CA 92093, USA
| | - Martin Ng
- Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA
| | - Michail Spanos
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Piyan Zhang
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - Tuoye Xu
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - Willi Cheung
- University of California San Diego, Department of Obstetrics, Gynecology, and Reproductive Medicine, La Jolla, CA 92093, USA
| | - Emeli Chatterjee
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Priyanka Gokulnath
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Natacha Carnel-Amar
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana Luisa Soares Chiaretti
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Jubin George
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Michelle Luo
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Abhik Chakraborty
- University of California San Diego, Department of Obstetrics, Gynecology, and Reproductive Medicine, La Jolla, CA 92093, USA
| | - Luiza Perucci
- University of California San Diego, Department of Obstetrics, Gynecology, and Reproductive Medicine, La Jolla, CA 92093, USA
| | - Jennifer C. Jones
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Peter De Hoff
- University of California San Diego, Department of Obstetrics, Gynecology, and Reproductive Medicine, La Jolla, CA 92093, USA
| | - Jeffrey L. Franklin
- Department of Medicine, Vanderbilt University Medical Center, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Robert L. Raffai
- Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA
- Department of Surgery, Division of Endovascular and Vascular Surgery, University of California, San Francisco, CA 94143, USA
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - John P. Nolan
- Scintillon Institute, San Diego, CA, 92121, USA
- Cellarcus Biosciences, La Jolla, CA, 92037, USA
| | - Al Charest
- Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - Louise C. Laurent
- University of California San Diego, Department of Obstetrics, Gynecology, and Reproductive Medicine, La Jolla, CA 92093, USA
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9
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Hussain MS, Moglad E, Afzal M, Sharma S, Gupta G, Sivaprasad GV, Deorari M, Almalki WH, Kazmi I, Alzarea SI, Shahwan M, Pant K, Ali H, Singh SK, Dua K, Subramaniyan V. Autophagy-associated non-coding RNAs: Unraveling their impact on Parkinson's disease pathogenesis. CNS Neurosci Ther 2024; 30:e14763. [PMID: 38790149 PMCID: PMC11126788 DOI: 10.1111/cns.14763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a degenerative neurological condition marked by the gradual loss of dopaminergic neurons in the substantia nigra pars compacta. The precise etiology of PD remains unclear, but emerging evidence suggests a significant role for disrupted autophagy-a crucial cellular process for maintaining protein and organelle integrity. METHODS This review focuses on the role of non-coding RNAs (ncRNAs) in modulating autophagy in PD. We conducted a comprehensive review of recent studies to explore how ncRNAs influence autophagy and contribute to PD pathophysiology. Special attention was given to the examination of ncRNAs' regulatory impacts in various PD models and patient samples. RESULTS Findings reveal that ncRNAs are pivotal in regulating key processes associated with PD progression, including autophagy, α-synuclein aggregation, mitochondrial dysfunction, and neuroinflammation. Dysregulation of specific ncRNAs appears to be closely linked to these pathogenic processes. CONCLUSION ncRNAs hold significant therapeutic potential for addressing autophagy-related mechanisms in PD. The review highlights innovative therapeutic strategies targeting autophagy-related ncRNAs and discusses the challenges and prospective directions for developing ncRNA-based therapies in clinical practice. The insights from this study underline the importance of ncRNAs in the molecular landscape of PD and their potential in novel treatment approaches.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical SciencesJaipur National UniversityJaipurRajasthanIndia
| | - Ehssan Moglad
- Department of Pharmaceutics, College of PharmacyPrince Sattam Bin Abdulaziz UniversityAl KharjSaudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy ProgramBatterjee Medical CollegeJeddahSaudi Arabia
| | - Shilpa Sharma
- Chandigarh Pharmacy College, Chandigarh Group of CollegesMohaliPunjabIndia
| | - Gaurav Gupta
- Centre of Medical and Bio‐allied Health Sciences ResearchAjman UniversityAjmanUnited Arab Emirates
- Chitkara College of PharmacyChitkara UniversityRajpuraPunjabIndia
| | - G. V. Sivaprasad
- Department of Basic Science & HumanitiesRaghu Engineering CollegeVisakhapatnamIndia
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical SciencesUttaranchal UniversityDehradunIndia
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of PharmacyUmm Al‐Qura UniversityMakkahSaudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of ScienceKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Sami I. Alzarea
- Department of Pharmacology, College of PharmacyJouf UniversitySakakaAl‐JoufSaudi Arabia
| | - Moyad Shahwan
- Centre of Medical and Bio‐allied Health Sciences ResearchAjman UniversityAjmanUnited Arab Emirates
- Department of Clinical Sciences, College of Pharmacy and Health SciencesAjman UniversityAjmanUnited Arab Emirates
| | - Kumud Pant
- Graphic Era (Deemed to be University)DehradunIndia
- Graphic Era Hill UniversityDehradunIndia
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical SciencesSaveetha UniversityChennaiIndia
- Department of PharmacologyKyrgyz State Medical CollegeBishkekKyrgyzstan
| | - Sachin Kumar Singh
- School of Pharmaceutical SciencesLovely Professional UniversityPhagwaraPunjabIndia
- Faculty of Health, Australian Research Centre in Complementary and Integrative MedicineUniversity of Technology SydneyUltimoNew South WalesAustralia
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative MedicineUniversity of Technology SydneyUltimoNew South WalesAustralia
