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Yu Y, Martins LM. Mitochondrial One-Carbon Metabolism and Alzheimer's Disease. Int J Mol Sci 2024; 25:6302. [PMID: 38928008 PMCID: PMC11203557 DOI: 10.3390/ijms25126302] [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: 03/12/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Mitochondrial one-carbon metabolism provides carbon units to several pathways, including nucleic acid synthesis, mitochondrial metabolism, amino acid metabolism, and methylation reactions. Late-onset Alzheimer's disease is the most common age-related neurodegenerative disease, characterised by impaired energy metabolism, and is potentially linked to mitochondrial bioenergetics. Here, we discuss the intersection between the molecular pathways linked to both mitochondrial one-carbon metabolism and Alzheimer's disease. We propose that enhancing one-carbon metabolism could promote the metabolic processes that help brain cells cope with Alzheimer's disease-related injuries. We also highlight potential therapeutic avenues to leverage one-carbon metabolism to delay Alzheimer's disease pathology.
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Affiliation(s)
- Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - L. Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
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2
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Mousavi H, Rimaz M, Zeynizadeh B. Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[ h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases. ACS Chem Neurosci 2024; 15:1828-1881. [PMID: 38647433 DOI: 10.1021/acschemneuro.4c00055] [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: 04/25/2024] Open
Abstract
Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.
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Affiliation(s)
- Hossein Mousavi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran 19395-3697, Iran
| | - Behzad Zeynizadeh
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
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3
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Yang L, Guttman L, Dawson VL, Dawson TM. Parthanatos: Mechanisms, modulation, and therapeutic prospects in neurodegenerative disease and stroke. Biochem Pharmacol 2024:116174. [PMID: 38552851 DOI: 10.1016/j.bcp.2024.116174] [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: 01/21/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Parthanatos is a cell death signaling pathway that has emerged as a compelling target for pharmaceutical intervention. It plays a pivotal role in the neuron loss and neuroinflammation that occurs in Parkinson's Disease (PD), Alzheimer's Disease (AD), Huntington's Disease (HD), Amyotrophic Lateral Sclerosis (ALS), and stroke. There are currently no treatments available to humans to prevent cell death in any of these diseases. This review provides an in-depth examination of the current understanding of the Parthanatos mechanism, with a particular focus on its implications in neuroinflammation and various diseases discussed herein. Furthermore, we thoroughly review potential intervention targets within the Parthanatos pathway. We dissect recent progress in inhibitory strategies, complimented by a detailed structural analysis of key Parthanatos executioners, PARP-1, AIF, and MIF, along with an assessment of their established inhibitors. We hope to introduce a new perspective on the feasibility of targeting components within the Parthanatos pathway, emphasizing its potential to bring about transformative outcomes in therapeutic interventions. By delineating therapeutic opportunities and known targets, we seek to emphasize the imperative of blocking Parthanatos as a precursor to developing disease-modifying treatments. This comprehensive exploration aims to catalyze a paradigm shift in our understanding of potential neurodegenerative disease therapeutics, advocating for the pursuit of effective interventions centered around Parthanatos inhibition.
