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Solano LE, D’Sa NM, Nikolaidis N. PRRGO: A Tool for Visualizing and Mapping Globally Expressed Genes in Public Gene Expression Omnibus RNA-Sequencing Studies to PageRank-scored Gene Ontology Terms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576540. [PMID: 38328158 PMCID: PMC10849496 DOI: 10.1101/2024.01.21.576540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
We herein report PageRankeR Gene Ontology (PRRGO), a downloadable web application that can integrate differentially expressed gene (DEG) data from the gene expression omnibus (GEO) GEO2R web tool with the gene ontology (GO) database [1]. Unlike existing tools, PRRGO computes the PageRank for the entire GO network and can generate both interactive GO networks on the web interface and comma-separated values (CSV) files containing the DEG statistics categorized by GO term. These hierarchical and tabular GO-DEG data are especially conducive to hypothesis generation and overlap studies with the use of PageRank data, which can provide a metric of GO term centrality. We verified the tool for accuracy and reliability across nine independent heat shock (HS) studies for which the RNA-seq data was publicly available on GEO and found that the tool produced increasing concordance between study DEGs, GO terms, and select HS-specific GO terms.
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Affiliation(s)
- Luis E. Solano
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA
| | - Nicholas M. D’Sa
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850
- University of California, Irvine, Irvine, CA
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850
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2
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Rashid H, Jali A, Akhter MS, Abdi SAH. Molecular Mechanisms of Oxidative Stress in Acute Kidney Injury: Targeting the Loci by Resveratrol. Int J Mol Sci 2023; 25:3. [PMID: 38203174 PMCID: PMC10779152 DOI: 10.3390/ijms25010003] [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: 09/26/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 01/12/2024] Open
Abstract
Reactive oxygen species are a group of cellular molecules that stand as double-edged swords, their good and bad being discriminated by a precise balance. Several metabolic reactions in the biological system generate these molecules that interact with cellular atoms to regulate functions ranging from cell homeostasis to cell death. A prooxidative state of the cell concomitant with decreased clearance of such molecules leads to oxidative stress, which contributes as a prime pathophysiological mechanism in various diseases including renal disorders, such as acute kidney injury. However, targeting the generation of oxidative stress in renal disorders by an antioxidant, resveratrol, is gaining considerable therapeutic importance and is known to improve the condition in preclinical studies. This review aims to discuss molecular mechanisms of oxidative stress in acute kidney injury and its amelioration by resveratrol. The major sources of data were PubMed and Google Scholar, with studies from the last five years primarily included, with significant earlier data also considered. Mitochondrial dysfunction, various enzymatic reactions, and protein misfolding are the major sources of reactive oxygen species in acute kidney injury, and interrupting these loci of generation or intersection with other cellular components by resveratrol can mitigate the severity of the condition.
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Affiliation(s)
- Hina Rashid
- Department of Pharmacology and Toxicology, College of Pharmacy, Jazan University, Jizan 45142, Saudi Arabia
| | - Abdulmajeed Jali
- Department of Pharmacology and Toxicology, College of Pharmacy, Jazan University, Jizan 45142, Saudi Arabia
| | - Mohammad Suhail Akhter
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jizan 45142, Saudi Arabia
| | - Sayed Aliul Hasan Abdi
- Department of Pharmacy, Faculty of Clinical Pharmacy, Al Baha University, Al Baha 65711, Saudi Arabia
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3
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Labbadia J. Potential roles for mitochondria-to-HSF1 signaling in health and disease. Front Mol Biosci 2023; 10:1332658. [PMID: 38164224 PMCID: PMC10757924 DOI: 10.3389/fmolb.2023.1332658] [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: 11/03/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024] Open
Abstract
The ability to respond rapidly and efficiently to protein misfolding is crucial for development, reproduction and long-term health. Cells respond to imbalances in cytosolic/nuclear protein homeostasis through the Heat Shock Response, a tightly regulated transcriptional program that enhances protein homeostasis capacity by increasing levels of protein quality control factors. The Heat Shock Response is driven by Heat Shock Factor 1, which is rapidly activated by the appearance of misfolded proteins and drives the expression of genes encoding molecular chaperones and protein degradation factors, thereby restoring proteome integrity. HSF1 is critical for organismal health, and this has largely been attributed to the preservation of cytosolic and nuclear protein homeostasis. However, evidence is now emerging that HSF1 is also a key mediator of mitochondrial function, raising the possibility that many of the health benefits conferred by HSF1 may be due to the maintenance of mitochondrial homeostasis. In this review, I will discuss our current understanding of the interplay between HSF1 and mitochondria and consider how mitochondria-to-HSF1 signaling may influence health and disease susceptibility.
