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Coulson-Gilmer C, Littler S, Barnes B, Brady R, Anagho H, Pillay N, Dey M, Macmorland W, Bronder D, Nelson L, Tighe A, Lin WH, Morgan R, Unwin R, Nielsen M, McGrail J, Taylor S. Intrinsic PARG inhibitor sensitivity is mimicked by TIMELESS haploinsufficiency and rescued by nucleoside supplementation. NAR Cancer 2024; 6:zcae030. [PMID: 39015544 PMCID: PMC11249981 DOI: 10.1093/narcan/zcae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024] Open
Abstract
A subset of cancer cells are intrinsically sensitive to inhibitors targeting PARG, the poly(ADP-ribose) glycohydrolase that degrades PAR chains. Sensitivity is accompanied by persistent DNA replication stress, and can be induced by inhibition of TIMELESS, a replisome accelerator. However, the nature of the vulnerability responsible for intrinsic sensitivity remains undetermined. To understand PARG activity dependency, we analysed Timeless model systems and intrinsically sensitive ovarian cancer cells. We show that nucleoside supplementation rescues all phenotypes associated with PARG inhibitor sensitivity, including replisome speed and fork stalling, S-phase completion and mitotic entry, proliferation dynamics and clonogenic potential. Importantly nucleoside supplementation restores PARG inhibitor resistance despite the continued presence of PAR chains, indicating that sensitivity does not correlate with PAR levels. In addition, we show that inhibition of thymidylate synthase, an enzyme required for dNTP homeostasis, induces PARG-dependency. Together, these observations suggest that PARG inhibitor sensitivity reflects an inability to control replisome speed and/or maintain helicase-polymerase coupling in response to nucleotide imbalances.
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Affiliation(s)
- Camilla Coulson-Gilmer
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Samantha Littler
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Bethany M Barnes
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Rosie M Brady
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Holda A Anagho
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nisha Pillay
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Malini Dey
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - William Macmorland
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Daniel Bronder
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Louisa Nelson
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Anthony Tighe
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Wei-Hsiang Lin
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Robert D Morgan
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester M20 4BX, UK
| | - Richard D Unwin
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Michael L Nielsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joanne C McGrail
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
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Soloveva NA, Novikova SE, Farafonova TE, Tikhonova OV, Zgoda VG, Archakov AI. Proteome of plasma extracellular vesicles as a source of colorectal cancer biomarkers. BIOMEDITSINSKAIA KHIMIIA 2024; 70:356-363. [PMID: 39324200 DOI: 10.18097/pbmc20247005356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
The search for minimally invasive methods for diagnostics of colorectal cancer (CRC) is the most important task for early diagnostics of the disease and subsequent successful treatment. Human plasma represents the main type of biological material used in the clinical practice; however, the complex dynamic range of substances circulating in it complicates determination of CRC protein markers by the mass spectrometric (MS) method. Studying the proteome of extracellular vesicles (EVs) isolated from human plasma represents an attractive approach for the discovery of tissue-secreted CRC markers. We performed shotgun mass spectrometry analysis of EV samples obtained from plasma of CRC patients and healthy volunteers. This MS analysis resulted in identification of 370 proteins (which were registered by at least two peptides). Stable isotope-free relative quantitation identified 55 proteins with altered abundance in EV samples obtained from plasma samples of CRC patients as compared to healthy controls. Among the EV proteins isolated from blood plasma we found components involved in cell adhesion and the VEGFA-VEGFR2 signaling pathway (TLN1, HSPA8, VCL, MYH9, and others), as well as proteins expressed predominantly by gastrointestinal tissues (polymeric immunoglobulin receptor, PIGR). The data obtained using the shotgun proteomic profiling may be added to the panel for targeted MS analysis of EV-associated protein markers, previously developed using CRC cell models.
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Affiliation(s)
- N A Soloveva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S E Novikova
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Middendorf PS, Wijnands LM, Boeren S, Zomer AL, Jacobs-Reitsma WF, den Besten HM, Abee T. Activation of the l-fucose utilization cluster in Campylobacter jejuni induces proteomic changes and enhances Caco-2 cell invasion and fibronectin binding. Heliyon 2024; 10:e34996. [PMID: 39220920 PMCID: PMC11365321 DOI: 10.1016/j.heliyon.2024.e34996] [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: 01/09/2024] [Revised: 07/16/2024] [Accepted: 07/21/2024] [Indexed: 09/04/2024] Open
Abstract
Most Campylobacter jejuni isolates carry the fucose utilization cluster (Cj0480c-Cj0489) that supports the metabolism of l-fucose and d-arabinose. In this study we quantified l-fucose and d-arabinose metabolism and metabolite production, and the impact on Caco-2 cell interaction and binding to fibronectin, using C. jejuni NCTC11168 and the closely related human isolate C. jejuni strain 286. When cultured with l-fucose and d-arabinose, both isolates showed increased survival and production of acetate, pyruvate and succinate, and the respective signature metabolites lactate and glycolic acid, in line with an overall upregulation of l-fucose cluster proteins. In vitro Caco-2 cell studies and fibronectin-binding experiments showed a trend towards higher invasion and a significantly higher fibronectin binding efficacy of C. jejuni NCTC11168 cells grown with l-fucose and d-arabinose, while no significant differences were found with C. jejuni 286. Both fibronectin binding proteins, CadF and FlpA, were detected in the two isolates, but were not significantly differentially expressed in l-fucose or d-arabinose grown cells. Comparative proteomics analysis linked the C. jejuni NCTC11168 phenotypes uniquely to the more than 135-fold upregulated protein Cj0608, putative TolC-like component MacC, which, together with the detected Cj0606 and Cj0607 proteins, forms the tripartite secretion system MacABC with putative functions in antibiotic resistance, cell envelope stress response and virulence in Gram negative pathogenic bacteria. Further studies are required to elucidate the role of the MacABC system in C. jejuni cell surface structure modulation and virulence.
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Affiliation(s)
- Pjotr S. Middendorf
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Lucas M. Wijnands
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Aldert L. Zomer
- Faculty of Veterinary Medicine, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, the Netherlands
- WHO Collaborating Center for Campylobacter/OIE Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | | | | | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
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54
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Odenwald J, Gabiatti B, Braune S, Shen S, Zoltner M, Kramer S. Detection of TurboID fusion proteins by fluorescent streptavidin outcompetes antibody signals and visualises targets not accessible to antibodies. eLife 2024; 13:RP95028. [PMID: 39206942 PMCID: PMC11361705 DOI: 10.7554/elife.95028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Immunofluorescence localises proteins via fluorophore-labelled antibodies. However, some proteins evade detection due to antibody-accessibility issues or because they are naturally low abundant or antigen density is reduced by the imaging method. Here, we show that the fusion of the target protein to the biotin ligase TurboID and subsequent detection of biotinylation by fluorescent streptavidin offers an 'all in one' solution to these restrictions. For all proteins tested, the streptavidin signal was significantly stronger than an antibody signal, markedly improving the sensitivity of expansion microscopy and correlative light and electron microscopy. Importantly, proteins within phase-separated regions, such as the central channel of the nuclear pores, the nucleolus, or RNA granules, were readily detected with streptavidin, while most antibodies failed. When TurboID is used in tandem with an HA epitope tag, co-probing with streptavidin and anti-HA can map antibody-accessibility and we created such a map for the trypanosome nuclear pore. Lastly, we show that streptavidin imaging resolves dynamic, temporally, and spatially distinct sub-complexes and, in specific cases, reveals a history of dynamic protein interaction. In conclusion, streptavidin imaging has major advantages for the detection of lowly abundant or inaccessible proteins and in addition, provides information on protein interactions and biophysical environment.
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Affiliation(s)
| | | | - Silke Braune
- Biocenter, University of WürzburgWürzburgGermany
| | - Siqi Shen
- Department of Parasitology, Faculty of Science, Charles University in PraguePragueCzech Republic
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in PraguePragueCzech Republic
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55
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Maclean AE, Sloan MA, Renaud EA, Argyle BE, Lewis WH, Ovciarikova J, Demolombe V, Waller RF, Besteiro S, Sheiner L. The Toxoplasma gondii mitochondrial transporter ABCB7L is essential for the biogenesis of cytosolic and nuclear iron-sulfur cluster proteins and cytosolic translation. mBio 2024:e0087224. [PMID: 39207139 DOI: 10.1128/mbio.00872-24] [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: 03/21/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous inorganic cofactors required for numerous essential cellular pathways. Since they cannot be scavenged from the environment, Fe-S clusters are synthesized de novo in cellular compartments such as the apicoplast, mitochondrion, and cytosol. The cytosolic Fe-S cluster biosynthesis pathway relies on the transport of an intermediate from the mitochondrial pathway. An ATP-binding cassette (ABC) transporter called ABCB7 is responsible for this role in numerous commonly studied organisms, but its role in the medically important apicomplexan parasites has not yet been studied. Here we identify and characterize a Toxoplasma gondii ABCB7 homolog, which we name ABCB7-like (ABCB7L). Genetic depletion shows that it is essential for parasite growth and that its disruption triggers partial stage conversion. Characterization of the knock-down line highlights a defect in the biogenesis of cytosolic and nuclear Fe-S proteins leading to defects in protein translation and other pathways including DNA and RNA replication and metabolism. Our work provides support for a broad conservation of the connection between mitochondrial and cytosolic pathways in Fe-S cluster biosynthesis and reveals its importance for parasite survival. IMPORTANCE Iron-sulfur (Fe-S) clusters are inorganic cofactors of proteins that play key roles in numerous essential biological processes, for example, respiration and DNA replication. Cells possess dedicated biosynthetic pathways to assemble Fe-S clusters, including a pathway in the mitochondrion and cytosol. A single transporter, called ABCB7, connects these two pathways, allowing an essential intermediate generated by the mitochondrial pathway to be used in the cytosolic pathway. Cytosolic and nuclear Fe-S proteins are dependent on the mitochondrial pathway, mediated by ABCB7, in numerous organisms studied to date. Here, we study the role of a homolog of ABCB7, which we name ABCB7-like (ABCB7L), in the ubiquitous unicellular apicomplexan parasite Toxoplasma gondii. We generated a depletion mutant of Toxoplasma ABCB7L and showed its importance for parasite fitness. Using comparative quantitative proteomic analysis and experimental validation of the mutants, we show that ABCB7L is required for cytosolic and nuclear, but not mitochondrial, Fe-S protein biogenesis. Our study supports the conservation of a protein homologous to ABCB7 and which has a similar function in apicomplexan parasites and provides insight into an understudied aspect of parasite metabolism.