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Affiliation(s)
- Liu Yang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lauren Guttman
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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4
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Wilson EL, Yu Y, Leal NS, Woodward JA, Patikas N, Morris JL, Field SF, Plumbly W, Paupe V, Chowdhury SR, Antrobus R, Lindop GE, Adia YM, Loh SHY, Prudent J, Martins LM, Metzakopian E. Genome-wide CRISPR/Cas9 screen shows that loss of GET4 increases mitochondria-endoplasmic reticulum contact sites and is neuroprotective. Cell Death Dis 2024; 15:203. [PMID: 38467609 PMCID: PMC10928201 DOI: 10.1038/s41419-024-06568-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] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024]
Abstract
Organelles form membrane contact sites between each other, allowing for the transfer of molecules and signals. Mitochondria-endoplasmic reticulum (ER) contact sites (MERCS) are cellular subdomains characterized by close apposition of mitochondria and ER membranes. They have been implicated in many diseases, including neurodegenerative, metabolic, and cardiac diseases. Although MERCS have been extensively studied, much remains to be explored. To uncover novel regulators of MERCS, we conducted a genome-wide, flow cytometry-based screen using an engineered MERCS reporter cell line. We found 410 genes whose downregulation promotes MERCS and 230 genes whose downregulation decreases MERCS. From these, 29 genes were selected from each population for arrayed screening and 25 were validated from the high population and 13 from the low population. GET4 and BAG6 were highlighted as the top 2 genes that upon suppression increased MERCS from both the pooled and arrayed screens, and these were subjected to further investigation. Multiple microscopy analyses confirmed that loss of GET4 or BAG6 increased MERCS. GET4 and BAG6 were also observed to interact with the known MERCS proteins, inositol 1,4,5-trisphosphate receptors (IP3R) and glucose-regulated protein 75 (GRP75). In addition, we found that loss of GET4 increased mitochondrial calcium uptake upon ER-Ca2+ release and mitochondrial respiration. Finally, we show that loss of GET4 rescues motor ability, improves lifespan and prevents neurodegeneration in a Drosophila model of Alzheimer's disease (Aβ42Arc). Together, these results suggest that GET4 is involved in decreasing MERCS and that its loss is neuroprotective.
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Affiliation(s)
- Emma L Wilson
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Nuno S Leal
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - James A Woodward
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Nikolaos Patikas
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - Jordan L Morris
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Sarah F Field
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - William Plumbly
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - Vincent Paupe
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Suvagata R Chowdhury
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Rd, Cambridge, CB2 0XY, UK
| | - Georgina E Lindop
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy Building, Downing Site, Cambridge, CB2 3DY, UK
| | - Yusuf M Adia
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Samantha H Y Loh
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Julien Prudent
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
| | - L Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK.
- bit bio, The Dorothy Hodgkin Building, Babraham Research Campus, Cambridge, CB22 3FH, UK.
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5
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Li F, Wu C, Wang G. Targeting NAD Metabolism for the Therapy of Age-Related Neurodegenerative Diseases. Neurosci Bull 2024; 40:218-240. [PMID: 37253984 PMCID: PMC10838897 DOI: 10.1007/s12264-023-01072-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/10/2023] [Indexed: 06/01/2023] Open
Abstract
As the aging population continues to grow rapidly, age-related diseases are becoming an increasing burden on the healthcare system and a major concern for the well-being of elderly individuals. While aging is an inevitable process for all humans, it can be slowed down and age-related diseases can be treated or alleviated. Nicotinamide adenine dinucleotide (NAD) is a critical coenzyme or cofactor that plays a central role in metabolism and is involved in various cellular processes including the maintenance of metabolic homeostasis, post-translational protein modifications, DNA repair, and immune responses. As individuals age, their NAD levels decline, and this decrease has been suggested to be a contributing factor to the development of numerous age-related diseases, such as cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. In pursuit of healthy aging, researchers have investigated approaches to boost or maintain NAD levels. Here, we provide an overview of NAD metabolism and the role of NAD in age-related diseases and summarize recent progress in the development of strategies that target NAD metabolism for the treatment of age-related diseases, particularly neurodegenerative diseases.
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Affiliation(s)
- Feifei Li
- School of Pharmaceutical Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Chou Wu
- School of Pharmaceutical Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gelin Wang
- School of Pharmaceutical Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.
