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Jusic A, Erpapazoglou Z, Dalgaard LT, Lakkisto P, de Gonzalo-Calvo D, Benczik B, Ágg B, Ferdinandy P, Fiedorowicz K, Schroen B, Lazou A, Devaux Y. Guidelines for mitochondrial RNA analysis. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102262. [PMID: 39091381 PMCID: PMC11292373 DOI: 10.1016/j.omtn.2024.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.
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Affiliation(s)
- Amela Jusic
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Zoi Erpapazoglou
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Päivi Lakkisto
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Bettina Benczik
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Bence Ágg
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | - Péter Ferdinandy
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
| | | | - Blanche Schroen
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
| | - Antigone Lazou
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - on behalf of EU-CardioRNA COST Action CA17129
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - AtheroNET COST Action CA21153
- HAYA Therapeutics SA, Route De La Corniche 6, SuperLab Suisse - Batiment Serine, 1066 Epalinges, Switzerland
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Ιnstitute for Fundamental Biomedical Research, B.S.R.C. “Alexander Fleming”, Vari, 16672 Athens, Greece
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Minerva Foundation Institute for Medical Research, 00290 Helsinki, Finland
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, 00014 Helsinki, Finland
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain
- Cardiometabolic and HUN-REN-SU System Pharmacology Research Group, Center for Pharmacology and Drug Research & Development, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1089 Budapest, Hungary
- Pharmahungary Group, 6722 Szeged, Hungary
- NanoBioMedical Centre, Adam Mickiewicz University in Poznan, 61614 Poznan, Poland
- Department of Physiology, Cardiovascular Research Institute Maastricht, Maastricht University, ER 6229 Maastricht, the Netherlands
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Arast Y, Sabbaghi M, Kamranfar F, Heidari F, Fazli Nejad SM, Hosseinabadi T, Pourahmad J. Selective cytotoxicity of standardised n-hexane extract of black soldier flies' larvae on cancerous skin cells mitochondria isolated from rat model of melanoma. Cutan Ocul Toxicol 2024:1-8. [PMID: 39115252 DOI: 10.1080/15569527.2024.2389193] [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: 12/27/2023] [Revised: 06/30/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024]
Abstract
INTRODUCTION Melanoma is known as a highly lethal cancer. In melanoma cells, apoptosis signalling which relies heavily on the acute activity of mitochondria and reactive oxygen species (ROS) formation is suppressed. Our previous studies on natural compounds on melanoma suggested that mitochondria are a potential target for the melanoma treatment by selective cytotoxic effect of them. The black soldier fly is an important environmental protectant insect that based on recent studies induces apoptosis in liver and colorectal carcinoma cells through the activation of caspase 3, 8, and 9 and ultimately inhibits the growth of cancer cells. PURPOSE This study was designed to evaluate the selective apoptotic effect of the n-hexane BSFL extract (BSFLE) on skin mitochondria. MATERIALS AND METHODS The mitochondria isolated from melanoma cells were treated with various concentrations (1500, 3000, and 6000 µg/ml) of n-hexane BSFLE Then MTT viability assay, ROS determination, Mitochondrial Membrane Potential (MMP), mitochondrial swelling, cytochrome c release determination, and % apoptosis were performed. RESULTS MTT assay showed that different concentrations of n-hexane BSFLE significantly (P < 0.05) decreased the SDH activity in cancerous skin mitochondria with the IC50. The ROS production and mitochondrial swelling results also showed that all concentrations of BSFL extracts significantly increased. MMP decline and the release of cytochrome c in cancer groups mitochondria. BSFLE increased apoptosis on melanoma cells. DISCUSSION AND CONCLUSION It is suggested that n-hexane BSFLE compounds selectively induce a cascade of proapoptotic events that are probably defective in cancer cells. Most of these compounds target the mitochondrial transient pore caused by disruption of the mitochondrial respiratory chain. These events lead to disruption of the temporary permeability of mitochondria, swelling of mitochondria and finally the formation of apoptosome in the cytosol.
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Affiliation(s)
- Yalda Arast
- Research Center of Environmental Pollutants, Qom University of Medical Sciences, Qom, Iran
| | - Mahya Sabbaghi
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences Tehran, Tehran, Iran
| | - Farzane Kamranfar
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences Tehran, Tehran, Iran
| | - Fatemeh Heidari
- Department of Anatomical Sciences, School of Medicine, Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | | | - Tahereh Hosseinabadi
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences Tehran, Tehran, Iran
| | - Jalal Pourahmad
- Department of Pharmacology and Toxicology, School of Pharmacy, Shahid Beheshti University of Medical Sciences Tehran, Tehran, Iran
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Zhao X, Wang F, Kam C, Wu MY, Zhang J, Xu C, Bao K, He Q, Ye R, Tang BZ, Chen S. Fluorescent Nanocable as a Biomedical Tool: Intracellular Self-Assembly Formed by a Natural Product Interconnects and Synchronizes Mitochondria. ACS NANO 2024; 18:21447-21458. [PMID: 39080909 PMCID: PMC11328177 DOI: 10.1021/acsnano.4c06186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
Self-assembly processes commonly occur in various biological contexts to form functional biological structures. However, the self-assembly of nanofibers within cells by heterologous molecules showing a biological function is rare. In this work, we reported the intracellular formation of fluorescent nanofibers by a natural small molecule, lycobetaine (LBT), which facilitated the direct physical connection between mitochondria and synchronized their membrane potential oscillations. The luminescent properties of LBT enabled the real-time observation of nanofiber formation, while the semiconductive nature of the LBT nanofiber facilitated electrical signal transduction among the connected mitochondria. This study introduces an approach to modulate mitochondrial connectivity within cells using "nano-cables" which facilitate studies on synchronized mitochondrial operations and the underlying mechanisms of drug action.
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Affiliation(s)
- Xueqian Zhao
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong 999077, China
| | - Fei Wang
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong 999077, China
| | - Chuen Kam
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong 999077, China
| | - Ming-Yu Wu
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong 999077, China
| | - Jianyu Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Changhuo Xu
- Ministry of Education Frontiers Science Center for Precision Oncology, Faculty of Health Sciences, University of Macau, Macao 999078, China
| | - Kai Bao
- Department of Materials Science and Engineering, Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Qiyuan He
- Department of Materials Science and Engineering, Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Ruquan Ye
- Department of Materials Science and Engineering, Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, and Guangdong-Hong Kong-Macau Joint Laboratory of Optoelectronic and Magnetic Functional Materials, The Hong Kong University of Science and Technology, Hong Kong 999077, China
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, China
| | - Sijie Chen
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong 999077, China
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Scheiblich H, Eikens F, Wischhof L, Opitz S, Jüngling K, Cserép C, Schmidt SV, Lambertz J, Bellande T, Pósfai B, Geck C, Spitzer J, Odainic A, Castro-Gomez S, Schwartz S, Boussaad I, Krüger R, Glaab E, Di Monte DA, Bano D, Dénes Á, Latz E, Melki R, Pape HC, Heneka MT. Microglia rescue neurons from aggregate-induced neuronal dysfunction and death through tunneling nanotubes. Neuron 2024:S0896-6273(24)00491-4. [PMID: 39059388 DOI: 10.1016/j.neuron.2024.06.029] [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: 10/26/2023] [Revised: 02/12/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
Microglia are crucial for maintaining brain health and neuron function. Here, we report that microglia establish connections with neurons using tunneling nanotubes (TNTs) in both physiological and pathological conditions. These TNTs facilitate the rapid exchange of organelles, vesicles, and proteins. In neurodegenerative diseases like Parkinson's and Alzheimer's disease, toxic aggregates of alpha-synuclein (α-syn) and tau accumulate within neurons. Our research demonstrates that microglia use TNTs to extract neurons from these aggregates, restoring neuronal health. Additionally, microglia share their healthy mitochondria with burdened neurons, reducing oxidative stress and normalizing gene expression. Disrupting mitochondrial function with antimycin A before TNT formation eliminates this neuroprotection. Moreover, co-culturing neurons with microglia and promoting TNT formation rescues suppressed neuronal activity caused by α-syn or tau aggregates. Notably, TNT-mediated aggregate transfer is compromised in microglia carrying Lrrk22(Gly2019Ser) or Trem2(T66M) and (R47H) mutations, suggesting a role in the pathology of these gene variants in neurodegenerative diseases.
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Affiliation(s)
- Hannah Scheiblich
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases, Bonn, Germany; Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Frederik Eikens
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases, Bonn, Germany; Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases, Bonn, Germany; Max-Planck-Institute for Biology of Ageing, Cologne, Germany
| | - Sabine Opitz
- Institute of Neuropathology, University of Bonn, Bonn, Germany
| | - Kay Jüngling
- Institute of Physiology I, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Csaba Cserép
- Institute of Experimental Medicine, Budapest, Hungary
| | - Susanne V Schmidt
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | | | - Tracy Bellande
- Institut François Jacob, CEA and Laboratory of Neurodegenerative Diseases, Fontenay-aux-Roses, France
| | - Balázs Pósfai
- Institute of Experimental Medicine, Budapest, Hungary
| | - Charlotte Geck
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Jasper Spitzer
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Alexandru Odainic
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, VIC, Australia
| | | | | | - Ibrahim Boussaad
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Daniele Bano
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Ádám Dénes
- Institute of Experimental Medicine, Budapest, Hungary
| | - Eike Latz
- German Center for Neurodegenerative Diseases, Bonn, Germany; Institute of innate immunity, University Hospital Bonn, Bonn, Germany
| | - Ronald Melki
- Institut François Jacob, CEA and Laboratory of Neurodegenerative Diseases, Fontenay-aux-Roses, France
| | - Hans-Christian Pape
- Institute of Physiology I, Westfälische Wilhelms-University Münster, Münster, Germany
| | - Michael T Heneka
- German Center for Neurodegenerative Diseases, Bonn, Germany; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg; Institute of innate immunity, University Hospital Bonn, Bonn, Germany; Department of Infectious Diseases and Immunology, University of Massachusetts, Medical School, Worcester, MA, USA.
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Cunha-Oliveira T, Ioannidis JPA, Oliveira PJ. Best practices for data management and sharing in experimental biomedical research. Physiol Rev 2024; 104:1387-1408. [PMID: 38451234 PMCID: PMC11380994 DOI: 10.1152/physrev.00043.2023] [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: 11/09/2023] [Revised: 02/07/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
Effective data management is crucial for scientific integrity and reproducibility, a cornerstone of scientific progress. Well-organized and well-documented data enable validation and building on results. Data management encompasses activities including organization, documentation, storage, sharing, and preservation. Robust data management establishes credibility, fostering trust within the scientific community and benefiting researchers' careers. In experimental biomedicine, comprehensive data management is vital due to the typically intricate protocols, extensive metadata, and large datasets. Low-throughput experiments, in particular, require careful management to address variations and errors in protocols and raw data quality. Transparent and accountable research practices rely on accurate documentation of procedures, data collection, and analysis methods. Proper data management ensures long-term preservation and accessibility of valuable datasets. Well-managed data can be revisited, contributing to cumulative knowledge and potential new discoveries. Publicly funded research has an added responsibility for transparency, resource allocation, and avoiding redundancy. Meeting funding agency expectations increasingly requires rigorous methodologies, adherence to standards, comprehensive documentation, and widespread sharing of data, code, and other auxiliary resources. This review provides critical insights into raw and processed data, metadata, high-throughput versus low-throughput datasets, a common language for documentation, experimental and reporting guidelines, efficient data management systems, sharing practices, and relevant repositories. We systematically present available resources and optimal practices for wide use by experimental biomedical researchers.
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Affiliation(s)
- Teresa Cunha-Oliveira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - John P A Ioannidis
- Meta-Research Innovation Center at Stanford (METRICS), Stanford, California, United States
- Department of Statistics, Stanford University, Stanford, California, United States
| | - Paulo J Oliveira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
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Parvanovova P, Evinova A, Grofik M, Hnilicova P, Tatarkova Z, Turcanova-Koprusakova M. Mitochondrial Dysfunction in Sporadic Amyotrophic Lateral Sclerosis Patients: Insights from High-Resolution Respirometry. Biomedicines 2024; 12:1294. [PMID: 38927501 PMCID: PMC11201269 DOI: 10.3390/biomedicines12061294] [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: 05/13/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Amyotrophic lateral sclerosis is a severe neurodegenerative disease whose exact cause is still unclear. Currently, research attention is turning to the mitochondrion as a critical organelle of energy metabolism. Current knowledge is sufficient to confirm the involvement of the mitochondria in the pathophysiology of the disease, since the mitochondria are involved in many processes in the cell; however, the exact mechanism of involvement is still unclear. We used peripheral blood mononuclear cells isolated from whole fresh blood from patients with amyotrophic lateral sclerosis for measurement and matched an age- and sex-matched set of healthy subjects. The group of patients consisted of patients examined and diagnosed at the neurological clinic of the University Hospital Martin. The set of controls consisted of healthy individuals who were actively searched, and controls were selected on the basis of age and sex. The group consisted of 26 patients with sporadic forms of ALS (13 women, 13 men), diagnosed based on the definitive criteria of El Escorial. The average age of patients was 54 years, and the average age of healthy controls was 56 years. We used a high-resolution O2K respirometry method, Oxygraph-2k, to measure mitochondrial respiration. Basal respiration was lower in patients by 29.48%, pyruvate-stimulated respiration (respiratory chain complex I) was lower by 29.26%, and maximal respiratory capacity was lower by 28.15%. The decrease in succinate-stimulated respiration (respiratory chain complex II) was 26.91%. Our data confirm changes in mitochondrial respiration in ALS patients, manifested by the reduced function of complex I and complex II of the respiratory chain. These defects are severe enough to confirm this disease's hypothesized mitochondrial damage. Therefore, research interest in the future should be directed towards a deeper understanding of the involvement of mitochondria and respiratory complexes in the pathophysiology of the disease. This understanding could develop new biomarkers in diagnostics and subsequent therapeutic interventions.
