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Romero-Moreno R, Czowski BJ, Harris L, Kuehn JF, White KA. Intracellular pH differentially regulates transcription of metabolic and signaling pathways in normal epithelial cells. J Biol Chem 2024:107658. [PMID: 39128712 DOI: 10.1016/j.jbc.2024.107658] [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: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
Intracellular pH (pHi) dynamics regulate normal cell function, and dysregulated pHi dynamics is an emerging hallmark of cancer (constitutively increased pHi) and neurodegeneration (constitutively decreased pHi). However, the molecular mechanisms by which pHi dynamics regulate cell biology are poorly understood. Here, we discovered that altering pHi in normal human breast epithelial cells triggers global transcriptional changes. We identified 176 genes differentially regulated by pHi, with pHi-dependent genes clustering in signaling and glycolytic pathways. Using various normal epithelial cell models, we showed pH-dependent Notch1 expression, with increased protein abundance at high pHi. This resulted in pH-dependent downstream signaling, with increased Notch1 signaling at high pHi. We also found that high pHi increased the expression of glycolytic enzymes and regulators of pyruvate fate, including lactate dehydrogenase and pyruvate dehydrogenase kinase. These transcriptional changes were sufficient to alter lactate production, with high pHi shifting these normal epithelial cells toward a glycolytic metabolism and increasing lactate production. Thus, pHi dynamics transcriptionally regulate signaling and metabolic pathways in normal epithelial cells. Our data reveal new molecular regulators of pHi-dependent biology and a role for increased pHi in driving the acquisition of cancer-associated signaling and metabolic changes in normal human epithelial cells.
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Affiliation(s)
- Ricardo Romero-Moreno
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Brandon J Czowski
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Lindsey Harris
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jessamine F Kuehn
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Katharine A White
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.
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2
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Nixon RA, Rubinsztein DC. Mechanisms of autophagy-lysosome dysfunction in neurodegenerative diseases. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00757-5. [PMID: 39107446 DOI: 10.1038/s41580-024-00757-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2024] [Indexed: 08/15/2024]
Abstract
Autophagy is a lysosome-based degradative process used to recycle obsolete cellular constituents and eliminate damaged organelles and aggregate-prone proteins. Their postmitotic nature and extremely polarized morphologies make neurons particularly vulnerable to disruptions caused by autophagy-lysosomal defects, especially as the brain ages. Consequently, mutations in genes regulating autophagy and lysosomal functions cause a wide range of neurodegenerative diseases. Here, we review the role of autophagy and lysosomes in neurodegenerative diseases such as Alzheimer disease, Parkinson disease and frontotemporal dementia. We also consider the strong impact of cellular ageing on lysosomes and autophagy as a tipping point for the late-age emergence of related neurodegenerative disorders. Many of these diseases have primary defects in autophagy, for example affecting autophagosome formation, and in lysosomal functions, especially pH regulation and calcium homeostasis. We have aimed to provide an integrative framework for understanding the central importance of autophagic-lysosomal function in neuronal health and disease.
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Affiliation(s)
- Ralph A Nixon
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, New York, NY, USA.
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA.
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA.
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA.
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK
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3
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Lu CY, Wu JZ, Yao HHY, Liu RJY, Li L, Pluthero FG, Freeman SA, Kahr WHA. Acidification of α-granules in megakaryocytes by vacuolar-type adenosine triphosphatase is essential for organelle biogenesis. J Thromb Haemost 2024; 22:2294-2305. [PMID: 38718926 DOI: 10.1016/j.jtha.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Platelets coordinate blood coagulation at sites of vascular injury and play fundamental roles in a wide variety of (patho)physiological processes. Key to many platelet functions is the transport and secretion of proteins packaged within α-granules, organelles produced by platelet precursor megakaryocytes. Prominent among α-granule cargo are fibrinogen endocytosed from plasma and endogenously synthesized von Willebrand factor. These and other proteins are known to require acidic pH for stable packaging. Luminal acidity has been confirmed for mature α-granules isolated from platelets, but direct measurement of megakaryocyte granule acidity has not been reported. OBJECTIVES To determine the luminal pH of α-granules and their precursors in megakaryocytes and assess the requirement of vacuolar-type adenosine triphosphatase (V-ATPase) activity to establish and maintain the luminal acidity and integrity of these organelles. METHODS Cresyl violet staining was used to detect acidic granules in megakaryocytes. Endocytosis of fibrinogen tagged with the pH-sensitive fluorescent dye fluorescein isothiocyanate was used to load a subset of these organelles. Ratiometric fluorescence analysis was used to determine their luminal pH. RESULTS We show that most of the acidic granules detected in megakaryocytes appear to be α-granules/precursors, for which we established a median luminal pH of 5.2 (IQR, 5.0-5.5). Inhibition of megakaryocyte V-ATPase activity led to enlargement of cargo-containing compartments detected by fluorescence microscopy and electron microscopy. CONCLUSION These observations reveal that V-ATPase activity is required to establish and maintain a luminal acidic pH in megakaryocyte α-granules/precursors, confirming its importance for stable packaging of cargo proteins such as von Willebrand factor.
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Affiliation(s)
- Chien-Yi Lu
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jing Ze Wu
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Helen H Y Yao
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Richard J Y Liu
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Ling Li
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fred G Pluthero
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Spencer A Freeman
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walter H A Kahr
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Division of Haematology/Oncology, Department of Paediatrics, University of Toronto and The Hospital for Sick Children, Toronto, Ontario, Canada.
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4
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Yousefnia S. A comprehensive review on lncRNA LOXL1-AS1: molecular mechanistic pathways of lncRNA LOXL1-AS1 in tumorigenicity of cancer cells. Front Oncol 2024; 14:1384342. [PMID: 39136001 PMCID: PMC11317273 DOI: 10.3389/fonc.2024.1384342] [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: 02/09/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are versatile RNAs that regulate various cellular processes, such as gene regulation, by acting as signals, decoys, guides, and scaffolds. A novel recognized lncRNA, LOXL1-antisense RNA 1 (LOXL1-AS1), is dysregulated in some diseases, including cancer, and acts as an oncogenic lncRNA in many types of cancer cells. Upregulation of LOXL1-AS1 has been involved in proliferation, migration, metastasis, and EMT, as well as inhibiting apoptosis in cancer cells. Most importantly, the malignant promoting activity of LOXL1-AS1 can be mostly mediated by sequestering specific miRNAs and inhibiting their binding to the 3´UTR of their target mRNAs, thereby indirectly regulating gene expression. Additionally, LOXL1-AS1 can decoy transcription factors and proteins and prevent their binding to their regulatory regions, inhibiting their mechanistic activity on the regulation of gene expression and signaling pathways. This review presents the mechanistic pathways of the oncogenic role of LOXL1-AS1 by modulating its target miRNAs and proteins in various cancer cells. Having information about the molecular mechanisms regulated by LOXL1-AS1 in cancer cells can open ways to find out particular prognostic biomarkers, as well as discover novel therapeutic approaches for different types of cancer.
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Affiliation(s)
- Saghar Yousefnia
- Department of Cell and Molecular Biology, Semnan University, Semnan, Iran
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5
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Hashmi F, Kane PM. V-ATPase Disassembly at the Yeast Lysosome-Like Vacuole Is a Phenotypic Driver of Lysosome Dysfunction in Replicative Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604825. [PMID: 39091794 PMCID: PMC11291124 DOI: 10.1101/2024.07.23.604825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Declines in lysosomal acidification and function with aging are observed in organisms ranging from yeast to humans. V-ATPases play a central role in organelle acidification and V-ATPase activity is regulated by reversible disassembly in many different settings. Using the yeast Saccharomyces cerevisiae as a replicative aging model, we demonstrate that V-ATPases disassemble into their V1 and V0 subcomplexes in aging cells, with release of V1 subunit C (Vma5) from the lysosome-like vacuole into the cytosol. Disassembly is observed after ≥5 cell divisions and results in overall vacuole alkalinization. Caloric restriction, an established mechanism for reversing many age-related outcomes, prevents V-ATPase disassembly in older cells and preserves vacuolar pH homeostasis. Reversible disassembly is controlled in part by the activity of two opposing and conserved factors, the RAVE complex and Oxr1. The RAVE complex promotes V-ATPase assembly and a rav1Δ mutant shortens replicative lifespan; Oxr1 promotes disassembly and an oxr1Δ mutation extends lifespan. Importantly, the level of Rav2, a key subunit of the RAVE complex, declines in aged cells. These data indicate that reduced V-ATPase assembly contributes to the loss of lysosome acidification with age, which affects replicative lifespan.
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Affiliation(s)
- Fiza Hashmi
- Department of Biochemistry and Molecular Biology , SUNY Upstate Medical University, Syracuse, NY USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology , SUNY Upstate Medical University, Syracuse, NY USA
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6
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Eaton AF, Danielson EC, Capen D, Merkulova M, Brown D. Dmxl1 Is an Essential Mammalian Gene that Is Required for V-ATPase Assembly and Function In Vivo. FUNCTION 2024; 5:zqae025. [PMID: 38984989 PMCID: PMC11237898 DOI: 10.1093/function/zqae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 07/11/2024] Open
Abstract
The proton pumping V-ATPase drives essential biological processes, such as acidification of intracellular organelles. Critically, the V-ATPase domains, V1 and VO, must assemble to produce a functional holoenzyme. V-ATPase dysfunction results in cancer, neurodegeneration, and diabetes, as well as systemic acidosis caused by reduced activity of proton-secreting kidney intercalated cells (ICs). However, little is known about the molecular regulation of V-ATPase in mammals. We identified a novel interactor of the mammalian V-ATPase, Drosophila melanogaster X chromosomal gene-like 1 (Dmxl1), aka Rabconnectin-3A. The yeast homologue of Dmxl1, Rav1p, is part of a complex that catalyzes the reversible assembly of the domains. We, therefore,hypothesized that Dmxl1 is a mammalian V-ATPase assembly factor. Here, we generated kidney IC-specific Dmxl1 knockout (KO) mice, which had high urine pH, like B1 V-ATPase KO mice, suggesting impaired V-ATPase function. Western blotting showed decreased B1 expression and B1 (V1) and a4 (VO) subunits were more intracellular and less colocalized in Dmxl1 KO ICs. In parallel, subcellular fractionation revealed less V1 associated B1 in the membrane fraction of KO cells relative to the cytosol. Furthermore, a proximity ligation assay performed using probes against B1 and a4 V-ATPase subunits also revealed decreased association. We propose that loss of Dmxl1 reduces V-ATPase holoenzyme assembly, thereby inhibiting proton pumping function. Dmxl1 may recruit the V1 domain to the membrane and facilitate assembly with the VO domain and in its absence V1 may be targeted for degradation. We conclude that Dmxl1 is a bona fide mammalian V-ATPase assembly factor.
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Affiliation(s)
- Amity F Eaton
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Elizabeth C Danielson
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Diane Capen
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Maria Merkulova
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dennis Brown
- Program in Membrane Biology and Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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7
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Jiménez J, Mishra R, Wang X, Magee CM, Bonning BC. Composition and abundance of midgut plasma membrane proteins in two major hemipteran vectors of plant viruses, Bemisia tabaci and Myzus persicae. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 116:e22133. [PMID: 39054788 DOI: 10.1002/arch.22133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/13/2024] [Accepted: 06/29/2024] [Indexed: 07/27/2024]
Abstract
Multiple species within the order Hemiptera cause severe agricultural losses on a global scale. Aphids and whiteflies are of particular importance due to their role as vectors for hundreds of plant viruses, many of which enter the insect via the gut. To facilitate the identification of novel targets for disruption of plant virus transmission, we compared the relative abundance and composition of the gut plasma membrane proteomes of adult Bemisia tabaci (Hemiptera: Aleyrodidae) and Myzus persicae (Hemiptera: Aphididae), representing the first study comparing the gut plasma membrane proteomes of two different insect species. Brush border membrane vesicles were prepared from dissected guts, and proteins extracted, identified and quantified from triplicate samples via timsTOF mass spectrometry. A total of 1699 B. tabaci and 1175 M. persicae proteins were identified. Following bioinformatics analysis and manual curation, 151 B. tabaci and 115 M. persicae proteins were predicted to localize to the plasma membrane of the gut microvilli. These proteins were further categorized based on molecular function and biological process according to Gene Ontology terms. The most abundant gut plasma membrane proteins were identified. The ten plasma membrane proteins that differed in abundance between the two insect species were associated with the terms "protein binding" and "viral processes." In addition to providing insight into the gut physiology of hemipteran insects, these gut plasma membrane proteomes provide context for appropriate identification of plant virus receptors based on a combination of bioinformatic prediction and protein localization on the surface of the insect gut.