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Affiliation(s)
- Andrew E Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Megan A Sloan
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Eléa A Renaud
- LPHI, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Blythe E Argyle
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - William H Lewis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Vincent Demolombe
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
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Zare A, Salehi S, Bader J, Schneider C, Fischer U, Veh A, Arampatzi P, Mann M, Briese M, Sendtner M. hnRNP R promotes O-GlcNAcylation of eIF4G and facilitates axonal protein synthesis. Nat Commun 2024; 15:7430. [PMID: 39198412 PMCID: PMC11358521 DOI: 10.1038/s41467-024-51678-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 08/12/2024] [Indexed: 09/01/2024] Open
Abstract
Motoneurons critically depend on precise spatial and temporal control of translation for axon growth and the establishment and maintenance of neuromuscular connections. While defects in local translation have been implicated in the pathogenesis of motoneuron disorders, little is known about the mechanisms regulating axonal protein synthesis. Here, we report that motoneurons derived from Hnrnpr knockout mice show reduced axon growth accompanied by lowered synthesis of cytoskeletal and synaptic components in axons. Mutant mice display denervated neuromuscular junctions and impaired motor behavior. In axons, hnRNP R is a component of translation initiation complexes and, through interaction with O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (Ogt), modulates O-GlcNAcylation of eIF4G. Restoring axonal O-GlcNAc levels rescued local protein synthesis and axon growth defects of hnRNP R knockout motoneurons. Together, these findings demonstrate a function of hnRNP R in controlling the local production of key factors required for axon growth and formation of neuromuscular innervations.
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Affiliation(s)
- Abdolhossein Zare
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Saeede Salehi
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Jakob Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Cornelius Schneider
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Alexander Veh
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | | | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Briese
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
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Angermann C, Heinemann B, Hansen J, Töpfer N, Braun HP, Hildebrandt TM. Proteome reorganization and amino acid metabolism during germination and seedling establishment in Lupinus albus. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4891-4903. [PMID: 38686677 DOI: 10.1093/jxb/erae197] [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: 11/29/2023] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
During germination plants rely entirely on their seed storage compounds to provide energy and precursors for the synthesis of macromolecular structures until the seedling has emerged from the soil and photosynthesis can be established. Lupin seeds use proteins as their major storage compounds, accounting for up to 40% of the seed dry weight. Lupins are therefore a valuable complement to soy as a source of plant protein for human and animal nutrition. The aim of this study was to elucidate how storage protein metabolism is coordinated with other metabolic processes to meet the requirements of the growing seedling. In a quantitative approach, we analysed seedling growth, as well as alterations in biomass composition, the proteome, and metabolite profiles during germination and seedling establishment in Lupinus albus. The reallocation of nitrogen resources from seed storage proteins to functional seed proteins was mapped based on a manually curated functional protein annotation database. Although classified as a protein crop, Lupinus albus does not use amino acids as a primary substrate for energy metabolism during germination. However, fatty acid and amino acid metabolism may be integrated at the level of malate synthase to combine stored carbon from lipids and proteins into gluconeogenesis.
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Affiliation(s)
- Cecile Angermann
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47a, 50674 Cologne, Germany
| | - Björn Heinemann
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47a, 50674 Cologne, Germany
| | - Jule Hansen
- Institute for Plant Genetics, Department of Plant Proteomics, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Nadine Töpfer
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Luxemburger Str. 90, 50939 Cologne, Germany
| | - Hans-Peter Braun
- Institute for Plant Genetics, Department of Plant Proteomics, Leibniz University Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Tatjana M Hildebrandt
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47a, 50674 Cologne, Germany
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Moulder R, Bhosale SD, Viiri K, Lahesmaa R. Comparative proteomics analysis of the mouse mini-gut organoid: insights into markers of gluten challenge from celiac disease intestinal biopsies. Front Mol Biosci 2024; 11:1446822. [PMID: 39263374 PMCID: PMC11387180 DOI: 10.3389/fmolb.2024.1446822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/05/2024] [Indexed: 09/13/2024] Open
Abstract
Introduction Organoid models enable three-dimensional representation of cellular systems, providing flexible and accessible research tools, and can highlight key biomolecules. Such models of the intestinal epithelium can provide significant knowledge for the study of celiac disease and provide an additional context for the nature of markers observed from patient biopsy data. Methods Using LC-MS/MS, the proteomes of the crypt and enterocyte-like states of a mouse mini-gut organoid model were measured. The data were further compared with published biopsy data by comparing the changes induced by gluten challenge after a gluten-free diet. Results and discussion These analyses identified 4,850 protein groups and revealed how 400 putative biomarkers of dietary challenge were differentially expressed in the organoid model. In addition to the extensive changes within the differentiated cells, the data reiterated the disruption of the crypt-villus axis after gluten challenge. The mass spectrometry data are available via ProteomeXchange with the identifier PXD025690.
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Affiliation(s)
- Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Keijo Viiri
- Celiac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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de Jaime-Soguero A, Hattemer J, Bufe A, Haas A, van den Berg J, van Batenburg V, Das B, di Marco B, Androulaki S, Böhly N, Landry JJM, Schoell B, Rosa VS, Villacorta L, Baskan Y, Trapp M, Benes V, Chabes A, Shahbazi M, Jauch A, Engel U, Patrizi A, Sotillo R, van Oudenaarden A, Bageritz J, Alfonso J, Bastians H, Acebrón SP. Developmental signals control chromosome segregation fidelity during pluripotency and neurogenesis by modulating replicative stress. Nat Commun 2024; 15:7404. [PMID: 39191776 DOI: 10.1038/s41467-024-51821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 08/09/2024] [Indexed: 08/29/2024] Open
Abstract
Human development relies on the correct replication, maintenance and segregation of our genetic blueprints. How these processes are monitored across embryonic lineages, and why genomic mosaicism varies during development remain unknown. Using pluripotent stem cells, we identify that several patterning signals-including WNT, BMP, and FGF-converge into the modulation of DNA replication stress and damage during S-phase, which in turn controls chromosome segregation fidelity in mitosis. We show that the WNT and BMP signals protect from excessive origin firing, DNA damage and chromosome missegregation derived from stalled forks in pluripotency. Cell signalling control of chromosome segregation declines during lineage specification into the three germ layers, but re-emerges in neural progenitors. In particular, we find that the neurogenic factor FGF2 induces DNA replication stress-mediated chromosome missegregation during the onset of neurogenesis, which could provide a rationale for the elevated chromosomal mosaicism of the developing brain. Our results highlight roles for morphogens and cellular identity in genome maintenance that contribute to somatic mosaicism during mammalian development.
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Affiliation(s)
| | - Janina Hattemer
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Anja Bufe
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Alexander Haas
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Jeroen van den Berg
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vincent van Batenburg
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Biswajit Das
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Barbara di Marco
- Department of Clinical Neurobiology, University Hospital Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefania Androulaki
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Nicolas Böhly
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Brigitte Schoell
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Laura Villacorta
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yagmur Baskan
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Marleen Trapp
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | | | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ulrike Engel
- Nikon Imaging Center at the University of Heidelberg, Bioquant, Heidelberg, Germany
| | - Annarita Patrizi
- Schaller Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
- KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Josephine Bageritz
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Julieta Alfonso
- Department of Clinical Neurobiology, University Hospital Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Holger Bastians
- Department of Molecular Oncology, Section for Cellular Oncology, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Sergio P Acebrón
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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Starkl P, Jonsson G, Artner T, Turnes BL, Gail LM, Oliveira T, Jain A, Serhan N, Stejskal K, Lakovits K, Hladik A, An M, Channon KM, Kim H, Köcher T, Weninger W, Stary G, Knapp S, Klang V, Gaudenzio N, Woolf CJ, Tikoo S, Jain R, Penninger JM, Cronin SJF. Mast cell-derived BH4 and serotonin are critical mediators of postoperative pain. Sci Immunol 2024; 9:eadh0545. [PMID: 39178277 DOI: 10.1126/sciimmunol.adh0545] [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: 02/14/2023] [Accepted: 08/01/2024] [Indexed: 08/25/2024]
Abstract
Postoperative pain affects most patients after major surgery and can transition to chronic pain. The considerable side effects and limited efficacy of current treatments underline the need for new therapeutic options. We observed increased amounts of the metabolites BH4 and serotonin after skin injury. Mast cells were primary postoperative sources of Gch1, the rate-limiting enzyme in BH4 synthesis, itself an obligate cofactor in serotonin production by tryptophan hydroxylase (Tph1). Mice deficient in mast cells or in mast cell-specific Gch1 or Tph1 showed drastically decreased postoperative pain. We found that injury induced the nociceptive neuropeptide substance P, mast cell degranulation, and granule nerve colocalization. Substance P triggered serotonin release in mouse and human mast cells, and substance P receptor blockade substantially ameliorated pain hypersensitivity. Our findings highlight the importance of mast cells at the neuroimmune interface and substance P-driven mast cell BH4 and serotonin production as a therapeutic target for postoperative pain treatment.