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6
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Brüll M, Geese N, Celardo I, Laumann M, Leist M. Preparation of Viable Human Neurites for Neurobiological and Neurodegeneration Studies. Cells 2024; 13:242. [PMID: 38334634 PMCID: PMC10854604 DOI: 10.3390/cells13030242] [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: 12/21/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
Few models allow the study of neurite damage in the human central nervous system. We used here dopaminergic LUHMES neurons to establish a culture system that allows for (i) the observation of highly enriched neurites, (ii) the preparation of the neurite fraction for biochemical studies, and (iii) the measurement of neurite markers and metabolites after axotomy. LUHMES-based spheroids, plated in culture dishes, extended neurites of several thousand µm length, while all somata remained aggregated. These cultures allowed an easy microscopic observation of live or fixed neurites. Neurite-only cultures (NOC) were produced by cutting out the still-aggregated somata. The potential application of such cultures was exemplified by determinations of their protein and RNA contents. For instance, the mitochondrial TOM20 protein was highly abundant, while nuclear histone H3 was absent. Similarly, mitochondrial-encoded RNAs were found at relatively high levels, while the mRNA for a histone or the neuronal nuclear marker NeuN (RBFOX3) were relatively depleted in NOC. Another potential use of NOC is the study of neurite degeneration. For this purpose, an algorithm to quantify neurite integrity was developed. Using this tool, we found that the addition of nicotinamide drastically reduced neurite degeneration. Also, the chelation of Ca2+ in NOC delayed the degeneration, while inhibitors of calpains had no effect. Thus, NOC proved to be suitable for biochemical analysis and for studying degeneration processes after a defined cut injury.
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Affiliation(s)
- Markus Brüll
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
| | - Nils Geese
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
| | - Ivana Celardo
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
| | - Michael Laumann
- Electron Microscopy Centre, University of Konstanz, 78457 Konstanz, Germany;
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, 78457 Konstanz, Germany; (M.B.); (N.G.); (I.C.)
- Center for Alternatives to Animal Testing in Europe (CAAT-Europe), University of Konstanz, 78457 Konstanz, Germany
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7
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Halder A, Drummond E. Strategies for translating proteomics discoveries into drug discovery for dementia. Neural Regen Res 2024; 19:132-139. [PMID: 37488854 PMCID: PMC10479849 DOI: 10.4103/1673-5374.373681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/25/2023] [Accepted: 04/06/2023] [Indexed: 07/26/2023] Open
Abstract
Tauopathies, diseases characterized by neuropathological aggregates of tau including Alzheimer's disease and subtypes of frontotemporal dementia, make up the vast majority of dementia cases. Although there have been recent developments in tauopathy biomarkers and disease-modifying treatments, ongoing progress is required to ensure these are effective, economical, and accessible for the globally ageing population. As such, continued identification of new potential drug targets and biomarkers is critical. "Big data" studies, such as proteomics, can generate information on thousands of possible new targets for dementia diagnostics and therapeutics, but currently remain underutilized due to the lack of a clear process by which targets are selected for future drug development. In this review, we discuss current tauopathy biomarkers and therapeutics, and highlight areas in need of improvement, particularly when addressing the needs of frail, comorbid and cognitively impaired populations. We highlight biomarkers which have been developed from proteomic data, and outline possible future directions in this field. We propose new criteria by which potential targets in proteomics studies can be objectively ranked as favorable for drug development, and demonstrate its application to our group's recent tau interactome dataset as an example.
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Affiliation(s)
- Aditi Halder
- School of Medical Sciences and Brain & Mind Center, University of Sydney, NSW, Sydney, Australia
- Department of Aged Care, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Eleanor Drummond
- School of Medical Sciences and Brain & Mind Center, University of Sydney, NSW, Sydney, Australia
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8
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Xu X, Sun B, Zhao C. Poly (ADP-Ribose) polymerase 1 and parthanatos in neurological diseases: From pathogenesis to therapeutic opportunities. Neurobiol Dis 2023; 187:106314. [PMID: 37783233 DOI: 10.1016/j.nbd.2023.106314] [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: 07/28/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP-1) is the most extensively studied member of the PARP superfamily, with its primary function being the facilitation of DNA damage repair processes. Parthanatos is a type of regulated cell death cascade initiated by PARP-1 hyperactivation, which involves multiple subroutines, including the accumulation of ADP-ribose polymers (PAR), binding of PAR and apoptosis-inducing factor (AIF), release of AIF from the mitochondria, the translocation of the AIF/macrophage migration inhibitory factor (MIF) complex, and massive MIF-mediated DNA fragmentation. Over the past few decades, the role of PARP-1 in central nervous system health and disease has received increasing attention. In this review, we discuss the biological functions of PARP-1 in neural cell proliferation and differentiation, memory formation, brain ageing, and epigenetic regulation. We then elaborate on the involvement of PARP-1 and PARP-1-dependant parthanatos in various neuropathological processes, such as oxidative stress, neuroinflammation, mitochondrial dysfunction, excitotoxicity, autophagy damage, and endoplasmic reticulum (ER) stress. Additional highlight contains PARP-1's implications in the initiation, progression, and therapeutic opportunities for different neurological illnesses, including neurodegenerative diseases, stroke, autism spectrum disorder (ASD), multiple sclerosis (MS), epilepsy, and neuropathic pain (NP). Finally, emerging insights into the repurposing of PARP inhibitors for the management of neurological diseases are provided. This review aims to summarize the exciting advancements in the critical role of PARP-1 in neurological disorders, which may open new avenues for therapeutic options targeting PARP-1 or parthanatos.