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Affiliation(s)
- Jaime Jiménez
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Ruchir Mishra
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Xinyue Wang
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Ciara M Magee
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Bryony C Bonning
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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8
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Bindschedler A, Schmuckli-Maurer J, Buchser S, Fischer TD, Wacker R, Davalan T, Brunner J, Heussler VT. LC3B labeling of the parasitophorous vacuole membrane of Plasmodium berghei liver stage parasites depends on the V-ATPase and ATG16L1. Mol Microbiol 2024; 121:1095-1111. [PMID: 38574236 DOI: 10.1111/mmi.15259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
The protozoan parasite Plasmodium, the causative agent of malaria, undergoes an obligatory stage of intra-hepatic development before initiating a blood-stage infection. Productive invasion of hepatocytes involves the formation of a parasitophorous vacuole (PV) generated by the invagination of the host cell plasma membrane. Surrounded by the PV membrane (PVM), the parasite undergoes extensive replication. During intracellular development in the hepatocyte, the parasites provoke the Plasmodium-associated autophagy-related (PAAR) response. This is characterized by a long-lasting association of the autophagy marker protein, and ATG8 family member, LC3B with the PVM. LC3B localization at the PVM does not follow the canonical autophagy pathway since upstream events specific to canonical autophagy are dispensable. Here, we describe that LC3B localization at the PVM of Plasmodium parasites requires the V-ATPase and its interaction with ATG16L1. The WD40 domain of ATG16L1 is crucial for its recruitment to the PVM. Thus, we provide new mechanistic insight into the previously described PAAR response targeting Plasmodium liver stage parasites.
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Affiliation(s)
- Annina Bindschedler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Sophie Buchser
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Tara D Fischer
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Rahel Wacker
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Tim Davalan
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jessica Brunner
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Volker T Heussler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
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Klössel S, Zhu Y, Amado L, Bisinski DD, Ruta J, Liu F, González Montoro A. Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase. EMBO J 2024; 43:1870-1897. [PMID: 38589611 PMCID: PMC11066047 DOI: 10.1038/s44318-024-00097-2] [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: 01/18/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 04/10/2024] Open
Abstract
Yeast vacuoles perform crucial cellular functions as acidic degradative organelles, storage compartments, and signaling hubs. These functions are mediated by important protein complexes, including the vacuolar-type H+-ATPase (V-ATPase), responsible for organelle acidification. To gain a more detailed understanding of vacuole function, we performed cross-linking mass spectrometry on isolated vacuoles, detecting many known as well as novel protein-protein interactions. Among these, we identified the uncharacterized TLDc-domain-containing protein Rtc5 as a novel interactor of the V-ATPase. We further analyzed the influence of Rtc5 and of Oxr1, the only other yeast TLDc-domain-containing protein, on V-ATPase function. We find that both Rtc5 and Oxr1 promote the disassembly of the vacuolar V-ATPase in vivo, counteracting the role of the RAVE complex, a V-ATPase assembly chaperone. Furthermore, Oxr1 is necessary for the retention of a Golgi-specific subunit of the V-ATPase in this compartment. Collectively, our results shed light on the in vivo roles of yeast TLDc-domain proteins as regulators of the V-ATPase, highlighting the multifaceted regulation of this crucial protein complex.
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Affiliation(s)
- Samira Klössel
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Ying Zhu
- Department of Structural Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin, 13125, Germany
| | - Lucia Amado
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Daniel D Bisinski
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Julia Ruta
- Department of Structural Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin, 13125, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, Berlin, 13125, Germany
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany
| | - Ayelén González Montoro
- Osnabrück University, Department of Biology/Chemistry, Cellular Communication Laboratory, Barbarastrasse 13, 49076, Osnabrück, Germany.
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076, Osnabrück, Germany.
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10
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Mulligan RJ, Magaj MM, Digilio L, Redemann S, Yap CC, Winckler B. Collapse of late endosomal pH elicits a rapid Rab7 response via the V-ATPase and RILP. J Cell Sci 2024; 137:jcs261765. [PMID: 38578235 PMCID: PMC11166203 DOI: 10.1242/jcs.261765] [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: 11/02/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Endosomal-lysosomal trafficking is accompanied by the acidification of endosomal compartments by the H+-V-ATPase to reach low lysosomal pH. Disruption of the correct pH impairs lysosomal function and the balance of protein synthesis and degradation (proteostasis). Here, we treated mammalian cells with the small dipeptide LLOMe, which is known to permeabilize lysosomal membranes, and find that LLOMe also impacts late endosomes (LEs) by neutralizing their pH without causing membrane permeabilization. We show that LLOMe leads to hyperactivation of Rab7 (herein referring to Rab7a), and disruption of tubulation and mannose-6-phosphate receptor (CI-M6PR; also known as IGF2R) recycling on pH-neutralized LEs. pH neutralization (NH4Cl) and expression of Rab7 hyperactive mutants alone can both phenocopy the alterations in tubulation and CI-M6PR trafficking. Mechanistically, pH neutralization increases the assembly of the V1G1 subunit (encoded by ATP6V1G1) of the V-ATPase on endosomal membranes, which stabilizes GTP-bound Rab7 via RILP, a known interactor of Rab7 and V1G1. We propose a novel pathway by which V-ATPase and RILP modulate LE pH and Rab7 activation in concert. This pathway might broadly contribute to pH control during physiologic endosomal maturation or starvation and during pathologic pH neutralization, which occurs via lysosomotropic compounds and in disease states.
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Affiliation(s)
- Ryan J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Magdalena M. Magaj
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA 22908, USA
| | - Laura Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Stefanie Redemann
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA
| | - Chan Choo Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908, USA
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11
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Sánchez-Ramón S, Fuentes-Antrás J, Rider NL, Pérez-Segura P, de la Fuente-Muñoz E, Fernández-Arquero M, Neves E, Pérez de Diego R, Ocaña A, Guevara-Hoyer K. Exploring gastric cancer genetics: A turning point in common variable immunodeficiency. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100203. [PMID: 38283086 PMCID: PMC10818086 DOI: 10.1016/j.jacig.2023.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 01/30/2024]
Abstract
Background Gastric cancer (GC) stands as a prominent cause of cancer-related mortality and ranks second among the most frequently diagnosed malignancies in individuals with common variable immunodeficiency (CVID). Objective We sought to conduct a comprehensive, large-scale genetic analysis to explore the CVID-associated germline variant landscape within gastric adenocarcinoma samples and to seek to delineate the transcriptomic similarities between GC and CVID. Methods We investigated the presence of CVID-associated germline variants in 1591 GC samples and assessed their impact on tumor mutational load. The progression of GC was evaluated in patients with and without these variants. Transcriptomic similarities were explored by matching differentially expressed genes in GC to healthy gastric tissue with a CVID transcriptomic signature. Results CVID-associated germline variants were found in 60% of GC samples. Our analysis revealed a significant association between the presence of CVID-related genetic variants and higher tumor mutational load in GC (P < .0001); high GC mutational load seems to be linked to immunotherapy response and worse prognosis. Transcriptomic similarities unveiled key genes and pathways implicated in innate immune responses and tumorigenesis. We identified upregulated genes related to oncogene drivers, inflammation, tumor suppression, DNA repair, and downregulated immunomodulatory genes shared between GC and CVID. Conclusions Our findings contribute to a deeper understanding of potential molecular modulators of GC and shed light on the intricate interplay between immunodeficiency and cancer. This study underscores the clinical relevance of CVID-related variants in influencing GC progression and opens avenues for further exploration into novel therapeutic approaches.
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Affiliation(s)
- Silvia Sánchez-Ramón
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Jesús Fuentes-Antrás
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nicholas L. Rider
- Division of Clinical Informatics, Pediatrics, Allergy and Immunology, Liberty University College of Osteopathic Medicine and Collaborative Health Partners, Lynchburg, Va
| | - Pedro Pérez-Segura
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
| | - Eduardo de la Fuente-Muñoz
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Miguel Fernández-Arquero
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Esmeralda Neves
- Department of Immunology, Centro Hospitalar e Universitário de Santo António, Porto, Portugal
| | - Rebeca Pérez de Diego
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Alberto Ocaña
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
| | - Kissy Guevara-Hoyer
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
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12
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Khan MM, Wilkens S. Molecular mechanism of Oxr1p mediated disassembly of yeast V-ATPase. EMBO Rep 2024; 25:2323-2347. [PMID: 38565737 PMCID: PMC11094088 DOI: 10.1038/s44319-024-00126-5] [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: 12/03/2023] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 04/04/2024] Open
Abstract
The eukaryotic vacuolar H+-ATPase (V-ATPase) is regulated by reversible disassembly into autoinhibited V1-ATPase and Vo proton channel subcomplexes. We recently reported that the TLDc protein Oxr1p induces V-ATPase disassembly in vitro. Whether and how Oxr1p is involved in enzyme disassembly in vivo, however, is not known. Here, using yeast genetics and fluorescence microscopy, we show that Oxr1p is essential for efficient V-ATPase disassembly in the cell. Supporting biochemical and biophysical in vitro experiments show that whereas Oxr1p-driven holoenzyme disassembly can occur in the absence of nucleotides, the presence of ATP greatly accelerates the process. ATP hydrolysis is needed, however, for subsequent release of Oxr1p so that the free V1 can adopt the autoinhibited conformation. Overall, our study unravels the molecular mechanism of Oxr1p-induced disassembly that occurs in vivo as part of the canonical V-ATPase regulation by reversible disassembly.
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Affiliation(s)
- Md Murad Khan
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Stephan Wilkens
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
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13
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Tang J, Fang D, Zhong J, Li M. Missing WD40 Repeats in ATG16L1 Delays Canonical Autophagy and Inhibits Noncanonical Autophagy. Int J Mol Sci 2024; 25:4493. [PMID: 38674078 PMCID: PMC11050548 DOI: 10.3390/ijms25084493] [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: 03/13/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Canonical autophagy is an evolutionarily conserved process that forms double-membrane structures and mediates the degradation of long-lived proteins (LLPs). Noncanonical autophagy (NCA) is an important alternative pathway involving the formation of microtubule-associated protein 1 light chain 3 (LC3)-positive structures that are independent of partial core autophagy proteins. NCA has been defined by the conjugation of ATG8s to single membranes (CASM). During canonical autophagy and NCA/CASM, LC3 undergoes a lipidation modification, and ATG16L1 is a crucial protein in this process. Previous studies have reported that the WDR domain of ATG16L1 is not necessary for canonical autophagy. However, our study found that WDR domain deficiency significantly impaired LLP degradation in basal conditions and slowed down LC3-II accumulation in canonical autophagy. We further demonstrated that the observed effect was due to a reduced interaction between ATG16L1 and FIP200/WIPI2, without affecting lysosome function or fusion. Furthermore, we also found that the WDR domain of ATG16L1 is crucial for chemical-induced NCA/CASM. The results showed that removing the WDR domain or introducing the K490A mutation in ATG16L1 significantly inhibited the NCA/CASM, which interrupted the V-ATPase-ATG16L1 axis. In conclusion, this study highlights the significance of the WDR domain of ATG16L1 for both canonical autophagy and NCA functions, improving our understanding of its role in autophagy.
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Affiliation(s)
- Jiuge Tang
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
| | - Dongmei Fang
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
| | - Jialing Zhong
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
| | - Min Li
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, Guangzhou 510006, China
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14
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Hong JM, Gerard-O'Riley RL, Acton D, Alam I, Econs MJ, Bruzzaniti A. The PDE4 Inhibitors Roflumilast and Rolipram Rescue ADO2 Osteoclast Resorption Dysfunction. Calcif Tissue Int 2024; 114:430-443. [PMID: 38483547 PMCID: PMC11239147 DOI: 10.1007/s00223-024-01191-7] [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: 09/04/2023] [Accepted: 01/29/2024] [Indexed: 03/22/2024]
Abstract
Autosomal Dominant Osteopetrosis type II (ADO2) is a rare bone disease of impaired osteoclastic bone resorption caused by heterozygous missense mutations in the chloride channel 7 (CLCN7). Adenylate cyclase, which catalyzes the formation of cAMP, is critical for lysosomal acidification in osteoclasts. We found reduced cAMP levels in ADO2 osteoclasts compared to wild-type (WT) osteoclasts, leading us to examine whether regulating cAMP would improve ADO2 osteoclast activity. Although forskolin, a known activator of adenylate cyclase and cAMP levels, negatively affected osteoclast number, it led to an overall increase in ADO2 and WT osteoclast resorption activity in vitro. Next, we examined cAMP hydrolysis by the phosphodiesterase 4 (PDE4) proteins in ADO2 versus WT osteoclasts. QPCR analysis revealed higher expression of the three major PDE4 subtypes (4a, 4b, 4d) in ADO2 osteoclasts compared in WT, consistent with reduced cAMP levels in ADO2 osteoclasts. In addition, we found that the PDE4 antagonists, rolipram and roflumilast, stimulated ADO2 and WT osteoclast formation in a dose-dependent manner. Importantly, roflumilast and rolipram displayed a concentration-dependent increase in osteoclast resorption activity which was greater in ADO2 than WT osteoclasts. Moreover, treatment with roflumilast rescued cAMP levels in ADO2 OCLs. The key findings from our studies demonstrate that osteoclasts from ADO2 mice exhibit reduced cAMP levels and PDE4 inhibition rescues cAMP levels and ADO2 osteoclast activity dysfunction in vitro. The mechanism of action of PDE4 inhibitors and their ability to reduce the high bone mass of ADO2 mice in vivo are currently under investigation. Importantly, these studies advance the understanding of the mechanisms underlying the ADO2 osteoclast dysfunction which is critical for the development of therapeutic approaches to treat clinically affected ADO2 patients.