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Affiliation(s)
- Philipp Starkl
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Gustav Jonsson
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Tyler Artner
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Bruna Lenfers Turnes
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Laura-Marie Gail
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tiago Oliveira
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Aakanksha Jain
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Nadine Serhan
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291 CNRS UMR5051, University of Toulouse III, Toulouse, France
| | - Karel Stejskal
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Karin Lakovits
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Anastasiya Hladik
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Meilin An
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Keith M Channon
- Radcliffe Department of Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Hail Kim
- Korea Advanced Institute of Science and Technology, Daejoen, Republic of Korea
| | - Thomas Köcher
- Vienna BioCenter Core Facilities (VBCF), 1030 Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Georg Stary
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sylvia Knapp
- Research Division of Infection Biology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Ignaz Semmelweis Institute, Interuniversity Institute for Infection Research, Medical University of Vienna, Vienna, Austria
| | - Victoria Klang
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Nicolas Gaudenzio
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291 CNRS UMR5051, University of Toulouse III, Toulouse, France
- Genoskin SAS, Toulouse, France
| | - Clifford J Woolf
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - Shweta Tikoo
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Rohit Jain
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Josef M Penninger
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shane J F Cronin
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
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Wang Z, Liu PK, Li L. A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics. ACS MEASUREMENT SCIENCE AU 2024; 4:315-337. [PMID: 39184361 PMCID: PMC11342459 DOI: 10.1021/acsmeasuresciau.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 08/27/2024]
Abstract
Recent advancements in mass spectrometry (MS) have revolutionized quantitative proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing accuracy, precision, and throughput. This tutorial review offers a comprehensive overview of multiplex isotope labeling techniques, including precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods. It details their fundamental principles, advantages, and inherent limitations along with strategies to mitigate the limitation of ratio-distortion. This review will also cover the applications and latest progress in these labeling techniques across various domains, including cancer biomarker discovery, neuroproteomics, post-translational modification analysis, cross-linking MS, and single-cell proteomics. This Review aims to provide guidance for researchers on selecting appropriate methods for their specific goals while also highlighting the potential future directions in this rapidly evolving field.
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Affiliation(s)
- Zicong Wang
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Peng-Kai Liu
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Lachman
Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Wisconsin
Center for NanoBioSystems, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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62
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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63
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Scharnow A, Solinski AE, Rowe S, Drechsel I, Zhang H, Shaw E, Page JE, Wu H, Sieber SA, Wuest WM. In Situ Biofilm Affinity-Based Protein Profiling Identifies the Streptococcal Hydrolase GbpB as the Target of a Carolacton-Inspired Chemical Probe. J Am Chem Soc 2024; 146:23449-23456. [PMID: 39133525 PMCID: PMC11345752 DOI: 10.1021/jacs.4c06658] [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: 05/17/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/13/2024]
Abstract
Natural products are important precursors for antibiotic drug design. These chemical scaffolds serve as synthetic inspiration for chemists who leverage their structures to develop novel antibacterials and chemical probes. We have previously studied carolacton, a natural product macrolactone fromSorangium cellulosum, and discovered a simplified derivative, A2, that maintained apparent biofilm inhibitory activity, although the biological target was unknown. Herein, we utilize affinity-based protein profiling (AfBPP) in situ during biofilm formation to identify the protein target using a photoexcitable cross-linking derivative of A2. From these studies, we identified glucan binding protein B (GbpB), a peptidoglycan hydrolase, as the primary target of A2. Further characterization of the interaction between A2 and GbpB, as well as PcsB, a closely related homologue from the more pathogenic S. pneumoniae, revealed binding to the catalytic CHAP (cysteine, histidine, aminopeptidase) domain. To the best of our knowledge, this is the first report of a small-molecule binder of a conserved and essential bacterial CHAP hydrolase, revealing its potential as an antibiotic target. This work also highlights A2 as a useful tool compound for streptococci and as an initial scaffold for the design of more potent CHAP binders.
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Affiliation(s)
- Amber
M. Scharnow
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Amy E. Solinski
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Sebastian Rowe
- Department
of Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ines Drechsel
- Department
of Chemistry, Center for Functional Protein Assemblies, Technical University of Munich, Garching D-85747, Germany
| | - Hua Zhang
- Departments
of Pediatric Dentistry, Microbiology, Schools of Dentistry and Medicine, University of Alabama at Birmingham, Birmingham 35294, Alabama, United States
| | - Elana Shaw
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Julia E. Page
- Department
of Microbiology, Blavatnik Institute, Harvard
Medical School, Boston, Massachusetts 02115, United States
| | - Hui Wu
- Departments
of Pediatric Dentistry, Microbiology, Schools of Dentistry and Medicine, University of Alabama at Birmingham, Birmingham 35294, Alabama, United States
| | - Stephan A. Sieber
- Department
of Chemistry, Center for Functional Protein Assemblies, Technical University of Munich, Garching D-85747, Germany
| | - William M. Wuest
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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64
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Noszka M, Strzałka A, Muraszko J, Hofreuter D, Abele M, Ludwig C, Stingl K, Zawilak-Pawlik A. CemR atypical response regulator impacts energy conversion in Campylobacteria. mSystems 2024; 9:e0078424. [PMID: 38980050 PMCID: PMC11334517 DOI: 10.1128/msystems.00784-24] [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: 06/09/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024] Open
Abstract
Campylobacter jejuni and Arcobacter butzleri are microaerobic food-borne human gastrointestinal pathogens that mainly cause diarrheal disease. These related species of the Campylobacteria class face variable atmospheric environments during infection and transmission, ranging from nearly anaerobic to aerobic conditions. Consequently, their lifestyles require that both pathogens need to adjust their metabolism and respiration to the changing oxygen concentrations of the colonization sites. Our transcriptomic and proteomic studies revealed that C. jejuni and A. butzleri, lacking a Campylobacteria-specific regulatory protein, C. jejuni Cj1608, or a homolog, A. butzleri Abu0127, are unable to reprogram tricarboxylic acid cycle or respiration pathways, respectively, to produce ATP efficiently and, in consequence, adjust growth to changing oxygen supply. We propose that these Campylobacteria energy and metabolism regulators (CemRs) are long-sought transcription factors controlling the metabolic shift related to oxygen availability, essential for these bacteria's survival and adaptation to the niches they inhabit. Besides their significant universal role in Campylobacteria, CemRs, as pleiotropic regulators, control the transcription of many genes, often specific to the species, under microaerophilic conditions and in response to oxidative stress. IMPORTANCE C. jejuni and A. butzleri are closely related pathogens that infect the human gastrointestinal tract. In order to infect humans successfully, they need to change their metabolism as nutrient and respiratory conditions change. A regulator called CemR has been identified, which helps them adapt their metabolism to changing conditions, particularly oxygen availability in the gastrointestinal tract so that they can produce enough energy for survival and spread. Without CemR, these bacteria, as well as a related species, Helicobacter pylori, produce less energy, grow more slowly, or, in the case of C. jejuni, do not grow at all. Furthermore, CemR is a global regulator that controls the synthesis of many genes in each species, potentially allowing them to adapt to their ecological niches as well as establish infection. Therefore, the identification of CemR opens new possibilities for studying the pathogenicity of C. jejuni and A. butzleri.
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Affiliation(s)
- Mateusz Noszka
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Agnieszka Strzałka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Jakub Muraszko
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Dirk Hofreuter
- Department of Biological Safety, Unit of Product Hygiene and Disinfection Strategies, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Kerstin Stingl
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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65
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Yu SB, Wang H, Sanchez RG, Carlson NM, Nguyen K, Zhang A, Papich ZD, Abushawish AA, Whiddon Z, Matysik W, Zhang J, Whisenant TC, Ghassemian M, Koberstein JN, Stewart ML, Myers SA, Pekkurnaz G. Neuronal activity-driven O-GlcNAcylation promotes mitochondrial plasticity. Dev Cell 2024; 59:2143-2157.e9. [PMID: 38843836 PMCID: PMC11338717 DOI: 10.1016/j.devcel.2024.05.008] [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: 01/12/2023] [Revised: 02/15/2024] [Accepted: 05/09/2024] [Indexed: 06/18/2024]
Abstract
Neuronal activity is an energy-intensive process that is largely sustained by instantaneous fuel utilization and ATP synthesis. However, how neurons couple ATP synthesis rate to fuel availability is largely unknown. Here, we demonstrate that the metabolic sensor enzyme O-linked N-acetyl glucosamine (O-GlcNAc) transferase regulates neuronal activity-driven mitochondrial bioenergetics in hippocampal and cortical neurons. We show that neuronal activity upregulates O-GlcNAcylation in mitochondria. Mitochondrial O-GlcNAcylation is promoted by activity-driven glucose consumption, which allows neurons to compensate for high energy expenditure based on fuel availability. To determine the proteins that are responsible for these adjustments, we mapped the mitochondrial O-GlcNAcome of neurons. Finally, we determine that neurons fail to meet activity-driven metabolic demand when O-GlcNAcylation dynamics are prevented. Our findings suggest that O-GlcNAcylation provides a fuel-dependent feedforward control mechanism in neurons to optimize mitochondrial performance based on neuronal activity. This mechanism thereby couples neuronal metabolism to mitochondrial bioenergetics and plays a key role in sustaining energy homeostasis.