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Affiliation(s)
- Petra Parvanovova
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia; (P.P.); (Z.T.)
| | - Andrea Evinova
- Biomedical Centre Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia; (A.E.); (P.H.)
| | - Milan Grofik
- Department of Neurology, University Hospital Martin, 036 01 Martin, Slovakia;
| | - Petra Hnilicova
- Biomedical Centre Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia; (A.E.); (P.H.)
| | - Zuzana Tatarkova
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia; (P.P.); (Z.T.)
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Zhao N, Wang J, Huang S, Zhang J, Bao J, Ni H, Gao X, Zhang C. The landscape of programmed cell death-related lncRNAs in Alzheimer's disease and Parkinson's disease. Apoptosis 2024:10.1007/s10495-024-01984-z. [PMID: 38853201 DOI: 10.1007/s10495-024-01984-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2024] [Indexed: 06/11/2024]
Abstract
This study delivers a thorough analysis of long non-coding RNAs (lncRNAs) in regulating programmed cell death (PCD), vital for neurodegenerative diseases like Alzheimer's disease (AD) and Parkinson's disease (PD). We propose a new framework PCDLnc, and identified 20 significant lncRNAs, including HEIH, SNHG15, and SNHG5, associated with PCD gene sets, which were known for roles in proliferation and apoptosis in neurodegenerative diseases. By using GREAT software, we identified regulatory functions of top lncRNAs in different neurodegenerative diseases. Moreover, lncRNAs cis-regulated mRNAs linked to neurodegeneration, including JAK2, AKT1, EGFR, CDC42, SNCA, and ADIPOQ, highlighting their therapeutic potential in neurodegenerative diseases. A further exploration into the differential expression of mRNA identified by PCDLnc revealed a role in apoptosis, ferroptosis and autophagy. Additionally, protein-protein interaction (PPI) network analysis exposed abnormal interactions among key genes, despite their consistent expression levels between disease and normal samples. The randomforest model effectively distinguished between disease samples, indicating a high level of accuracy. Shared gene subsets in AD and PD might serve as potential biomarkers, along with disease-specific gene sets. Besides, we also found the strong relationship between AD and immune infiltration. This research highlights the role of lncRNAs and their associated genes in PCD in neurodegenerative diseases, offering potential therapeutic targets and diagnostic markers for future study and clinical application.
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Affiliation(s)
- Ning Zhao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Junyi Wang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shan Huang
- The Second Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jingyu Zhang
- The Fourth Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jin Bao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Haisen Ni
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Xinhang Gao
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Chunlong Zhang
- College of Computer and Control Engineering, Northeast Forestry University, Harbin, Heilongjiang, China.
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Isei MO, Girardi PA, Rodwell-Bullock J, Nehrke K, Johnson GVW. Site-specific phosphorylation of tau impacts mitochondrial function and response to stressors. J Neurochem 2024; 168:1019-1029. [PMID: 37787052 PMCID: PMC10987400 DOI: 10.1111/jnc.15975] [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: 02/17/2023] [Revised: 08/31/2023] [Accepted: 09/14/2023] [Indexed: 10/04/2023]
Abstract
Phosphorylation of tau at sites associated with Alzheimer's disease (AD) likely plays a role in the disease progression. Mitochondrial impairment, correlating with increased presence of phosphorylated tau, has been identified as a contributing factor to neurodegenerative processes in AD. However, how tau phosphorylated at specific sites impacts mitochondrial function has not been fully defined. We examined how AD-relevant phosphomimetics of tau impact selected aspects of mitochondrial biology. To mimic phosphorylation at AD-associated sites, the serine/threonine (Ser/Thr) sites in wild-type green fluorescent protein (GFP)-tagged tau (T4) were converted to glutamic acid (E) to make pseudo-phosphorylated GFP-tagged Ser-396/404 (2EC) and GFP-tagged Thr-231/Ser-235 (2EM) constructs. These constructs were expressed in immortalized mouse hippocampal neuronal cell lines, and their impact on specific mitochondrial functions and responses to stressors were measured. Phosphomimetic tau altered mitochondrial distribution. Specifically, mitochondria accumulated in the soma of cells expressing either 2EC or 2EM and neurite-like extensions in 2EC cells were shorter. Additionally, adenosine triphosphate levels were reduced in both 2EC- and 2EM-expressing cells, and reactive oxygen species (ROS) production increased in 2EC cells during oxidation of succinate when compared to T4-expressing cells. Thapsigargin reduced mitochondrial membrane potential and increased ROS production in both 2EC and 2EM cells relative to T4 cells, with no significant difference in the effects of rotenone. These results show that tau phosphorylation at specific AD-relevant epitopes negatively affects mitochondria, with the extent of dysfunction and stress response varying according to the sites of phosphorylation. Altogether, these findings show that phosphorylated tau increases mitochondrial susceptibility to stressors and extend our understanding of potential mechanisms whereby phosphorylated tau promotes mitochondria dysfunction in tauopathies, including AD.
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Affiliation(s)
- Michael O Isei
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
| | - Peter A Girardi
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
| | - Joel Rodwell-Bullock
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
| | - Keith Nehrke
- University of Rochester, Department of Medicine, Nephrology Division, Rochester, New York, USA
| | - Gail VW Johnson
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
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Jörg M, Plehn JE, Kristen M, Lander M, Walz L, Lietz C, Wijns J, Pichot F, Rojas-Charry L, Wirtz Martin KM, Ruffini N, Kreim N, Gerber S, Motorin Y, Endres K, Rossmanith W, Methner A, Helm M, Friedland K. N1-methylation of adenosine (m 1A) in ND5 mRNA leads to complex I dysfunction in Alzheimer's disease. Mol Psychiatry 2024; 29:1427-1439. [PMID: 38287100 PMCID: PMC11189808 DOI: 10.1038/s41380-024-02421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024]
Abstract
One mechanism of particular interest to regulate mRNA fate post-transcriptionally is mRNA modification. Especially the extent of m1A mRNA methylation is highly discussed due to methodological differences. However, one single m1A site in mitochondrial ND5 mRNA was unanimously reported by different groups. ND5 is a subunit of complex I of the respiratory chain. It is considered essential for the coupling of oxidation and proton transport. Here we demonstrate that this m1A site might be involved in the pathophysiology of Alzheimer's disease (AD). One of the pathological hallmarks of this neurodegenerative disease is mitochondrial dysfunction, mainly induced by Amyloid β (Aβ). Aβ mainly disturbs functions of complex I and IV of the respiratory chain. However, the molecular mechanism of complex I dysfunction is still not fully understood. We found enhanced m1A methylation of ND5 mRNA in an AD cell model as well as in AD patients. Formation of this m1A methylation is catalyzed by increased TRMT10C protein levels, leading to translation repression of ND5. As a consequence, here demonstrated for the first time, TRMT10C induced m1A methylation of ND5 mRNA leads to mitochondrial dysfunction. Our findings suggest that this newly identified mechanism might be involved in Aβ-induced mitochondrial dysfunction.
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Affiliation(s)
- Marko Jörg
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Johanna E Plehn
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marco Kristen
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lukas Walz
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Christine Lietz
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Julie Wijns
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Florian Pichot
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Liliana Rojas-Charry
- Institute of Molecular Medicine, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Katja M Wirtz Martin
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Nicolas Ruffini
- Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany
| | - Nastasja Kreim
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany
| | - Yuri Motorin
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor CNRS, Université de Lorraine-INSERM, Biopôle, 9 Avenue de la Forêt de Haye, 54505, Vandœuvre-lès-Nancy, France
- IMoPA, UMR7365 CNRS, Université de Lorraine, Biopôle, 9 Avenue de la Forêt de Haye, 54505, Vandœuvre-lès-Nancy, France
| | - Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Center of the Johannes Gutenberg University Mainz, Untere Zahlbacher Str. 8, 55131, Mainz, Germany
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straβe 13, 1090, Vienna, Austria
| | - Axel Methner
- Institute of Molecular Medicine, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany.
| | - Kristina Friedland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany.
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10
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Dithmar S, Zare A, Salehi S, Briese M, Sendtner M. hnRNP R regulates mitochondrial movement and membrane potential in axons of motoneurons. Neurobiol Dis 2024; 193:106454. [PMID: 38408684 DOI: 10.1016/j.nbd.2024.106454] [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: 12/12/2023] [Revised: 02/12/2024] [Accepted: 02/23/2024] [Indexed: 02/28/2024] Open
Abstract
Axonal mitochondria defects are early events in the pathogenesis of motoneuron disorders such as spinal muscular atrophy and amyotrophic lateral sclerosis. The RNA-binding protein hnRNP R interacts with different motoneuron disease-related proteins such as SMN and TDP-43 and has important roles in axons of motoneurons, including axonal mRNA transport. However, whether hnRNP R also modulates axonal mitochondria is currently unknown. Here, we show that axonal mitochondria exhibit altered function and motility in hnRNP R-deficient motoneurons. Motoneurons lacking hnRNP R show decreased anterograde and increased retrograde transport of mitochondria in axons. Furthermore, hnRNP R-deficiency leads to mitochondrial hyperpolarization, caused by decreased complex I and reversed complex V activity within the respiratory chain. Taken together, our data indicate a role for hnRNP R in regulating transport and maintaining functionality of axonal mitochondria in motoneurons.
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Affiliation(s)
- Sophia Dithmar
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Abdolhossein Zare
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Saeede Salehi
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Michael Briese
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
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11
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Fan RZ, Sportelli C, Lai Y, Salehe SS, Pinnell JR, Brown HJ, Richardson JR, Luo S, Tieu K. A partial Drp1 knockout improves autophagy flux independent of mitochondrial function. Mol Neurodegener 2024; 19:26. [PMID: 38504290 PMCID: PMC10953112 DOI: 10.1186/s13024-024-00708-w] [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: 10/03/2023] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Dynamin-related protein 1 (Drp1) plays a critical role in mitochondrial dynamics. Partial inhibition of this protein is protective in experimental models of neurological disorders such as Parkinson's disease and Alzheimer's disease. The protective mechanism has been attributed primarily to improved mitochondrial function. However, the observations that Drp1 inhibition reduces protein aggregation in such neurological disorders suggest the involvement of autophagy. To investigate this potential novel protective mechanism of Drp1 inhibition, a model with impaired autophagy without mitochondrial involvement is needed. METHODS We characterized the effects of manganese (Mn), which causes parkinsonian-like symptoms in humans, on autophagy and mitochondria by performing dose-response studies in two cell culture models (stable autophagy HeLa reporter cells and N27 rat immortalized dopamine neuronal cells). Mitochondrial function was assessed using the Seahorse Flux Analyzer. Autophagy flux was monitored by quantifying the number of autophagosomes and autolysosomes, as well as the levels of other autophagy proteins. To strengthen the in vitro data, multiple mouse models (autophagy reporter mice and mutant Drp1+/- mice and their wild-type littermates) were orally treated with a low chronic Mn regimen that was previously reported to increase α-synuclein aggregation and transmission via exosomes. RNAseq, laser captured microdissection, immunofluorescence, immunoblotting, stereological cell counting, and behavioural studies were used. RESULTS IN VITRO: data demonstrate that at low non-toxic concentrations, Mn impaired autophagy flux but not mitochondrial function and morphology. In the mouse midbrain, RNAseq data further confirmed autophagy pathways were dysregulated but not mitochondrial related genes. Additionally, Mn selectively impaired autophagy in the nigral dopamine neurons but not the nearby nigral GABA neurons. In cells with a partial Drp1-knockdown and Drp1+/- mice, Mn induced autophagic impairment was significantly prevented. Consistent with these observations, Mn increased the levels of proteinase-K resistant α-synuclein and Drp1-knockdown protected against this pathology. CONCLUSIONS This study demonstrates that improved autophagy flux is a separate mechanism conferred by Drp1 inhibition independent of its role in mitochondrial fission. Given that impaired autophagy and mitochondrial dysfunction are two prominent features of neurodegenerative diseases, the combined protective mechanisms targeting these two pathways conferred by Drp1 inhibition make this protein an attractive therapeutic target.
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Affiliation(s)
- Rebecca Z Fan
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Carolina Sportelli
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Yanhao Lai
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Said S Salehe
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Jennifer R Pinnell
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Harry J Brown
- Department of Environmental Health Sciences, Florida International University, Miami, USA
- Biomolecular Sciences Institute, Florida International University, Miami, USA
| | - Jason R Richardson
- Department of Environmental Health Sciences, Florida International University, Miami, USA
| | - Shouqing Luo
- Peninsula Schools of Medicine and Dentistry, Plymouth University, Plymouth, UK
| | - Kim Tieu
- Department of Environmental Health Sciences, Florida International University, Miami, USA.
- Biomolecular Sciences Institute, Florida International University, Miami, USA.
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12
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Popgeorgiev N, Gil C, Berthenet K, Bertolin G, Ichim G. Shedding light on mitochondrial outer-membrane permeabilization and membrane potential: State of the art methods and biosensors. Semin Cell Dev Biol 2024; 156:58-65. [PMID: 37438211 DOI: 10.1016/j.semcdb.2023.07.003] [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: 04/02/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Membrane structural integrity is essential for optimal mitochondrial function. These organelles produce the energy needed for all vital processes, provided their outer and inner membranes are intact. This prevents the release of mitochondrial apoptogenic factors into the cytosol and ensures intact mitochondrial membrane potential (ΔΨm) to sustain ATP production. Cell death by apoptosis is generally triggered by outer mitochondrial membrane permeabilization (MOMP), tightly coupled with loss of ΔΨ m. As these two processes are essential for both mitochondrial function and cell death, researchers have devised various techniques to assess them. Here, we discuss current methods and biosensors available for detecting MOMP and measuring ΔΨ m, focusing on their advantages and limitations and discuss what new imaging tools are needed to improve our knowledge of mitochondrial function.