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Affiliation(s)
- Xiaoxue Xu
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China; Key Laboratory of Neurological Disease Big Data of Liaoning Province, Shenyang, China.
| | - Bowen Sun
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China; Key Laboratory of Neurological Disease Big Data of Liaoning Province, Shenyang, China
| | - Chuansheng Zhao
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China; Key Laboratory of Neurological Disease Big Data of Liaoning Province, Shenyang, China.
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9
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Yu Y. Links between Sleep Apnoea and Insomnia in a British Cohort. Clocks Sleep 2023; 5:552-565. [PMID: 37754354 PMCID: PMC10529849 DOI: 10.3390/clockssleep5030036] [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: 08/05/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023] Open
Abstract
Poor sleep is a major public health problem with implications for a wide range of critical health outcomes. Insomnia and sleep apnoea are the two most common causes of poor sleep, and recent studies have shown that these disorders frequently co-occur. Comorbid insomnia and sleep apnoea can substantially impair quality of life and increase the overall risk of mortality. However, the causal and physiological links between sleep apnoea and insomnia are unclear. It is also unknown whether having a higher risk for one condition can increase the risk of developing the other. Here, we investigated links between sleep apnoea and insomnia in a British population using a combination of self-reported questionnaires and causal inference. We found that 54.3% of the cohort had moderate insomnia, 9.4% had moderate sleep apnoea, and that 6.2% scored high for both conditions. Importantly, having a higher risk of sleep apnoea was associated with a higher risk of insomnia and vice versa. To determine the causal directionality between sleep apnoea and insomnia, we used Mendelian randomisation and found evidence that sleep apnoea could cause insomnia, but not the reverse. To elucidate how both sleep apnoea and insomnia were linked to each other, we looked at the behavioural markers of poor sleep. We found that feeling fatigued after sleeping and having noticeable sleep problems were linked to a higher burden of both sleep apnoea and insomnia. In conclusion, our results show that sleep apnoea increases the risk of developing insomnia, and both conditions can result in fatigue. We highlight the importance of considering and treating the symptoms of both conditions.