- Discipline of Pharmacy, Graduate School of HealthUniversity of Technology SydneyUltimoNew South WalesAustralia
- Uttaranchal Institute of Pharmaceutical SciencesUttaranchal UniversityDehradunIndia
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaBandar SunwaySelangor Darul EhsanMalaysia
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10
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Ferrucci M, Lenzi P, Lazzeri G, Busceti CL, Frati A, Puglisi-Allegra S, Fornai F. Combined light and electron microscopy (CLEM) to quantify methamphetamine-induced alpha-synuclein-related pathology. J Neural Transm (Vienna) 2024; 131:335-358. [PMID: 38367081 PMCID: PMC11016004 DOI: 10.1007/s00702-024-02741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/19/2024]
Abstract
Methamphetamine (METH) produces a cytopathology, which is rather specific within catecholamine neurons both in vitro and ex vivo, in animal models and chronic METH abusers. This led some authors to postulate a sort of parallelism between METH cytopathology and cell damage in Parkinson's disease (PD). In fact, METH increases and aggregates alpha-syn proto-fibrils along with producing spreading of alpha-syn. Although alpha-syn is considered to be the major component of aggregates and inclusions developing within diseased catecholamine neurons including classic Lewy body (LB), at present, no study provided a quantitative assessment of this protein in situ, neither following METH nor in LB occurring in PD. Similarly, no study addressed the quantitative comparison between occurrence of alpha-syn and other key proteins and no investigation measured the protein compared with non-protein structure within catecholamine cytopathology. Therefore, the present study addresses these issues using an oversimplified model consisting of a catecholamine cell line where the novel approach of combined light and electron microscopy (CLEM) was used measuring the amount of alpha-syn, which is lower compared with p62 or poly-ubiquitin within pathological cell domains. The scenario provided by electron microscopy reveals unexpected findings, which are similar to those recently described in the pathology of PD featuring packing of autophagosome-like vesicles and key proteins shuttling autophagy substrates. Remarkably, small seed-like areas, densely packed with p62 molecules attached to poly-ubiquitin within wide vesicular domains occurred. The present data shed new light about quantitative morphometry of catecholamine cell damage in PD and within the addicted brain.
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Affiliation(s)
- Michela Ferrucci
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Paola Lenzi
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Gloria Lazzeri
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Carla L Busceti
- Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Neuromed, Via Atinense 18, 86077, Pozzilli, Italy
| | - Alessandro Frati
- Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Neuromed, Via Atinense 18, 86077, Pozzilli, Italy
- Neurosurgery Division, Human Neurosciences Department, Sapienza University, 00135, Rome, Italy
| | - Stefano Puglisi-Allegra
- Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Neuromed, Via Atinense 18, 86077, Pozzilli, Italy
| | - Francesco Fornai
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Via Roma 55, 56126, Pisa, Italy.
- Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Neuromed, Via Atinense 18, 86077, Pozzilli, Italy.
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11
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Zhou A, Bian F. Editorial: Proteostasis in central nervous system disorders. Front Mol Neurosci 2024; 17:1394171. [PMID: 38562165 PMCID: PMC10982507 DOI: 10.3389/fnmol.2024.1394171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
- An Zhou
- Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA, United States
| | - Fang Bian
- Department of Bioengineering, Office of Research and Innovation, The University of Texas at Dallas, Richardson, TX, United States
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12
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Sipos A, Kim KJ, Alvarez JR, Crandall ED. Real-Time Autophagic Flux Measurements in Live Cells Using a Novel Fluorescent Marker DAPRed. Bio Protoc 2024; 14:e4949. [PMID: 38464942 PMCID: PMC10917693 DOI: 10.21769/bioprotoc.4949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/05/2023] [Accepted: 01/31/2024] [Indexed: 03/12/2024] Open
Abstract
Autophagy is a conserved homeostatic mechanism involved in cellular homeostasis and many disease processes. Although it was first described in yeast cells undergoing starvation, we have learned over the years that autophagy gets activated in many stress conditions and during development and aging in mammalian cells. Understanding the fundamental mechanisms underlying autophagy effects can bring us closer to better insights into the pathogenesis of many disease conditions (e.g., cardiac muscle necrosis, Alzheimer's disease, and chronic lung injury). Due to the complex and dynamic nature of the autophagic processes, many different techniques (e.g., western blotting, fluorescent labeling, and genetic modifications of key autophagy proteins) have been developed to delineate autophagy effects. Although these methods are valid, they are not well suited for the assessment of time-dependent autophagy kinetics. Here, we describe a novel approach: the use of DAPRed for autophagic flux measurement via live cell imaging, utilizing A549 cells, that can visualize and quantify autophagic flux in real time in single live cells. This approach is relatively straightforward in comparison to other experimental procedures and should be applicable to any in vitro cell/tissue models. Key features • Allows real-time qualitative imaging of autophagic flux at single-cell level. • Primary cells and cell lines can also be utilized with this technique. • Use of confocal microscopy allows visualization of autophagy without disturbing cellular functions.