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Affiliation(s)
- Nikolay Popgeorgiev
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France; Institut Universitaire de France (IUF), Paris, France
| | - Clara Gil
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France
| | - Kevin Berthenet
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Institute of Genetics and Development of Rennes), Rennes, France.
| | - Gabriel Ichim
- Cancer Cell Death laboratory, part of LabEX DEVweCAN, Cancer Initiation and Tumoral Cell Identity Department, CRCL, U1052 INSERM, UMR CNRS 5286, Centre Léon Bérard, Université Lyon I, Institut Convergence PLAsCAN Lyon, France.
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13
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Ke W, Xie Y, Chen Y, Ding H, Ye L, Qiu H, Li H, Zhang L, Chen L, Tian X, Shen Z, Song Z, Fan X, Zong JF, Guo Z, Ma X, Xiao M, Liao G, Liu CH, Yin WB, Dong Z, Yang F, Jiang YY, Perlin DS, Chen Y, Fu YV, Wang L. Fungicide-tolerant persister formation during cryptococcal pulmonary infection. Cell Host Microbe 2024; 32:276-289.e7. [PMID: 38215741 DOI: 10.1016/j.chom.2023.12.012] [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: 06/08/2023] [Revised: 09/25/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
Bacterial persisters, a subpopulation of genetically susceptible cells that are normally dormant and tolerant to bactericides, have been studied extensively because of their clinical importance. In comparison, much less is known about the determinants underlying fungicide-tolerant fungal persister formation in vivo. Here, we report that during mouse lung infection, Cryptococcus neoformans forms persisters that are highly tolerant to amphotericin B (AmB), the standard of care for treating cryptococcosis. By exploring stationary-phase indicator molecules and developing single-cell tracking strategies, we show that in the lung, AmB persisters are enriched in cryptococcal cells that abundantly produce stationary-phase molecules. The antioxidant ergothioneine plays a specific and key role in AmB persistence, which is conserved in phylogenetically distant fungi. Furthermore, the antidepressant sertraline (SRT) shows potent activity specifically against cryptococcal AmB persisters. Our results provide evidence for and the determinant of AmB-tolerant persister formation in pulmonary cryptococcosis, which has potential clinical significance.
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Affiliation(s)
- Weixin Ke
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuyan Xie
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingying Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Ding
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leixin Ye
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haoning Qiu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Li
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Lanyue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuyun Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenghao Shen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zili Song
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Jian-Fa Zong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoyu Ma
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing 100730, China
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Cui Hua Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Yang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yuan-Ying Jiang
- Department of Pharmacy, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - David S Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Yihua Chen
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu V Fu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Linqi Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Matveeva A, Watters O, Rukhadze A, Khemka N, Gentile D, Perez IF, Llorente-Folch I, Farrell C, Lo Cacciato E, Jackson J, Piazzesi A, Wischhof L, Woods I, Halang L, Hogg M, Muñoz AG, Dillon ET, Matallanas D, Arijs I, Lambrechts D, Bano D, Connolly NMC, Prehn JHM. Integrated analysis of transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:135-149. [PMID: 37779364 DOI: 10.1080/21678421.2023.2261979] [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: 04/22/2023] [Accepted: 09/10/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE Sporadic and familial amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease that results in loss of motor neurons and, in some patients, associates with frontotemporal dementia (FTD). Apart from the accumulation of proteinaceous deposits, emerging literature indicates that aberrant mitochondrial bioenergetics may contribute to the onset and progression of ALS/FTD. Here we sought to investigate the pathophysiological signatures of mitochondrial dysfunction associated with ALS/FTD. METHODS By means of label-free mass spectrometry (MS) and mRNA sequencing (mRNA-seq), we report pre-symptomatic changes in the cortices of TDP-43 and FUS mutant mouse models. Using tissues from transgenic mouse models of mitochondrial diseases as a reference, we performed comparative analyses and extracted unique and common mitochondrial signatures that revealed neuroprotective compensatory mechanisms in response to early damage. RESULTS In this regard, upregulation of both Acyl-CoA Synthetase Long-Chain Family Member 3 (ACSL3) and mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) were the most representative change in pre-symptomatic ALS/FTD tissues, suggesting that fatty acid beta-oxidation and mitochondrial protein translation are mechanisms of adaptation in response to ALS/FTD pathology. CONCLUSIONS Together, our unbiased integrative analyses unveil novel molecular components that may influence mitochondrial homeostasis in the earliest phase of ALS.
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Affiliation(s)
- Anna Matveeva
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Orla Watters
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
| | - Ani Rukhadze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Niraj Khemka
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Debora Gentile
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ivan Fernandez Perez
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Irene Llorente-Folch
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Cliona Farrell
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | | | - Joshua Jackson
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ina Woods
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Luise Halang
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Marion Hogg
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
- Department of Biosciences, Nottingham Trent University, Clifton Campus, Nottingham, UK
| | - Amaya Garcia Muñoz
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Belfield, Ireland
| | - Eugène T Dillon
- Mass Spectrometry Resource, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - David Matallanas
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Belfield, Ireland
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Niamh M C Connolly
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jochen H M Prehn
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
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15
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Ratan Y, Rajput A, Pareek A, Pareek A, Jain V, Sonia S, Farooqui Z, Kaur R, Singh G. Advancements in Genetic and Biochemical Insights: Unraveling the Etiopathogenesis of Neurodegeneration in Parkinson's Disease. Biomolecules 2024; 14:73. [PMID: 38254673 PMCID: PMC10813470 DOI: 10.3390/biom14010073] [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: 11/21/2023] [Revised: 12/15/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative movement disorder worldwide, which is primarily characterized by motor impairments. Even though multiple hypotheses have been proposed over the decades that explain the pathogenesis of PD, presently, there are no cures or promising preventive therapies for PD. This could be attributed to the intricate pathophysiology of PD and the poorly understood molecular mechanism. To address these challenges comprehensively, a thorough disease model is imperative for a nuanced understanding of PD's underlying pathogenic mechanisms. This review offers a detailed analysis of the current state of knowledge regarding the molecular mechanisms underlying the pathogenesis of PD, with a particular emphasis on the roles played by gene-based factors in the disease's development and progression. This study includes an extensive discussion of the proteins and mutations of primary genes that are linked to PD, including α-synuclein, GBA1, LRRK2, VPS35, PINK1, DJ-1, and Parkin. Further, this review explores plausible mechanisms for DAergic neural loss, non-motor and non-dopaminergic pathologies, and the risk factors associated with PD. The present study will encourage the related research fields to understand better and analyze the current status of the biochemical mechanisms of PD, which might contribute to the design and development of efficacious and safe treatment strategies for PD in future endeavors.
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Affiliation(s)
- Yashumati Ratan
- Department of Pharmacy, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India; (A.R.); (A.P.); (A.P.)
| | - Aishwarya Rajput
- Department of Pharmacy, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India; (A.R.); (A.P.); (A.P.)
| | - Ashutosh Pareek
- Department of Pharmacy, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India; (A.R.); (A.P.); (A.P.)
| | - Aaushi Pareek
- Department of Pharmacy, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India; (A.R.); (A.P.); (A.P.)
| | - Vivek Jain
- Department of Pharmaceutical Sciences, Mohan Lal Sukhadia University, Udaipur 313001, Rajasthan, India;
| | - Sonia Sonia
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar 143005, Punjab, India;
| | - Zeba Farooqui
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA;
| | - Ranjeet Kaur
- Adesh Institute of Dental Sciences and Research, Bathinda 151101, Punjab, India;
| | - Gurjit Singh
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL 60607, USA;
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16
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Gnaiger E. Complex II ambiguities-FADH 2 in the electron transfer system. J Biol Chem 2024; 300:105470. [PMID: 38118236 PMCID: PMC10772739 DOI: 10.1016/j.jbc.2023.105470] [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: 07/03/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 12/22/2023] Open
Abstract
The prevailing notion that reduced cofactors NADH and FADH2 transfer electrons from the tricarboxylic acid cycle to the mitochondrial electron transfer system creates ambiguities regarding respiratory Complex II (CII). CII is the only membrane-bound enzyme in the tricarboxylic acid cycle and is part of the electron transfer system of the mitochondrial inner membrane feeding electrons into the coenzyme Q-junction. The succinate dehydrogenase subunit SDHA of CII oxidizes succinate and reduces the covalently bound prosthetic group FAD to FADH2 in the canonical forward tricarboxylic acid cycle. However, several graphical representations of the electron transfer system depict FADH2 in the mitochondrial matrix as a substrate to be oxidized by CII. This leads to the false conclusion that FADH2 from the β-oxidation cycle in fatty acid oxidation feeds electrons into CII. In reality, dehydrogenases of fatty acid oxidation channel electrons to the Q-junction but not through CII. The ambiguities surrounding Complex II in the literature and educational resources call for quality control, to secure scientific standards in current communications of bioenergetics, and ultimately support adequate clinical applications. This review aims to raise awareness of the inherent ambiguity crisis, complementing efforts to address the well-acknowledged issues of credibility and reproducibility.
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17
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Shen M, Sirois CL, Guo Y, Li M, Dong Q, Méndez-Albelo NM, Gao Y, Khullar S, Kissel L, Sandoval SO, Wolkoff NE, Huang SX, Xu Z, Bryan JE, Contractor AM, Korabelnikov T, Glass IA, Doherty D, Levine JE, Sousa AMM, Chang Q, Bhattacharyya A, Wang D, Werling DM, Zhao X. Species-specific FMRP regulation of RACK1 is critical for prenatal cortical development. Neuron 2023; 111:3988-4005.e11. [PMID: 37820724 PMCID: PMC10841112 DOI: 10.1016/j.neuron.2023.09.014] [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: 01/30/2023] [Revised: 07/20/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Fragile X messenger ribonucleoprotein 1 protein (FMRP) deficiency leads to fragile X syndrome (FXS), an autism spectrum disorder. The role of FMRP in prenatal human brain development remains unclear. Here, we show that FMRP is important for human and macaque prenatal brain development. Both FMRP-deficient neurons in human fetal cortical slices and FXS patient stem cell-derived neurons exhibit mitochondrial dysfunctions and hyperexcitability. Using multiomics analyses, we have identified both FMRP-bound mRNAs and FMRP-interacting proteins in human neurons and unveiled a previously unknown role of FMRP in regulating essential genes during human prenatal development. We demonstrate that FMRP interaction with CNOT1 maintains the levels of receptor for activated C kinase 1 (RACK1), a species-specific FMRP target. Genetic reduction of RACK1 leads to both mitochondrial dysfunctions and hyperexcitability, resembling FXS neurons. Finally, enhancing mitochondrial functions rescues deficits of FMRP-deficient cortical neurons during prenatal development, demonstrating targeting mitochondrial dysfunction as a potential treatment.
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Affiliation(s)
- Minjie Shen
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Carissa L Sirois
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yu Guo
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Meng Li
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Qiping Dong
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Natasha M Méndez-Albelo
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yu Gao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Saniya Khullar
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Departments of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Lee Kissel
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Soraya O Sandoval
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Natalie E Wolkoff
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sabrina X Huang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zhiyan Xu
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Graduate Program in Cell and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jonathan E Bryan
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Departments of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Amaya M Contractor
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Tomer Korabelnikov
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ian A Glass
- Birth Defects Research Laboratory, University of Washington, Seattle, WA 98195, USA
| | - Dan Doherty
- Birth Defects Research Laboratory, University of Washington, Seattle, WA 98195, USA
| | - Jon E Levine
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Qiang Chang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neurology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Departments of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Donna M Werling
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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18
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Bagnoli E, Trotier A, McMahon J, Quinlan LR, Biggs M, Pandit A, FitzGerald U. Prodromal Parkinson's disease and the catecholaldehyde hypothesis: Insight from olfactory bulb organotypic cultures. FASEB J 2023; 37:e23272. [PMID: 37997495 DOI: 10.1096/fj.202301253r] [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: 06/22/2023] [Revised: 09/15/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023]
Abstract
Parkinson's disease (PD) is a progressive, neurodegenerative disorder with an increasing incidence, unknown etiology, and is currently incurable. Advances in understanding the pathological mechanisms at a molecular level have been slow, with little attention focused on the early prodromal phase of the disease. Consequently, the development of early-acting disease-modifying therapies has been hindered. The olfactory bulb (OB), the brain region responsible for initial processing of olfactory information, is particularly affected early in PD at both functional and molecular levels but there is little information on how the cells in this region are affected by disease. Organotypic and primary OB cultures were developed and characterized. These platforms were then used to assess the effects of 3,4-dihydroxyphenylacetylaldehyde (DOPAL), a metabolite of dopamine present in increased levels in post-mortem PD tissue and which is thought to contribute to PD pathogenesis. Our findings showed that DOPAL exposure can recapitulate many aspects of PD pathology. Oxidative stress, depolarization of mitochondrial membranes, and neurodegeneration were all induced by DOPAL addition, as were measured transcriptomic changes consistent with those reported in PD clinical studies. These olfactory models of prodromal disease lend credence to the catecholaldehyde hypothesis of PD and provide insight into the mechanisms by which the OB may be involved in disease progression.