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Affiliation(s)
- Yizhou Yu
- International Sleep Charity, Shedfield, Southampton SO32 2HN, UK;
- MRC Toxicology Unit, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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10
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Abstract
Biomolecular condensates are reversible compartments that form through a process called phase separation. Post-translational modifications like ADP-ribosylation can nucleate the formation of these condensates by accelerating the self-association of proteins. Poly(ADP-ribose) (PAR) chains are remarkably transient modifications with turnover rates on the order of minutes, yet they can be required for the formation of granules in response to oxidative stress, DNA damage, and other stimuli. Moreover, accumulation of PAR is linked with adverse phase transitions in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In this review, we provide a primer on how PAR is synthesized and regulated, the diverse structures and chemistries of ADP-ribosylation modifications, and protein-PAR interactions. We review substantial progress in recent efforts to determine the molecular mechanism of PAR-mediated phase separation, and we further delineate how inhibitors of PAR polymerases may be effective treatments for neurodegenerative pathologies. Finally, we highlight the need for rigorous biochemical interrogation of ADP-ribosylation in vivo and in vitro to clarify the exact pathway from PARylation to condensate formation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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11
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Fontana P, Buch-Larsen SC, Suyari O, Smith R, Suskiewicz MJ, Schützenhofer K, Ariza A, Rack JGM, Nielsen ML, Ahel I. Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling. Nat Commun 2023; 14:3200. [PMID: 37268618 PMCID: PMC10238386 DOI: 10.1038/s41467-023-38793-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
In the mammalian DNA damage response, ADP-ribosylation signalling is of crucial importance to mark sites of DNA damage as well as recruit and regulate repairs factors. Specifically, the PARP1:HPF1 complex recognises damaged DNA and catalyses the formation of serine-linked ADP-ribosylation marks (mono-Ser-ADPr), which are extended into ADP-ribose polymers (poly-Ser-ADPr) by PARP1 alone. Poly-Ser-ADPr is reversed by PARG, while the terminal mono-Ser-ADPr is removed by ARH3. Despite its significance and apparent evolutionary conservation, little is known about ADP-ribosylation signalling in non-mammalian Animalia. The presence of HPF1, but absence of ARH3, in some insect genomes, including Drosophila species, raises questions regarding the existence and reversal of serine-ADP-ribosylation in these species. Here we show by quantitative proteomics that Ser-ADPr is the major form of ADP-ribosylation in the DNA damage response of Drosophila melanogaster and is dependent on the dParp1:dHpf1 complex. Moreover, our structural and biochemical investigations uncover the mechanism of mono-Ser-ADPr removal by Drosophila Parg. Collectively, our data reveal PARP:HPF1-mediated Ser-ADPr as a defining feature of the DDR in Animalia. The striking conservation within this kingdom suggests that organisms that carry only a core set of ADP-ribosyl metabolising enzymes, such as Drosophila, are valuable model organisms to study the physiological role of Ser-ADPr signalling.
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Affiliation(s)
- Pietro Fontana
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Sara C Buch-Larsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Marcin J Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071, Orléans, France
| | - Kira Schützenhofer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, UK.
| | - Michael L Nielsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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12
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Popovic R, Yu Y, Leal NS, Fedele G, Loh SHY, Martins LM. Upregulation of Tribbles decreases body weight and increases sleep duration. Dis Model Mech 2023; 16:dmm049942. [PMID: 37083954 PMCID: PMC10151826 DOI: 10.1242/dmm.049942] [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: 10/12/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023] Open
Abstract
Eukaryotic Tribbles proteins are pseudoenzymes that regulate multiple aspects of intracellular signalling. Both Drosophila melanogaster and mammalian members of this family of pseudokinases act as negative regulators of insulin signalling. Mammalian tribbles pseudokinase (TRIB) genes have also been linked to insulin resistance and type 2 diabetes mellitus. Type 2 diabetes mellitus is associated with increased body weight, sleep problems and increased long-term mortality. Here, we investigated how manipulating the expression of Tribbles impacts body weight, sleep and mortality. We showed that the overexpression of Drosophila tribbles (trbl) in the fly fat body reduces both body weight and lifespan in adult flies without affecting food intake. Furthermore, it decreases the levels of Drosophila insulin-like peptide 2 (DILP2; ILP2) and increases night-time sleep. The three genes encoding TRIBs of mammals, TRIB1, TRIB2 and TRIB3, show both common and unique features. As the three human TRIB genes share features with Drosophila trbl, we further explored the links between TRIB genetic variants and both body weight and sleep in the human population. We identified associations between the polymorphisms and expression levels of the pseudokinases and markers of body weight and sleep duration. We conclude that Tribbles pseudokinases are involved in the control of body weight, lifespan and sleep.