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Affiliation(s)
- Arnold Sipos
- Will Rogers Institute Pulmonary Research Center and Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kwang-Jin Kim
- Will Rogers Institute Pulmonary Research Center and Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Juan R Alvarez
- Will Rogers Institute Pulmonary Research Center and Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Edward D Crandall
- Will Rogers Institute Pulmonary Research Center and Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
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13
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Jiang H, Tang M, Xu Z, Wang Y, Li M, Zheng S, Zhu J, Lin Z, Zhang M. CRISPR/Cas9 system and its applications in nervous system diseases. Genes Dis 2024; 11:675-686. [PMID: 37692518 PMCID: PMC10491921 DOI: 10.1016/j.gendis.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/05/2023] [Indexed: 09/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is an acquired immune system of many bacteria and archaea, comprising CRISPR loci, Cas genes, and its associated proteins. This system can recognize exogenous DNA and utilize the Cas9 protein's nuclease activity to break DNA double-strand and to achieve base insertion or deletion by subsequent DNA repair. In recent years, multiple laboratory and clinical studies have revealed the therapeutic role of the CRISPR/Cas9 system in neurological diseases. This article reviews the CRISPR/Cas9-mediated gene editing technology and its potential for clinical application against neurological diseases.
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Affiliation(s)
- Haibin Jiang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mengyan Tang
- The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zidi Xu
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yanan Wang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mopu Li
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Shuyin Zheng
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jianghu Zhu
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Zhenlang Lin
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Min Zhang
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
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14
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Ryan L, Rubinsztein DC. The autophagy of stress granules. FEBS Lett 2024; 598:59-72. [PMID: 38101818 DOI: 10.1002/1873-3468.14787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/20/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023]
Abstract
Our understanding of stress granule (SG) biology has deepened considerably in recent years, and with this, increased understanding of links has been made between SGs and numerous neurodegenerative diseases. One of the proposed mechanisms by which SGs and any associated protein aggregates may become pathological is based upon defects in their autophagic clearance, and so the precise processes governing the degradation of SGs are important to understand. Mutations and disease-associated variants implicated in amyotrophic lateral sclerosis, Huntington's disease, Parkinson's disease and frontotemporal lobar dementia compromise autophagy, whilst autophagy-inhibiting drugs or knockdown of essential autophagy proteins result in the persistence of SGs. In this review, we will consider the current knowledge regarding the autophagy of SG.
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Affiliation(s)
- Laura Ryan
- Department of Medical Genetics, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
- UK Dementia Research Institute, Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
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15
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Hwang ES, Song SB. Impaired Autophagic Flux in Glucose-Deprived Cells: An Outcome of Lysosomal Acidification Failure Exacerbated by Mitophagy Dysfunction. Mol Cells 2023; 46:655-663. [PMID: 37867391 PMCID: PMC10654461 DOI: 10.14348/molcells.2023.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 10/24/2023] Open
Abstract
Autophagy dysfunction is associated with human diseases and conditions including neurodegenerative diseases, metabolic issues, and chronic infections. Additionally, the decline in autophagic activity contributes to tissue and organ dysfunction and aging-related diseases. Several factors, such as down-regulation of autophagy components and activators, oxidative damage, microinflammation, and impaired autophagy flux, are linked to autophagy decline. An autophagy flux impairment (AFI) has been implicated in neurological disorders and in certain other pathological conditions. Here, to enhance our understanding of AFI, we conducted a comprehensive literature review of findings derived from two well-studied cellular stress models: glucose deprivation and replicative senescence. Glucose deprivation is a condition in which cells heavily rely on oxidative phosphorylation for ATP generation. Autophagy is activated, but its flux is hindered at the autolysis step, primarily due to an impairment of lysosomal acidity. Cells undergoing replicative senescence also experience AFI, which is also known to be caused by lysosomal acidity failure. Both glucose deprivation and replicative senescence elevate levels of reactive oxygen species (ROS), affecting lysosomal acidification. Mitochondrial alterations play a crucial role in elevating ROS generation and reducing lysosomal acidity, highlighting their association with autophagy dysfunction and disease conditions. This paper delves into the underlying molecular and cellular pathways of AFI in glucose-deprived cells, providing insights into potential strategies for managing AFI that is driven by lysosomal acidity failure. Furthermore, the investigation on the roles of mitochondrial dysfunction sheds light on the potential effectiveness of modulating mitochondrial function to overcome AFI, offering new possibilities for therapeutic interventions.