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Affiliation(s)
- Jung Min Hong
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, 1121 West Michigan Street, DS266, Indianapolis, IN, 46202, USA
| | - Rita L Gerard-O'Riley
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dena Acton
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Imranul Alam
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Michael J Econs
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Angela Bruzzaniti
- Department of Biomedical Sciences and Comprehensive Care, Indiana University School of Dentistry, 1121 West Michigan Street, DS266, Indianapolis, IN, 46202, USA.
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15
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Yanagisawa S, Bukhari ZA, Parra KJ, Frasch WD. Eukaryotic yeast V 1-ATPase rotary mechanism insights revealed by high-resolution single-molecule studies. Front Mol Biosci 2024; 11:1269040. [PMID: 38567099 PMCID: PMC10985318 DOI: 10.3389/fmolb.2024.1269040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 02/07/2024] [Indexed: 04/04/2024] Open
Abstract
Vacuolar ATP-dependent proton pumps (V-ATPases) belong to a super-family of rotary ATPases and ATP synthases. The V1 complex consumes ATP to drive rotation of a central rotor that pumps protons across membranes via the Vo complex. Eukaryotic V-ATPases are regulated by reversible disassembly of subunit C, V1 without C, and VO. ATP hydrolysis is thought to generate an unknown rotary state that initiates regulated disassembly. Dissociated V1 is inhibited by subunit H that traps it in a specific rotational position. Here, we report the first single-molecule studies with high resolution of time and rotational position of Saccharomyces cerevisiae V1-ATPase lacking subunits H and C (V1ΔHC), which resolves previously elusive dwells and angular velocity changes. Rotation occurred in 120° power strokes separated by dwells comparable to catalytic dwells observed in other rotary ATPases. However, unique V1ΔHC rotational features included: 1) faltering power stroke rotation during the first 60°; 2) a dwell often occurring ∼45° after the catalytic dwell, which did not increase in duration at limiting MgATP; 3) a second dwell, ∼2-fold longer occurring 112° that increased in duration and occurrence at limiting MgATP; 4) limiting MgATP-dependent decreases in power stroke angular velocity where dwells were not observed. The results presented here are consistent with MgATP binding to the empty catalytic site at 112° and MgADP released at ∼45°, and provide important new insight concerning the molecular basis for the differences in rotary positions of substrate binding and product release between V-type and F-type ATPases.
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Affiliation(s)
- Seiga Yanagisawa
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Zain A. Bukhari
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Karlett J. Parra
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Wayne D. Frasch
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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16
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Liu L, Chen X, Wu L, Huang K, Wang Z, Zheng Y, Zheng C, Zhang Z, Chen J, Wei J, Chen S, Jin W, Chen J, Wei D, Xu Y. Ubiquitin ligase subunit FBXO9 inhibits V-ATPase assembly and impedes lung cancer metastasis. Exp Hematol Oncol 2024; 13:32. [PMID: 38486234 PMCID: PMC10938814 DOI: 10.1186/s40164-024-00497-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The evolutionarily conserved protein FBXO9 acts as a substrate receptor for the SKP1-cullin-1-RBX1 ubiquitin ligase and is implicated in cancer, exhibiting either tumor-suppressive or oncogenic effects depending on the specific tumor type. However, their role in lung cancer metastasis remains unclear. METHODS Lentiviral vectors carrying miRNA-based shRNA sequences for gene-specific knockdown were generated, and Lenti-CRISPR-Cas9 vectors containing gene-specific sgRNA sequences were designed. Gene overexpression was achieved using doxycycline-inducible lentiviral constructs, while gene knockdown or knockout cells were generated using shRNA and CRISPR-Cas9, respectively. Functional assays included migration, clonogenic survival assays, tumor sphere assays, and protein interaction studies using mass spectrometry, immunoprecipitation, and immunoblot analysis. RESULTS This study identified FBXO9 as a crucial regulator that suppresses lung cancer cell migration, tumor sphere growth and restricts metastasis. We showed that FBXO9 facilitates the ubiquitination of the catalytic subunit A (ATP6V1A) of the Vacuolar-type H+-ATPase (V-ATPase), resulting in its interaction with the cytoplasmic chaperone HSPA8 and subsequent sequestration within the cytoplasm. This process hinders the assembly of functional V-ATPase, resulting in reduced vesicular acidification. In contrast, depletion of FBXO9 reduced ATP6V1A ubiquitination, resulting in increased V-ATPase assembly and vesicular acidification, thus promoting pro-metastatic Wnt signaling and metastasis of lung cancer cells. Furthermore, we demonstrated the effectiveness of inhibitors targeting V-ATPase in inhibiting lung cancer metastasis in a mouse model. Finally, we established a correlation between lower FBXO9 levels and poorer survival outcomes in patients with lung cancer. CONCLUSION These findings collectively elucidate the critical role of FBXO9 in regulating V-ATPase assembly and provide a molecular basis for FBXO9's function in inhibiting lung cancer metastasis. This highlights the potential therapeutic opportunities of FBXO9 supplementation.
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Affiliation(s)
- Liang Liu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China
- Institute of Clinical Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaodong Chen
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, Zhejiang Province, China
| | - Leilei Wu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China
| | - Kaizong Huang
- Department of Clinical Pharmacology Lab, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Zhenyi Wang
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, Zhejiang Province, China
| | - Yaolin Zheng
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China
| | - Cheng Zheng
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, Zhejiang Province, China
| | - Zhenshan Zhang
- Department of Radiation Oncology, Shanghai Proton and Heavy Ion Center, Fudan University Cancer Center, Shanghai, 200032, China
| | - Jiayan Chen
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jiaming Wei
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, 223300, Jiangsu, China
| | - Song Chen
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, 223300, Jiangsu, China
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450053, Henan, China
| | - Weilin Jin
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, China
| | - Jinfei Chen
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 730000, Zhejiang Province, China
| | - Dongping Wei
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, Zhejiang Province, China.
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.
| | - Yaping Xu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China.
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17
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Giambra M, Di Cristofori A, Raimondo F, Rigolio R, Conconi D, Chiarello G, Tabano SM, Antolini L, Nicolini G, Bua M, Ferlito D, Carrabba G, Giussani CG, Lavitrano M, Bentivegna A. Vacuolar Proton-Translocating ATPase May Take Part in the Drug Resistance Phenotype of Glioma Stem Cells. Int J Mol Sci 2024; 25:2743. [PMID: 38473989 DOI: 10.3390/ijms25052743] [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: 01/31/2024] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
The vacuolar proton-translocating ATPase (V-ATPase) is a transmembrane multi-protein complex fundamental in maintaining a normal intracellular pH. In the tumoral contest, its role is crucial since the metabolism underlying carcinogenesis is mainly based on anaerobic glycolytic reactions. Moreover, neoplastic cells use the V-ATPase to extrude chemotherapy drugs into the extra-cellular compartment as a drug resistance mechanism. In glioblastoma (GBM), the most malignant and incurable primary brain tumor, the expression of this pump is upregulated, making it a new possible therapeutic target. In this work, the bafilomycin A1-induced inhibition of V-ATPase in patient-derived glioma stem cell (GSC) lines was evaluated together with temozolomide, the first-line therapy against GBM. In contrast with previous published data, the proposed treatment did not overcome resistance to the standard therapy. In addition, our data showed that nanomolar dosages of bafilomycin A1 led to the blockage of the autophagy process and cellular necrosis, making the drug unusable in models which are more complex. Nevertheless, the increased expression of V-ATPase following bafilomycin A1 suggests a critical role of the proton pump in GBM stem components, encouraging the search for novel strategies to limit its activity in order to circumvent resistance to conventional therapy.
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Affiliation(s)
- Martina Giambra
- PhD Program in Neuroscience, University of Milano-Bicocca, 20900 Monza, Italy
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Andrea Di Cristofori
- PhD Program in Neuroscience, University of Milano-Bicocca, 20900 Monza, Italy
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Neurosurgery, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Francesca Raimondo
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Roberta Rigolio
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Donatella Conconi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Gaia Chiarello
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- Pathology, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Silvia Maria Tabano
- Laboratory of Medical Genetics, Ospedale Maggiore Policlinico, IRCCS Ca' Granda, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Laura Antolini
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Gabriella Nicolini
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Miriam Bua
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Neurosurgery, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Davide Ferlito
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Neurosurgery, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Giorgio Carrabba
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Neurosurgery, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Carlo Giorgio Giussani
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Neurosurgery, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Marialuisa Lavitrano
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Angela Bentivegna
- GBM-BI-TRACE (GlioBlastoMa-BIcocca-TRAnslational-CEnter), University of Milano-Bicocca, 20900 Monza, Italy
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
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18
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Mulligan R, Magaj M, Digilio L, Redemann S, Yap C, Winckler B. Collapse of late endosomal pH elicits a rapid Rab7 response via V-ATPase and RILP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.24.563658. [PMID: 37961579 PMCID: PMC10634777 DOI: 10.1101/2023.10.24.563658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Endosomal-lysosomal trafficking is accompanied by the acidification of endosomal compartments by the H+-V-ATPase to reach low lysosomal pH. Disruption of proper pH impairs lysosomal function and the balance of protein synthesis and degradation (proteostasis). We used the small dipeptide LLOMe, which is known to permeabilize lysosomal membranes, and find that LLOMe also impacts late endosomes (LEs) by neutralizing their pH without causing membrane permeabilization. We show that LLOMe leads to hyper-activation of Rab7 and disruption of tubulation and mannose-6-phosphate receptor (CI-M6PR) recycling on pH-neutralized LEs. Either pH neutralization (NH4Cl) or Rab7 hyper-active mutants alone can phenocopy the alterations in tubulation and CI-M6PR trafficking. Mechanistically, pH neutralization increases the assembly of the V1G1 subunit of the V-ATPase on endosomal membranes, which stabilizes GTP-bound Rab7 via RILP, a known interactor of Rab7 and V1G1. We propose a novel pathway by which V-ATPase and RILP modulate LE pH and Rab7 activation in concert. This pathway might broadly contribute to pH control during physiologic endosomal maturation or starvation and during pathologic pH neutralization, which occurs via lysosomotropic compounds or in disease states.
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Affiliation(s)
- R.J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA
| | - M.M. Magaj
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville VA
- Cell and Developmental Biology Graduate Program, University of Virginia, Charlottesville, VA
| | - L. Digilio
- Department of Cell Biology, University of Virginia, Charlottesville, VA
| | - S. Redemann
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville VA
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA
| | - C.C. Yap
- Department of Cell Biology, University of Virginia, Charlottesville, VA
| | - B Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA
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19
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Portela M, Mukherjee S, Paul S, La Marca JE, Parsons LM, Veraksa A, Richardson HE. The Drosophila tumour suppressor Lgl and Vap33 activate the Hippo pathway through a dual mechanism. J Cell Sci 2024; 137:jcs261917. [PMID: 38240353 PMCID: PMC10911279 DOI: 10.1242/jcs.261917] [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: 12/19/2023] [Accepted: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
The tumour suppressor, Lethal (2) giant larvae [Lgl; also known as L(2)gl], is an evolutionarily conserved protein that was discovered in the vinegar fly Drosophila, where its depletion results in tissue overgrowth and loss of cell polarity. Lgl links cell polarity and tissue growth through regulation of the Notch and the Hippo signalling pathways. Lgl regulates the Notch pathway by inhibiting V-ATPase activity via Vap33. How Lgl regulates the Hippo pathway was unclear. In this current study, we show that V-ATPase activity inhibits the Hippo pathway, whereas Vap33 acts to activate Hippo signalling. Vap33 physically and genetically interacts with the actin cytoskeletal regulators RtGEF (Pix) and Git, which also bind to the Hippo protein (Hpo) and are involved in the activation of the Hippo pathway. Additionally, we show that the ADP ribosylation factor Arf79F (Arf1), which is a Hpo interactor, is involved in the inhibition of the Hippo pathway. Altogether, our data suggest that Lgl acts via Vap33 to activate the Hippo pathway by a dual mechanism: (1) through interaction with RtGEF, Git and Arf79F, and (2) through interaction and inhibition of the V-ATPase, thereby controlling epithelial tissue growth.