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Affiliation(s)
- Seungyoon B Yu
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Haoming Wang
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard G Sanchez
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Natasha M Carlson
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Khanh Nguyen
- Laboratory for Immunochemical Circuits, Center of Autoimmunity and Inflammation, and Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA 92093, USA
| | - Andrew Zhang
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zachary D Papich
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ahmed A Abushawish
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zachary Whiddon
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Weronika Matysik
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jie Zhang
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas C Whisenant
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - John N Koberstein
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa L Stewart
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, Center of Autoimmunity and Inflammation, and Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA 92093, USA; Department of Pharmacology, Program in Immunology, and Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Gulcin Pekkurnaz
- Neurobiology Department, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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66
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Mukherjee A, Spanos C, Marston AL. Distinct roles of spindle checkpoint proteins in meiosis. Curr Biol 2024; 34:3820-3829.e5. [PMID: 39079532 DOI: 10.1016/j.cub.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/12/2024] [Accepted: 07/03/2024] [Indexed: 08/22/2024]
Abstract
Gametes are produced via meiosis, a specialized cell division associated with frequent errors that cause birth defects and infertility. Uniquely in meiosis I, homologous chromosomes segregate to opposite poles, usually requiring their linkage by chiasmata, the products of crossover recombination.1 The spindle checkpoint delays cell-cycle progression until all chromosomes are properly attached to microtubules,2 but the steps leading to the capture and alignment of chromosomes on the meiosis I spindle remain poorly understood. In budding yeast meiosis I, Mad2 and Mad3BUBR1 are equally important for spindle checkpoint delay, but biorientation of homologs on the meiosis I spindle requires Mad2, but not Mad3BUBR1.3,4 Here we reveal the distinct functions of Mad2 and Mad3BUBR1 in meiosis I chromosome segregation. Mad2 promotes the prophase to metaphase I transition, while Mad3BUBR1 associates with the TOGL1 domain of Stu1CLASP, a conserved plus-end microtubule protein that is important for chromosome capture onto the spindle. Homologous chromosome pairs that are proficient in crossover formation but fail to biorient rely on Mad3BUBR1-Stu1CLASP to ensure their efficient attachment to microtubules and segregation during meiosis I. Furthermore, we show that Mad3BUBR1-Stu1CLASP are essential to rescue the segregation of mini-chromosomes lacking crossovers. Our findings define a new pathway ensuring microtubule-dependent chromosome capture and demonstrate that spindle checkpoint proteins safeguard the fidelity of chromosome segregation both by actively promoting chromosome alignment and by delaying cell-cycle progression until this has occurred.
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Affiliation(s)
- Anuradha Mukherjee
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Christos Spanos
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Adele L Marston
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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67
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Zhang T, Jia L, Li X, Niu Z, Zhang S, Dong W, Peng L, Ma M, Wang H, Tang X, Chen Q. Integrative proteome and metabolome analyses reveal molecular basis of the tail resorption during the metamorphic climax of Nanorana pleskei. Front Cell Dev Biol 2024; 12:1431173. [PMID: 39224435 PMCID: PMC11366584 DOI: 10.3389/fcell.2024.1431173] [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: 05/11/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
During the metamorphosis of anuran amphibians, the tail resorption process is a necessary and crucial change. One subject that has received relatively little or no attention is the expression patterns of proteins and metabolites in the different tail portions during metamorphosis, especially in highland amphibians. The mechanisms of tail resorption in three portions (the tip, middle and root) of the tail were investigated in N. pleskei G43 tadpole based on two omics (proteomic and metabolomic). Integrin αVβ3 was found to be high expressed in the distal portion of the tail, which could improve the sensitiveness to thyroid hormones in the distal portion of the tail. Muscle regression displayed a spatial pattern with stronger regression in distal and weaker one in proximal portion. Probably, this stronger regression was mainly performed by the proteases of proteasome from the active translation by ribosomes. The suicide model and murder model coexisted in the tail resorption. Meanwhile, fatty acids, amino acids, pyrimidine, and purine which derived from the breakdown of tissues can be used as building blocks or energy source for successful metamorphosis. Our data improved a better comprehension of the tail resorption mechanisms underlying the metamorphism of N. pleskei tadpole through identifying important participating proteins and metabolites.
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Affiliation(s)
- Tao Zhang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lun Jia
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xinying Li
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhiyi Niu
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Siping Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Weijun Dong
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Liang Peng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Miaojun Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Huihui Wang
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Xiaolong Tang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiang Chen
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
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Yun D, Bae S, Gao Y, Lopez L, Han D, Nicora CD, Kim TY, Moon KC, Kim DK, Fillmore TL, Kim YS, Rosenberg AZ, Wang W, Sarder P, Qian WJ, Afkarian M, Han SS. Urine complement proteins are associated with kidney disease progression of type 2 diabetes in Korean and American cohorts. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.15.24312080. [PMID: 39211860 PMCID: PMC11361241 DOI: 10.1101/2024.08.15.24312080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Background Mechanisms of progression of diabetic kidney disease (DKD) are not completely understood. This study uses untargeted and targeted mass spectrometry-based proteomics in two independent cohorts on two continents to decipher the mechanisms of DKD in patients with type 2 diabetes. Methods We conducted untargeted mass spectrometry on urine samples collected at the time of kidney biopsy from Korean patients with type 2 diabetes and biopsy-proven diabetic nephropathy at Seoul National University Hospital (SNUH-DN cohort; n = 64). These findings were validated using targeted mass spectrometry in urine samples from a Chronic Renal Insufficiency Cohort subgroup with type 2 diabetes and DKD (CRIC-T2D; n = 282). Urinary biomarkers/pathways associated with kidney disease progression (doubling of serum creatinine, ≥50% decrease in estimated glomerular filtration rates, or the development of end-stage kidney disease) were identified. Results SNUH-DN patients had an estimated glomerular filtration rate (eGFR) of 55 mL/min/1.73 m 2 (interquartile range [IQR], 44-75) and random urine protein-to-creatinine ratio of 3.1 g/g (IQR, 1.7-7.0). Urine proteins clustered into two groups, with cluster 2 having a 4.6-fold greater hazard (95% confidence interval [CI], 1.9-11.5) of disease progression than cluster 1 in multivariable-adjusted, time-to-event analyses. Proteins in cluster 2 mapped to 10 pathways, four of the top five of which were complement or complement-related. A high complement score, constructed from urine complement protein abundance, was strongly correlated to 4 of 5 histopathologic DN features and was associated with a 2.4-fold greater hazard (95% CI, 1.0-5.4) of disease progression than a low complement score. Targeted mass spectrometry of the CRIC-T2D participants, who had an eGFR of 42 mL/min/1.73 m 2 (IQR, 37-49) and 24-hr urine protein of 0.48 g (IQR, 0.10-1.87), showed that the complement score similarly segregated them into rapid and slow DKD progression groups. In both cohorts, the complement score had a linear association with disease progression. Conclusions Urinary proteomic profiling confirms the association between the complement pathway and rapid DKD progression in two independent cohorts. These results suggest a need to further investigate complement pathway inhibition as a novel treatment for DKD.
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Čunátová K, Vrbacký M, Puertas-Frias G, Alán L, Vanišová M, Saucedo-Rodríguez MJ, Houštěk J, Fernández-Vizarra E, Neužil J, Pecinová A, Pecina P, Mráček T. Mitochondrial translation is the primary determinant of secondary mitochondrial complex I deficiencies. iScience 2024; 27:110560. [PMID: 39184436 PMCID: PMC11342289 DOI: 10.1016/j.isci.2024.110560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/28/2024] [Accepted: 07/17/2024] [Indexed: 08/27/2024] Open
Abstract
Individual complexes of the mitochondrial oxidative phosphorylation system (OXPHOS) are not linked solely by their function; they also share dependencies at the maintenance/assembly level, where one complex depends on the presence of a different individual complex. Despite the relevance of this "interdependence" behavior for mitochondrial diseases, its true nature remains elusive. To understand the mechanism that can explain this phenomenon, we examined the consequences of the aberration of different OXPHOS complexes in human cells. We demonstrate here that the complete disruption of each of the OXPHOS complexes resulted in a decrease in the complex I (cI) level and that the major reason for this is linked to the downregulation of mitochondrial ribosomal proteins. We conclude that the secondary cI defect is due to mitochondrial protein synthesis attenuation, while the responsible signaling pathways could differ based on the origin of the OXPHOS defect.