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Affiliation(s)
- Enrico Bagnoli
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
- Galway Neuroscience Centre, University of Galway, Galway, Ireland
| | - Alexandre Trotier
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
- Galway Neuroscience Centre, University of Galway, Galway, Ireland
| | - Jill McMahon
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
- Galway Neuroscience Centre, University of Galway, Galway, Ireland
| | - Leo R Quinlan
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
- Physiology, School of Medicine, Galway, Ireland
| | - Manus Biggs
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
- Galway Neuroscience Centre, University of Galway, Galway, Ireland
| | - Abhay Pandit
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
- Galway Neuroscience Centre, University of Galway, Galway, Ireland
| | - Una FitzGerald
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
- Galway Neuroscience Centre, University of Galway, Galway, Ireland
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19
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Strogulski NR, Portela LV, Polster BM, Loane DJ. Fundamental Neurochemistry Review: Microglial immunometabolism in traumatic brain injury. J Neurochem 2023; 167:129-153. [PMID: 37759406 PMCID: PMC10655864 DOI: 10.1111/jnc.15959] [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: 07/05/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023]
Abstract
Traumatic brain injury (TBI) is a devastating neurological disorder caused by a physical impact to the brain that promotes diffuse damage and chronic neurodegeneration. Key mechanisms believed to support secondary brain injury include mitochondrial dysfunction and chronic neuroinflammation. Microglia and brain-infiltrating macrophages are responsible for neuroinflammatory cytokine and reactive oxygen species (ROS) production after TBI. Their production is associated with loss of homeostatic microglial functions such as immunosurveillance, phagocytosis, and immune resolution. Beyond providing energy support, mitochondrial metabolic pathways reprogram the pro- and anti-inflammatory machinery in immune cells, providing a critical immunometabolic axis capable of regulating immunologic response to noxious stimuli. In the brain, the capacity to adapt to different environmental stimuli derives, in part, from microglia's ability to recognize and respond to changes in extracellular and intracellular metabolite levels. This capacity is met by an equally plastic metabolism, capable of altering immune function. Microglial pro-inflammatory activation is associated with decreased mitochondrial respiration, whereas anti-inflammatory microglial polarization is supported by increased oxidative metabolism. These metabolic adaptations contribute to neuroimmune responses, placing mitochondria as a central regulator of post-traumatic neuroinflammation. Although it is established that profound neurometabolic changes occur following TBI, key questions related to metabolic shifts in microglia remain unresolved. These include (a) the nature of microglial mitochondrial dysfunction after TBI, (b) the hierarchical positions of different metabolic pathways such as glycolysis, pentose phosphate pathway, glutaminolysis, and lipid oxidation during secondary injury and recovery, and (c) how immunometabolism alters microglial phenotypes, culminating in chronic non-resolving neuroinflammation. In this basic neurochemistry review article, we describe the contributions of immunometabolism to TBI, detail primary evidence of mitochondrial dysfunction and metabolic impairments in microglia and macrophages, discuss how major metabolic pathways contribute to post-traumatic neuroinflammation, and set out future directions toward advancing immunometabolic phenotyping in TBI.
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Affiliation(s)
- Nathan R. Strogulski
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Luis V. Portela
- Neurotrauma and Biomarkers Laboratory, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Brian M. Polster
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - David J. Loane
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
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20
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Chen SY, Li YP, You YP, Zhang HR, Shi ZJ, Liang QQ, Yuan T, Xu R, Xu LH, Zha QB, Ou-Yang DY, He XH. Theaflavin mitigates acute gouty peritonitis and septic organ injury in mice by suppressing NLRP3 inflammasome assembly. Acta Pharmacol Sin 2023; 44:2019-2036. [PMID: 37221235 PMCID: PMC10545837 DOI: 10.1038/s41401-023-01105-7] [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: 11/30/2022] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Activation of NLR family pyrin domain-containing 3 (NLRP3) inflammasome plays important role in defending against infections, but its aberrant activation is causally linked to many inflammatory diseases, thus being a therapeutic target for these diseases. Theaflavin, one major ingredient of black tea, exhibits potent anti-inflammatory and anti-oxidative activities. In this study, we investigated the therapeutic effects of theaflavin against NLRP3 inflammasome activation in macrophages in vitro and in animal models of related diseases. We showed that theaflavin (50, 100, 200 μM) dose-dependently inhibited NLRP3 inflammasome activation in LPS-primed macrophages stimulated with ATP, nigericin or monosodium urate crystals (MSU), evidenced by reduced release of caspase-1p10 and mature interleukin-1β (IL-1β). Theaflavin treatment also inhibited pyroptosis as shown by decreased generation of N-terminal fragment of gasdermin D (GSDMD-NT) and propidium iodide incorporation. Consistent with these, theaflavin treatment suppressed ASC speck formation and oligomerization in macrophages stimulated with ATP or nigericin, suggesting reduced inflammasome assembly. We revealed that theaflavin-induced inhibition on NLRP3 inflammasome assembly and pyroptosis resulted from ameliorated mitochondrial dysfunction and reduced mitochondrial ROS production, thereby suppressing interaction between NLRP3 and NEK7 downstream of ROS. Moreover, we showed that oral administration of theaflavin significantly attenuated MSU-induced mouse peritonitis and improved the survival of mice with bacterial sepsis. Consistently, theaflavin administration significantly reduced serum levels of inflammatory cytokines including IL-1β and attenuated liver inflammation and renal injury of mice with sepsis, concomitant with reduced generation of caspase-1p10 and GSDMD-NT in the liver and kidney. Together, we demonstrate that theaflavin suppresses NLRP3 inflammasome activation and pyroptosis by protecting mitochondrial function, thus mitigating acute gouty peritonitis and bacterial sepsis in mice, highlighting a potential application in treating NLRP3 inflammasome-related diseases.
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Affiliation(s)
- Si-Yuan Chen
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Ya-Ping Li
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yi-Ping You
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Hong-Rui Zhang
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Zi-Jian Shi
- Department of Fetal Medicine, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Qi-Qi Liang
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Tao Yuan
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Rong Xu
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Li-Hui Xu
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Qing-Bing Zha
- Department of Fetal Medicine, the First Affiliated Hospital of Jinan University, Guangzhou, 510630, China.
- Department of Clinical Laboratory, the Fifth Affiliated Hospital of Jinan University, Heyuan, 517000, China.
| | - Dong-Yun Ou-Yang
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Xian-Hui He
- Department of Immunobiology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
- Department of Clinical Laboratory, the Fifth Affiliated Hospital of Jinan University, Heyuan, 517000, China.
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21
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Menduti G, Boido M. Recent Advances in High-Content Imaging and Analysis in iPSC-Based Modelling of Neurodegenerative Diseases. Int J Mol Sci 2023; 24:14689. [PMID: 37834135 PMCID: PMC10572296 DOI: 10.3390/ijms241914689] [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: 08/13/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In the field of neurodegenerative pathologies, the platforms for disease modelling based on patient-derived induced pluripotent stem cells (iPSCs) represent a valuable molecular diagnostic/prognostic tool. Indeed, they paved the way for the in vitro recapitulation of the pathological mechanisms underlying neurodegeneration and for characterizing the molecular heterogeneity of disease manifestations, also enabling drug screening approaches for new therapeutic candidates. A major challenge is related to the choice and optimization of the morpho-functional study designs in human iPSC-derived neurons to deeply detail the cell phenotypes as markers of neurodegeneration. In recent years, the specific combination of high-throughput screening with subcellular resolution microscopy for cell-based high-content imaging (HCI) screening allowed in-depth analyses of cell morphology and neurite trafficking in iPSC-derived neuronal cells by using specific cutting-edge microscopes and automated computational assays. The present work aims to describe the main recent protocols and advances achieved with the HCI analysis in iPSC-based modelling of neurodegenerative diseases, highlighting technical and bioinformatics tips and tricks for further uses and research. To this end, microscopy requirements and the latest computational pipelines to analyze imaging data will be explored, while also providing an overview of the available open-source high-throughput automated platforms.
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Affiliation(s)
- Giovanna Menduti
- Department of Neuroscience “Rita Levi Montalcini”, Neuroscience Institute Cavalieri Ottolenghi, University of Turin, Regione Gonzole 10, Orbassano, 10043 Turin, TO, Italy;
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22
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Rohatgi N, Zou W, Li Y, Cho K, Collins PL, Tycksen E, Pandey G, DeSelm CJ, Patti GJ, Dey A, Teitelbaum SL. BAP1 promotes osteoclast function by metabolic reprogramming. Nat Commun 2023; 14:5923. [PMID: 37740028 PMCID: PMC10516877 DOI: 10.1038/s41467-023-41629-4] [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: 12/03/2021] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Treatment of osteoporosis commonly diminishes osteoclast number which suppresses bone formation thus compromising fracture prevention. Bone formation is not suppressed, however, when bone degradation is reduced by retarding osteoclast functional resorptive capacity, rather than differentiation. We find deletion of deubiquitinase, BRCA1-associated protein 1 (Bap1), in myeloid cells (Bap1∆LysM), arrests osteoclast function but not formation. Bap1∆LysM osteoclasts fail to organize their cytoskeleton which is essential for bone degradation consequently increasing bone mass in both male and female mice. The deubiquitinase activity of BAP1 modifies osteoclast function by metabolic reprogramming. Bap1 deficient osteoclast upregulate the cystine transporter, Slc7a11, by enhanced H2Aub occupancy of its promoter. SLC7A11 controls cellular reactive oxygen species levels and redirects the mitochondrial metabolites away from the tricarboxylic acid cycle, both being necessary for osteoclast function. Thus, in osteoclasts BAP1 appears to regulate the epigenetic-metabolic axis and is a potential target to reduce bone degradation while maintaining osteogenesis in osteoporotic patients.
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Affiliation(s)
- Nidhi Rohatgi
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Wei Zou
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yongjia Li
- Department of Pharmacology, Jiangsu University School of Medicine, Zhenjiang, Jiangsu Province, 212013, PR China
| | - Kevin Cho
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Patrick L Collins
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, 43210, USA
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Gaurav Pandey
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Carl J DeSelm
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Steven L Teitelbaum
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
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23
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Shao X, Meng C, Song W, Zhang T, Chen Q. Subcellular visualization: Organelle-specific targeted drug delivery and discovery. Adv Drug Deliv Rev 2023; 199:114977. [PMID: 37391014 DOI: 10.1016/j.addr.2023.114977] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Organelles perform critical biological functions due to their distinct molecular composition and internal environment. Disorders in organelles or their interacting networks have been linked to the incidence of numerous diseases, and the research of pharmacological actions at the organelle level has sparked pharmacists' interest. Currently, cell imaging has evolved into a critical tool for drug delivery, drug discovery, and pharmacological research. The introduction of advanced imaging techniques in recent years has provided researchers with richer biological information for viewing and studying the ultrastructure of organelles, protein interactions, and gene transcription activities, leading to the design and delivery of precision-targeted drugs. Therefore, this reviews the research on organelles-targeted drugs based upon imaging technologies and development of fluorescent molecules for medicinal purposes. We also give a thorough analysis of a number of subcellular-level elements of drug development, including subcellular research instruments and methods, organelle biological event investigation, subcellular target and drug identification, and design of subcellular delivery systems. This review will make it possible to promote drug research from the individual/cellular level to the subcellular level, as well as give a new focus based on newly found organelle activities.
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Affiliation(s)
- Xintian Shao
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Caicai Meng
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Wenjing Song
- School of Life Sciences, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China; School of Pharmaceutical Sciences & Institute of Materia Medica, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Key Laboratory for Biotechnology Drugs of National Health Commission, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China
| | - Tao Zhang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong Province 250014, PR China
| | - Qixin Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Key Laboratory for Biotechnology Drugs of National Health Commission, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, PR China.
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24
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Debruyne AC, Okkelman IA, Dmitriev RI. Balance between the cell viability and death in 3D. Semin Cell Dev Biol 2023; 144:55-66. [PMID: 36117019 DOI: 10.1016/j.semcdb.2022.09.005] [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: 04/19/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/25/2022]
Abstract
Cell death is a phenomenon, frequently perceived as an absolute event for cell, tissue and the organ. However, the rising popularity and complexity of such 3D multicellular 'tissue building blocks' as heterocellular spheroids, organoids, and 'assembloids' prompts to revise the definition and quantification of cell viability and death. It raises several questions on the overall viability of all the cells within 3D volume and on choosing the appropriate, continuous, and non-destructive viability assay enabling for a single-cell analysis. In this review, we look at cell viability and cell death modalities with attention to the intrinsic features of such 3D models as spheroids, organoids, and bioprints. Furthermore, we look at emerging and promising methodologies, which can help define and understand the balance between cell viability and death in dynamic and complex 3D environments. We conclude that the recent innovations in biofabrication, biosensor probe development, and fluorescence microscopy can help answer these questions.
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Affiliation(s)
- Angela C Debruyne
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
| | - Irina A Okkelman
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium
| | - Ruslan I Dmitriev
- Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent 9000, Belgium.
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25
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Alqahtani T, Deore SL, Kide AA, Shende BA, Sharma R, Chakole RD, Nemade LS, Kale NK, Borah S, Deokar SS, Behera A, Dhawal Bhandari D, Gaikwad N, Azad AK, Ghosh A. Mitochondrial dysfunction and oxidative stress in Alzheimer's disease, and Parkinson's disease, Huntington's disease and Amyotrophic Lateral Sclerosis -An updated review. Mitochondrion 2023:S1567-7249(23)00051-X. [PMID: 37269968 DOI: 10.1016/j.mito.2023.05.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Misfolded proteins in the central nervous system can induce oxidative damage, which can contribute to neurodegenerative diseases in the mitochondria. Neurodegenerative patients face early mitochondrial dysfunction, impacting energy utilization. Amyloid-ß and tau problems both have an effect on mitochondria, which leads to mitochondrial malfunction and, ultimately, the onset of Alzheimer's disease. Cellular oxygen interaction yields reactive oxygen species within mitochondria, initiating oxidative damage to mitochondrial constituents. Parkinson's disease, linked to oxidative stress, α-synuclein aggregation, and inflammation, results from reduced brain mitochondria activity. Mitochondrial dynamics profoundly influence cellular apoptosis via distinct causative mechanisms. The condition known as Huntington's disease is characterized by an expansion of polyglutamine, primarily impactingthe cerebral cortex and striatum. Research has identified mitochondrial failure as an early pathogenic mechanism contributing to HD's selective neurodegeneration. The mitochondria are organelles that exhibit dynamism by undergoing fragmentation and fusion processes to attain optimal bioenergetic efficiency. They can also be transported along microtubules and regulateintracellular calcium homeostasis through their interaction with the endoplasmic reticulum. Additionally, the mitochondria produce free radicals. The functions of eukaryotic cells, particularly in neurons, have significantly deviated from the traditionally assigned role of cellular energy production. Most of them areimpaired in HD, which may lead to neuronal dysfunction before symptoms manifest. This article summarises the most important changes in mitochondrial dynamics that come from neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's and Amyotrophic Lateral Sclerosis. Finally, we discussed about novel techniques that can potentially treat mitochondrial malfunction and oxidative stress in four most dominating neuro disorders.