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Affiliation(s)
- Marta Portela
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3002, Australia
| | - Swastik Mukherjee
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Sayantanee Paul
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - John E. La Marca
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
- Blood Cells and Blood Cancer Division, Water and Eliza Hall Institute, Melbourne, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, 3084, Australia
| | - Linda M. Parsons
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3002, Australia
| | - Alexey Veraksa
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Helena E. Richardson
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, 3002, Australia
- Sir Peter MacCallum Department of Oncology, Department of Anatomy and Neuroscience, Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, 3010, Australia
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Mitra C, Winkley S, Kane PM. Human V-ATPase a-subunit isoforms bind specifically to distinct phosphoinositide phospholipids. J Biol Chem 2023; 299:105473. [PMID: 37979916 PMCID: PMC10755780 DOI: 10.1016/j.jbc.2023.105473] [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: 05/12/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases) are highly conserved multisubunit enzymes that maintain the distinct pH of eukaryotic organelles. The integral membrane a-subunit is encoded by tissue- and organelle-specific isoforms, and its cytosolic N-terminal domain (aNT) modulates organelle-specific regulation and targeting of V-ATPases. Organelle membranes have specific phosphatidylinositol phosphate (PIP) lipid enrichment linked to maintenance of organelle pH. In yeast, the aNT domains of the two a-subunit isoforms bind PIP lipids enriched in the organelle membranes where they reside; these interactions affect activity and regulatory properties of the V-ATPases containing each isoform. Humans have four a-subunit isoforms, and we hypothesize that the aNT domains of these isoforms will also bind to specific PIP lipids. The a1 and a2 isoforms of human V-ATPase a-subunits are localized to endolysosomes and Golgi, respectively. We determined that bacterially expressed Hua1NT and Hua2NT bind specifically to endolysosomal PIP lipids PI(3)P and PI(3,5)P2 and Golgi enriched PI(4)P, respectively. Despite the lack of canonical PIP-binding sites, we identified potential binding sites in the HuaNT domains by sequence comparisons and existing subunit structures and models. We found that mutations at a similar location in the distal loops of both HuaNT isoforms compromise binding to their cognate PIP lipids, suggesting that these loops encode PIP specificity of the a-subunit isoforms. These data suggest a mechanism through which PIP lipid binding could stabilize and activate V-ATPases in distinct organelles.
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Affiliation(s)
- Connie Mitra
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Samuel Winkley
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.
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21
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Li H, Li J, Qu X, Dai H, Liu J, Ma M, Wang J, Dong W, Wang W. Establishment and validation of a novel lysosome-related gene signature for predicting prognosis and immune landscape in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:17543-17557. [PMID: 37903936 DOI: 10.1007/s00432-023-05477-5] [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: 06/12/2023] [Accepted: 10/12/2023] [Indexed: 11/01/2023]
Abstract
BACKGROUND Recent studies have shown that lysosomes not only provide energy for tumor cell growth, but also participate in the occurrence and development of malignant tumors by regulating various ways of tumor cell death. However, the role of lysosome associated genes (LSAGs) in hepatocellular carcinoma (HCC) remains unclear. METHODS Transcriptome data and clinical data of HCC were downloaded from the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. We identified differential expression of LSAGs by comparing tumor tissue with normal liver tissue. Subsequently, we used univariate COX analysis and least absolute shrinkage and selection operator (LASSO) COX regression to construct the prognostic feature of LSAGs. Kaplan-Meier survival curve and receiver operating characteristic curve were used to evaluate the predictive ability of LSAGs feature. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for functional enrichment analysis of risk differential genes. The relationship between LSAGs score and tumor microenvironment and chemotherapy drug sensitivity was analyzed. Finally, the cellular communication of tumor cells with high and low expression of model LSAGs was explored. RESULTS We identified sixteen prognostic associated LSAGs, four of which were selected to construct prognostic feature of LSAGs. Patients in the low LSAGs group had a better prognosis than those in the high LSAGs group. GO and KEGG analyses showed that risk differential genes were enriched in leukocyte migration, cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway. The group with low LSAGs score had lower immune score. Patients in the high LSAGs group were more sensitive to drugs for chemotherapy. In addition, tumor cells with high expression of model LSAGs showed stronger association with immune cells through the interleukin-2 (IL2), fibroblast growth factor (FGF), adiponectin, and bone morphogenetic proteins (BMP) signaling pathways. CONCLUSION We established a LSAGs signature that had the ability to predict clinical prognosis and immune landscape, proposing potential therapeutic targets for HCC.
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Affiliation(s)
- Haoling Li
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Anhui, 233030, China
- Department of Clinical Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Jing Li
- Department of Pharmacy, Shanghai Pudong New Area People's Hospital, Shanghai, 201299, China
| | - Xiangyu Qu
- Department of Clinical Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Hengwen Dai
- Department of Clinical Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Junjie Liu
- Department of Clinical Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Mengxi Ma
- Department of Clinical Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Jian Wang
- Department of Pharmacy, Shanghai Pudong New Area People's Hospital, Shanghai, 201299, China.
| | - Wei Dong
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, 200438, China.
| | - Wenrui Wang
- Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Anhui, 233030, China.
- Department of Biotechnology, School of Life Sciences, Bengbu Medical College, Anhui, 233030, China.
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22
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Hou W, Huang LJ, Huang H, Liu SL, Dai W, Li ZM, Zhang ZY, Xin SY, Wang JY, Zhang ZY, Ouyang X, Lan JX. Bioactivities and Mechanisms of Action of Diphyllin and Its Derivatives: A Comprehensive Systematic Review. Molecules 2023; 28:7874. [PMID: 38067601 PMCID: PMC10707837 DOI: 10.3390/molecules28237874] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Natural products are treasure houses for modern drug discovery. Diphyllin is a natural arylnaphthalene lignan lactone isolated from the leaf of Astilboides tabularis. Studies have found that it possesses plenty of bioactivity characteristics. In this paper, we reviewed the structure, bioactivity, and mechanism of action of diphyllin and its derivatives. The references were obtained from PubMed, Web of Science, and Science Direct databases up to August 2023. Papers without a bio-evaluation were excluded. Diphyllin and its derivatives have demonstrated V-ATPase inhibition, anti-tumor, anti-virus, anti-biofilm, anti-inflammatory, and anti-oxidant activities. The most studied activities of diphyllin and its derivatives are V-ATPase inhibition, anti-tumor activities, and anti-virus activities. Furthermore, V-ATPase inhibition activity is the mechanism of many bioactivities, including anti-tumor, anti-virus, and anti-inflammatory activities. We also found that the galactosylated modification of diphyllin is a common phenomenon in plants, and therefore, galactosylated modification is applied by researchers in the laboratory to obtain more excellent diphyllin derivatives. This review will provide useful information for the development of diphyllin-based anti-tumor and anti-virus compounds.
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Affiliation(s)
- Wen Hou
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Le-Jun Huang
- College of Rehabilitation, Gannan Medical University, Ganzhou 341000, China;
| | - Hao Huang
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Sheng-Lan Liu
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Wei Dai
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Zeng-Min Li
- Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou 341000, China;
| | - Zhen-Yu Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Su-Ya Xin
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Jin-Yang Wang
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Zi-Yun Zhang
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Xi Ouyang
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China; (W.H.); (H.H.); (S.-L.L.); (W.D.); (Z.-Y.Z.); (S.-Y.X.); (J.-Y.W.); (Z.-Y.Z.); (X.O.)
| | - Jin-Xia Lan
- College of Public Health and Health Management, Gannan Medical University, Ganzhou 341000, China
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23
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Cheng CY, Romero DP, Zoltner M, Yao MC, Turkewitz AP. Structure and dynamics of the contractile vacuole complex in Tetrahymena thermophila. J Cell Sci 2023; 136:jcs261511. [PMID: 37902010 PMCID: PMC10729820 DOI: 10.1242/jcs.261511] [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: 07/25/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023] Open
Abstract
The contractile vacuole complex (CVC) is a dynamic and morphologically complex membrane organelle, comprising a large vesicle (bladder) linked with a tubular reticulum (spongiome). CVCs provide key osmoregulatory roles across diverse eukaryotic lineages, but probing the mechanisms underlying their structure and function is hampered by the limited tools available for in vivo analysis. In the experimentally tractable ciliate Tetrahymena thermophila, we describe four proteins that, as endogenously tagged constructs, localize specifically to distinct CVC zones. The DOPEY homolog Dop1p and the CORVET subunit Vps8Dp localize both to the bladder and spongiome but with different local distributions that are sensitive to osmotic perturbation, whereas the lipid scramblase Scr7p colocalizes with Vps8Dp. The H+-ATPase subunit Vma4 is spongiome specific. The live imaging permitted by these probes revealed dynamics at multiple scales including rapid exchange of CVC-localized and soluble protein pools versus lateral diffusion in the spongiome, spongiome extension and branching, and CVC formation during mitosis. Although the association with DOP1 and VPS8D implicate the CVC in endosomal trafficking, both the bladder and spongiome might be isolated from bulk endocytic input.
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Affiliation(s)
- Chao-Yin Cheng
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Daniel P. Romero
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Martin Zoltner
- Biotechnology Biomedicine Centre of the Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Meng-Chao Yao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Aaron P. Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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24
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Li J, Krause GJ, Gui Q, Kaushik S, Rona G, Zhang Q, Liang FX, Dhabaria A, Anerillas C, Martindale JL, Vasilyev N, Askenazi M, Ueberheide B, Nudler E, Gorospe M, Cuervo AM, Pagano M. A noncanonical function of SKP1 regulates the switch between autophagy and unconventional secretion. SCIENCE ADVANCES 2023; 9:eadh1134. [PMID: 37831778 PMCID: PMC10575587 DOI: 10.1126/sciadv.adh1134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Intracellular degradation of proteins and organelles by the autophagy-lysosome system is essential for cellular quality control and energy homeostasis. Besides degradation, endolysosomal organelles can fuse with the plasma membrane and contribute to unconventional secretion. Here, we identify a function for mammalian SKP1 in endolysosomes that is independent of its established role as an essential component of the family of SCF/CRL1 ubiquitin ligases. We found that, under nutrient-poor conditions, SKP1 is phosphorylated on Thr131, allowing its interaction with V1 subunits of the vacuolar ATPase (V-ATPase). This event, in turn, promotes V-ATPase assembly to acidify late endosomes and enhance endolysosomal degradation. Under nutrient-rich conditions, SUMOylation of phosphorylated SKP1 allows its binding to and dephosphorylation by the PPM1B phosphatase. Dephosphorylated SKP1 interacts with SEC22B to promote unconventional secretion of the content of less acidified hybrid endosomal/autophagic compartments. Collectively, our study implicates SKP1 phosphorylation as a switch between autophagy and unconventional secretion in a manner dependent on cellular nutrient status.
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Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gregory J. Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qi Gui
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Susmita Kaushik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Avantika Dhabaria
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L. Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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25
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Fabri LM, Garçon DP, Moraes CM, Pinto MR, McNamara JC, Leone FA. A kinetic characterization of the gill V(H +)-ATPase from two hololimnetic populations of the Amazon River shrimp Macrobrachium amazonicum. Comp Biochem Physiol B Biochem Mol Biol 2023; 268:110880. [PMID: 37517460 DOI: 10.1016/j.cbpb.2023.110880] [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: 05/08/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
This investigation examines the kinetic characteristics and effect of acclimation to a brackish medium (21 ‰S) on gill V(H+)-ATPase activity in two hololimnetic populations of M. amazonicum. We also investigate the cellular immunolocalization of the enzyme. Immunofluorescence findings demonstrate that the V(H+)-ATPase c-subunit is distributed in the apical pillar cells of shrimps in fresh water but is absent after acclimation to 21 ‰S for 10 days. V(H+)-ATPase activity from the Tietê River population is ≈50% greater than the Grande River population, comparable to a wild population from the Santa Elisa Reservoir, but is 2-fold less than in cultivated shrimps. V(H+)-ATPase activity in the Tietê and the Grande River shrimps is abolished after 21 ‰S acclimation. The apparent affinities of the V(H+)-ATPase for ATP (0.27 ± 0.04 and 0.16 ± 0.03 mmol L-1, respectively) and Mg2+ (0.28 ± 0.05 and 0.14 ± 0.02 mmol L-1, respectively) are similar in both populations. The absence of V(H+)-ATPase activity in salinity-acclimated shrimps and its apical distribution in shrimps in fresh water underpins the importance of the crustacean V(H+)-ATPase for ion uptake in fresh water.
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Affiliation(s)
- Leonardo M Fabri
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Brazil
| | - Daniela P Garçon
- Universidade Federal do Triângulo Mineiro, Campus Universitário de Iturama, 38280-000, Brazil
| | - Cintya M Moraes
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Brazil
| | - Marcelo R Pinto
- Laboratory of Biopathology and Molecular Biology, University of Uberaba, Uberaba, Minas Gerais, Brazil
| | - John C McNamara
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil.; Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, 11000-600, Brazil. https://twitter.com/maracoani
| | - Francisco A Leone
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil.