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Affiliation(s)
- Kristýna Čunátová
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Marek Vrbacký
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Guillermo Puertas-Frias
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Lukáš Alán
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Marie Vanišová
- Laboratory for Study of Mitochondrial Disorders, First Faculty of Medicine, Charles University and General University Hospital, 12808 Prague, Czech Republic
| | - María José Saucedo-Rodríguez
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Josef Houštěk
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Erika Fernández-Vizarra
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Veneto Institute of Molecular Medicine, 35129 Padova, Italy
| | - Jiří Neužil
- School of Pharmacy and Medical Science, Griffith University, Southport, Qld 4222, Australia
- Laboratory of Molecular Therapy, Institute of Biotechnology, Czech Academy of Sciences, 25250 Prague, Czech Republic
- Department of Pediatrics and Inherited Diseases, First Faculty of Medicine, Charles University, 12108 Prague, Czech Republic
- Department of Physiology, Faculty of Science, Charles University, 12800 Prague, Czech Republic
| | - Alena Pecinová
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Petr Pecina
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
| | - Tomáš Mráček
- Laboratory of Bioenergetics, Institute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic
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Tanaka A, Ogawa M, Zhou Y, Otani Y, Hendrickson RC, Miele MM, Li Z, Klimstra DS, Wang JY, Roehrl MH. Proteogenomic characterization of pancreatic neuroendocrine tumors uncovers hypoxia and immune signatures in clinically aggressive subtypes. iScience 2024; 27:110544. [PMID: 39206147 PMCID: PMC11350455 DOI: 10.1016/j.isci.2024.110544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/15/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024] Open
Abstract
Pancreatic neuroendocrine tumors (PanNETs) represent well-differentiated endocrine neoplasms with variable clinical outcomes. Predicting patient outcomes using the current tumor grading system is challenging. In addition, traditional systemic treatment options for PanNETs, such as somatostatin analogs or cytotoxic chemotherapies, are very limited. To address these issues, we characterized PanNETs using integrated proteogenomics and identified four subtypes. Two proteomic subtypes showed high recurrence rates, suggesting clinical aggressiveness that was missed by current classification. Hypoxia and inflammatory pathways were significantly enriched in the clinically aggressive subtypes. Detailed analyses revealed metabolic adaptation via glycolysis upregulation and oxidative phosphorylation downregulation under hypoxic conditions. Inflammatory signature analysis revealed that immunosuppressive molecules were enriched in immune hot tumors and might be immunotherapy targets. In this study, we characterized clinically aggressive proteomic subtypes of well-differentiated PanNETs and identified candidate therapeutic targets.
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Affiliation(s)
- Atsushi Tanaka
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Makiko Ogawa
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yihua Zhou
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- ICU Department, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yusuke Otani
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ronald C. Hendrickson
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew M. Miele
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S. Klimstra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Michael H. Roehrl
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Grepper D, Tabasso C, Zanou N, Aguettaz AK, Castro-Sepulveda M, Ziegler DV, Lagarrigue S, Arribat Y, Martinotti A, Ebrahimi A, Daraspe J, Fajas L, Amati F. BCL2L13 at endoplasmic reticulum-mitochondria contact sites regulates calcium homeostasis to maintain skeletal muscle function. iScience 2024; 27:110510. [PMID: 39175772 PMCID: PMC11340602 DOI: 10.1016/j.isci.2024.110510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/17/2024] [Accepted: 07/11/2024] [Indexed: 08/24/2024] Open
Abstract
The physical connection between mitochondria and endoplasmic reticulum (ER) is an essential signaling hub to ensure organelle and cellular functions. In skeletal muscle, ER-mitochondria calcium (Ca2+) signaling is crucial to maintain cellular homeostasis during physical activity. High expression of BCL2L13, a member of the BCL-2 family, was suggested as an adaptive response in endurance-trained human subjects. In adult zebrafish, we found that the loss of Bcl2l13 impairs skeletal muscle structure and function. Ca2+ signaling is altered in Bcl2l13 knockout animals and mitochondrial complexes activity is decreased. Organelle fractioning in mammalian cells shows BCL2L13 at mitochondria, ER, and mitochondria-associated membranes. ER-mitochondria contact sites number is not modified by BCL2L13 modulation, but knockdown of BCL2L13 in C2C12 cells changes cytosolic Ca2+ release and mitochondrial Ca2+ uptake. This suggests that BCL2L13 interaction with mitochondria and ER, and its role in Ca2+ signaling, contributes to proper skeletal muscle function.
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Affiliation(s)
- Dogan Grepper
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
| | - Cassandra Tabasso
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
| | - Nadège Zanou
- Institute of Sport Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud 1015, Switzerland
| | - Axel K.F. Aguettaz
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
- Service of Endocrinology, Diabetes and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Vaud 1011, Switzerland
| | - Mauricio Castro-Sepulveda
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
| | - Dorian V. Ziegler
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud 1015, Switzerland
| | - Sylviane Lagarrigue
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
| | - Yoan Arribat
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
| | - Adrien Martinotti
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
- Service of Endocrinology, Diabetes and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Vaud 1011, Switzerland
| | - Ammar Ebrahimi
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
- Service of Endocrinology, Diabetes and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Vaud 1011, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud 1015, Switzerland
| | - Lluis Fajas
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud 1015, Switzerland
| | - Francesca Amati
- Aging and Muscle Metabolism Lab, Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Bugnon 7, Lausanne, Vaud 1005, Switzerland
- Service of Endocrinology, Diabetes and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Vaud 1011, Switzerland
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Cui G, Di Y, Yang S, Chen Y, Li Y, Chen D. Proteomic analysis reveals key differences in pro-stromal corneal tissue between highly myopic males and females. Front Med (Lausanne) 2024; 11:1406748. [PMID: 39219796 PMCID: PMC11361967 DOI: 10.3389/fmed.2024.1406748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/06/2024] [Indexed: 09/04/2024] Open
Abstract
Background and purpose Nowadays, myopia has become a highly prevalent disease globally, especially in East Asia. Epidemiological studies have found that there may be sex differences in the occurrence and progression of myopia, with females having a higher incidence of myopia and higher risk of myopia progression. The purpose of this study was to explore the sex differences in myopic cornea using corneal stroma removed by small incision lenticule extraction (SMILE) surgery. Methods The corneal stroma of females with high myopia (FH) and males with high myopia (MH) were subjected to proteomic assays. Proteomic-related data were statistically analyzed using software such as MaxQuan, KAAS, Proteome Discovery, etc. The total number of proteins in the cornea and the proteins specifically expressed in the two groups were counted, and the differentially expressed proteins in the two groups were identified by expression fold change >2 and p-value <0.05, and volcano plots were constructed, and functional enrichment analysis, subcellular organelle analysis, and molecular interaction were implemented. Results Ten samples from each group were analyzed. Twenty-seven proteins were down-regulated and 27 proteins were up-regulated in the FH group, of which 23 proteins were up-regulated in the range of 2-10-fold and 4 proteins were up-regulated in the range of >10-fold. Comparative proteomic analysis of the cornea of male and female patients with high myopia revealed that the expression of corneal extracellular matrix and collagen I, III, V, and VIII-associated proteins were increased in the cornea of female patients, and the transforming growth factor-β (TGF-β)/Smad pathway was an important pathway obtained by functional analysis. Conclusion Comparative proteomic analysis of cornea from male and female patients with high myopia revealed increased expression of proteins related to extracellular matrix and collagen I, III, V, and VIII in female patients, and the TGF-β/Smad pathway was an important pathway obtained from the functional analysis, suggesting that extracellular matrix remodeling and collagen fiber synthesis may be more active in the cornea of female patients.
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Affiliation(s)
- Ge Cui
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Di
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shan Yang
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Youxin Chen
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ying Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Di Chen
- Department of Ophthalmology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Key Laboratory of Ocular Fundus Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Laybourn HA, Hellemann Polhaus C, Kristensen C, Lyngfeldt Henriksen B, Zhang Y, Brogaard L, Larsen CA, Trebbien R, Larsen LE, Kalogeropoulos K, Auf dem Keller U, Skovgaard K. Multi-omics analysis reveals the impact of influenza a virus host adaptation on immune signatures in pig tracheal tissue. Front Immunol 2024; 15:1432743. [PMID: 39247193 PMCID: PMC11378526 DOI: 10.3389/fimmu.2024.1432743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/29/2024] [Indexed: 09/10/2024] Open
Abstract
Introduction Influenza A virus (IAV) infection is a global respiratory disease, which annually leads to 3-5 million cases of severe illness, resulting in 290,000-650,000 deaths. Additionally, during the past century, four global IAV pandemics have claimed millions of human lives. The epithelial lining of the trachea plays a vital role during IAV infection, both as point of viral entry and replication as well as in the antiviral immune response. Tracheal tissue is generally inaccessible from human patients, which makes animal models crucial for the study of the tracheal host immune response. Method In this study, pigs were inoculated with swine- or human-adapted H1N1 IAV to gain insight into how host adaptation of IAV shapes the innate immune response during infection. In-depth multi-omics analysis (global proteomics and RNA sequencing) of the host response in upper and lower tracheal tissue was conducted, and results were validated by microfluidic qPCR. Additionally, a subset of samples was selected for histopathological examination. Results A classical innate antiviral immune response was induced in both upper and lower trachea after infection with either swine- or human-adapted IAV with upregulation of genes and higher abundance of proteins associated with viral infection and recognition, accompanied by a significant induction of interferon stimulated genes with corresponding higher proteins concentrations. Infection with the swine-adapted virus induced a much stronger immune response compared to infection with a human-adapted IAV strain in the lower trachea, which could be a consequence of a higher viral load and a higher degree of inflammation. Discussion Central components of the JAK-STAT pathway, apoptosis, pyrimidine metabolism, and the cytoskeleton were significantly altered depending on infection with swine- or human-adapted virus and might be relevant mechanisms in relation to antiviral immunity against putative zoonotic IAV. Based on our findings, we hypothesize that during host adaptation, IAV evolve to modulate important host cell elements to favor viral infectivity and replication.