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Affiliation(s)
- Eun Seong Hwang
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Seon Beom Song
- Department of Life Science, University of Seoul, Seoul 02504, Korea
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16
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Guil-Luna S, Sanchez-Montero MT, Rodríguez-Ariza A. S-Nitrosylation at the intersection of metabolism and autophagy: Implications for cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:189012. [PMID: 37918453 DOI: 10.1016/j.bbcan.2023.189012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Metabolic plasticity, which determines tumour growth and metastasis, is now understood to be a flexible and context-specific process in cancer metabolism. One of the major pathways contributing to metabolic adaptations in eucaryotic cells is autophagy, a cellular degradation and recycling process that is activated during periods of starvation or stress to maintain metabolite and biosynthetic intermediate levels. Consequently, there is a close association between the metabolic adaptive capacity of tumour cells and autophagy-related pathways in cancer. Additionally, nitric oxide regulates protein function and signalling through S-nitrosylation, a post-translational modification that can also impact metabolism and autophagy. The primary objective of this review is to provide an up-to-date overview of the role of S-nitrosylation at the intersection of metabolism and autophagy in cancer. First, we will outline the involvement of S-nitrosylation in the metabolic adaptations that occur in tumours. Then, we will discuss the multifaceted role of autophagy in cancer, the interplay between metabolism and autophagy during tumour progression, and the contribution of S-nitrosylation to autophagic dysregulation in cancer. Finally, we will present insights into relevant therapeutic aspects and discuss prospects for the future.
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Affiliation(s)
- Silvia Guil-Luna
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain; Department of Comparative Anatomy and Pathology, Faculty of Veterinary Medicine of Córdoba, University of Córdoba, Córdoba, Spain
| | | | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain; Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain.
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17
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Mazina A, Shumilina J, Gazizova N, Repkin E, Frolov A, Minibayeva F. S-Nitrosylated Proteins Involved in Autophagy in Triticum aestivum Roots: A Bottom-Up Proteomics Approach and In Silico Predictive Algorithms. Life (Basel) 2023; 13:2024. [PMID: 37895406 PMCID: PMC10608115 DOI: 10.3390/life13102024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/23/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Autophagy is a highly conserved catabolic process in eukaryotic cells. Reactive nitrogen species play roles as inductors and signaling molecules of autophagy. A key mechanism of NO-mediated signaling is S-nitrosylation, a post-translational modification (PTM) of proteins at cysteine residues. In the present work, we analyzed the patterns of protein S-nitrosylation during the induction of autophagy in Triticum aestivum roots. The accumulation of S-nitrosylated proteins in the cells during autophagy induced with KNO2 and antimycin A was visualized using monoclonal antibodies with a Western blot analysis, and proteins were identified using a standard bottom-up proteomics approach. Protein S-nitrosylation is a labile and reversible PTM, and therefore the SNO group can be lost during experimental procedures. A subsequent bioinformatic analysis using predictive algorithms and protein-ligand docking showed that identified proteins possess hypothetical S-nitrosylation sites. Analyzing protein-protein interaction networks enabled us to discover the targets that can directly interact with autophagic proteins, and those that can interact with them indirectly via key multifunctional regulatory proteins. In this study, we show that S-nitrosylation is a key mechanism of NO-mediated regulation of autophagy in wheat roots. A combination of in silico predictive algorithms with a mass spectrometry analysis provides a targeted approach for the identification of S-nitrosylated proteins.
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Affiliation(s)
- Anastasia Mazina
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia; (A.M.); (N.G.)
| | - Julia Shumilina
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.F.)
| | - Natalia Gazizova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia; (A.M.); (N.G.)
| | - Egor Repkin
- Centre for Molecular and Cell Technologies, Saint Petersburg State University, Universitetskaya Embankment, 7/9, 199034 Saint Petersburg, Russia;
| | - Andrej Frolov
- Laboratory of Analytical Biochemistry and Biotechnology, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, 127276 Moscow, Russia; (J.S.); (A.F.)
| | - Farida Minibayeva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia; (A.M.); (N.G.)
- Open Lab ‘Biomarker’, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
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18
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Shi X, Wu W, Feng Z, Fan P, Shi R, Zhang X. MARCH7-mediated ubiquitination decreases the solubility of ATG14 to inhibit autophagy. Cell Rep 2023; 42:113045. [PMID: 37632749 DOI: 10.1016/j.celrep.2023.113045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/07/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023] Open
Abstract
Autophagy is a fundamental biological process critical to all eukaryotic cellular life. Although autophagy has been increasingly studied, how its process is precisely coordinated remains an open question. ATG14 (ATG14L/Barkor) is known to play a crucial role in both autophagosome formation and autophagosome-lysosome fusion. However, how ATG14 is regulated, especially at the post-translation level, is still not clear. Here, we report that MARCH7 (membrane-associated ring-CH-type finger 7), an E3 ubiquitin ligase, inhibits autophagy by ubiquitinating ATG14. MARCH7 significantly promotes K6-, K11-, and K63-linked mixed polyubiquitination on ATG14, triggering the aggregation of ATG14 and reducing its solubility in cells. Functionally, we find that MARCH7 depletion decreases the number of aggresome-like induced structures (ALISs). Mechanistically, we show that ubiquitinated ATG14 has fewer interactions with STX17, leading to the inhibition of autophagy flux. Collectively, our study reveals a mechanism in regulating autophagy and suggests a potential strategy for the treatment of autophagy-related diseases.