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Affiliation(s)
- Taha Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia.
| | | | | | | | - Ritika Sharma
- University institute of pharma sciences, Chandigarh University, Mohali, Punjab.
| | - Rita Dadarao Chakole
- Government College of Pharmacy Vidyanagar Karad Dist Satara Maharashtra Pin 415124.
| | - Lalita S Nemade
- Govindrao Nikam College of Pharmacy Sawarde Maharashtra 415606.
| | | | - Sudarshana Borah
- Department of Pharmacognosy, University of Science and Technology Meghalaya Technocity, Ri-Bhoi District Meghalaya.
| | | | - Ashok Behera
- Faculty of Pharmacy, DIT University, Dehradun,Uttarakhand.
| | - Divya Dhawal Bhandari
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014. India.
| | - Nikita Gaikwad
- Department of Pharmaceutics, P.E.S. Modern College of Pharmacy, Nigdi, Pune-411044.
| | - Abul Kalam Azad
- Faculty of Pharmacy MAHSA University Bandar Saujana putra, 42610, Selangor, Malaysia
| | - Arabinda Ghosh
- Department of Botany, Gauhati University, Guwahati, 781014, Assam, India
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26
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Acin‐Perez R, Benincá C, Fernandez del Rio L, Shu C, Baghdasarian S, Zanette V, Gerle C, Jiko C, Khairallah R, Khan S, Rincon Fernandez Pacheco D, Shabane B, Erion K, Masand R, Dugar S, Ghenoiu C, Schreiner G, Stiles L, Liesa M, Shirihai OS. Inhibition of ATP synthase reverse activity restores energy homeostasis in mitochondrial pathologies. EMBO J 2023; 42:e111699. [PMID: 36912136 PMCID: PMC10183817 DOI: 10.15252/embj.2022111699] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 03/14/2023] Open
Abstract
The maintenance of cellular function relies on the close regulation of adenosine triphosphate (ATP) synthesis and hydrolysis. ATP hydrolysis by mitochondrial ATP Synthase (CV) is induced by loss of proton motive force and inhibited by the mitochondrial protein ATPase inhibitor (ATPIF1). The extent of CV hydrolytic activity and its impact on cellular energetics remains unknown due to the lack of selective hydrolysis inhibitors of CV. We find that CV hydrolytic activity takes place in coupled intact mitochondria and is increased by respiratory chain defects. We identified (+)-Epicatechin as a selective inhibitor of ATP hydrolysis that binds CV while preventing the binding of ATPIF1. In cells with Complex-III deficiency, we show that inhibition of CV hydrolytic activity by (+)-Epichatechin is sufficient to restore ATP content without restoring respiratory function. Inhibition of CV-ATP hydrolysis in a mouse model of Duchenne Muscular Dystrophy is sufficient to improve muscle force without any increase in mitochondrial content. We conclude that the impact of compromised mitochondrial respiration can be lessened using hydrolysis-selective inhibitors of CV.
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Affiliation(s)
- Rebeca Acin‐Perez
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Cristiane Benincá
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Lucia Fernandez del Rio
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Cynthia Shu
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Siyouneh Baghdasarian
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Vanessa Zanette
- Department of BioinformaticsUniversity Federal of ParanaCuritibaBrazil
| | - Christoph Gerle
- Institute for Protein ResearchOsaka UniversitySuitaJapan
- RIKEN SPring‐8 CenterSayo‐gunJapan
| | - Chimari Jiko
- Institute for Integrated Radiation and Nuclear ScienceKyoto UniversityKyotoJapan
| | | | | | | | - Byourak Shabane
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | | | | | | | | | | | - Linsey Stiles
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Department of Molecular and Medical PharmacologyUniversity of CaliforniaLos AngelesCAUSA
| | - Marc Liesa
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Department of Molecular and Medical PharmacologyUniversity of CaliforniaLos AngelesCAUSA
- Molecular Cellular Integrative PhysiologyUniversity of CaliforniaLos AngelesCAUSA
- Institut de Biologia Molecular de Barcelona, IBMB, CSICBarcelonaCataloniaSpain
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Metabolism Theme, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Department of Molecular and Medical PharmacologyUniversity of CaliforniaLos AngelesCAUSA
- Molecular Cellular Integrative PhysiologyUniversity of CaliforniaLos AngelesCAUSA
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27
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Szabo L, Grimm A, García-León JA, Verfaillie CM, Eckert A. Genetically Engineered Triple MAPT-Mutant Human-Induced Pluripotent Stem Cells (N279K, P301L, and E10+16 Mutations) Exhibit Impairments in Mitochondrial Bioenergetics and Dynamics. Cells 2023; 12:1385. [PMID: 37408218 DOI: 10.3390/cells12101385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 07/07/2023] Open
Abstract
Pathological abnormalities in the tau protein give rise to a variety of neurodegenerative diseases, conjointly termed tauopathies. Several tau mutations have been identified in the tau-encoding gene MAPT, affecting either the physical properties of tau or resulting in altered tau splicing. At early disease stages, mitochondrial dysfunction was highlighted with mutant tau compromising almost every aspect of mitochondrial function. Additionally, mitochondria have emerged as fundamental regulators of stem cell function. Here, we show that compared to the isogenic wild-type triple MAPT-mutant human-induced pluripotent stem cells, bearing the pathogenic N279K, P301L, and E10+16 mutations, exhibit deficits in mitochondrial bioenergetics and present altered parameters linked to the metabolic regulation of mitochondria. Moreover, we demonstrate that the triple tau mutations disturb the cellular redox homeostasis and modify the mitochondrial network morphology and distribution. This study provides the first characterization of disease-associated tau-mediated mitochondrial impairments in an advanced human cellular tau pathology model at early disease stages, ranging from mitochondrial bioenergetics to dynamics. Consequently, comprehending better the influence of dysfunctional mitochondria on the development and differentiation of stem cells and their contribution to disease progression may thus assist in the potential prevention and treatment of tau-related neurodegeneration.
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Affiliation(s)
- Leonora Szabo
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, 4002 Basel, Switzerland
- Neurobiology Lab for Brain Aging and Mental Health, University Psychiatric Clinics Basel, 4002 Basel, Switzerland
| | - Amandine Grimm
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, 4002 Basel, Switzerland
- Neurobiology Lab for Brain Aging and Mental Health, University Psychiatric Clinics Basel, 4002 Basel, Switzerland
- Department of Biomedicine, University of Basel, 4055 Basel, Switzerland
| | - Juan Antonio García-León
- Departamento Biologia Celular, Genetica y Fisiologia, Instituto de Investigacion Biomedica de Malaga-IBIMA, Facultad de Ciencias, Universidad de Malaga, 29071 Malaga, Spain
- Centro de Investigacion Biomedica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28031 Madrid, Spain
| | - Catherine M Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, 3000 Leuven, Belgium
| | - Anne Eckert
- Research Cluster Molecular and Cognitive Neurosciences, University of Basel, 4002 Basel, Switzerland
- Neurobiology Lab for Brain Aging and Mental Health, University Psychiatric Clinics Basel, 4002 Basel, Switzerland
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28
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Westi EW, Andersen JV, Aldana BI. Using stable isotope tracing to unravel the metabolic components of neurodegeneration: Focus on neuron-glia metabolic interactions. Neurobiol Dis 2023; 182:106145. [PMID: 37150307 DOI: 10.1016/j.nbd.2023.106145] [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: 02/23/2023] [Revised: 04/17/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023] Open
Abstract
Disrupted brain metabolism is a critical component of several neurodegenerative diseases. Energy metabolism of both neurons and astrocytes is closely connected to neurotransmitter recycling via the glutamate/GABA-glutamine cycle. Neurons and astrocytes hereby work in close metabolic collaboration which is essential to sustain neurotransmission. Elucidating the mechanistic involvement of altered brain metabolism in disease progression has been aided by the advance of techniques to monitor cellular metabolism, in particular by mapping metabolism of substrates containing stable isotopes, a technique known as isotope tracing. Here we review key aspects of isotope tracing including advantages, drawbacks and applications to different cerebral preparations. In addition, we narrate how isotope tracing has facilitated the discovery of central metabolic features in neurodegeneration with a focus on the metabolic cooperation between neurons and astrocytes.
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Affiliation(s)
- Emil W Westi
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jens V Andersen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Blanca I Aldana
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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29
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Kiriyama Y, Nochi H. Role of Microbiota-Modified Bile Acids in the Regulation of Intracellular Organelles and Neurodegenerative Diseases. Genes (Basel) 2023; 14:825. [PMID: 37107583 PMCID: PMC10137455 DOI: 10.3390/genes14040825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Bile acids (BAs) are amphiphilic steroidal molecules generated from cholesterol in the liver and facilitate the digestion and absorption of fat-soluble substances in the gut. Some BAs in the intestine are modified by the gut microbiota. Because BAs are modified in a variety of ways by different types of bacteria present in the gut microbiota, changes in the gut microbiota can affect the metabolism of BAs in the host. Although most BAs absorbed from the gut are transferred to the liver, some are transferred to the systemic circulation. Furthermore, BAs have also been detected in the brain and are thought to migrate into the brain through the systemic circulation. Although BAs are known to affect a variety of physiological functions by acting as ligands for various nuclear and cell-surface receptors, BAs have also been found to act on mitochondria and autophagy in the cell. This review focuses on the BAs modified by the gut microbiota and their roles in intracellular organelles and neurodegenerative diseases.
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Affiliation(s)
- Yoshimitsu Kiriyama
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Kagawa 769-2193, Japan
- Institute of Neuroscience, Tokushima Bunri University, Kagawa 769-2193, Japan
| | - Hiromi Nochi
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Kagawa 769-2193, Japan
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30
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Linciano P, Sorbi C, Rossino G, Rossi D, Marsala A, Denora N, Bedeschi M, Marino N, Miserocchi G, Dondio G, Peviani M, Tesei A, Collina S, Franchini S. Novel S1R agonists counteracting NMDA excitotoxicity and oxidative stress: A step forward in the discovery of neuroprotective agents. Eur J Med Chem 2023; 249:115163. [PMID: 36716640 DOI: 10.1016/j.ejmech.2023.115163] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
Sigma-1 receptor (S1R) has been considered a promising therapeutic target for several neurodegenerative diseases and S1R agonists have shown neuroprotective activity against glutamate excitotoxicity and oxidative stress. Starting from a previously identified low nanomolar S1R agonist, in this work we prepared and tested novel benzylpiperidine/benzylpiperazine-based compounds designed by applying a ring opening strategy. Among them, 4-benzyl-1-(2-phenoxyethyl)piperidine 6b (S1R Ki = 0.93 nM) and 4-benzyl-1-(3-phenoxypropyl)piperidine 8b (S1R Ki = 1.1 nM) emerged as high affinity S1R ligands and showed selectivity over S2R and N-methyl-d-aspartate receptor (NMDAR). Candidate compounds behaved as potent S1R agonists being able to enhance the neurite outgrowth induced by nerve growth factor (NGF) in PC12 cell lines. In SH-SY5Y neuroblastoma cell lines they exhibited a neuroprotective effect against rotenone- and NMDA-mediated toxic insults. The neuroprotective activity of 6b and 8b was reverted by co-treatment with an S1R antagonist, PB212. Compounds 6b and 8b were tested for cytotoxicity in-vitro against three human cancer cell lines (A549, LoVo and Panc-1) and in-vivo zebrafish model, resulting in a good efficacy/safety profile, comparable or superior to the reference drug memantine. Overall, these results encourage further preclinical investigations of 6b and 8b on in-vivo models of neurodegenerative diseases.
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Affiliation(s)
- Pasquale Linciano
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Claudia Sorbi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Andrea Marsala
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Nunzio Denora
- Dipartimento di Farmacia - Scienze del Farmaco, Università, degli Studi di Bari Aldo Moro, 70126, Bari, Italy
| | - Martina Bedeschi
- BioScience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Noemi Marino
- BioScience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Giacomo Miserocchi
- BioScience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Giulio Dondio
- Aphad SrL, Via della Resistenza, 65, Buccinasco, 20090, Italy
| | - Marco Peviani
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Anna Tesei
- BioScience Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Silvia Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy.
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31
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Anto EM, Sruthi CR, Krishnan L, Raghu KG, Purushothaman J. Tangeretin alleviates Tunicamycin-induced endoplasmic reticulum stress and associated complications in skeletal muscle cells. Cell Stress Chaperones 2023; 28:151-165. [PMID: 36653727 PMCID: PMC10050522 DOI: 10.1007/s12192-023-01322-3] [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: 06/14/2022] [Revised: 11/10/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Endoplasmic reticulum (ER) stress and associated oxidative stress are involved in the genesis and progression of skeletal muscle diseases such as myositis and atrophy or muscle wasting. Targeting the ER stress and associated downstream pathways can aid in the development of better treatment strategies for these diseases with limited therapeutic approaches. There is a growing interest in identifying natural products against ER stress due to the lower toxicity and cost effectiveness. In the present study, we investigated the protective effect of Tangeretin, a citrus methoxyflavone found in citrus peels against Tunicamycin (pharmacological ER stress inducer)-induced ER stress and associated complications in rat skeletal muscle L6 cell lines. Treatment with Tunicamycin for a period of 24 h resulted in the upregulation of ER stress marker proteins, ER resident oxidoreductases and cellular reactive oxygen species (ROS). Co-treatment with Tangeretin was effective in alleviating Tunicamycin-induced ER stress and associated redox-related complications by significantly downregulating the unfolded protein response (UPR), ER resident oxidoreductase proteins, cellular ROS and improving the antioxidant enzyme activity. Tunicamycin also induced upregulation of phosphorylated p38 MAP Kinase and loss of mitochondrial membrane potential. Tangeretin significantly reduced the levels of phosphorylated p38 MAP Kinase and improved the mitochondrial membrane potential. From the results, it is evident that Tangeretin can be explored further as a potential candidate for skeletal muscle diseases involving protein misfolding and ER stress.