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26
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Gu SH, Lin PL, Chang CH. Expressions of sugar transporter genes during Bombyx mori embryonic development. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:788-798. [PMID: 37407486 DOI: 10.1002/jez.2729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Sugar transporters (Sts) play important roles in controlling carbohydrate transport and are responsible for mediating the movement of sugars into cells. Few studies have been conducted on expressions of Sts during insect embryonic development. In the present study, we investigated temporal expressions of St genes during the embryonic diapause process in Bombyx mori. We found that in HCl-treated developing eggs, high gene expressions of trehalose transporter 1 (Tret1) were detected during middle and later embryonic development. St4 and St3 gene expressions gradually increased during the early stages, reached a small peak on Day 3, and large peaks were again detected on Day 7. However, in diapause eggs, expression levels of the Tret1, St4, and St3 genes all remained at low levels. Differential temporal changes in expressions of the Tret1, St4, and St3 genes found between diapause and HCl-treated eggs were further confirmed using nondiapause eggs. Our results showed that nondiapause eggs exhibited similar changing patterns as those of HCl-treated eggs, thus clearly indicating potential correlations between expressions of these genes and embryonic development. In addition, high gene expressions of Tret1 were also detected when dechorionated eggs were incubated in the medium. The addition of LY294002 (a specific phosphatidylinositol 3-kinase [PI3K] inhibitor) and U0126 (a mitogen-activated protein kinase/extracellular signal-regulated kinase [ERK] kinase [MEK] inhibitor) partially inhibited Tret1 gene expression in dechorionated eggs, but did not affect either ecdysteroid-phosphate phosphatase gene expression or ecdysteroid biosynthesis, clearly indicating that both PI3K and ERK are involved in increased gene expression of Tret1 that was independent of ecdysteroid levels. To our knowledge, this is the first comprehensive report to demonstrate the transcriptional regulation of St genes during embryonic development, thus providing useful information for a clearer understanding of insect egg diapause mechanisms.
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Affiliation(s)
- Shi-Hong Gu
- Department of Biology, National Museum of Natural Science, Taiwan, Taichung, Republic of China
| | - Pei-Ling Lin
- Department of Biology, National Museum of Natural Science, Taiwan, Taichung, Republic of China
| | - Chia-Hao Chang
- Department of Biology, National Museum of Natural Science, Taiwan, Taichung, Republic of China
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27
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Mulligan RJ, Winckler B. Regulation of Endosomal Trafficking by Rab7 and Its Effectors in Neurons: Clues from Charcot-Marie-Tooth 2B Disease. Biomolecules 2023; 13:1399. [PMID: 37759799 PMCID: PMC10527268 DOI: 10.3390/biom13091399] [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: 08/27/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Intracellular endosomal trafficking controls the balance between protein degradation and synthesis, i.e., proteostasis, but also many of the cellular signaling pathways that emanate from activated growth factor receptors after endocytosis. Endosomal trafficking, sorting, and motility are coordinated by the activity of small GTPases, including Rab proteins, whose function as molecular switches direct activity at endosomal membranes through effector proteins. Rab7 is particularly important in the coordination of the degradative functions of the pathway. Rab7 effectors control endosomal maturation and the properties of late endosomal and lysosomal compartments, such as coordination of recycling, motility, and fusion with downstream compartments. The spatiotemporal regulation of endosomal receptor trafficking is particularly challenging in neurons because of their enormous size, their distinct intracellular domains with unique requirements (dendrites vs. axons), and their long lifespans as postmitotic, differentiated cells. In Charcot-Marie-Tooth 2B disease (CMT2B), familial missense mutations in Rab7 cause alterations in GTPase cycling and trafficking, leading to an ulcero-mutilating peripheral neuropathy. The prevailing hypothesis to account for CMT2B pathologies is that CMT2B-associated Rab7 alleles alter endocytic trafficking of the neurotrophin NGF and its receptor TrkA and, thereby, disrupt normal trophic signaling in the peripheral nervous system, but other Rab7-dependent pathways are also impacted. Here, using TrkA as a prototypical endocytic cargo, we review physiologic Rab7 effector interactions and control in neurons. Since neurons are among the largest cells in the body, we place particular emphasis on the temporal and spatial regulation of endosomal sorting and trafficking in neuronal processes. We further discuss the current findings in CMT2B mutant Rab7 models, the impact of mutations on effector interactions or balance, and how this dysregulation may confer disease.
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Affiliation(s)
- Ryan J. Mulligan
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, USA
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA 22903, USA
| | - Bettina Winckler
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22903, USA
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28
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Morello G, Guarnaccia M, La Cognata V, Latina V, Calissano P, Amadoro G, Cavallaro S. Transcriptomic Analysis in the Hippocampus and Retina of Tg2576 AD Mice Reveals Defective Mitochondrial Oxidative Phosphorylation and Recovery by Tau 12A12mAb Treatment. Cells 2023; 12:2254. [PMID: 37759477 PMCID: PMC10527038 DOI: 10.3390/cells12182254] [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: 06/27/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Increasing evidence implicates decreased energy metabolism and mitochondrial dysfunctions among the earliest pathogenic events of Alzheimer's disease (AD). However, the molecular mechanisms underlying bioenergetic dysfunctions in AD remain, to date, largely unknown. In this work, we analyzed transcriptomic changes occurring in the hippocampus and retina of a Tg2576 AD mouse model and wild-type controls, evaluating their functional implications by gene set enrichment analysis. The results revealed that oxidative phosphorylation and mitochondrial-related pathways are significantly down-regulated in both tissues of Tg2576 mice, supporting the role of these processes in the pathogenesis of AD. In addition, we also analyzed transcriptomic changes occurring in Tg2576 mice treated with the 12A12 monoclonal antibody that neutralizes an AD-relevant tau-derived neurotoxic peptide in vivo. Our analysis showed that the mitochondrial alterations observed in AD mice were significantly reverted by treatment with 12A12mAb, supporting bioenergetic pathways as key mediators of its in vivo neuroprotective and anti-amyloidogenic effects. This study provides, for the first time, a comprehensive characterization of molecular events underlying the disrupted mitochondrial bioenergetics in AD pathology, laying the foundation for the future development of diagnostic and therapeutic tools.
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Affiliation(s)
- Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), Via Paolo Gaifami, 18, 95126 Catania, Italy; (G.M.); (M.G.); (V.L.C.)
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), Via Paolo Gaifami, 18, 95126 Catania, Italy; (G.M.); (M.G.); (V.L.C.)
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), Via Paolo Gaifami, 18, 95126 Catania, Italy; (G.M.); (M.G.); (V.L.C.)
| | - Valentina Latina
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy; (V.L.); (P.C.); (G.A.)
| | - Pietro Calissano
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy; (V.L.); (P.C.); (G.A.)
| | - Giuseppina Amadoro
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy; (V.L.); (P.C.); (G.A.)
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), Via Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council (CNR-IRIB), Via Paolo Gaifami, 18, 95126 Catania, Italy; (G.M.); (M.G.); (V.L.C.)
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Darmayanti S, Lesmana R, Meiliana A, Abdulah R. V-ATPase subunit C 1 and IKBIP as tandem prospective biomarkers for diabetic nephropathy. Diabetes Res Clin Pract 2023; 203:110887. [PMID: 37604283 DOI: 10.1016/j.diabres.2023.110887] [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: 04/10/2023] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
AIMS The appearance of low-molecular-weight (LMW) protein in the urine indicates any disruption in the structural integrity of the glomerular capillary wall; therefore, the presence of LMW protein may be a potential predictive marker for DN. METHODS The urine proteomic profiling of T2DM patients (n = 94) and control group (n = 32) was compared by liquid chromatography-tandem mass spectrometry, and the untargeted LMW protein was identified by Progenesis Q1 For Proteomics v4.2. RESULTS A total of 73 LMW proteins were identified and quantified, of which, 32 proteins were found to be altered significantly (p < 0.05). Further analysis with heat maps identified two potential proteins with the highest folding alterations in urine. V-ATPase subunit C 1 abundance was significantly inversely correlated with microalbumin and significantly decreased in urine, whereas increased IKBIP was positively correlated with microalbumin. The level of those proteins was significantly different among the control, T2DM, and DN groups, implying an association with the progression of DN. CONCLUSIONS The present findings of our study indicate that the decreasing V-ATPase subunit C 1 together with increasing IKBIP in urine, were found to be closely associated with DN complications and signifying their value as biomarkers for predicting the risk of DN at initial diagnosis.
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Affiliation(s)
- Siska Darmayanti
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia; Prodia Clinical Laboratory, Jakarta, Indonesia
| | - Ronny Lesmana
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Jatinangor, Indonesia; Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Jatinangor, Indonesia.
| | - Anna Meiliana
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia; Prodia Clinical Laboratory, Jakarta, Indonesia
| | - Rizky Abdulah
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia; Center of Excellence for Pharmaceutical Care Innovation, Universitas Padjadjaran, Jatinangor, Indonesia
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30
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Tang HS, Gates CR, Schultz MC. Biochemical evidence that the whole compartment activity behavior of GAPDH differs between the cytoplasm and nucleus. PLoS One 2023; 18:e0290892. [PMID: 37651389 PMCID: PMC10470895 DOI: 10.1371/journal.pone.0290892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
Some metabolic enzymes normally occur in the nucleus and cytoplasm. These compartments differ in molecular composition. Since post-translational modification and interaction with allosteric effectors can tune enzyme activity, it follows that the behavior of an enzyme as a catalyst may differ between the cytoplasm and nucleus. We explored this possibility for the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Homogenates of pristine nuclei and cytoplasms isolated from Xenopus laevis oocytes were used for whole compartment activity profiling in a near-physiological buffer. Titrations of NAD+ revealed similar whole compartment activity profiles for GAPDH in nuclear and cytoplasmic homogenates. Surprisingly however GAPDH in these compartments did not have the same behavior in assays of the dependence of initial velocity (v0) on G3P concentration. First, the peak v0 for nuclear GAPDH was up to 2.5-fold higher than the peak for cytoplasmic GAPDH. Second, while Michaelis Menten-like behavior was observed in all assays of cytoplasm, the v0 versus [G3P] plots for nuclear GAPDH typically exhibited a non-Michaelis Menten (sigmoidal) profile. Apparent Km and Vmax (G3P) values for nuclear GAPDH activity were highly variable, even between replicates of the same sample. Possible sources of this variability include in vitro processing of a metabolite that allosterically regulates GAPDH, turnover of a post-translational modification of the enzyme, and fluctuation of the state of interaction of GAPDH with other proteins. Collectively these findings are consistent with the hypothesis that the environment of the nucleus is distinct from the environment of the cytoplasm with regard to GAPDH activity and its modulation. This finding warrants further comparison of the regulation of nuclear and cytoplasmic GAPDH, as well as whole compartment activity profiling of other enzymes of metabolism with cytosolic and nuclear pools.
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Affiliation(s)
- Helen S. Tang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Chelsea R. Gates
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael C. Schultz
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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31
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Nasu T, Hori A, Hotta N, Kihara C, Kubo A, Katanosaka K, Suzuki M, Mizumura K. Vacuolar-ATPase-mediated muscle acidification caused muscular mechanical nociceptive hypersensitivity after chronic stress in rats, which involved extracellular matrix proteoglycan and ASIC3. Sci Rep 2023; 13:13585. [PMID: 37604935 PMCID: PMC10442418 DOI: 10.1038/s41598-023-39633-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/28/2023] [Indexed: 08/23/2023] Open
Abstract
Although widespread pain, such as fibromyalgia, is considered to have a central cause, peripheral input is important. We used a rat repeated cold stress (RCS) model with many characteristics common to fibromyalgia and studied the possible involvement of decreased muscle pH in muscle mechanical hyperalgesia. After a 5-day RCS, the muscle pH and the muscular mechanical withdrawal threshold (MMWT) decreased significantly. Subcutaneously injected specific inhibitor of vacuolar ATPase (V-ATPase), bafilomycin A1, reversed both changes almost completely. It also reversed the increased mechanical response of muscle thin-fibre afferents after RCS. These results show that V-ATPase activation caused muscle pH drop, which led to mechanical hypersensitivity after RCS. Since extracellular matrix proteoglycan and acid sensitive ion channels (TRPV1 and ASIC3) have been considered as possible mechanisms for sensitizing/activating nociceptors by protons, we investigated their involvement. Manipulating the extracellular matrix proteoglycan with chondroitin sulfate and chondroitinase ABC reversed the MMWT decrease after RCS, supporting the involvement of the extracellular mechanism. Inhibiting ASIC3, but not TRPV1, reversed the decreased MMWT after RCS, and ASIC3 mRNA and protein in the dorsal root ganglia were upregulated, indicating ASIC3 involvement. These findings suggest that extracellular mechanism and ASIC3 play essential roles in proton-induced mechanical hyperalgesia after RCS.