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Affiliation(s)
- Xue Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfeng Wu
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China
| | - Zhenhuan Feng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peiyang Fan
- SanQuan College, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - Ruona Shi
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510530, China.
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19
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Chen C, Cai N, Niu Q, Tian Y, Hu Y, Yan X. Quantitative assessment of lipophilic membrane dye-based labelling of extracellular vesicles by nano-flow cytometry. J Extracell Vesicles 2023; 12:e12351. [PMID: 37525378 PMCID: PMC10390660 DOI: 10.1002/jev2.12351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023] Open
Abstract
Although lipophilic membrane dyes (LMDs) or probes (LMPs) are widely used to label extracellular vesicles (EVs) for detection and purification, their labelling performance has not been systematically characterized. Through concurrent side scattering and fluorescence detection of single EVs as small as 40 nm in diameter by a laboratory-built nano-flow cytometer (nFCM), present study identified that (1) PKH67 and PKH26 could maximally label ∼60%-80% of EVs isolated from the conditioned cell culture medium (purity of ∼88%) and ∼40%-70% of PFP-EVs (purity of ∼73%); (2) excessive PKH26 could cause damage to the EV structure; (3) di-8-ANEPPS and high concentration of DiI could achieve efficient and uniform labelling of EVs with nearly 100% labelling efficiency for di-8-ANEPPS and 70%-100% for DiI; (4) all the four tested LMDs can aggregate and form micelles that exhibit comparable side scatter and fluorescence intensity with those of labelled EVs and thus hardly be differentiate from each other; (5) as the LMD concentration went up, the particle number of self-aggregates increased while the fluorescence intensity of aggregates remained constant; (6) PKH67 and PKH26 tend to form more aggregated micelles than di-8-ANEPPS and DiI, and the effect of LMD self-aggregation can be negligible at optimal staining conditions. (7) All the four tested LMDs can label almost all the very-low-density lipoprotein (VLDL) particles, indicating potential confounding factor in plasma-EV labelling. Besides, it was discovered that DSPE-PEG2000 -biotin can only label ∼50% of plasma-EVs. The number of LMP inserted into the membrane of single EVs was measured for the first time and it was confirmed that membrane labelling by lipophilic dyes did not interfere with the immunophenotyping of EVs. nFCM provides a unique perspective for a better understanding of EV labelling by LMD/LMP.
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Affiliation(s)
- Chen Chen
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen UniversityXiamenPeople's Republic of China
| | - Niangui Cai
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen UniversityXiamenPeople's Republic of China
| | - Qian Niu
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen UniversityXiamenPeople's Republic of China
| | - Ye Tian
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen UniversityXiamenPeople's Republic of China
| | - Yunyun Hu
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen UniversityXiamenPeople's Republic of China
| | - Xiaomei Yan
- Department of Chemical Biology, MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen UniversityXiamenPeople's Republic of China
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20
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Ramzan F, Abrar F, Mishra GG, Liao LMQ, Martin DDO. Lost in traffic: consequences of altered palmitoylation in neurodegeneration. Front Physiol 2023; 14:1166125. [PMID: 37324388 PMCID: PMC10268010 DOI: 10.3389/fphys.2023.1166125] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023] Open
Abstract
One of the first molecular events in neurodegenerative diseases, regardless of etiology, is protein mislocalization. Protein mislocalization in neurons is often linked to proteostasis deficiencies leading to the build-up of misfolded proteins and/or organelles that contributes to cellular toxicity and cell death. By understanding how proteins mislocalize in neurons, we can develop novel therapeutics that target the earliest stages of neurodegeneration. A critical mechanism regulating protein localization and proteostasis in neurons is the protein-lipid modification S-acylation, the reversible addition of fatty acids to cysteine residues. S-acylation is more commonly referred to as S-palmitoylation or simply palmitoylation, which is the addition of the 16-carbon fatty acid palmitate to proteins. Like phosphorylation, palmitoylation is highly dynamic and tightly regulated by writers (i.e., palmitoyl acyltransferases) and erasers (i.e., depalmitoylating enzymes). The hydrophobic fatty acid anchors proteins to membranes; thus, the reversibility allows proteins to be re-directed to and from membranes based on local signaling factors. This is particularly important in the nervous system, where axons (output projections) can be meters long. Any disturbance in protein trafficking can have dire consequences. Indeed, many proteins involved in neurodegenerative diseases are palmitoylated, and many more have been identified in palmitoyl-proteomic studies. It follows that palmitoyl acyl transferase enzymes have also been implicated in numerous diseases. In addition, palmitoylation can work in concert with cellular mechanisms, like autophagy, to affect cell health and protein modifications, such as acetylation, nitrosylation, and ubiquitination, to affect protein function and turnover. Limited studies have further revealed a sexually dimorphic pattern of protein palmitoylation. Therefore, palmitoylation can have wide-reaching consequences in neurodegenerative diseases.