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Affiliation(s)
- Eveline M Anto
- Department of Biochemistry, Agro-Processing & Technology Division, CSIR-National Institute for Interdisciplinary Science & Technology, Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - C R Sruthi
- Department of Biochemistry, Agro-Processing & Technology Division, CSIR-National Institute for Interdisciplinary Science & Technology, Thiruvananthapuram, 695019, Kerala, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Lekshmy Krishnan
- Department of Biochemistry, Agro-Processing & Technology Division, CSIR-National Institute for Interdisciplinary Science & Technology, Thiruvananthapuram, 695019, Kerala, India
| | - K G Raghu
- Department of Biochemistry, Agro-Processing & Technology Division, CSIR-National Institute for Interdisciplinary Science & Technology, Thiruvananthapuram, 695019, Kerala, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Jayamurthy Purushothaman
- Department of Biochemistry, Agro-Processing & Technology Division, CSIR-National Institute for Interdisciplinary Science & Technology, Thiruvananthapuram, 695019, Kerala, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Arast Y, Jabbarzadeh A, Tanbakosazan F, Arjmand A, Vazirizadeh A, Pourahmad J. Toxicity of Persian Gulf shell-less marine mollusc (Peronia peronii) methanolic extract on melanoma tumor mitochondria. Cutan Ocul Toxicol 2023; 42:12-18. [PMID: 36433797 DOI: 10.1080/15569527.2022.2152041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Melanoma is known as an aggressive and highly lethal cancer. The poor prognosis and resistance to treatment are characteristics of melanoma. In melanoma cells, apoptosis signaling which relies heavily on the acute activity of mitochondria and reactive oxygen species (ROS) formation is suppressed. Studies have shown that compounds isolated from marine herbs and animals, have been shown to have cytotoxic consequences on cancerous cells in prior research. This study was designed to evaluate the apoptotic effect of methanolic extract of Persian Gulf shell-less marine mollusc (Peronia peronii) on skin mitochondria isolated from animal model of melanoma. PURPOSE Melanoma mitochondria obtained from skin of melanoma animal model are studied in this research to see whether extracts from Persian Gulf shell-less marine mollusc (Peronia peronii), has a cytotoxic impact on them. MATERIAL AND METHOD In this study, the mitochondria were isolated from melanoma cells via differential centrifugation were treated with various concentrations (650, 1300 and 2600 µg/ml) of methanolic extract of Peronia peronii. Then MTT(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) viability assay, Reactive oxygen species (ROS) determination, Mitochondrial Membrane Potential (MMP) decline assay, mitochondrial swelling and cytochrome c release determination were performed. Flow cytometry assay of % apoptotic vs necrotic phenotypes was also performed on extract treated melanoma cells. RESULTS The results of MTT assay showed that different concentrations of Peronia peronii extract significantly (P < 0.05) decreased the SDH activity in cancerous skin mitochondria with the IC50(1300 μg/ml). The ROS results also showed that all concentrations of Peronia peronii extracts significantly increased ROS production, MMP decline and the release of cytochrome c in cancer groups mitochondria. The swelling of mitochondria was significantly increased compared to the control group. In addition, the results of apoptosis assay showed that addition of root extract of Peronia peronii on melanoma cells increased apoptosis, while it had no effect on control non tumour cells. DISCUSSION AND CONCLUSION Based on these results, the presence of potentially bioactive compounds in Peronia peronii make this Persian Gulf coastal herb a strong candidate for further molecular studies and clinical research in the field of melanoma cancer therapy.
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Affiliation(s)
- Yalda Arast
- Research center of Environmental Pollutants, Qom University of Medical Sciences, Qom, Iran
| | - Aida Jabbarzadeh
- Department of Toxicology and Pharmacology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farahnaz Tanbakosazan
- Department of Toxicology and Pharmacology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdollah Arjmand
- Department of Toxicology and Pharmacology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Vazirizadeh
- Persian Gulf Research Institute, Marine Biology and Fishery Sciences Department, Persian Gulf University, Busher, Iran
| | - Jalal Pourahmad
- Department of Toxicology and Pharmacology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Isei MO, Girardi PA, Rodwell-Bullock J, Nehrke K, Johnson GVW. Site-specific phosphorylation of tau impacts mitochondrial biology and response to stressors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.529131. [PMID: 36824940 PMCID: PMC9949115 DOI: 10.1101/2023.02.19.529131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Phosphorylation of tau at sites associated with Alzheimer's disease (AD) likely plays a role in the disease progression. Mitochondrial impairment, correlating with increased presence of phosphorylated tau, has been identified as a contributing factor to neurodegenerative processes in AD. However, how tau phosphorylated at specific sites impacts mitochondrial function has not been fully defined. We examined how AD-relevant phosphomimetics of tau impact selected aspects of mitochondrial biology. To mimic phosphorylation at AD-associated sites, the Ser/Thr sites in wild-type GFP tagged-tau (T4) were converted to glutamic acid (E) to make pseudophosphorylated GFP tagged-Ser-396/404 (2EC) and GFP tagged-Thr-231/Ser-235 (2EM) constructs. These constructs were expressed in neuronal HT22 cells and their impact on specific mitochondrial functions and responses to stressors were measured. Phosphomimetic tau altered mitochondrial distribution. Specifically, mitochondria accumulated in the soma of cells expressing either 2EC or 2EM, and neurite-like extensions in 2EC cells were shorter. Additionally, ATP levels were reduced in both 2EC and 2EM expressing cells, and ROS production increased in 2EC cells during oxidation of succinate when compared to T4 expressing cells. Thapsigargin reduced mitochondrial membrane potential (Ψ m ) and increased ROS production in both 2EC and 2EM cells relative to T4 cells, with no significant difference in the effects of rotenone. These results show that tau phosphorylation at specific AD-relevant epitopes negatively affects mitochondria, with the extent of dysfunction and stress response varying according to the sites of phosphorylation. Altogether, these findings extend our understanding of potential mechanisms whereby phosphorylated tau promotes mitochondria dysfunction in tauopathies, including AD. Funding information R01 AG067617.
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Affiliation(s)
- Michael O Isei
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
| | - Peter A Girardi
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
| | - Joel Rodwell-Bullock
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
| | - Keith Nehrke
- University of Rochester, Department of Medicine, Nephrology Division, Rochester, New York, USA
| | - Gail VW Johnson
- University of Rochester, Department of Anesthesiology & Perioperative Medicine, Rochester, New York, USA
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Ma G, Li C, Ji P, Chen Y, Li A, Hu Q, Song Z, Tang BQ, Jia D, Wei Y, Li T. Association of traditional Chinese medicine body constitution and cold syndrome with leukocyte mitochondrial functions: An observational study. Medicine (Baltimore) 2023; 102:e32694. [PMID: 36749256 PMCID: PMC9902006 DOI: 10.1097/md.0000000000032694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/28/2022] [Indexed: 02/08/2023] Open
Abstract
Body constitution in traditional Chinese medicine (TCM) refers to the holistic and relatively durable state of an individual, based on the qi and blood assessment, and TCM syndrome is defined as the theoretical abstraction of disease-symptom profiles. The biological basis as related to mitochondria, which produce most of the cellular energy, has not been well studied. This study aimed to elucidate the association of mitochondrial function with TCM body constitution and cold syndrome. Body constitution and cold syndrome in TCM were assessed using the Constitution in Chinese Medicine Questionnaire (CCMQ). The mitochondrial function of peripheral leukocytes was evaluated based on oxygen consumption rate (OCR) and enzyme activity; OCR reflects mitochondrial activity and the capacity to produce adenosine triphosphate (ATP). Cellular adenosine nucleotides and malondialdehyde levels were determined using high-performance liquid chromatography to assess the potential bioenergetic mechanisms. A total of 283 adults participated in this study. Leukocytes from subjects with a balanced constitution had higher OCRs than those with unbalanced constitutions. Yang deficiency and cold syndrome also demonstrated lower energy metabolism, as indicated by reduced basal metabolic rate and cellular levels of ATP and malondialdehyde. Decreased mitochondrial enzyme activity has been observed in individuals with the cold syndrome. Unbalanced body constitutions in TCM impair mitochondrial function in leukocytes, which may contribute to the high disease susceptibility. Cold syndrome is characterized by reduced mitochondrial mass, which may explain its symptoms of low-energy metabolism and cold intolerance.
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Affiliation(s)
- Guangyin Ma
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Caixia Li
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Peng Ji
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Yanjie Chen
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Ang Li
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Qingchuan Hu
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Zehua Song
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Bruce Qing Tang
- Ennova Institute of Life Science and Technology, Langfang, China
| | - Dexian Jia
- Beijing University of Chinese Medicine, Beijing, China
| | - Yulong Wei
- Beijing University of Chinese Medicine, Beijing, China
| | - Tongju Li
- Ennova Institute of Life Science and Technology, Langfang, China
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35
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Greeck VB, Williams SK, Haas J, Wildemann B, Fairless R. Alterations in Lymphocytic Metabolism-An Emerging Hallmark of MS Pathophysiology? Int J Mol Sci 2023; 24:ijms24032094. [PMID: 36768415 PMCID: PMC9917089 DOI: 10.3390/ijms24032094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS) characterised by acute inflammation and subsequent neuro-axonal degeneration resulting in progressive neurological impairment. Aberrant immune system activation in the periphery and subsequent lymphocyte migration to the CNS contribute to the pathophysiology. Recent research has identified metabolic dysfunction as an additional feature of MS. It is already well known that energy deficiency in neurons caused by impaired mitochondrial oxidative phosphorylation results in ionic imbalances that trigger degenerative pathways contributing to white and grey matter atrophy. However, metabolic dysfunction in MS appears to be more widespread than the CNS. This review focuses on recent research assessing the metabolism and mitochondrial function in peripheral immune cells of MS patients and lymphocytes isolated from murine models of MS. Emerging evidence suggests that pharmacological modulation of lymphocytic metabolism may regulate their subtype differentiation and rebalance pro- and anti-inflammatory functions. As such, further understanding of MS immunometabolism may aid the identification of novel treatments to specifically target proinflammatory immune responses.
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Affiliation(s)
- Viktoria B. Greeck
- Department of Neurology, University Clinic Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit (CCU) Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah K. Williams
- Department of Neurology, University Clinic Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit (CCU) Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jürgen Haas
- Department of Neurology, University Clinic Heidelberg, 69120 Heidelberg, Germany
| | - Brigitte Wildemann
- Department of Neurology, University Clinic Heidelberg, 69120 Heidelberg, Germany
| | - Richard Fairless
- Department of Neurology, University Clinic Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit (CCU) Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Correspondence:
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Abstract
Mortality in acute kidney injury (AKI) remains very high, yet the cause of death is often failure of extrarenal organs. We and others have demonstrated remote organ dysfunction after renal ischemia. The term "cardiorenal syndrome" was first applied to the "cross talk" between the organs by the National Heart, Lung, and Blood Institute of the National Institutes of Health, and the clinical importance is being increasingly appreciated. Nevertheless, more information is needed to effectively address the consequences of renal injury on the heart. Since AKI often occurs in patients with comorbidities, we investigated the effect of renal ischemia in the setting of existing cardiac failure. We hypothesized that the cardiac effects of renal ischemia would be significantly amplified in experimental cardiomyopathy. Male Sprague-Dawley rats with preexisting cardiac and renal injury due to low-dose doxorubicin were subjected to bilateral renal artery occlusion. Cardiac structure and function were examined 2 days after reperfusion. Loss of functional myocardial tissue with decreases in left ventricular pressure, increases in apoptotic cell death, inflammation, and collagen, and greater disruption in ultrastructure with mitochondrial fragmentation were seen in the doxorubicin/ischemia group compared with animals in the groups treated with doxorubicin alone or following ischemia alone. Systemic inflammation and cardiac abnormalities persisted for at least 21 wk. These results suggest that preexisting comorbidities can result in much more severe distant organ effects of acute renal injury. The results of this study are relevant to human AKI.NEW & NOTEWORTHY Acute kidney injury is common, expensive, and deadly, yet morbidity and mortality are often secondary to remote organ dysfunction. We hypothesized that the effects of renal ischemia would be amplified in the setting of comorbidities. Sustained systemic inflammation and loss of functional myocardium with significantly decreased systolic and diastolic function, apoptotic cell death, and increased collagen and inflammatory cells were found in the heart after renal ischemia in the doxorubicin cardiomyopathy model (vs. renal ischemia alone). Understanding the remote effects of renal ischemia has the potential to improve outcomes in acute kidney injury.