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Affiliation(s)
- Helena Aagaard Laybourn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Charlotte Kristensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Yaolei Zhang
- Qingdao Key Laboratory of Marine Genomics, BGI-Qingdao, Qingdao, China
| | - Louise Brogaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Cathrine Agnete Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ramona Trebbien
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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Jing SY, Liu D, Feng N, Dong H, Wang HQ, Yan X, Chen XF, Qu MC, Lin P, Yi B, Feng F, Chen L, Wang HY, Li H, He YF. Spatial multiomics reveals a subpopulation of fibroblasts associated with cancer stemness in human hepatocellular carcinoma. Genome Med 2024; 16:98. [PMID: 39138551 PMCID: PMC11320883 DOI: 10.1186/s13073-024-01367-8] [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: 11/14/2023] [Accepted: 07/23/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Cancer-associated fibroblasts (CAFs) are the prominent cell type in the tumor microenvironment (TME), and CAF subsets have been identified in various tumors. However, how CAFs spatially coordinate other cell populations within the liver TME to promote cancer progression remains unclear. METHODS We combined multi-region proteomics (6 patients, 24 samples), 10X Genomics Visium spatial transcriptomics (11 patients, 25 samples), and multiplexed imaging (92 patients, 264 samples) technologies to decipher the expression heterogeneity, functional diversity, spatial distribution, colocalization, and interaction of fibroblasts. The newly identified CAF subpopulation was validated by cells isolated from 5 liver cancer patients and in vitro functional assays. RESULTS We identified a liver CAF subpopulation, marked by the expression of COL1A2, COL4A1, COL4A2, CTGF, and FSTL1, and named F5-CAF. F5-CAF is preferentially located within and around tumor nests and colocalizes with cancer cells with higher stemness in hepatocellular carcinoma (HCC). Multiplexed staining of 92 patients and the bulk transcriptome of 371 patients demonstrated that the abundance of F5-CAFs in HCC was associated with a worse prognosis. Further in vitro experiments showed that F5-CAFs isolated from liver cancer patients can promote the proliferation and stemness of HCC cells. CONCLUSIONS We identified a CAF subpopulation F5-CAF in liver cancer, which is associated with cancer stemness and unfavorable prognosis. Our results provide potential mechanisms by which the CAF subset in the TME promotes the development of liver cancer by supporting the survival of cancer stem cells.
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Affiliation(s)
- Si-Yu Jing
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Dan Liu
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Na Feng
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Hui Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Shanghai, 200438, People's Republic of China
| | - He-Qi Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Xi Yan
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Xu-Feng Chen
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Min-Cheng Qu
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Ping Lin
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Bin Yi
- Department of Organ Transplantation, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Feiling Feng
- Department of Biliary Tract Surgery I, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China
| | - Lei Chen
- National Center for Liver Cancer and International Cooperation Laboratory On Signal Transduction, Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, 200438, People's Republic of China.
| | - Hong-Yang Wang
- National Center for Liver Cancer and International Cooperation Laboratory On Signal Transduction, Eastern Hepatobiliary Surgery Institute/Hospital, Shanghai, 200438, People's Republic of China.
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education and Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai, 200438, People's Republic of China.
| | - Hong Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China.
| | - Yu-Fei He
- Molecular Pathology Laboratory, National Center for Liver Cancer, Eastern Hepatobiliary Surgery Hospital, Shanghai, 201800, People's Republic of China.
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Arce RC, Mayta ML, Melzer M, Hajirezaei MR, Lodeyro AF, Carrillo N. Introduction of a terminal electron sink in chloroplasts decreases leaf cell expansion associated with higher proteasome activity and lower endoreduplication. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4625-4640. [PMID: 38364822 DOI: 10.1093/jxb/erae039] [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: 11/30/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
Foliar development involves successive phases of cell proliferation and expansion that determine the final leaf size, and is characterized by an early burst of reactive oxygen species generated in the photosynthetic electron transport chain (PETC). Introduction of the alternative PETC acceptor flavodoxin in tobacco chloroplasts led to a reduction in leaf size associated to lower cell expansion, without affecting cell number per leaf. Proteomic analysis showed that the biogenesis of the PETC proceeded stepwise in wild-type leaves, with accumulation of light-harvesting proteins preceding that of electron transport components, which might explain the increased energy and electron transfer to oxygen and reactive oxygen species build-up at this stage. Flavodoxin expression did not affect biogenesis of the PETC but prevented hydroperoxide formation through its function as electron sink. Mature leaves from flavodoxin-expressing plants were shown to contain higher levels of transcripts encoding components of the proteasome, a key negative modulator of organ size. Proteome profiling revealed that this differential accumulation was initiated during expansion and led to increased proteasomal activity, whereas a proteasome inhibitor reverted the flavodoxin-dependent size phenotype. Cells expressing plastid-targeted flavodoxin displayed lower endoreduplication, also associated to decreased organ size. These results provide novel insights into the regulation of leaf growth by chloroplast-generated redox signals, and highlight the potential of alternative electron shuttles to investigate the link(s) between photosynthesis and plant development.
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Affiliation(s)
- Rocío C Arce
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
| | - Martín L Mayta
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
- Centro Interdisciplinario de Investigaciones en Ciencias de la Salud y del Comportamiento (CIICSAC), Facultad de Ciencias de la Salud, Universidad Adventista del Plata, 25 de Mayo 99, E3103XAF, Libertador San Martín, Entre Ríos, Argentina
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Corrensstrasse, D-06466 Stadt Seeland, Germany
| | - Mohammad-Reza Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben, Corrensstrasse, D-06466 Stadt Seeland, Germany
| | - Anabella F Lodeyro
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
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76
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Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A framework for quality control in quantitative proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589318. [PMID: 38645098 PMCID: PMC11030400 DOI: 10.1101/2024.04.12.589318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and on ProteomeXchange under the identifier PXD051318 .
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Affiliation(s)
- Kristine A. Tsantilas
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Julia E. Robbins
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Jea Park
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Washington 98195, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Josh Eckels
- LabKey, 500 Union St #1000, Seattle, Washington 98101, United States
| | - Christine C. Wu
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael S. Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607
| | - Sandra E. Spencer
- Canada’s Michael Smith Genome Sciences Centre (BC Cancer Research Institute), University of British Columbia, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew N. Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Washington 98195, United States
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77
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Lin MH, Jensen MK, Elrod ND, Chu HF, Haseley M, Beam AC, Huang KL, Chiang W, Russell WK, Williams K, Pröschel C, Wagner EJ, Tong L. Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function. Mol Cell 2024; 84:2900-2917.e10. [PMID: 39032490 PMCID: PMC11316654 DOI: 10.1016/j.molcel.2024.06.017] [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: 11/08/2023] [Revised: 06/04/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024]
Abstract
INTS11 and CPSF73 are metal-dependent endonucleases for Integrator and pre-mRNA 3'-end processing, respectively. Here, we show that the INTS11 binding partner BRAT1/CG7044, a factor important for neuronal fitness, stabilizes INTS11 in the cytoplasm and is required for Integrator function in the nucleus. Loss of BRAT1 in neural organoids leads to transcriptomic disruption and precocious expression of neurogenesis-driving transcription factors. The structures of the human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes reveal that the conserved C terminus of BRAT1/CG7044 is captured in the active site of INTS11, with a cysteine residue directly coordinating the metal ions. Inspired by these observations, we find that UBE3D is a binding partner for CPSF73, and UBE3D likely also uses a conserved cysteine residue to directly coordinate the active site metal ions. Our studies have revealed binding partners for INTS11 and CPSF73 that behave like cytoplasmic chaperones with a conserved impact on the nuclear functions of these enzymes.
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Affiliation(s)
- Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Madeline K Jensen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Hsu-Feng Chu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - MaryClaire Haseley
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Alissa C Beam
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Wesley Chiang
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Kelsey Williams
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Christoph Pröschel
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Eric J Wagner
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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78
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Ivanov MV, Kopeykina AS, Gorshkov MV. Reanalysis of DIA Data Demonstrates the Capabilities of MS/MS-Free Proteomics to Reveal New Biological Insights in Disease-Related Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1775-1785. [PMID: 38938158 DOI: 10.1021/jasms.4c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Data-independent acquisition (DIA) at the shortened data acquisition time is becoming a method of choice for quantitative proteomic applications requiring high throughput analysis of large cohorts of samples. With the advent of the combination of high resolution mass spectrometry with an asymmetric track lossless analyzer, these DIA capabilities were further extended with the recent demonstration of quantitative analyses at the speed of up to hundreds of samples per day. In particular, the proteomic data for the brain samples related to multiple system atrophy disease were acquired using 7 and 28 min chromatography gradients (Guzman et al., Nat. Biotech. 2024). In this work, we applied the recently introduced DirectMS1 method to reanalysis of these data using only MS1 spectra. Both DirectMS1 and DIA results were matched against long gradient DDA analysis from the earlier study of the same sample cohort. While the quantitation efficiency of DirectMS1 was comparable with DIA on the same data sets, we found an additional five proteins of biological significance relevant to the analyzed tissue samples. Among the findings, DirectMS1 was able to detect decreased caspase activity for Vimentin protein in the multiple system atrophy samples missed by the MS/MS-based quantitation methods. Our study suggests that DirectMS1 can be an efficient MS1-only addition to the analysis of DIA data in high-throughput quantitative proteomic studies.