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21
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Pinjala P, Tryphena KP, Prasad R, Khatri DK, Sun W, Singh SB, Gugulothu D, Srivastava S, Vora L. CRISPR/Cas9 assisted stem cell therapy in Parkinson's disease. Biomater Res 2023; 27:46. [PMID: 37194005 DOI: 10.1186/s40824-023-00381-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/16/2023] [Indexed: 05/18/2023] Open
Abstract
Since its discovery in 2012, CRISPR Cas9 has been tried as a direct treatment approach to correct the causative gene mutation and establish animal models in neurodegenerative disorders. Since no strategy developed until now could completely cure Parkinson's disease (PD), neuroscientists aspire to use gene editing technology, especially CRISPR/Cas9, to induce a permanent correction in genetic PD patients expressing mutated genes. Over the years, our understanding of stem cell biology has improved. Scientists have developed personalized cell therapy using CRISPR/Cas9 to edit embryonic and patient-derived stem cells ex-vivo. This review details the importance of CRISPR/Cas9-based stem cell therapy in Parkinson's disease in developing PD disease models and developing therapeutic strategies after elucidating the possible pathophysiological mechanisms.
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Affiliation(s)
- Poojitha Pinjala
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana-500037, Hyderabad, India
| | - Kamatham Pushpa Tryphena
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana-500037, Hyderabad, India
| | - Renuka Prasad
- Department of Anatomy, Korea University College of Medicine, Moonsuk Medical Research Building, 73 Inchon-Ro, Seongbuk-Gu, Seoul, 12841, Republic of Korea
| | - Dharmendra Kumar Khatri
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana-500037, Hyderabad, India.
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Moonsuk Medical Research Building, 73 Inchon-Ro, Seongbuk-Gu, Seoul, 12841, Republic of Korea
| | - Shashi Bala Singh
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana-500037, Hyderabad, India
| | - Dalapathi Gugulothu
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Saurabh Srivastava
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana-500037, Hyderabad, India
| | - Lalitkumar Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK.
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22
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Sipos A, Kim KJ, Sioutas C, Crandall ED. Kinetics of autophagic activity in nanoparticle-exposed lung adenocarcinoma (A549) cells. AUTOPHAGY REPORTS 2023; 2:2186568. [PMID: 37520337 PMCID: PMC10373127 DOI: 10.1080/27694127.2023.2186568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 08/01/2023]
Abstract
Autophagy, a homeostatic mechanism, is crucial in maintaining normal cellular function. Although dysregulation of autophagic processes is recognized in certain diseases, it is unknown how maintenance of cellular homeostasis might be affected by the kinetics of autophagic activity in response to various stimuli. In this study, we assessed those kinetics in lung adenocarcinoma (A549) cells in response to exposure to nanoparticles (NP) and/or Rapamycin. Since NP are known to induce autophagy, we wished to determine if this phenomenon could be a driver of the harmful effects seen in lung tissues exposed to air pollution. A549 cells were loaded with a fluorescent marker (DAPRed) that labels autophagosomes and autolysosomes. Autophagic activity was assessed based on the fluorescence intensity of DAPRed measured over the entire cell volume of live single cells using confocal laser scanning microscopy (CLSM). Autophagic activity over time was determined during exposure of A549 cells to single agents (50 nM Rapamycin; 80 μg/mL, 20 nm carboxylated polystyrene NP (PNP); or, 1 μg/mL ambient ultrafine particles (UFP) (<180 nm)), or double agents (Rapamycin + PNP or Rapamycin + UFP; concomitant and sequential), known to stimulate autophagy. Autophagic activity increased in all experimental modalities, including both single agent and double agent exposures, and reached a steady state in all cases ~2 times control from ~8 to 24 hrs, suggesting the presence of an upper limit to autophagic capacity. These results are consistent with the hypothesis that environmental stressors might exert their harmful effects, at least in part, by limiting available autophagic response to additional stimulation, thereby making nanoparticle-exposed cells more susceptible to secondary injury due to autophagic overload.
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Affiliation(s)
- Arnold Sipos
- Will Rogers Institute Pulmonary Research Center and Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kwang-Jin Kim
- Will Rogers Institute Pulmonary Research Center and Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neurosciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Constantinos Sioutas
- Sonny Astani Department of Civil and Environmental Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Edward D. Crandall
- Will Rogers Institute Pulmonary Research Center and Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Mork Family Department of Chemical Engineering and Materials Science, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
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23
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Ghatak S, Nakamura T, Lipton SA. Aberrant protein S-nitrosylation contributes to hyperexcitability-induced synaptic damage in Alzheimer's disease: Mechanistic insights and potential therapies. Front Neural Circuits 2023; 17:1099467. [PMID: 36817649 PMCID: PMC9932935 DOI: 10.3389/fncir.2023.1099467] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Alzheimer's disease (AD) is arguably the most common cause of dementia in the elderly and is marked by progressive synaptic degeneration, which in turn leads to cognitive decline. Studies in patients and in various AD models have shown that one of the early signatures of AD is neuronal hyperactivity. This excessive electrical activity contributes to dysregulated neural network function and synaptic damage. Mechanistically, evidence suggests that hyperexcitability accelerates production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) that contribute to neural network impairment and synapse loss. This review focuses on the pathways and molecular changes that cause hyperexcitability and how RNS-dependent posttranslational modifications, represented predominantly by protein S-nitrosylation, mediate, at least in part, the deleterious effects of hyperexcitability on single neurons and the neural network, resulting in synaptic loss in AD.