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Affiliation(s)
- Teruaki Nasu
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Matsumoto-Cho, Kasugai, 487-8501, Japan
| | - Amane Hori
- Graduate School of Life and Health Sciences, Chubu University, Matsumoto-Cho, Kasugai, 487-8501, Japan
- Japan Society for the Promotion of Science, Kojimachi, Chiyoda-Ku, Tokyo, 102-8472, Japan
| | - Norio Hotta
- Department of Lifelong Sports and Health Sciences, College of Life and Health Sciences, Chubu University, Matsumoto-Cho, Kasugai, 487-8501, Japan
| | - Chiaki Kihara
- Graduate School of Life and Health Sciences, Chubu University, Matsumoto-Cho, Kasugai, 487-8501, Japan
| | - Asako Kubo
- Department of Physiology, Nihon University School of Dentistry, 1-8-13 Kandasurugadai, Chiyoda-Ku, Tokyo, 101-8310, Japan
- Department of Acupuncture and Moxibustion, Faculty of Rehabilitation, Niigata University of Health and Welfare, Niigata, 950-3198, Japan
| | - Kimiaki Katanosaka
- Department of Biomedical Sciences, College of Life and Health Sciences, Chubu University, Matsumoto-Cho, Kasugai, 487-8501, Japan
| | - Masamitsu Suzuki
- Central Research Laboratories, ZERIA Pharmaceutical Co. Ltd., 2512-1 Numagami, Oshikiri, Kumagaya, Saitama, 360-0111, Japan
| | - Kazue Mizumura
- Department of Physiology, Nihon University School of Dentistry, 1-8-13 Kandasurugadai, Chiyoda-Ku, Tokyo, 101-8310, Japan.
- Department of Physical Therapy, College of Life and Health Sciences, Chubu University, Matsumoto-Cho, Kasugai, 487-8501, Japan.
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32
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Vriens E, De Ruysscher D, Weir ANM, Dekimpe S, Steurs G, Shemy A, Persoons L, Santos AR, Williams C, Daelemans D, Crump MP, Voet A, De Borggraeve W, Lescrinier E, Masschelein J. Polyketide Synthase-Mediated O-Methyloxime Formation in the Biosynthesis of the Oximidine Anticancer Agents. Angew Chem Int Ed Engl 2023; 62:e202304476. [PMID: 37218580 DOI: 10.1002/anie.202304476] [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: 03/28/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are modular megaenzymes that employ unusual catalytic domains to assemble diverse bioactive natural products. One such PKS is responsible for the biosynthesis of the oximidine anticancer agents, oxime-substituted benzolactone enamides that inhibit vacuolar H+ -ATPases. Here, we describe the identification of the oximidine gene cluster in Pseudomonas baetica and the characterization of four novel oximidine variants, including a structurally simpler intermediate that retains potent anticancer activity. Using a combination of in vivo, in vitro and computational approaches, we experimentally elucidate the oximidine biosynthetic pathway and reveal an unprecedented mechanism for O-methyloxime formation. We show that this process involves a specialized monooxygenase and methyltransferase domain and provide insight into their activity, mechanism and specificity. Our findings expand the catalytic capabilities of trans-AT PKSs and identify potential strategies for the production of novel oximidine analogues.
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Affiliation(s)
- Eveline Vriens
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Dries De Ruysscher
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Angus N M Weir
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Sofie Dekimpe
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Gert Steurs
- Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Ahmed Shemy
- Laboratory for Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Leentje Persoons
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | | | | | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Arnout Voet
- Laboratory for Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Wim De Borggraeve
- Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
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Wilkens S, Khan MM, Knight K, Oot R. Tender love and disassembly: How a TLDc domain protein breaks the V-ATPase. Bioessays 2023; 45:e2200251. [PMID: 37183929 PMCID: PMC10392918 DOI: 10.1002/bies.202200251] [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: 12/31/2022] [Revised: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Vacuolar ATPases (V-ATPases, V1 Vo -ATPases) are rotary motor proton pumps that acidify intracellular compartments, and, when localized to the plasma membrane, the extracellular space. V-ATPase is regulated by a unique process referred to as reversible disassembly, wherein V1 -ATPase disengages from Vo proton channel in response to diverse environmental signals. Whereas the disassembly step of this process is ATP dependent, the (re)assembly step is not, but requires the action of a heterotrimeric chaperone referred to as the RAVE complex. Recently, an alternative pathway of holoenzyme disassembly was discovered that involves binding of Oxidation Resistance 1 (Oxr1p), a poorly characterized protein implicated in oxidative stress response. Unlike conventional reversible disassembly, which depends on enzyme activity, Oxr1p induced dissociation can occur in absence of ATP. Yeast Oxr1p belongs to the family of TLDc domain containing proteins that are conserved from yeast to mammals, and have been implicated in V-ATPase function in a variety of tissues. This brief perspective summarizes what we know about the molecular mechanisms governing both reversible (ATP dependent) and Oxr1p driven (ATP independent) V-ATPase dissociation into autoinhibited V1 and Vo subcomplexes.
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Affiliation(s)
- Stephan Wilkens
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Md. Murad Khan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Kassidy Knight
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Rebecca Oot
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
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34
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Tuli F, Kane PM. The cytosolic N-terminal domain of V-ATPase a-subunits is a regulatory hub targeted by multiple signals. Front Mol Biosci 2023; 10:1168680. [PMID: 37398550 PMCID: PMC10313074 DOI: 10.3389/fmolb.2023.1168680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases) acidify several organelles in all eukaryotic cells and export protons across the plasma membrane in a subset of cell types. V-ATPases are multisubunit enzymes consisting of a peripheral subcomplex, V1, that is exposed to the cytosol and an integral membrane subcomplex, Vo, that contains the proton pore. The Vo a-subunit is the largest membrane subunit and consists of two domains. The N-terminal domain of the a-subunit (aNT) interacts with several V1 and Vo subunits and serves to bridge the V1 and Vo subcomplexes, while the C-terminal domain contains eight transmembrane helices, two of which are directly involved in proton transport. Although there can be multiple isoforms of several V-ATPase subunits, the a-subunit is encoded by the largest number of isoforms in most organisms. For example, the human genome encodes four a-subunit isoforms that exhibit a tissue- and organelle-specific distribution. In the yeast S. cerevisiae, the two a-subunit isoforms, Golgi-enriched Stv1 and vacuolar Vph1, are the only V-ATPase subunit isoforms. Current structural information indicates that a-subunit isoforms adopt a similar backbone structure but sequence variations allow for specific interactions during trafficking and in response to cellular signals. V-ATPases are subject to several types of environmental regulation that serve to tune their activity to their cellular location and environmental demands. The position of the aNT domain in the complex makes it an ideal target for modulating V1-Vo interactions and regulating enzyme activity. The yeast a-subunit isoforms have served as a paradigm for dissecting interactions of regulatory inputs with subunit isoforms. Importantly, structures of yeast V-ATPases containing each a-subunit isoform are available. Chimeric a-subunits combining elements of Stv1NT and Vph1NT have provided insights into how regulatory inputs can be integrated to allow V-ATPases to support cell growth under different stress conditions. Although the function and distribution of the four mammalian a-subunit isoforms present additional complexity, it is clear that the aNT domains of these isoforms are also subject to multiple regulatory interactions. Regulatory mechanisms that target mammalian a-subunit isoforms, and specifically the aNT domains, will be described. Altered V-ATPase function is associated with multiple diseases in humans. The possibility of regulating V-ATPase subpopulations via their isoform-specific regulatory interactions are discussed.
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Affiliation(s)
| | - Patricia M. Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
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35
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Kara N, Ayoub N, Ilgu H, Fotiadis D, Ilgu M. Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications. Molecules 2023; 28:molecules28093728. [PMID: 37175137 PMCID: PMC10180177 DOI: 10.3390/molecules28093728] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Many biological processes (physiological or pathological) are relevant to membrane proteins (MPs), which account for almost 30% of the total of human proteins. As such, MPs can serve as predictive molecular biomarkers for disease diagnosis and prognosis. Indeed, cell surface MPs are an important class of attractive targets of the currently prescribed therapeutic drugs and diagnostic molecules used in disease detection. The oligonucleotides known as aptamers can be selected against a particular target with high affinity and selectivity by iterative rounds of in vitro library evolution, known as Systematic Evolution of Ligands by EXponential Enrichment (SELEX). As an alternative to antibodies, aptamers offer unique features like thermal stability, low-cost, reuse, ease of chemical modification, and compatibility with various detection techniques. Particularly, immobilized-aptamer sensing platforms have been under investigation for diagnostics and have demonstrated significant value compared to other analytical techniques. These "aptasensors" can be classified into several types based on their working principle, which are commonly electrochemical, optical, or mass-sensitive. In this review, we review the studies on aptamer-based MP-sensing technologies for diagnostic applications and have included new methodological variations undertaken in recent years.
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Affiliation(s)
- Nilufer Kara
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Nooraldeen Ayoub
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Huseyin Ilgu
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Muslum Ilgu
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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36
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Mitra C, Kane PM. Human V-ATPase a-subunit isoforms bind specifically to distinct phosphoinositide phospholipids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538068. [PMID: 37162989 PMCID: PMC10168244 DOI: 10.1101/2023.04.24.538068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
V-ATPases are highly conserved multi-subunit enzymes that maintain the distinct pH of eukaryotic organelles. The integral membrane a-subunit is encoded by tissue and organelle specific isoforms, and its cytosolic N-terminal domain (aNT) modulates organelle specific regulation and targeting of V-ATPases. Organelle membranes have specific phosphatidylinositol phosphate (PIP) lipid enrichment linked to maintenance of organelle pH. In yeast, the aNT domains of the two a-subunit isoforms bind PIP lipids enriched in the organelle membranes where they reside; these interactions affect activity and regulatory properties of the V-ATPases containing each isoform. Humans have four a-subunit isoforms. We hypothesize that the aNT domains of the human isoforms will also bind to specific PIP lipids. The a1 and a2 isoforms of human V-ATPase a-subunits are localized to endolysosomes and Golgi, respectively. Bacterially expressed Hua1NT and Hua2NT bind specifically to endolysosomal PIP lipids PI(3)P and PI(3,5)P2 and Golgi enriched PI(4)P, respectively. Despite the lack of canonical PIP binding sites, potential binding sites in the HuaNT domains were identified by sequence comparisons and existing subunit structures and models. Mutations at a similar location in the distal loops of both HuaNT isoforms compromise binding to their cognate PIP lipids, suggesting that these loops encode PIP specificity of the a-subunit isoforms. These data also suggest a mechanism through which PIP lipid binding could stabilize and activate V-ATPases in distinct organelles.
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Affiliation(s)
- Connie Mitra
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
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37
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Pelster B. The rete mirabile: a possible control site for swimbladder function. J Comp Physiol B 2023; 193:307-313. [PMID: 37060451 DOI: 10.1007/s00360-023-01486-5] [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: 03/01/2023] [Revised: 03/25/2023] [Accepted: 03/31/2023] [Indexed: 04/16/2023]
Abstract
In a recent study, a large number of transport proteins was detected in the transcriptome and proteome of saline perfused rete mirabile tissue of the European eel. In this study, the data set was reanalyzed for the presence of receptor proteins and proteins involved in intracellular signaling pathways. A large number of expressed receptor proteins and proteins involved in intracellular signal transduction was detected. Several G-protein-coupled receptor signal pathways were significantly enriched in their expression level, in particular receptors and signaling pathways involved in the control of blood flow. The enriched signaling pathways also include pathways involved in trafficking of crucial transport proteins like, monocarboxylate transporters, V-ATPase, and aquaporin. The data, therefore, suggest that the rete mirabile has the capacity to control swimbladder function by regulating blood flow and by modifying countercurrent multiplication.
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Affiliation(s)
- Bernd Pelster
- Institute for Zoology, Leopold-Franzens-Universität Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria.
- Center for Molecular Biosciences, Universität Innsbruck, Innsbruck, Austria.