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Affiliation(s)
- Johnathan Labbadia
- Department of Genetics, Evolution and Environment, Division of Biosciences, Institute of Healthy Ageing, University College London, London, United Kingdom
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Taouktsi E, Kyriakou E, Voulgaraki E, Verganelakis D, Krokou S, Rigas S, Voutsinas GE, Syntichaki P. Mitochondrial p38 Mitogen-Activated Protein Kinase: Insights into Its Regulation of and Role in LONP1-Deficient Nematodes. Int J Mol Sci 2023; 24:17209. [PMID: 38139038 PMCID: PMC10743222 DOI: 10.3390/ijms242417209] [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: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
p38 Mitogen-Activated Protein Kinase (MAPK) cascades are central regulators of numerous physiological cellular processes, including stress response signaling. In C. elegans, mitochondrial dysfunction activates a PMK-3/p38 MAPK signaling pathway (MAPKmt), but its functional role still remains elusive. Here, we demonstrate the induction of MAPKmt in worms deficient in the lonp-1 gene, which encodes the worm ortholog of mammalian mitochondrial LonP1. This induction is subjected to negative regulation by the ATFS-1 transcription factor through the CREB-binding protein (CBP) ortholog CBP-3, indicating an interplay between both activated MAPKmt and mitochondrial Unfolded Protein Response (UPRmt) surveillance pathways. Our results also reveal a genetic interaction in lonp-1 mutants between PMK-3 kinase and the ZIP-2 transcription factor. ZIP-2 has an established role in innate immunity but can also modulate the lifespan by maintaining mitochondrial homeostasis during ageing. We show that in lonp-1 animals, ZIP-2 is activated in a PMK-3-dependent manner but does not confer increased survival to pathogenic bacteria. However, deletion of zip-2 or pmk-3 shortens the lifespan of lonp-1 mutants, suggesting a possible crosstalk under conditions of mitochondrial perturbation that influences the ageing process. Furthermore, loss of pmk-3 specifically diminished the extreme heat tolerance of lonp-1 worms, highlighting the crucial role of PMK-3 in the heat shock response upon mitochondrial LONP-1 inactivation.
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Affiliation(s)
- Eirini Taouktsi
- Laboratory of Molecular Genetics of Aging, Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, 11527 Athens, Greece; (E.T.); (E.K.); (E.V.); (D.V.); (S.K.)
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece;
| | - Eleni Kyriakou
- Laboratory of Molecular Genetics of Aging, Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, 11527 Athens, Greece; (E.T.); (E.K.); (E.V.); (D.V.); (S.K.)
| | - Evangelia Voulgaraki
- Laboratory of Molecular Genetics of Aging, Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, 11527 Athens, Greece; (E.T.); (E.K.); (E.V.); (D.V.); (S.K.)
| | - Dimitris Verganelakis
- Laboratory of Molecular Genetics of Aging, Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, 11527 Athens, Greece; (E.T.); (E.K.); (E.V.); (D.V.); (S.K.)
- Department of Biological Applications & Technology, University of Ioannina, 45500 Ioannina, Greece
| | - Stefania Krokou
- Laboratory of Molecular Genetics of Aging, Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, 11527 Athens, Greece; (E.T.); (E.K.); (E.V.); (D.V.); (S.K.)
| | - Stamatis Rigas
- Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece;
| | - Gerassimos E. Voutsinas
- Laboratory of Molecular Carcinogenesis and Rare Disease Genetics, Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, 15341 Athens, Greece;
| | - Popi Syntichaki
- Laboratory of Molecular Genetics of Aging, Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, 11527 Athens, Greece; (E.T.); (E.K.); (E.V.); (D.V.); (S.K.)
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Ghosh S, Villacorta-Martin C, Lindstrom-Vautrin J, Kenney D, Golden CS, Edwards CV, Sanchorawala V, Connors LH, Giadone RM, Murphy GJ. Mapping cellular response to destabilized transthyretin reveals cell- and amyloidogenic protein-specific signatures. Amyloid 2023; 30:379-393. [PMID: 37439769 DOI: 10.1080/13506129.2023.2224494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/04/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND In ATTR amyloidosis, transthyretin (TTR) protein is secreted from the liver and deposited as toxic aggregates at downstream target tissues. Despite recent advancements in treatments for ATTR amyloidosis, the mechanisms underlying misfolded TTR-mediated cellular damage remain elusive. METHODS In an effort to define early events of TTR-associated stress, we exposed neuronal (SH-SY5Y) and cardiac (AC16) cells to wild-type and destabilized TTR variants (TTRV122I (p.V142I) and TTRL55P (p.L70P)) and performed transcriptional (RNAseq) and epigenetic (ATACseq) profiling. We subsequently compared TTR-responsive signatures to cells exposed to destabilized antibody light chain protein associated with AL amyloidosis as well as ER stressors (thapsigargin, heat shock). RESULTS In doing so, we observed overlapping, yet distinct cell type- and amyloidogenic protein-specific signatures, suggesting unique responses to each amyloidogenic variant. Moreover, we identified chromatin level changes in AC16 cells exposed to mutant TTR that resolved upon pre-incubation with kinetic stabilizer tafamidis. CONCLUSIONS Collectively, these data provide insight into the mechanisms underlying destabilized protein-mediated cellular damage and provide a robust resource representing cellular responses to aggregation-prone proteins and ER stress.