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Affiliation(s)
- Swagata Ghatak
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
| | - Tomohiro Nakamura
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States,*Correspondence: Tomohiro Nakamura,
| | - Stuart A. Lipton
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States,Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, United States,Stuart A. Lipton,
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24
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Yang H, Oh CK, Amal H, Wishnok JS, Lewis S, Schahrer E, Trudler D, Nakamura T, Tannenbaum SR, Lipton SA. Mechanistic insight into female predominance in Alzheimer's disease based on aberrant protein S-nitrosylation of C3. SCIENCE ADVANCES 2022; 8:eade0764. [PMID: 36516243 PMCID: PMC9750152 DOI: 10.1126/sciadv.ade0764] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein S-nitros(yl)ation (SNO) is a posttranslational modification involved in diverse processes in health and disease and can contribute to synaptic damage in Alzheimer's disease (AD). To identify SNO proteins in AD brains, we used triaryl phosphine (SNOTRAP) combined with mass spectrometry (MS). We detected 1449 SNO proteins with 2809 SNO sites, representing a wide range of S-nitrosylated proteins in 40 postmortem AD and non-AD human brains from patients of both sexes. Integrative protein ranking revealed the top 10 increased SNO proteins, including complement component 3 (C3), p62 (SQSTM1), and phospholipase D3. Increased levels of S-nitrosylated C3 were present in female over male AD brains. Mechanistically, we show that formation of SNO-C3 is dependent on falling β-estradiol levels, leading to increased synaptic phagocytosis and thus synapse loss and consequent cognitive decline. Collectively, we demonstrate robust alterations in the S-nitrosoproteome that contribute to AD pathogenesis in a sex-dependent manner.
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Affiliation(s)
- Hongmei Yang
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130021, China
| | - Chang-ki Oh
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Haitham Amal
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - John S. Wishnok
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sarah Lewis
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Emily Schahrer
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dorit Trudler
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tomohiro Nakamura
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven R. Tannenbaum
- Departments of Biological Engineering and Chemistry, and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Corresponding author. (S.R.T.); (S.A.L.)
| | - Stuart A. Lipton
- Department of Molecular Medicine and Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla CA 92093, USA
- Corresponding author. (S.R.T.); (S.A.L.)
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25
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Kim KR, Cho EJ, Eom JW, Oh SS, Nakamura T, Oh CK, Lipton SA, Kim YH. S-Nitrosylation of cathepsin B affects autophagic flux and accumulation of protein aggregates in neurodegenerative disorders. Cell Death Differ 2022; 29:2137-2150. [PMID: 35462559 PMCID: PMC9613756 DOI: 10.1038/s41418-022-01004-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 01/05/2023] Open
Abstract
Protein S-nitrosylation is known to regulate enzymatic function. Here, we report that nitric oxide (NO)-related species can contribute to Alzheimer's disease (AD) by S-nitrosylating the lysosomal protease cathepsin B (forming SNO-CTSB), thereby inhibiting CTSB activity. This posttranslational modification inhibited autophagic flux, increased autolysosomal vesicles, and led to accumulation of protein aggregates. CA-074Me, a CTSB chemical inhibitor, also inhibited autophagic flux and resulted in accumulation of protein aggregates similar to the effect of SNO-CTSB. Inhibition of CTSB activity also induced caspase-dependent neuronal apoptosis in mouse cerebrocortical cultures. To examine which cysteine residue(s) in CTSB are S-nitrosylated, we mutated candidate cysteines and found that three cysteines were susceptible to S-nitrosylation. Finally, we observed an increase in SNO-CTSB in both 5XFAD transgenic mouse and flash-frozen postmortem human AD brains. These results suggest that S-nitrosylation of CTSB inhibits enzymatic activity, blocks autophagic flux, and thus contributes to AD pathogenesis.
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Affiliation(s)
- Ki-Ryeong Kim
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, 05006, Republic of Korea
| | - Eun-Jung Cho
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, 05006, Republic of Korea
| | - Jae-Won Eom
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, 05006, Republic of Korea
| | - Sang-Seok Oh
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, 05006, Republic of Korea
| | - Tomohiro Nakamura
- Neurodegeneration New Medicines Center, Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chang-Ki Oh
- Neurodegeneration New Medicines Center, Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Stuart A Lipton
- Neurodegeneration New Medicines Center, Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA, 92093, USA.
| | - Yang-Hee Kim
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, 05006, Republic of Korea.