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Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna S Kopeykina
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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79
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Ball B, Sukumaran A, Pladwig S, Kazi S, Chan N, Honeywell E, Modrakova M, Geddes-McAlister J. Proteome signatures reveal homeostatic and adaptive oxidative responses by a putative co-chaperone, Wos2, to influence fungal virulence determinants in cryptococcosis. Microbiol Spectr 2024; 12:e0015224. [PMID: 38953322 PMCID: PMC11302251 DOI: 10.1128/spectrum.00152-24] [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: 01/16/2024] [Accepted: 05/27/2024] [Indexed: 07/04/2024] Open
Abstract
The increasing prevalence of invasive fungal pathogens is dramatically changing the clinical landscape of infectious diseases, posing an imminent threat to public health. Specifically, Cryptococcus neoformans, the human opportunistic pathogen, expresses elaborate virulence mechanisms and is equipped with sophisticated adaptation strategies to survive in harsh host environments. This study extensively characterizes Wos2, an Hsp90 co-chaperone homolog, featuring bilateral functioning for both cryptococcal adaptation and the resulting virulence response. In this study, we evaluated the proteome and secretome signatures associated with wos2 deletion in enriched and infection-mimicking conditions to reveal Wos2-dependent regulation of the oxidative stress response through global translational reprogramming. The wos2Δ strain demonstrates defective intracellular and extracellular antioxidant protection systems, measurable through a decreased abundance of critical antioxidant enzymes and reduced growth in the presence of peroxide stress. Additional Wos2-associated stress phenotypes were observed upon fungal challenge with heat shock, osmotic stress, and cell membrane stressors. We demonstrate the importance of Wos2 for intracellular lifestyle of C. neoformans during in vitro macrophage infection and provide evidence for reduced phagosomal replication levels associated with wos2Δ. Accordingly, wos2Δ featured significantly reduced virulence within impacting fungal burden in a murine model of cryptococcosis. Our study highlights a vulnerable point in the fungal chaperone network that offers a therapeutic opportunity to interfere with both fungal virulence and fitness.IMPORTANCEThe global impact of fungal pathogens, both emerging and emerged, is undeniable, and the alarming increase in antifungal resistance rates hampers our ability to protect the global population from deadly infections. For cryptococcal infections, a limited arsenal of antifungals and increasing rates of resistance demand alternative therapeutic strategies, including an anti-virulence approach, which disarms the pathogen of critical virulence factors, empowering the host to remove the pathogens and clear the infection. To this end, we apply state-of-the-art mass spectrometry-based proteomics to evaluate the impact of a recently defined novel co-chaperone, Wos2, toward cryptococcal virulence using in vitro and in vivo models of infection. We explore global proteome and secretome remodeling driven by the protein and uncover the novel role in modulating the fungal oxidative stress response. Complementation of proteome findings with in vitro infectivity assays demonstrated the protective role of Wos2 within the macrophage phagosome, influencing fungal replication and survival. These results underscore differential cryptococcal survivability and weakened patterns of dissemination in the absence of wos2. Overall, our study establishes Wos2 as an important contributor to fungal pathogenesis and warrants further research into critical proteins within global stress response networks as potential druggable targets to reduce fungal virulence and clear infection.
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Affiliation(s)
- Brianna Ball
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Arjun Sukumaran
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Samanta Pladwig
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Samiha Kazi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Norris Chan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Effie Honeywell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Manuela Modrakova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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80
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Fábián Z, Kakulidis ES, Hendriks IA, Kühbacher U, Larsen NB, Oliva-Santiago M, Wang J, Leng X, Dirac-Svejstrup AB, Svejstrup JQ, Nielsen ML, Caldecott K, Duxin JP. PARP1-dependent DNA-protein crosslink repair. Nat Commun 2024; 15:6641. [PMID: 39103378 PMCID: PMC11300803 DOI: 10.1038/s41467-024-50912-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 07/25/2024] [Indexed: 08/07/2024] Open
Abstract
DNA-protein crosslinks (DPCs) are toxic lesions that inhibit DNA related processes. Post-translational modifications (PTMs), including SUMOylation and ubiquitylation, play a central role in DPC resolution, but whether other PTMs are also involved remains elusive. Here, we identify a DPC repair pathway orchestrated by poly-ADP-ribosylation (PARylation). Using Xenopus egg extracts, we show that DPCs on single-stranded DNA gaps can be targeted for degradation via a replication-independent mechanism. During this process, DPCs are initially PARylated by PARP1 and subsequently ubiquitylated and degraded by the proteasome. Notably, PARP1-mediated DPC resolution is required for resolving topoisomerase 1-DNA cleavage complexes (TOP1ccs) induced by camptothecin. Using the Flp-nick system, we further reveal that in the absence of PARP1 activity, the TOP1cc-like lesion persists and induces replisome disassembly when encountered by a DNA replication fork. In summary, our work uncovers a PARP1-mediated DPC repair pathway that may underlie the synergistic toxicity between TOP1 poisons and PARP inhibitors.
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Affiliation(s)
- Zita Fábián
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ellen S Kakulidis
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ivo A Hendriks
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Ulrike Kühbacher
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Nicolai B Larsen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Marta Oliva-Santiago
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Junhui Wang
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RH, UK
| | - Xueyuan Leng
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - A Barbara Dirac-Svejstrup
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Keith Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RH, UK
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark.
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81
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Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman JE, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579775. [PMID: 38405833 PMCID: PMC10888908 DOI: 10.1101/2024.02.10.579775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The intricate molecular environment of the native membrane profoundly influences every aspect of membrane protein (MP) biology. Despite this, the most prevalent method of studying MPs uses detergent-like molecules that disrupt and remove this vital local membrane context. This severely impedes our ability to quantitatively decipher the local molecular context and comprehend its regulatory role in the structure, function, and biogenesis of MPs. Using a library of membrane-active polymers we have developed a platform for the high-throughput analysis of the membrane proteome. The platform enables near-complete spatially resolved extraction of target MPs directly from their endogenous membranes into native nanodiscs that maintain the local membrane context. We accompany this advancement with an open-access database that quantifies the polymer-specific extraction variability for 2065 unique mammalian MPs and provides the most optimized condition for each of them. Our method enables rapid and near-complete extraction and purification of target MPs directly from their endogenous organellar membranes at physiological expression levels while maintaining the nanoscale local membrane environment. Going beyond the plasma membrane proteome, our platform enables extraction from any target organellar membrane including the endoplasmic reticulum, mitochondria, lysosome, Golgi, and even transient organelles such as the autophagosome. To further validate this platform, we took several independent MPs and demonstrated how our resource can enable rapid extraction and purification of target MPs from different organellar membranes with high efficiency and purity. Further, taking two synaptic vesicle MPs, we show how the database can be extended to capture multiprotein complexes between overexpressed MPs. We expect these publicly available resources to empower researchers across disciplines to efficiently capture membrane 'nano-scoops' containing a target MP and interface with structural, functional, and other bioanalytical approaches. We demonstrate an example of this by combining our extraction platform with single-molecule TIRF imaging to demonstrate how it can enable rapid determination of homo-oligomeric states of target MPs in native cell membranes.
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Affiliation(s)
- Caroline Brown
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Snehasish Ghosh
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - Rachel McAllister
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Mukesh Kumar
- F.M. Kirby Neurobiology Center, Department of Neurobiology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gerard Walker
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Eric Sun
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Talat Aman
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Shailesh Kumar
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Jeff Coleman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University, New Haven, CT, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - James E Rothman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
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82
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Ahola S, Pazurek LA, Mayer F, Lampe P, Hermans S, Becker L, Amarie OV, Fuchs H, Gailus-Durner V, de Angelis MH, Riedel D, Nolte H, Langer T. Opa1 processing is dispensable in mouse development but is protective in mitochondrial cardiomyopathy. SCIENCE ADVANCES 2024; 10:eadp0443. [PMID: 39093974 PMCID: PMC11296347 DOI: 10.1126/sciadv.adp0443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024]
Abstract
Mitochondrial fusion and fission accompany adaptive responses to stress and altered metabolic demands. Inner membrane fusion and cristae morphogenesis depends on optic atrophy 1 (Opa1), which is expressed in different isoforms and is cleaved from a membrane-bound, long to a soluble, short form. Here, we have analyzed the physiological role of Opa1 isoforms and Opa1 processing by generating mouse lines expressing only one cleavable Opa1 isoform or a non-cleavable variant thereof. Our results show that expression of a single cleavable or non-cleavable Opa1 isoform preserves embryonic development and the health of adult mice. Opa1 processing is dispensable under metabolic and thermal stress but prolongs life span and protects against mitochondrial cardiomyopathy in OXPHOS-deficient Cox10-/- mice. Mechanistically, loss of Opa1 processing disturbs the balance between mitochondrial biogenesis and mitophagy, suppressing cardiac hypertrophic growth in Cox10-/- hearts. Our results highlight the critical regulatory role of Opa1 processing, mitochondrial dynamics, and metabolism for cardiac hypertrophy.