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Affiliation(s)
- Jesus H Dominguez
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Danhui Xie
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - K J Kelly
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.,Roudebush Veterans Affairs Medical Center, Indianapolis, Indiana
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Rey F, Messa L, Maghraby E, Casili G, Ottolenghi S, Barzaghini B, Raimondi MT, Cereda C, Cuzzocrea S, Zuccotti G, Esposito E, Paterniti I, Carelli S. Oxygen Sensing in Neurodegenerative Diseases: Current Mechanisms, Implication of Transcriptional Response, and Pharmacological Modulation. Antioxid Redox Signal 2023; 38:160-182. [PMID: 35793106 DOI: 10.1089/ars.2022.0046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Significance: Oxygen (O2) sensing is the fundamental process through which organisms respond to changes in O2 levels. Complex networks exist allowing the maintenance of O2 levels through the perception, capture, binding, transport, and delivery of molecular O2. The brain extreme sensitivity to O2 balance makes the dysregulation of related processes crucial players in the pathogenesis of neurodegenerative diseases (NDs). In this study, we wish to review the most relevant advances in O2 sensing in relation to Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Recent Advances: Over the years, it has been clarified that most NDs share common pathways, a great number of which are in relation to O2 imbalance. These include hypoxia, hyperoxia, reactive oxygen species production, metabolism of metals, protein misfolding, and neuroinflammation. Critical Issues: There is still a gap in knowledge concerning how O2 sensing plays a role in the above indicated neurodegenerations. Specifically, O2 concentrations are perceived in body sites that are not limited to the brain, but primarily reside in other organs. Moreover, the mechanisms of O2 sensing, gene expression, and signal transduction seem to correlate with neurodegeneration, but many aspects are mechanistically still unexplained. Future Directions: Future studies should focus on the precise characterization of O2 level disruption and O2 sensing mechanisms in NDs. Moreover, advances need to be made also concerning the techniques used to assess O2 sensing dysfunctions in these diseases. There is also the need to develop innovative therapies targeting this precise mechanism rather than its secondary effects, as early intervention is necessary. Antioxid. Redox Signal. 38, 160-182.
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Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
| | - Letizia Messa
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
| | - Erika Maghraby
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
| | - Giovanna Casili
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Sara Ottolenghi
- Department of Medicine and Surgery, University of Milano Bicocca, Milano, Italy
| | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta," Politecnico di Milano, Milano, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta," Politecnico di Milano, Milano, Italy
| | - Cristina Cereda
- Department of Women, Mothers and Neonatal Care, Children's Hospital "V. Buzzi," Milano, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy.,Department of Pediatrics, Children's Hospital "V. Buzzi," Milano, 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
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences, University of Milano, Milano, Italy.,Department of Biomedical and Clinical Sciences, Pediatric Research Center "Romeo ed Enrica Invernizzi," University of Milano, Milano, Italy
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Ahmad F, Ramamorthy S, Areeshi MY, Ashraf GM, Haque S. Isolated Mitochondrial Preparations and In organello Assays: A Powerful and Relevant Ex vivo Tool for Assessment of Brain (Patho)physiology. Curr Neuropharmacol 2023; 21:1433-1449. [PMID: 36872352 PMCID: PMC10324330 DOI: 10.2174/1570159x21666230303123555] [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: 05/16/2022] [Revised: 10/30/2022] [Accepted: 12/29/2022] [Indexed: 03/07/2023] Open
Abstract
Mitochondria regulate multiple aspects of neuronal development, physiology, plasticity, and pathology through their regulatory roles in bioenergetic, calcium, redox, and cell survival/death signalling. While several reviews have addressed these different aspects, a comprehensive discussion focussing on the relevance of isolated brain mitochondria and their utilities in neuroscience research has been lacking. This is relevant because the employment of isolated mitochondria rather than their in situ functional evaluation, offers definitive evidence of organelle-specificity, negating the interference from extra mitochondrial cellular factors/signals. This mini-review was designed primarily to explore the commonly employed in organello analytical assays for the assessment of mitochondrial physiology and its dysfunction, with a particular focus on neuroscience research. The authors briefly discuss the methodologies for biochemical isolation of mitochondria, their quality assessment, and cryopreservation. Further, the review attempts to accumulate the key biochemical protocols for in organello assessment of a multitude of mitochondrial functions critical for neurophysiology, including assays for bioenergetic activity, calcium and redox homeostasis, and mitochondrial protein translation. The purpose of this review is not to examine each and every method or study related to the functional assessment of isolated brain mitochondria, but rather to assemble the commonly used protocols of in organello mitochondrial research in a single publication. The hope is that this review will provide a suitable platform aiding neuroscientists to choose and apply the required protocols and tools to address their particular mechanistic, diagnostic, or therapeutic question dealing within the confines of the research area of mitochondrial patho-physiology in the neuronal perspective.
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Affiliation(s)
- Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences and Technology (SBST), Vellore Institute of Technology, Vellore, 632014, India
| | - Siva Ramamorthy
- Department of Biotechnology, School of Bio Sciences and Technology (SBST), Vellore Institute of Technology, Vellore, 632014, India
| | - Mohammed Y. Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, 45142, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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39
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Pozdnyakov DI, Zolotykh DS, Vihor AA. [An effect of ethylmethylhydroxypyridine succinate and ethylmethylhydroxypyridine malate on changes in mitochondrial function under conditions of focal cerebral ischemia]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:111-116. [PMID: 37994896 DOI: 10.17116/jnevro2023123111111] [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] [Indexed: 11/24/2023]
Abstract
OBJECTIVE To evaluate an effect of ethylmethylhydroxypyridine succinate and ethylmethylhydroxypyridine malate on changes in mitochondrial function under experimental focal cerebral ischemia. MATERIAL AND METHODS Focal cerebral ischemia was modeled in Wistar rats by thermocoagulation of the middle cerebral artery. Ethylmethylhydroxypyridine succinate («Mexidol») and ethylmethylhydroxypyridine malate («Ethoxidol») were injected into the tail vein 30 minutes after ischemia simulation and then for 3 days at doses of 50 mg/kg, 100 mg/kg and 150 mg/kg. After 72 hours, changes in neurological deficits, aerobic and anaerobic respiration activity, the concentration of mitochondrial hydrogen peroxide and apoptosis-inducing factor, as well as the activity of succinate dehydrogenase and cytochrome c oxidase in brain tissue supernatants were assessed. RESULTS The course administration of ethylmethylhydroxypyridine succinate and ethylmethylhydroxypyridine malate dose-dependently contributed to a decrease in the concentration of mitochondrial hydrogen peroxide and apoptosis-inducing factor in the brain tissue. The restoration of mitochondrial energy function was also shown with the use of ethylmethylhydroxypyridine succinate in all studied doses, while the administration of ethylmethylhydroxypyridine malate led to the restoration of mitochondrial-dependent energy production only at higher doses (100 mg/kg and 150 mg/kg). CONCLUSION The effect of malic acid and succinic acid salts of ethylmethylhydroxypyridine on the change in the redox and apoptosis-regulating function of mitochondria does not depend on the type of anion, whereas the change in the energy function of mitochondria is associated with the salt residue included in the drug structure and its dosage.
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Affiliation(s)
- D I Pozdnyakov
- Pyatigorsk Medical and Pharmaceutical Institute - Branch of the Volgograd State Medical University, Pyatigorsk, Russia
| | - D S Zolotykh
- Pyatigorsk Medical and Pharmaceutical Institute - Branch of the Volgograd State Medical University, Pyatigorsk, Russia
| | - A A Vihor
- Pyatigorsk Medical and Pharmaceutical Institute - Branch of the Volgograd State Medical University, Pyatigorsk, Russia
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40
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Magaña JC, Deus CM, Giné-Garriga M, Montané J, Pereira SP. Exercise-Boosted Mitochondrial Remodeling in Parkinson's Disease. Biomedicines 2022; 10:biomedicines10123228. [PMID: 36551984 PMCID: PMC9775656 DOI: 10.3390/biomedicines10123228] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a movement disorder characterized by the progressive degeneration of dopaminergic neurons resulting in dopamine deficiency in the striatum. Given the estimated escalation in the number of people with PD in the coming decades, interventions aimed at minimizing morbidity and improving quality of life are crucial. Mitochondrial dysfunction and oxidative stress are intrinsic factors related to PD pathogenesis. Accumulating evidence suggests that patients with PD might benefit from various forms of exercise in diverse ways, from general health improvements to disease-specific effects and, potentially, disease-modifying effects. However, the signaling and mechanism connecting skeletal muscle-increased activity and brain remodeling are poorly elucidated. In this review, we describe skeletal muscle-brain crosstalk in PD, with a special focus on mitochondrial effects, proposing mitochondrial dysfunction as a linker in the muscle-brain axis in this neurodegenerative disease and as a promising therapeutic target. Moreover, we outline how exercise secretome can improve mitochondrial health and impact the nervous system to slow down PD progression. Understanding the regulation of the mitochondrial function by exercise in PD may be beneficial in defining interventions to delay the onset of this neurodegenerative disease.
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Affiliation(s)
- Juan Carlos Magaña
- Blanquerna Faculty of Psychology, Education and Sport Sciences, Ramon Llull University, 08022 Barcelona, Spain
| | - Cláudia M. Deus
- CNC—Center for Neuroscience and Cell Biology, CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- Correspondence: (C.M.D.); (J.M.)
| | - Maria Giné-Garriga
- Blanquerna Faculty of Psychology, Education and Sport Sciences, Ramon Llull University, 08022 Barcelona, Spain
- Blanquerna Faculty of Health Sciences, Ramon Llull University, 08025 Barcelona, Spain
| | - Joel Montané
- Blanquerna Faculty of Psychology, Education and Sport Sciences, Ramon Llull University, 08022 Barcelona, Spain
- Blanquerna Faculty of Health Sciences, Ramon Llull University, 08025 Barcelona, Spain
- Correspondence: (C.M.D.); (J.M.)
| | - Susana P. Pereira
- CNC—Center for Neuroscience and Cell Biology, CIBB—Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, 4150-564 Porto, Portugal
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41
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Terracina S, Petrella C, Francati S, Lucarelli M, Barbato C, Minni A, Ralli M, Greco A, Tarani L, Fiore M, Ferraguti G. Antioxidant Intervention to Improve Cognition in the Aging Brain: The Example of Hydroxytyrosol and Resveratrol. Int J Mol Sci 2022; 23:15674. [PMID: 36555317 PMCID: PMC9778814 DOI: 10.3390/ijms232415674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/30/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Both physiological and pathological aging processes induce brain alterations especially affecting the speed of processing, working memory, conceptual reasoning and executive functions. Many therapeutic approaches to reduce the impact of brain aging on cognitive functioning have been tested; unfortunately, there are no satisfactory results as a single therapy. As aging is partly contributed by free radical reactions, it has been proposed that exogenous antioxidants could have a positive impact on both aging and its associated manifestations. The aim of this report is to provide a summary and a subsequent review of the literature evidence on the role of antioxidants in preventing and improving cognition in the aging brain. Manipulation of endogenous cellular defense mechanisms through nutritional antioxidants or pharmacological compounds represents an innovative approach to therapeutic intervention in diseases causing brain tissue damage, such as neurodegeneration. Coherently with this notion, antioxidants, especially those derived from the Mediterranean diet such as hydroxytyrosol and resveratrol, seem to be able to delay and modulate the cognitive brain aging processes and decrease the occurrence of its effects on the brain. The potential preventive activity of antioxidants should be evaluated in long-term exposure clinical trials, using preparations with high bioavailability, able to bypass the blood-brain barrier limitation, and that are well standardized.
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Affiliation(s)
- Sergio Terracina
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Carla Petrella
- Institute of Biochemistry and Cell Biology, IBBC—CNR, 00185 Rome, Italy
| | - Silvia Francati
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Christian Barbato
- Institute of Biochemistry and Cell Biology, IBBC—CNR, 00185 Rome, Italy
| | - Antonio Minni
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy
| | - Massimo Ralli
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy
| | - Antonio Greco
- Department of Sense Organs, Sapienza University of Rome, 00185 Rome, Italy
| | - Luigi Tarani
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Fiore
- Institute of Biochemistry and Cell Biology, IBBC—CNR, 00185 Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy
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How does metabolic rate in plant shoot tips change after cryopreservation? Cryobiology 2022; 109:1-9. [PMID: 36356915 DOI: 10.1016/j.cryobiol.2022.10.003] [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: 06/03/2022] [Revised: 10/26/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
Cryopreservation allows the long-term storage of plant germplasm, but can cause damage to plant tissues, which must be repaired for survival to occur. This repair process is fuelled by the metabolic function of mitochondria; however, little is known about how metabolic function is affected by the cryopreservation process in plants. We compared metabolic rates of shoot tips of two Australian native species, Androcalva perlaria and Anigozanthos viridis. Overall, cryopreservation resulted in a significant reduction in the metabolic rates of shoot tips from both species, even in tissues that regenerated after cryopreservation. Metabolic rate did not increase within 48 h after of thawing, even in shoot tips which later regenerated. When examined in isolation, both pre-treatment on desiccation medium and exposure to cryoprotective agents significantly decreased metabolic rates in regenerating shoot tips of A. viridis, however both caused a significant increase in shoot tips of A. perlaria, suggesting diversity of response to cryopreservation stresses across species. Measurements of shoot tip metabolic rate during cryopreservation will inform investigations into cellular energy production and provide critical information on the state of shoot health after exposure to different cryoprotective treatments, which could play a useful role in guiding protocol optimisation for threatened species to maximise post-cryopreservation regeneration.