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26
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Taha HB, Kearney B, Bitan G. A minute fraction of α-synuclein in extracellular vesicles may be a major contributor to α-synuclein spreading following autophagy inhibition. Front Mol Neurosci 2022; 15:1001382. [PMID: 36245921 PMCID: PMC9554483 DOI: 10.3389/fnmol.2022.1001382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hash Brown Taha
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Brian Kearney
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: Gal Bitan
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27
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Oh CK, Nakamura T, Lipton SA. Inhibition of autophagic flux by S-nitrosylation of SQSTM1/p62 promotes neuronal secretion and cell-to-cell transmission of SNCA/α-synuclein in Parkinson disease and Lewy body dementia. AUTOPHAGY REPORTS 2022; 1:223-225. [PMID: 38098743 PMCID: PMC10721282 DOI: 10.1080/27694127.2022.2076770] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Autophagy (in the form of macroautophagy) is the major intracellular protein quality control system for removal of damaged organelles and abnormally aggregated proteins. We and others have shown that dysregulated autophagic pathways contribute to accumulation and spread of misfolded proteins in many neurodegenerative disorders, including Parkinson disease (PD) and Lewy body dementia (LBD). Additionally, generation of excessive reactive oxygen and nitrogen species, such as nitric oxide (NO), accelerates neuronal and synaptic damage mediated, at least in part, via aberrant protein S-nitrosylation. Using cell-based models, including human induced pluripotent stem cell (hiPSC)-derived neurons, CRISPR-Cas9 technology, and transgenic PD/LBD mice, plus vetting in human postmortem brains, we found that S-nitrosylation of the autophagic receptor protein SQSTM1/p62 (forming SNO-SQSTM1/p62) inhibits autophagic flux, thus contributing to accumulation of misfolded SNCA/α-synuclein. Consequently, this impairment in autophagy increases extracellular vesicle-dependent secretion and spread of aggregated SNCA. Taken together, our evidence suggests that aberrant formation of SNO-SQSTM1/p62 represents a pathogenic event contributing not only to inhibition of autophagic flux and potentiation of neuronal damage, but also to propagation of α-synucleinopathy between cells in the diseased brain.
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Affiliation(s)
- Chang-ki Oh
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - Tomohiro Nakamura
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
| | - Stuart A. Lipton
- Neurodegeneration New Medicines Center and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037
- Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, California 92093
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28
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Nagatsu T, Nakashima A, Watanabe H, Ito S, Wakamatsu K. Neuromelanin in Parkinson's Disease: Tyrosine Hydroxylase and Tyrosinase. Int J Mol Sci 2022; 23:4176. [PMID: 35456994 PMCID: PMC9029562 DOI: 10.3390/ijms23084176] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/02/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023] Open
Abstract
Parkinson's disease (PD) is an aging-related disease and the second most common neurodegenerative disease after Alzheimer's disease. The main symptoms of PD are movement disorders accompanied with deficiency of neurotransmitter dopamine (DA) in the striatum due to cell death of the nigrostriatal DA neurons. Two main histopathological hallmarks exist in PD: cytosolic inclusion bodies termed Lewy bodies that mainly consist of α-synuclein protein, the oligomers of which produced by misfolding are regarded to be neurotoxic, causing DA cell death; and black pigments termed neuromelanin (NM) that are contained in DA neurons and markedly decrease in PD. The synthesis of human NM is regarded to be similar to that of melanin in melanocytes; melanin synthesis in skin is via DOPAquinone (DQ) by tyrosinase, whereas NM synthesis in DA neurons is via DAquinone (DAQ) by tyrosine hydroxylase (TH) and aromatic L-amino acid decarboxylase (AADC). DA in cytoplasm is highly reactive and is assumed to be oxidized spontaneously or by an unidentified tyrosinase to DAQ and then, synthesized to NM. Intracellular NM accumulation above a specific threshold has been reported to be associated with DA neuron death and PD phenotypes. This review reports recent progress in the biosynthesis and pathophysiology of NM in PD.
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Affiliation(s)
- Toshiharu Nagatsu
- Center for Research Promotion and Support, School of Medicine, Fujita Health University, Toyoake 470-1192, Aichi, Japan
| | - Akira Nakashima
- Department of Physiological Chemistry, School of Medicine, Fujita Health University, Toyoake 470-1192, Aichi, Japan;
| | - Hirohisa Watanabe
- Department of Neurology, School of Medicine, Fujita Health University, Toyoake 470-1192, Aichi, Japan;
| | - Shosuke Ito
- Institute for Melanin Chemistry, Fujita Health University, Toyoake 470-1192, Aichi, Japan; (S.I.); (K.W.)
| | - Kazumasa Wakamatsu
- Institute for Melanin Chemistry, Fujita Health University, Toyoake 470-1192, Aichi, Japan; (S.I.); (K.W.)
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