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38
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Zheng S, Hu H, Hou M, Zhu K, Wu Z, Qi L, Xia H, Liu G, Ren Y, Xu Y, Yan C, Zhao B. Proton pump inhibitor-enhanced nanocatalytic ferroptosis induction for stimuli-responsive dual-modal molecular imaging guided cancer radiosensitization. Acta Biomater 2023; 162:72-84. [PMID: 36931419 DOI: 10.1016/j.actbio.2023.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/19/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
Although radiotherapeutic efficiency has been revealed to be positively correlated with ferroptosis, the neutral/alkaline cytoplasm pH value of tumor cells remains an intrinsic challenge for efficient Fenton/Fenton-like reaction-based ferroptosis induction. Herein, PEGylated hollow mesoporous organosilica nanotheranostics (HMON)-GOx@MnO2 nanoparticles (HGMP NPs) were designed as a ferroptosis inducer, which could specifically release Mn2+ in tumor cells to activate the Fenton-like reaction for ferroptosis induction. Proton pump inhibitors (PPIs) were synchronously administered for cytoplasm pH level regulation by inhibiting V-H+-ATPases activity, enhancing Fenton-like reaction-based ferroptosis induction. Moreover, reactive oxygen species production was facilitated via the glucose oxidase triggered cascade catalytic reaction by utilizing intracellular β-D-glucose for H2O2 self-supply and generation of additional cytoplasm H+. The PPI enhanced ferroptosis inducing nanosystem effectively inhibited tumor growth both in vitro and in vivo for tumor-specific ferroptosis induction and radiotherapy sensitization, suggesting that PPI administration could be an efficient adjuvant to reinforce Fenton/Fenton-like reaction-based ferroptosis induction for radiosensitization. STATEMENT OF SIGNIFICANCE: The cytoplasm pH value of tumor cells is typically neutral to alkaline, which is higher than that of the Fenton/Fenton-like reaction desired acidic environments, hindering its efficiency. In this study, PEGylated hollow mesoporous organosilica nanotheranostics (HMON)-GOx@MnO2 nanoparticles were synthesized as a ferroptosis inducer, which could specifically release Mn2+ via depleting glutathione and then activate the Fenton-like reaction in the tumor microenvironment. The glucose oxidase was applied for H2O2 self-supply and addition of cytoplasm H+ to further boost the Fenton-like reaction. We found that proton pump inhibitors (PPIs) increased intracellular acidification by inhibiting the activity of V-H+-ATPases to enhance the Fenton reaction-based ferroptosis induction, suggesting PPIs administration could be a feasible strategy to reinforce ferroptosis induction for radiosensitization.
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Affiliation(s)
- Shuting Zheng
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China; Guangzhou Key Laboratory of Tumor Immunology Research, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Honglei Hu
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China; Guangzhou Key Laboratory of Tumor Immunology Research, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Meirong Hou
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China; Guangzhou Key Laboratory of Tumor Immunology Research, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Kai Zhu
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China; Guangzhou Key Laboratory of Tumor Immunology Research, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Zede Wu
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China; Guangzhou Key Laboratory of Tumor Immunology Research, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Li Qi
- Guangdong Provincial Key Laboratory of Medical Image Processing, School of Biomedical Engineering, Southern Medical University, Guangzhou, 510515, PR China
| | - Hui Xia
- Institute of Electrical Engineering Chinese Academy of Sciences, Beijing 100190, PR China
| | - Guoqiang Liu
- Institute of Electrical Engineering Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yunyan Ren
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China
| | - Yikai Xu
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China.
| | - Chenggong Yan
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, PR China.
| | - Bingxia Zhao
- Guangzhou Key Laboratory of Tumor Immunology Research, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China; Experiment Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, PR China.
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Structural and Functional Diversity of Two ATP-Driven Plant Proton Pumps. Int J Mol Sci 2023; 24:ijms24054512. [PMID: 36901943 PMCID: PMC10003446 DOI: 10.3390/ijms24054512] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Two ATP-dependent proton pumps function in plant cells. Plasma membrane H+-ATPase (PM H+-ATPase) transfers protons from the cytoplasm to the apoplast, while vacuolar H+-ATPase (V-ATPase), located in tonoplasts and other endomembranes, is responsible for proton pumping into the organelle lumen. Both enzymes belong to two different families of proteins and, therefore, differ significantly in their structure and mechanism of action. The plasma membrane H+-ATPase is a member of the P-ATPases that undergo conformational changes, associated with two distinct E1 and E2 states, and autophosphorylation during the catalytic cycle. The vacuolar H+-ATPase represents rotary enzymes functioning as a molecular motor. The plant V-ATPase consists of thirteen different subunits organized into two subcomplexes, the peripheral V1 and the membrane-embedded V0, in which the stator and rotor parts have been distinguished. In contrast, the plant plasma membrane proton pump is a functional single polypeptide chain. However, when the enzyme is active, it transforms into a large twelve-protein complex of six H+-ATPase molecules and six 14-3-3 proteins. Despite these differences, both proton pumps can be regulated by the same mechanisms (such as reversible phosphorylation) and, in some processes, such as cytosolic pH regulation, may act in a coordinated way.
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Knobbe TJ, Kremer D, Douwes RM, Eisenga MF, Gomes-Neto AW, Annema C, Swarte JC, Klont F, Navis G, Berger SP, Bakker SJL, Bodewes FAJA, de Boer MT, Damman K, de Borst MH, Diepstra A, Dijkstra G, Doorenbos CSE, Erasmus ME, Gan CT, Hak E, Hepkema BG, Leuvenink HGD, Lexmond WS, de Meijer VE, Niesters HGM, Pelt LJV, Pol RA, Porte RJ, Ranchor AV, Sanders JSF, Siebelink MJ, Slart RJHJA, Touw DJ, van den Heuvel MC, van Leer-Buter C, van Londen M, Verschuuren EAM, Vos MJ, Weersma RK. Proton Pump Inhibitor Use, Fatigue, and Health-Related Quality of Life in Kidney Transplant Recipients: Results From the TransplantLines Biobank and Cohort Study. Am J Kidney Dis 2023:S0272-6386(23)00532-2. [PMID: 36801431 DOI: 10.1053/j.ajkd.2022.12.012] [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: 07/01/2022] [Accepted: 12/21/2022] [Indexed: 02/19/2023]
Abstract
RATIONALE & OBJECTIVE Prior studies report that the use of proton pump inhibitors (PPIs) can adversely affect gut microbiota and gastrointestinal uptake of micronutrients, in particular iron and magnesium, and are used frequently by kidney transplant recipients. Altered gut microbiota, iron deficiency, and magnesium deficiency have been implicated in the pathogenesis of chronic fatigue. Therefore, we hypothesized that PPI use may be an important and underappreciated cause of fatigue and reduced health-related quality of life (HRQoL) in this population. STUDY DESIGN Cross-sectional study. SETTING & PARTICIPANTS Kidney transplant recipients (≥1 year after transplantation) enrolled in the TransplantLines Biobank and Cohort Study. EXPOSURE PPI use, PPI type, PPI dosage, and duration of PPI use. OUTCOME Fatigue and HRQoL, assessed using the validated Checklist Individual Strength 20 Revised questionnaire and Short Form-36 questionnaire. ANALYTICAL APPROACH Logistic and linear regression. RESULTS We included 937 kidney transplant recipients (mean age 56±13 years, 39% female) at a median of 3 (1-10) years after transplantation. PPI use was associated with fatigue severity (regression coefficient 4.02, 95% CI, 2.18 to 5.85, P<0.001), a higher risk of severe fatigue (OR 2.05, 95% CI, 1.48 to 2.84, P<0.001), lower physical HRQoL (regression coefficient-8.54, 95% CI, -11.54 to-5.54, P<0.001), and lower mental HRQoL (regression coefficient-4.66, 95% CI, -7.15 to-2.17, P<0.001). These associations were independent of potential confounders including age, time since transplantation, history of upper gastrointestinal disease, antiplatelet therapy, and the total number of medications. They were present among all individually assessed PPI types and were dose dependent. Duration of PPI exposure was only associated with fatigue severity. LIMITATIONS Residual confounding and inability to assess causal relationships. CONCLUSIONS PPI use is independently associated with fatigue and lower HRQoL among kidney transplant recipients. PPI use might be an easily accessible target for alleviating fatigue and improving HRQoL among kidney transplant recipients. Further studies examining the effect of PPI exposure in this population are warranted.
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Affiliation(s)
- Tim J Knobbe
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen.
| | - Daan Kremer
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
| | - Rianne M Douwes
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
| | - Michele F Eisenga
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
| | - António W Gomes-Neto
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
| | - Coby Annema
- Department of Health Sciences, Section of Nursing Research, University Medical Center Groningen
| | - J Casper Swarte
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
| | - Frank Klont
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen; Unit of PharmacoTherapy, -Epidemiology and -Economics, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, the Netherlands
| | - Gerjan Navis
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
| | - Stefan P Berger
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen
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41
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Li H, Wang X, Yang Q, Cheng L, Zeng HL. Identification of iron metabolism-related genes as diagnostic signatures in sepsis by blood transcriptomic analysis. Open Life Sci 2023; 18:20220549. [PMID: 36820206 PMCID: PMC9938542 DOI: 10.1515/biol-2022-0549] [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: 09/30/2022] [Revised: 11/17/2022] [Accepted: 12/14/2022] [Indexed: 02/11/2023] Open
Abstract
Iron metabolism is considered to play the principal role in sepsis, but the key iron metabolism-related genetic signatures are unclear. In this study, we analyzed and identified the genetic signatures related to the iron-metabolism in sepsis by using a bioinformatics analysis of four transcriptomic datasets from the GEO database. A total of 21 differentially expressed iron metabolism-related signatures were identified including 9 transporters, 8 enzymes, and 4 regulatory factors. Among them, lipocalin 2 was found to have the highest diagnostic value as its expression showed significant differences in all the comparisons including sepsis vs healthy controls, sepsis vs non-sepsis diseases, and mild forms vs severe forms of sepsis. Besides, the cytochrome P450 gene CYP1B1 also showed diagnostic values for sepsis from the non-sepsis diseases. The CYP4V2, LTF, and GCLM showed diagnostic values for distinguishing the severe forms from mild forms of sepsis. Our analysis identified 21 sepsis-associated iron metabolism-related genetic signatures, which may represent diagnostic and therapeutic biomarkers of sepsis, and will improve our understanding of the molecular mechanism underlying the occurrence of sepsis.
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Affiliation(s)
- Huijun Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xu Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Yang
- Institute of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao-Long Zeng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Chen F, Zhu S, Kang R, Tang D, Liu J. ATP6V0D1 promotes alkaliptosis by blocking STAT3-mediated lysosomal pH homeostasis. Cell Rep 2023; 42:111911. [PMID: 36640329 DOI: 10.1016/j.celrep.2022.111911] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
Alkaliptosis, a type of regulated cell death driven by intracellular alkalization, was first described in pancreatic ductal adenocarcinoma (PDAC) cells after treatment with the opioid analgesic drug JTC801. Here, we used mass-spectrometry-based drug target identification, cellular thermal shift assay, and point mutation technologies to reveal ATP6V0D1 as a direct JTC801 target that drives alkaliptosis in human PDAC cells. Functionally, the protein stability of ATP6V0D1, when mediated by JTC801, increases the interaction between ATP6V0D1 and STAT3, resulting in increased expression and activity of STAT3 for sustaining lysosome homeostasis. Consequently, the pharmacological or genetic inhibition of STAT3 restores the sensitivity of ATP6V0D1-deficient cells to alkaliptosis in vitro or in suitable mouse models. Clinically, a high expression of ATP6V0D1 correlates with prolonged survival of patients with PDAC. Together, these results illustrate a link between ATP6V0D1 and PDAC and advance our understanding of alkaliptosis in targeted therapy.
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Affiliation(s)
- Fangquan Chen
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, China; Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Shan Zhu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Jiao Liu
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, China; Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, Guangdong 511436, China.
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43
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Litvinov I, Salova A, Aksenov N, Kornilova E, Belyaeva T. Microenvironmental Impact on InP/ZnS-Based Quantum Dots in In Vitro Models and in Living Cells: Spectrally- and Time-Resolved Luminescence Analysis. Int J Mol Sci 2023; 24:ijms24032699. [PMID: 36769021 PMCID: PMC9916881 DOI: 10.3390/ijms24032699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/15/2023] [Accepted: 01/21/2023] [Indexed: 02/04/2023] Open
Abstract
Quantum dots (QDs) have attracted great attention as tools for theranostics that combine the possibility of simultaneous biological target visualization and medicine delivery. Here, we address whether core/shell InP/ZnS QDs (InP-QDs) may be an alternative to toxic Cd-based QDs. We analyze InP-QD photophysical characteristics in cell culture medium, salt solutions, and directly in the cells. It was demonstrated that InP-QDs were internalized into endolysosomes in HeLa and A549 cells with dynamics similar to Cd-based QDs of the same design, but the two cell lines accumulated them with different efficiencies. InP-QDs were reliably detected in the endosomes despite their low quantum yields. Cell culture medium efficiently decreased the InP-QD photoluminescence lifetime by 50%, acidic pH (4.0) had a moderate effect (20-25% reduction), and quenching by salt solutions typical of intra-endosomal medium composition resulted in a decrease of about 10-15%. The single-vesicle fluorescence-lifetime imaging microscopy analysis of QDs inside and outside the cells shows that the scatter between endosomes in the same cell can be significant, which indicates the complex impact of the abovementioned factors on the state of InP-QDs. The PI test and MTT test demonstrate that InP-QDs are toxic for both cell lines at concentrations higher than 20 nM. Possible reasons for InP-QD toxicity are discussed.