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43
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Wakhloo D, Oberhauser J, Madira A, Mahajani S. From cradle to grave: neurogenesis, neuroregeneration and neurodegeneration in Alzheimer's and Parkinson's diseases. Neural Regen Res 2022; 17:2606-2614. [PMID: 35662189 PMCID: PMC9165389 DOI: 10.4103/1673-5374.336138] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/16/2021] [Accepted: 12/02/2021] [Indexed: 11/29/2022] Open
Abstract
Two of the most common neurodegenerative disorders - Alzheimer's and Parkinson's diseases - are characterized by synaptic dysfunction and degeneration that culminate in neuronal loss due to abnormal protein accumulation. The intracellular aggregation of hyper-phosphorylated tau and the extracellular aggregation of amyloid beta plaques form the basis of Alzheimer's disease pathology. The major hallmark of Parkinson's disease is the loss of dopaminergic neurons in the substantia nigra pars compacta, following the formation of Lewy bodies, which consists primarily of alpha-synuclein aggregates. However, the discrete mechanisms that contribute to neurodegeneration in these disorders are still poorly understood. Both neuronal loss and impaired adult neurogenesis have been reported in animal models of these disorders. Yet these findings remain subject to frequent debate due to a lack of conclusive evidence in post mortem brain tissue from human patients. While some publications provide significant findings related to axonal regeneration in Alzheimer's and Parkinson's diseases, they also highlight the limitations and obstacles to the development of neuroregenerative therapies. In this review, we summarize in vitro and in vivo findings related to neurogenesis, neuroregeneration and neurodegeneration in the context of Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Debia Wakhloo
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Jane Oberhauser
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Angela Madira
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Sameehan Mahajani
- Deparment of Neuropathology, Stanford University, School of Medicine, Stanford, CA, USA
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44
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Peterson AA, Rangwala AM, Thakur MK, Ward PS, Hung C, Outhwaite IR, Chan AI, Usanov DL, Mootha VK, Seeliger MA, Liu DR. Discovery and molecular basis of subtype-selective cyclophilin inhibitors. Nat Chem Biol 2022; 18:1184-1195. [PMID: 36163383 PMCID: PMC9596378 DOI: 10.1038/s41589-022-01116-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/19/2022] [Indexed: 11/25/2022]
Abstract
Although cyclophilins are attractive targets for probing biology and therapeutic intervention, no subtype-selective cyclophilin inhibitors have been described. We discovered novel cyclophilin inhibitors from the in vitro selection of a DNA-templated library of 256,000 drug-like macrocycles for cyclophilin D (CypD) affinity. Iterated macrocycle engineering guided by ten X-ray co-crystal structures yielded potent and selective inhibitors (half maximal inhibitory concentration (IC50) = 10 nM) that bind the active site of CypD and also make novel interactions with non-conserved residues in the S2 pocket, an adjacent exo-site. The resulting macrocycles inhibit CypD activity with 21- to >10,000-fold selectivity over other cyclophilins and inhibit mitochondrial permeability transition pore opening in isolated mitochondria. We further exploited S2 pocket interactions to develop the first cyclophilin E (CypE)-selective inhibitor, which forms a reversible covalent bond with a CypE S2 pocket lysine, and exhibits 30- to >4,000-fold selectivity over other cyclophilins. These findings reveal a strategy to generate isoform-selective small-molecule cyclophilin modulators, advancing their suitability as targets for biological investigation and therapeutic development.
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Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aziz M Rangwala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Manish K Thakur
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Patrick S Ward
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Christie Hung
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Ian R Outhwaite
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Alix I Chan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Dmitry L Usanov
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Vamsi K Mootha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute and Departments of Molecular Biology and Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Maguire E, Connor-Robson N, Shaw B, O’Donoghue R, Stöberl N, Hall-Roberts H. Assaying Microglia Functions In Vitro. Cells 2022; 11:3414. [PMID: 36359810 PMCID: PMC9654693 DOI: 10.3390/cells11213414] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Microglia, the main immune modulators of the central nervous system, have key roles in both the developing and adult brain. These functions include shaping healthy neuronal networks, carrying out immune surveillance, mediating inflammatory responses, and disposing of unwanted material. A wide variety of pathological conditions present with microglia dysregulation, highlighting the importance of these cells in both normal brain function and disease. Studies into microglial function in the context of both health and disease thus have the potential to provide tremendous insight across a broad range of research areas. In vitro culture of microglia, using primary cells, cell lines, or induced pluripotent stem cell derived microglia, allows researchers to generate reproducible, robust, and quantifiable data regarding microglia function. A broad range of assays have been successfully developed and optimised for characterizing microglial morphology, mediation of inflammation, endocytosis, phagocytosis, chemotaxis and random motility, and mediation of immunometabolism. This review describes the main functions of microglia, compares existing protocols for measuring these functions in vitro, and highlights common pitfalls and future areas for development. We aim to provide a comprehensive methodological guide for researchers planning to characterise microglial functions within a range of contexts and in vitro models.
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Affiliation(s)
- Emily Maguire
- UK Dementia Research Institute (UK DRI), School of Medicine, Cardiff University, Cardiff CF10 3AT, UK
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Liu ZF, Liu K, Liu ZQ, Cong L, Lei MY, Li J, Ma Z, Deng Y, Liu W, Xu B. Melatonin attenuates manganese-induced mitochondrial fragmentation by suppressing the Mst1/JNK signaling pathway in primary mouse neurons. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 844:157134. [PMID: 35792268 DOI: 10.1016/j.scitotenv.2022.157134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/18/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Manganese (Mn) toxicity is mainly caused by excessive Mn content in drinking water and occupational exposure. Moreover, overexposure to Mn can impair mental, cognitive, memory, and motor capacities. Although melatonin (Mel) can protect against Mn-induced neuronal damage and mitochondrial fragmentation, the underlying mechanism remains elusive. Here, we examined the related molecular mechanisms underlying Mel attenuating Mn-induced mitochondrial fragmentation through the mammalian sterile 20-like kinase-1 (Mst1)/JNK signaling path. To test the role of Mst1 in mitochondrial fragmentation, we treated mouse primary neurons overexpressing Mst1 with Mel and Mn stimulation. In normal neurons, 10 μM Mel reduced the effects of Mn (200 μM) on Mst1 expression at the mRNA and protein levels and on phosphorylation of JNK and Drp1, Drp1 mitochondrial translocation, and mitochondrial fragmentation. Conversely, overexpression of Mst1 hindered the protective effect of Mel (10 μM) against Mn-induced mitochondrial fragmentation. Anisomycin (ANI), an activator of JNK signaling, was similarly found to inhibit the protective effect of Mel on mitochondria, while Mst1 levels were not significantly changed. Thus, our results demonstrated that 10 μM Mel negatively regulated the Mst1-JNK pathway, thereby reducing excessive mitochondrial fission, maintaining the mitochondrial network, and alleviating Mn-induced mitochondrial dysfunction.
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Affiliation(s)
- Zhuo-Fan Liu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Kuan Liu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Zhi-Qi Liu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Lin Cong
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Meng-Yu Lei
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Jing Li
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Zhuo Ma
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, China.
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A systemic cell stress signal confers neuronal resilience toward oxidative stress in a Hedgehog-dependent manner. Cell Rep 2022; 41:111488. [PMID: 36260999 PMCID: PMC9623505 DOI: 10.1016/j.celrep.2022.111488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/04/2022] [Accepted: 09/21/2022] [Indexed: 11/22/2022] Open
Abstract
Cells possess several conserved adaptive mechanisms to respond to stress. Stress signaling is initiated to reestablish cellular homeostasis, but its effects on the tissue or systemic levels are far less understood. We report that the secreted luminal domain of the endoplasmic reticulum (ER) stress transducer CREB3L2 (which we name TAILS [transmissible activator of increased cell livability under stress]) is an endogenous, cell non-autonomous activator of neuronal resilience. In response to oxidative insults, neurons secrete TAILS, which potentiates hedgehog signaling through direct interaction with Sonic hedgehog (SHH) and its receptor PTCH1, leading to improved antioxidant signaling and mitochondrial function in neighboring neurons. In an in vivo model of ischemic brain injury, administration of TAILS enables survival of CNS neurons and fully preserves cognitive function in behavioral tests. Our findings reveal an SHH-mediated, cell non-autonomous branch of cellular stress signaling that confers resilience to oxidative stress in the mature brain, providing protection from ischemic neurodegeneration. Whether and how neurons can communicate stress to other neurons is poorly understood. Chung et al. demonstrate that oxidative stress in neurons leads to secretion of cell non-autonomous stress signaling protein. This protein, TAILS, induces neuronal resilience against cell stress in recipient cells in an SHH-dependent manner.
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Leman G, Pavel P, Hermann M, Crumrine D, Elias PM, Minzaghi D, Goudounèche D, Roshardt Prieto NM, Cavinato M, Wanner A, Blunder S, Gruber R, Jansen-Dürr P, Dubrac S. Mitochondrial Activity Is Upregulated in Nonlesional Atopic Dermatitis and Amenable to Therapeutic Intervention. J Invest Dermatol 2022; 142:2623-2634.e12. [PMID: 35341734 DOI: 10.1016/j.jid.2022.01.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 12/12/2022]
Abstract
Previous work has shown increased expression of genes related to oxidative stress in nonlesional atopic dermatitis (ADNL) skin. Although mitochondria are key regulators of ROS production, their function in AD has never been investigated. Energy metabolism and the oxidative stress response were studied in keratinocytes (KCs) from patients with ADNL or healthy controls. Moreover, ADNL human epidermal equivalents were treated with tigecycline or MitoQ. We found that pyruvate and glucose were used as energy substrates by ADNL KCs. Increased mitochondrial oxidation of (very) long-chain fatty acids, associated with enhanced complexes I and II activities, was observed in ADNL KCs. Metabolomic analysis revealed increased tricarboxylic acid cycle turnover. Increased aerobic metabolism generated oxidative stress in ADNL KCs. ADNL human epidermal equivalents displayed increased mitochondrial function and an enhanced oxidative stress response compared with controls. Treatment of ADNL human epidermal equivalents with tigecycline or MitoQ largely corrected the AD profile, including high p-65 NF-κB, abnormal lamellar bodies, and cellular damage. Furthermore, we found that glycolysis supports but does not supersede mitochondrial metabolism in ADNL KCs. Thus, aerobic metabolism predominates in ADNL but leads to oxidative stress. Therefore, mitochondria could be a reservoir of potential therapeutic targets in atopic dermatitis.
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Affiliation(s)
- Geraldine Leman
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Petra Pavel
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Hermann
- Department of Anesthesiology and Critical Care Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Debra Crumrine
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Peter M Elias
- Department of Dermatology, University of California San Francisco, San Francisco, California
| | - Deborah Minzaghi
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominique Goudounèche
- Center of Electron Microscopy Applied to Biology, Faculty of Medicine Rangueil, Toulouse III, Paul Sabatier University, Toulouse, France
| | - Natalia M Roshardt Prieto
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Maria Cavinato
- Research Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Andrea Wanner
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefan Blunder
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Robert Gruber
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Pidder Jansen-Dürr
- Research Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - Sandrine Dubrac
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria.
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Novel Role of CETP in Macrophages: Reduction of Mitochondrial Oxidants Production and Modulation of Cell Immune-Metabolic Profile. Antioxidants (Basel) 2022; 11:antiox11091734. [PMID: 36139808 PMCID: PMC9495589 DOI: 10.3390/antiox11091734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 01/22/2023] Open
Abstract
Plasma cholesteryl ester transfer protein (CETP) activity diminishes HDL-cholesterol levels and thus may increase atherosclerosis risk. Experimental evidence suggests CETP may also exhibit anti-inflammatory properties, but local tissue-specific functions of CETP have not yet been clarified. Since oxidative stress and inflammation are major features of atherogenesis, we investigated whether CETP modulates macrophage oxidant production, inflammatory and metabolic profiles. Comparing macrophages from CETP-expressing transgenic mice and non-expressing littermates, we observed that CETP expression reduced mitochondrial superoxide anion production and H2O2 release, increased maximal mitochondrial respiration rates, and induced elongation of the mitochondrial network and expression of fusion-related genes (mitofusin-2 and OPA1). The expression of pro-inflammatory genes and phagocytic activity were diminished in CETP-expressing macrophages. In addition, CETP-expressing macrophages had less unesterified cholesterol under basal conditions and after exposure to oxidized LDL, as well as increased HDL-mediated cholesterol efflux. CETP knockdown in human THP1 cells increased unesterified cholesterol and abolished the effects on mitofusin-2 and TNFα. In summary, the expression of CETP in macrophages modulates mitochondrial structure and function to promote an intracellular antioxidant state and oxidative metabolism, attenuation of pro-inflammatory gene expression, reduced cholesterol accumulation, and phagocytosis. These localized functions of CETP may be relevant for the prevention of atherosclerosis and other inflammatory diseases.
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Integration of Human Protein Sequence and Protein-Protein Interaction Data by Graph Autoencoder to Identify Novel Protein-Abnormal Phenotype Associations. Cells 2022; 11:cells11162485. [PMID: 36010562 PMCID: PMC9406402 DOI: 10.3390/cells11162485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding gene functions and their associated abnormal phenotypes is crucial in the prevention, diagnosis and treatment against diseases. The Human Phenotype Ontology (HPO) is a standardized vocabulary for describing the phenotype abnormalities associated with human diseases. However, the current HPO annotations are far from completion, and only a small fraction of human protein-coding genes has HPO annotations. Thus, it is necessary to predict protein-phenotype associations using computational methods. Protein sequences can indicate the structure and function of the proteins, and interacting proteins are more likely to have same function. It is promising to integrate these features for predicting HPO annotations of human protein. We developed GraphPheno, a semi-supervised method based on graph autoencoders, which does not require feature engineering to capture deep features from protein sequences, while also taking into account the topological properties in the protein–protein interaction network to predict the relationships between human genes/proteins and abnormal phenotypes. Cross validation and independent dataset tests show that GraphPheno has satisfactory prediction performance. The algorithm is further confirmed on automatic HPO annotation for no-knowledge proteins under the benchmark of the second Critical Assessment of Functional Annotation, 2013–2014 (CAFA2), where GraphPheno surpasses most existing methods. Further bioinformatics analysis shows that predicted certain phenotype-associated genes using GraphPheno share similar biological properties with known ones. In a case study on the phenotype of abnormality of mitochondrial respiratory chain, top prioritized genes are validated by recent papers. We believe that GraphPheno will help to reveal more associations between genes and phenotypes, and contribute to the discovery of drug targets.
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