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Affiliation(s)
- Rebeka Popovic
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Nuno Santos Leal
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Giorgio Fedele
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Samantha H. Y. Loh
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - L. Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
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13
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Gene Self-Expressive Networks as a Generalization-Aware Tool to Model Gene Regulatory Networks. Biomolecules 2023; 13:biom13030526. [PMID: 36979461 PMCID: PMC10046116 DOI: 10.3390/biom13030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Self-expressiveness is a mathematical property that aims at characterizing the relationship between instances in a dataset. This property has been applied widely and successfully in computer-vision tasks, time-series analysis, and to infer underlying network structures in domains including protein signaling interactions and social-networks activity. Nevertheless, despite its potential, self-expressiveness has not been explicitly used to infer gene networks. In this article, we present Generalizable Gene Self-Expressive Networks, a new, interpretable, and generalization-aware formalism to model gene networks, and we propose two methods: GXN•EN and GXN•OMP, based respectively on ElasticNet and OMP (Orthogonal Matching Pursuit), to infer and assess Generalizable Gene Self-Expressive Networks. We evaluate these methods on four Microarray datasets from the DREAM5 benchmark, using both internal and external metrics. The results obtained by both methods are comparable to those obtained by state-of-the-art tools, but are fast to train and exhibit high levels of sparsity, which make them easier to interpret. Moreover we applied these methods to three complex datasets containing RNA-seq informations from different mammalian tissues/cell-types. Lastly, we applied our methodology to compare a normal vs. a disease condition (Alzheimer), which allowed us to detect differential expression of genes’ sub-networks between these two biological conditions. Globally, the gene networks obtained exhibit a sparse and modular structure, with inner communities of genes presenting statistically significant over/under-expression on specific cell types, as well as significant enrichment for some anatomical GO terms, suggesting that such communities may also drive important functional roles.
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14
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Metabolic Activation of PARP as a SARS-CoV-2 Therapeutic Target-Is It a Bait for the Virus or the Best Deal We Could Ever Make with the Virus? Is AMBICA the Potential Cure? Biomolecules 2023; 13:biom13020374. [PMID: 36830743 PMCID: PMC9953159 DOI: 10.3390/biom13020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
The COVID-19 pandemic has had a great impact on global health and is an economic burden. Even with vaccines and anti-viral medications we are still scrambling to get a balance. In this perspective, we have shed light upon an extremely feasible approach by which we can control the SARS-CoV-2 infection and the associated complications, bringing some solace to this ongoing turmoil. We are providing some insights regarding an ideal agent which could prevent SARS-CoV-2 multiplication. If we could identify an agent which is an activator of metabolism and is also bioactive, we could prevent corona activation (AMBICA). Some naturally occurring lipid molecules best fit this identity as an agent which has the capacity to replenish our host cells, specifically immune cells, with ATP. It could also act as a source for providing a substrate for host cell PARP family members for MARylation and PARylation processes, leading to manipulation of the viral macro domain function, resulting in curbing the virulence and propagation of SARS-CoV-2. Identification of the right lipid molecule or combination of lipid molecules will fulfill the criteria. This perspective has focused on a unique angle of host-pathogen interaction and will open up a new dimension in treating COVID-19 infection.
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15
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Chiu LY, Huang DY, Lin WW. PARP-1 regulates inflammasome activity by poly-ADP-ribosylation of NLRP3 and interaction with TXNIP in primary macrophages. Cell Mol Life Sci 2022; 79:108. [PMID: 35098371 PMCID: PMC8801414 DOI: 10.1007/s00018-022-04138-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/17/2021] [Accepted: 01/06/2022] [Indexed: 12/28/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) plays an essential role in DNA repair by catalyzing the polymerization of ADP-ribose unit to target proteins. Several studies have shown that PARP-1 can regulate inflammatory responses in various disease models. The intracellular Nod-like receptor NLRP3 has emerged as the most crucial innate immune receptor because of its broad specificity in mediating immune response to pathogen invasion and danger signals associated with cellular damage. In our study, we found NLRP3 stimuli-induced caspase-1 maturation and IL-1β production were impaired by PARP-1 knockout or PARP-1 inhibition in bone marrow-derived macrophages (BMDM). The step 1 signal of NLRP3 inflammasome activation was not affected by PARP-1 deficiency. Moreover, ATP-induced cytosolic ROS production was lower in Parp-1-/- BMDM, resulting in the decreased inflammasome complex assembly. PARP-1 can translocate to cytosol upon ATP stimulation and trigger the PARylation modification on NLRP3, leading to NLRP3 inflammasome assembly. PARP-1 was also a bridge between NLRP3 and thioredoxin-interacting protein (TXNIP) and participated in NLRP3/TXNIP complex formation for inflammasome activation. Overall, PARP-1 positively regulates NLRP3 inflammasome activation via increasing ROS production and interaction with TXNIP and NLRP3, leading to PARylation of NLRP3. Our data demonstrate a novel regulatory mechanism for NLRP3 inflammasome activation by PARP-1. Therefore, PARP-1 can serve as a potential target in the treatment of IL-1β associated inflammatory diseases.