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Affiliation(s)
- Sabrina Ghosh
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
| | | | | | - Devin Kenney
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Carly S Golden
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Camille V Edwards
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Vaishali Sanchorawala
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Lawreen H Connors
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Richard M Giadone
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
| | - George J Murphy
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
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Todosenko N, Khaziakhmatova O, Malashchenko V, Yurova K, Bograya M, Beletskaya M, Vulf M, Gazatova N, Litvinova L. Mitochondrial Dysfunction Associated with mtDNA in Metabolic Syndrome and Obesity. Int J Mol Sci 2023; 24:12012. [PMID: 37569389 PMCID: PMC10418437 DOI: 10.3390/ijms241512012] [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: 07/04/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Metabolic syndrome (MetS) is a precursor to the major health diseases associated with high mortality in industrialized countries: cardiovascular disease and diabetes. An important component of the pathogenesis of the metabolic syndrome is mitochondrial dysfunction, which is associated with tissue hypoxia, disruption of mitochondrial integrity, increased production of reactive oxygen species, and a decrease in ATP, leading to a chronic inflammatory state that affects tissues and organ systems. The mitochondrial AAA + protease Lon (Lonp1) has a broad spectrum of activities. In addition to its classical function (degradation of misfolded or damaged proteins), enzymatic activity (proteolysis, chaperone activity, mitochondrial DNA (mtDNA)binding) has been demonstrated. At the same time, the spectrum of Lonp1 activity extends to the regulation of cellular processes inside mitochondria, as well as outside mitochondria (nuclear localization). This mitochondrial protease with enzymatic activity may be a promising molecular target for the development of targeted therapy for MetS and its components. The aim of this review is to elucidate the role of mtDNA in the pathogenesis of metabolic syndrome and its components as a key component of mitochondrial dysfunction and to describe the promising and little-studied AAA + LonP1 protease as a potential target in metabolic disorders.
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Affiliation(s)
- Natalia Todosenko
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Olga Khaziakhmatova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Vladimir Malashchenko
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Kristina Yurova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Bograya
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Beletskaya
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Vulf
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Natalia Gazatova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Larisa Litvinova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
- Laboratory of Cellular and Microfluidic Technologies, Siberian State Medical University, 634050 Tomsk, Russia
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Zanini G, Selleri V, De Gaetano A, Gibellini L, Malerba M, Mattioli AV, Nasi M, Apostolova N, Pinti M. Differential Expression of Lonp1 Isoforms in Cancer Cells. Cells 2022; 11:cells11233940. [PMID: 36497197 PMCID: PMC9739308 DOI: 10.3390/cells11233940] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/26/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Lonp1 is a mitochondrial protease that degrades oxidized and damaged proteins, assists protein folding, and contributes to the maintenance of mitochondrial DNA. A higher expression of LonP1 has been associated with higher tumour aggressiveness. Besides the full-length isoform (ISO1), we identified two other isoforms of Lonp1 in humans, resulting from alternative splicing: Isoform-2 (ISO2) lacking aa 42-105 and isoform-3 (ISO3) lacking aa 1-196. An inspection of the public database TSVdb showed that ISO1 was upregulated in lung, bladder, prostate, and breast cancer, ISO2 in all the cancers analysed (including rectum, colon, cervical, bladder, prostate, breast, head, and neck), ISO3 did not show significant changes between cancer and normal tissue. We overexpressed ISO1, ISO2, and ISO3 in SW620 cells and found that the ISO1 isoform was exclusively mitochondrial, ISO2 was present in the organelle and in the cytoplasm, and ISO3 was exclusively cytoplasmatic. The overexpression of ISO1 and, at a letter extent, of ISO2 enhanced basal, ATP-linked, and maximal respiration without altering the mitochondria number or network, mtDNA amount. or mitochondrial dynamics. A higher extracellular acidification rate was observed in ISO1 and ISO2, overexpressing cells, suggesting an increase in glycolysis. Cells overexpressing the different isoforms did not show a difference in the proliferation rate but showed a great increase in anchorage-independent growth. ISO1 and ISO2, but not ISO3, determined an upregulation of EMT-related proteins, which appeared unrelated to higher mitochondrial ROS production, nor due to the activation of the MEK ERK pathway, but rather to global metabolic reprogramming of cells.
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Affiliation(s)
- Giada Zanini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Valentina Selleri
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- National Institute for Cardiovascular Research (INRC), 40126 Bologna, Italy
| | - Anna De Gaetano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Mara Malerba
- Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Anna Vittoria Mattioli
- National Institute for Cardiovascular Research (INRC), 40126 Bologna, Italy
- Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Milena Nasi
- Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41124 Modena, Italy
| | - Nadezda Apostolova
- Department of Pharmacology, University of Valencia, 46010 Valencia, Spain
- FISABIO—Hospital Universitario Dr. Peset, 46017 Valencia, Spain
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Correspondence: ; Tel.: +39-059-205-5386
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