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Affiliation(s)
- Ilia Litvinov
- Institute of Cytology, Russian Academy of Sciences,194064 Saint Petersburg, Russia
| | - Anna Salova
- Institute of Cytology, Russian Academy of Sciences,194064 Saint Petersburg, Russia
| | - Nikolay Aksenov
- Institute of Cytology, Russian Academy of Sciences,194064 Saint Petersburg, Russia
| | - Elena Kornilova
- Institute of Cytology, Russian Academy of Sciences,194064 Saint Petersburg, Russia
- Higher School of Biomedical Systems and Technologies, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
- Correspondence: ; Tel.: +7-921-302-59-05
| | - Tatiana Belyaeva
- Institute of Cytology, Russian Academy of Sciences,194064 Saint Petersburg, Russia
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44
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Ngo C, Ekanayake A, Zhang C. Identification of Covalent Ligands – from Single Targets to Whole Proteome. Isr J Chem 2023. [DOI: 10.1002/ijch.202200105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Chau Ngo
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
| | - Arunika Ekanayake
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
- Current address: Department of Chemistry University of Alberta T6G 2G2 Edmonton AB Canada
| | - Chao Zhang
- Department of Chemistry Loker Hydrocarbon Research Institute University of Southern California 90089 Los Angeles California USA
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Durgan J, Florey O. Many roads lead to CASM: Diverse stimuli of noncanonical autophagy share a unifying molecular mechanism. SCIENCE ADVANCES 2022; 8:eabo1274. [PMID: 36288315 PMCID: PMC9604613 DOI: 10.1126/sciadv.abo1274] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Autophagy is a fundamental catabolic process coordinated by a network of autophagy-related (ATG) proteins. These ATG proteins also perform an important parallel role in "noncanonical" autophagy, a lysosome-associated signaling pathway with key functions in immunity, inflammation, cancer, and neurodegeneration. While the noncanonical autophagy pathway shares the common ATG machinery, it bears key mechanistic and functional distinctions, and is characterized by conjugation of ATG8 to single membranes (CASM). Here, we review the diverse, and still expanding, collection of stimuli and processes now known to harness the noncanonical autophagy pathway, including engulfment processes, drug treatments, TRPML1 and STING signaling, viral infection, and other pathogenic factors. We discuss the multiple associated routes to CASM and assess their shared and distinctive molecular features. By integrating these findings, we propose an updated and unifying mechanism for noncanonical autophagy, centered on ATG16L1 and V-ATPase.
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46
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Lin BC, Higgins NR, Phung TH, Monteiro MJ. UBQLN proteins in health and disease with a focus on UBQLN2 in ALS/FTD. FEBS J 2022; 289:6132-6153. [PMID: 34273246 PMCID: PMC8761781 DOI: 10.1111/febs.16129] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023]
Abstract
Ubiquilin (UBQLN) proteins are a dynamic and versatile family of proteins found in all eukaryotes that function in the regulation of proteostasis. Besides their canonical function as shuttle factors in delivering misfolded proteins to the proteasome and autophagy systems for degradation, there is emerging evidence that UBQLN proteins play broader roles in proteostasis. New information suggests the proteins function as chaperones in protein folding, protecting proteins prior to membrane insertion, and as guardians for mitochondrial protein import. In this review, we describe the evidence for these different roles, highlighting how different domains of the proteins impart these functions. We also describe how changes in the structure and phase separation properties of UBQLNs may regulate their activity and function. Finally, we discuss the pathogenic mechanisms by which mutations in UBQLN2 cause amyotrophic lateral sclerosis and frontotemporal dementia. We describe the animal model systems made for different UBQLN2 mutations and how lessons learnt from these systems provide fundamental insight into the molecular mechanisms by which UBQLN2 mutations drive disease pathogenesis through disturbances in proteostasis.
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Affiliation(s)
- Brian C. Lin
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicole R. Higgins
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Trong H. Phung
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mervyn J. Monteiro
- Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA,Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA,Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
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47
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Tian Y, Gao M, Huang L, Zhou H, Wang J. ATP6AP1 is a potential prognostic biomarker and is associated with iron metabolism in breast cancer. Front Genet 2022; 13:958290. [PMID: 36147483 PMCID: PMC9486317 DOI: 10.3389/fgene.2022.958290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer occurrence and progression may be facilitated by aberrant expression of ATPase H+ transporting accessory protein 1 (ATP6AP1). However, the clinical relevance of ATP6AP1 in breast cancer remains unclear. In this study, we investigated the association between ATP6AP1 and breast cancer. Data collected from patients with breast cancer from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were used in this study. To determine the relationship between ATP6AP1 and breast cancer survival rates, Kaplan-Meier analysis was used. To determine the prognostic value of ATP6AP1, a receiver operating characteristic (ROC) curve was constructed. To identify the major pathways involving ATP6AP1, we performed functional enrichment analysis using gene set enrichment analysis (GSEA). We analyzed the association between ATP6AP1 expression and tumor immunity using the ESTIMATE algorithm and single-sample GSEA (ssGSEA). A nomogram based on a Cox regression analysis was constructed to predict the impact of ATP6AP1 on prognosis. ATP6AP1 expression was significantly upregulated in breast cancer tissues. Moreover, patients with elevated ATP6AP1 expression had shorter total survival rates than those with lower expression levels (p = 0.032). The area under the receiver operating characteristic curve for ATP6AP1 was 0.939. Gene set enrichment analysis revealed that reaction iron uptake and transport, proteasome degradation, glutathione metabolism, and pyruvate metabolism were enriched in the ATP6AP1 high expression phenotype. The relationship between immune infiltration cells and ATP6AP1 expression, including macrophages, B cells, dendritic cells, cytotoxic cells, NK cells, and T cells, was found to be negative, suggesting that ATP6AP1 overexpression results in immunosuppression. Based on the Cox regression analyses, the calibration plot of the nomogram demonstrated effective performance in predicting breast cancer patients. ATP6AP1 may facilitate breast cancer progression by inhibiting antitumor immunity and promoting iron metabolism and may be a biomarker for breast cancer prognosis.
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Affiliation(s)
- Ye Tian
- Department of Thyroid and Breast Surgery, Wuhan No, 1 Hospital, Wuhan, China
| | - Ming Gao
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Huang
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hu Zhou
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Wang
- Department of Blood Transfusion, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Juan Wang,
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A Novel Oxidative Phosphorylation-Associated Gene Signature for Prognosis Prediction in Patients with Hepatocellular Carcinoma. DISEASE MARKERS 2022; 2022:3594901. [PMID: 36105252 PMCID: PMC9467772 DOI: 10.1155/2022/3594901] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/25/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022]
Abstract
Hepatocellular carcinoma (HCC) is a common type of malignant tumor with high morbidity and mortality. The oxidative phosphorylation (OXPHOS) metabolic pathway produces adenosine triphosphate (ATP) by delivering electrons to transmembrane protein complexes in the mitochondria. This research was dedicated to identifying an OXPHOS-associated signature for the assessment of prognosis of HCC patients. A total of 371 HCC patients from the Cancer Genome Atlas (TCGA) and 231 HCC patients from the International Cancer Genome Consortium (ICGC) with RNA expression data and clinical data were employed as construction and validation cohorts, respectively. The least absolute shrinkage and selection operator (LASSO) Cox regression was applied to establish a multigene signature in the TCGA cohort, and the ICGC cohort was used for validation. The prognostic value of the risk signature was evaluated using univariate and multivariate Cox regression, Kaplan–Meier curves, and receiver operating characteristic (ROC) curves. The potential enrichment of biological functions was investigated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Meanwhile, we analyzed the correlation between the risk score and the tumor microenvironment (TME). A five-gene signature including ATP6V0B, ATP6V1C1, ATP6V1E1, TIMM9, and UQCRH was identified by LASSO Cox regression to classify patients into low- and high-risk groups. ROC curve analysis indicated that the five-gene signature is a prospective prognostic factor in HCC patients. Univariate and multivariate Cox regression analyses demonstrated that the risk score was an independent prognostic factor for overall survival (OS). Functional analysis showed that differentially expressed genes (DEGs) between the low- and high-risk groups were enriched in mitosis and the cell cycle pathway. In addition, the five-gene signature was associated with innate immune cell infiltration, immune subtypes, and tumor stemness. A novel OXPHOS-associated gene signature can be used for prognostic prediction for patients with HCC.
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Yuan L, Li P, Jing H, Zheng Q, Xiao H. trim-21 promotes proteasomal degradation of CED-1 for apoptotic cell clearance in C. elegans. eLife 2022; 11:76436. [PMID: 35929733 PMCID: PMC9388098 DOI: 10.7554/elife.76436] [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: 12/16/2021] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
The phagocytic receptor CED-1 mediates apoptotic cell recognition by phagocytic cells, enabling cell corpse clearance in Caenorhabditis elegans. Whether appropriate levels of CED-1 are maintained for executing the engulfment function remains unknown. Here, we identified the C. elegans E3 ubiquitin ligase tripartite motif containing-21 (TRIM-21) as a component of the CED-1 pathway for apoptotic cell clearance. When the NPXY motif of CED-1 was bound to the adaptor protein CED-6 or the YXXL motif of CED-1 was phosphorylated by tyrosine kinase SRC-1 and subsequently bound to the adaptor protein NCK-1 containing the SH2 domain, TRIM-21 functioned in conjunction with UBC-21 to catalyze K48-linked poly-ubiquitination on CED-1, targeting it for proteasomal degradation. In the absence of TRIM-21, CED-1 accumulated post-translationally and drove cell corpse degradation defects, as evidenced by direct binding to VHA-10. These findings reveal a unique mechanism for the maintenance of appropriate levels of CED-1 to regulate apoptotic cell clearance.
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Affiliation(s)
- Lei Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'An, China
| | - Peiyao Li
- College of Life Sciences, Shaanxi Normal University, Xi'An, China
| | - Huiru Jing
- College of Life Sciences, Shaanxi Normal University, Xi'An, China
| | - Qian Zheng
- College of Life Sciences, Shaanxi Normal University, Xi'An, China
| | - Hui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi'An, China
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50
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Edelman WC, Kiianitsa K, Virmani T, Martinez RA, Young JE, Keene CD, Bird TD, Raskind WH, Korvatska O. Reduced gene dosage is a common mechanism of neuropathologies caused by ATP6AP2 splicing mutations. Parkinsonism Relat Disord 2022; 101:31-38. [PMID: 35779466 PMCID: PMC10012809 DOI: 10.1016/j.parkreldis.2022.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/26/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Mutations that alter splicing of X-linked ATP6AP2 cause a spectrum of neurodevelopmental and neurodegenerative pathologies including parkinsonism in affected males. All previously reported splicing mutations increase the level of a minor isoform with skipped exon 4 (Δe4) that encodes a functionally deficient protein. OBJECTIVES We investigated the pathogenic mechanism of a novel c.168+6T>A variant reported in a family with X-linked intellectual disability, epilepsy, and parkinsonism. We also analyzed ATP6AP2 splicing defects in brains of carriers of a c.345C>T variant associated with X-linked spasticity and parkinsonism. METHODS We generated induced pluripotent stem cells from patients with c.168+6T>A, reprogrammed them to neural progenitor cells and analyzed them by RNA-Seq and qRT-PCR. We also quantified ATP6AP2 isoforms in the brains of c.345C>T carriers by Nanostring nCounter. RESULTS The c.168+6T>A increased skipping of ATP6AP2 exon 2 and usage of cryptic intronic donor splice sites. This results in out-of-frame splicing products and a reciprocal 50% reduction in functional full-length ATP6AP2 transcripts. Neural progenitors of patients with c.168+6T>A exhibited downregulated neural development gene networks. Analysis of blood transcriptomes of c.168+6T>A carriers identified potential biomarkers of ATP6AP2 deficiency in non-neural tissues. The c.345C>T variant increased exon 4 skipping with concomitant decrease of full length ATP6AP2 in brains of carriers. CONCLUSION A common pathogenic consequence of splicing mutations affecting inclusion of different ATP6AP2 exons is reduction of the functional full-length transcript. The exacerbated ATP6AP2 splicing defect in brains of c.345C>T carriers is consistent with their CNS-restricted clinical presentations.
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Affiliation(s)
- William C Edelman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Tuhin Virmani
- Department of Neurology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Refugio A Martinez
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jessica E Young
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle, WA, USA; Geriatric Research, Education and Clinical Center (GRECC), VA Puget Sound Medical Center, Seattle, WA, USA
| | - Wendy H Raskind
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, USA; Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Medical Center, Seattle, WA, USA
| | - Olena Korvatska
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, USA; Mental Illness Research, Education and Clinical Center (MIRECC), VA Puget Sound Medical Center, Seattle, WA, USA.
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