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Affiliation(s)
- Ling-Ya Chiu
- Department of Pharmacology, College of Medicine, National Taiwan University, Rm. 1119, 11F., No. 1, Sec. 1, Ren Ai Rd., Zhongzheng Dist., Taipei, 100, Taiwan
| | - Duen-Yi Huang
- Department of Pharmacology, College of Medicine, National Taiwan University, Rm. 1119, 11F., No. 1, Sec. 1, Ren Ai Rd., Zhongzheng Dist., Taipei, 100, Taiwan
| | - Wan-Wan Lin
- Department of Pharmacology, College of Medicine, National Taiwan University, Rm. 1119, 11F., No. 1, Sec. 1, Ren Ai Rd., Zhongzheng Dist., Taipei, 100, Taiwan.
- Department and Graduate Institute of Pharmacology, National Defense Medical Center, Taipei, Taiwan.
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan.
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16
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Mani S, Swargiary G, Singh M, Agarwal S, Dey A, Ojha S, Jha NK. Mitochondrial defects: An emerging theranostic avenue towards Alzheimer's associated dysregulations. Life Sci 2021; 285:119985. [PMID: 34592237 DOI: 10.1016/j.lfs.2021.119985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/10/2021] [Accepted: 09/18/2021] [Indexed: 01/02/2023]
Abstract
Mitochondria play a crucial role in expediting the energy homeostasis under varying environmental conditions. As mitochondria are controllers of both energy production and apoptotic pathways, they are also distinctively involved in controlling the neuronal cell survival and/or death. Numerous factors are responsible for mitochondria to get degraded with aging and huge functional failures in mitochondria are also found to be associated with the commencement of numerous neurodegenerative conditions, including Alzheimer's disease (AD). A large number of existing literatures promote the pivotal role of mitochondrial damage and oxidative impairment in the pathogenesis of AD. Numerous mitochondria associated processes such as mitochondrial biogenesis, fission, fusion, mitophagy, transportation and bioenergetics are crucial for proper functioning of mitochondria but are reported to be defective in AD patients. Though, the knowledge on the precise and in-depth mechanisms of these actions is still in infancy. Based upon the outcome of various significant studies, mitochondria are also being considered as therapeutic targets for AD. Here, we review the current status of mitochondrial defects in AD and also summarize the possible role of these defects in the pathogenesis of AD. The various approaches for developing the mitochondria-targeted therapies are also discussed here in detail. Consequently, it is suggested that improving mitochondrial activity via pharmacological and/or non-pharmacological interventions could postpone the onset and slow the development of AD. Further research and consequences of ongoing clinical trials should extend our understanding and help to validate conclusions regarding the causation of AD.
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Affiliation(s)
- Shalini Mani
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida, UP 201307, India.
| | - Geeta Swargiary
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida, UP 201307, India
| | - Manisha Singh
- Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida, UP 201307, India
| | | | - Abhijit Dey
- Department of Life Sciences, Presidency University, College Street, Kolkata 700073, India
| | - Shreesh Ojha
- Department of Internal Medicine, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 17666, United Arab Emirates
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh 201310, India
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