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Affiliation(s)
- Sofia Ahola
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Fiona Mayer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Philipp Lampe
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Steffen Hermans
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Lore Becker
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg
| | - Dietmar Riedel
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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83
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Hemmati M, Wudy SI, Hackbarth F, Mittermeier-Kleßinger VK, Coleman OI, Haller D, Ludwig C, Dawid C, Kleigrewe K. Development of a Global Metabo-Lipid-Prote-omics Workflow to Compare Healthy Proximal and Distal Colonic Epithelium in Mice. J Proteome Res 2024; 23:3124-3140. [PMID: 39052308 DOI: 10.1021/acs.jproteome.3c00771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
A multimetabo-lipid-prote-omics workflow was developed to characterize the molecular interplay within proximal (PC) and distal (DC) colonic epithelium of healthy mice. This multiomics data set lays the foundation to better understand the two tissue types and can be used to study, for example, colon-related diseases like colorectal cancer or inflammatory bowel disease. First, the methyl tert-butyl ether extraction method was optimized, so that from a single tissue biopsy >350 reference-matched metabolites, >1850 reference-matched lipids, and >4500 proteins were detected by using targeted and untargeted metabolomics, untargeted lipidomics, and proteomics. Next, each omics-data set was analyzed individually and then merged with the additional omics disciplines to generate a deep understanding of the underlying complex regulatory network within the colon. Our data demonstrates, for example, differences in mucin formation, detected on substrate level as well as on enzyme level, and altered lipid metabolism by the detection of phospholipases hydrolyzing sphingomyelins to ceramides. In conclusion, the combination of the three mass spectrometry-based omics techniques can better entangle the functional and regional differences between PC and DC tissue compared to each single omics technique.
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Affiliation(s)
- Maryam Hemmati
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Susanne I Wudy
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Franziska Hackbarth
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Verena K Mittermeier-Kleßinger
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Olivia I Coleman
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Corinna Dawid
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Professorship for Functional Phytometabolomics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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84
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Bataclan M, Leoni C, Moro SG, Pecoraro M, Wong EH, Heissmeyer V, Monticelli S. Crosstalk between Regnase-1 and -3 shapes mast cell survival and cytokine expression. Life Sci Alliance 2024; 7:e202402784. [PMID: 38830770 PMCID: PMC11147952 DOI: 10.26508/lsa.202402784] [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: 04/22/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
Post-transcriptional regulation of immune-related transcripts by RNA-binding proteins (RBPs) impacts immune cell responses, including mast cell functionality. Despite their importance in immune regulation, the functional role of most RBPs remains to be understood. By manipulating the expression of specific RBPs in murine mast cells, coupled with mass spectrometry and transcriptomic analyses, we found that the Regnase family of proteins acts as a potent regulator of mast cell physiology. Specifically, Regnase-1 is required to maintain basic cell proliferation and survival, whereas both Regnase-1 and -3 cooperatively regulate the expression of inflammatory transcripts upon activation, with Tnf being a primary target in both human and mouse cells. Furthermore, Regnase-3 directly interacts with Regnase-1 in mast cells and is necessary to restrain Regnase-1 expression through the destabilization of its transcript. Overall, our study identifies protein interactors of endogenously expressed Regnase factors, characterizes the regulatory interplay between Regnase family members in mast cells, and establishes their role in the control of mast cell homeostasis and inflammatory responses.
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Affiliation(s)
- Marian Bataclan
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Cristina Leoni
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Simone G Moro
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Matteo Pecoraro
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Elaine H Wong
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| | - Silvia Monticelli
- https://ror.org/05gfswd81 Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
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85
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Montoya MR, Quanrud GM, Mei L, Moñtano JL, Hong C, Genereux JC. Factors affecting protein recovery during Hsp40 affinity profiling. Anal Bioanal Chem 2024; 416:4249-4260. [PMID: 38850318 PMCID: PMC11271386 DOI: 10.1007/s00216-024-05362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/30/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024]
Abstract
The identification and quantification of misfolded proteins from complex mixtures is important for biological characterization and disease diagnosis, but remains a major bioanalytical challenge. We have developed Hsp40 Affinity Profiling as a bioanalytical approach to profile protein stability in response to cellular stress. In this assay, we ectopically introduce the Hsp40 FlagDNAJB8H31Q into cells and use quantitative proteomics to determine how protein affinity for DNAJB8 changes in the presence of cellular stress, without regard for native clients. Herein, we evaluate potential approaches to improve the performance of this bioanalytical assay. We find that although intracellular crosslinking increases recovery of protein interactors, this is not enough to overcome the relative drop in DNAJB8 recovery. While the J-domain promotes Hsp70 association, it does not affect the yield of protein association with DNAJB8 under basal conditions. By contrast, crosslinking and J-domain ablation both substantially increase relative protein interactor recovery with the structurally distinct Class B Hsp40 DNAJB1 but are completely compensated by poorer yield of DNAJB1 itself. Cellular thermal stress promotes increased affinity between DNAJB8H31Q and interacting proteins, as expected for interactions driven by recognition of misfolded proteins. DNAJB8WT does not demonstrate such a property, suggesting that under stress misfolded proteins are handed off to Hsp70. Hence, we find that DNAJB8H31Q is still our most effective recognition element for the recovery of destabilized client proteins following cellular stress.
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Affiliation(s)
- Maureen R Montoya
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Guy M Quanrud
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Liangyong Mei
- Department of Chemistry, University of North Florida, Jacksonville, FL, USA
| | - José L Moñtano
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Caleb Hong
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, 501 Big Springs Rd, Riverside, CA, 92521, USA.
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86
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Janusova S, Paprckova D, Michalik J, Uleri V, Drobek A, Salyova E, Chorfi L, Neuwirth A, Andreyeva A, Prochazka J, Sedlacek R, Draber P, Stepanek O. ABIN1 is a negative regulator of effector functions in cytotoxic T cells. EMBO Rep 2024; 25:3456-3485. [PMID: 38877170 PMCID: PMC11315980 DOI: 10.1038/s44319-024-00179-6] [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: 12/02/2023] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
T cells are pivotal in the adaptive immune defense, necessitating a delicate balance between robust response against infections and self-tolerance. Their activation involves intricate cross-talk among signaling pathways triggered by the T-cell antigen receptors (TCR) and co-stimulatory or inhibitory receptors. The molecular regulation of these complex signaling networks is still incompletely understood. Here, we identify the adaptor protein ABIN1 as a component of the signaling complexes of GITR and OX40 co-stimulation receptors. T cells lacking ABIN1 are hyper-responsive ex vivo, exhibit enhanced responses to cognate infections, and superior ability to induce experimental autoimmune diabetes in mice. ABIN1 negatively regulates p38 kinase activation and late NF-κB target genes. P38 is at least partially responsible for the upregulation of the key effector proteins IFNG and GZMB in ABIN1-deficient T cells after TCR stimulation. Our findings reveal the intricate role of ABIN1 in T-cell regulation.
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MESH Headings
- Animals
- Humans
- Mice
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Glucocorticoid-Induced TNFR-Related Protein
- Interferon-gamma/metabolism
- Lymphocyte Activation/immunology
- Lymphocyte Activation/genetics
- Mice, Inbred C57BL
- Mice, Knockout
- NF-kappa B/metabolism
- p38 Mitogen-Activated Protein Kinases/metabolism
- Receptors, Antigen, T-Cell/metabolism
- Receptors, OX40/metabolism
- Receptors, OX40/genetics
- Signal Transduction
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Sarka Janusova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Darina Paprckova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Juraj Michalik
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Valeria Uleri
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Ales Drobek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eva Salyova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Louise Chorfi
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ales Neuwirth
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Arina Andreyeva
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Peter Draber
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Immunity & Cell Communication, Division BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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87
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Zhang L, Elkahal J, Wang T, Rimmer R, Genzelinakh A, Bassat E, Wang J, Perez D, Kain D, Lendengolts D, Winkler R, Bueno-Levy H, Umansky KB, Mishaly D, Shakked A, Miyara S, Sarusi-Portuguez A, Goldfinger N, Prior A, Morgenstern D, Levin Y, Addadi Y, Li B, Rotter V, Katz U, Tanaka EM, Krizhanovsky V, Sarig R, Tzahor E. Egr1 regulates regenerative senescence and cardiac repair. NATURE CARDIOVASCULAR RESEARCH 2024; 3:915-932. [PMID: 39196027 DOI: 10.1038/s44161-024-00493-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/16/2024] [Indexed: 08/29/2024]
Abstract
Senescence plays a key role in various physiological and pathological processes. We reported that injury-induced transient senescence correlates with heart regeneration, yet the multi-omics profile and molecular underpinnings of regenerative senescence remain obscure. Using proteomics and single-cell RNA sequencing, here we report the regenerative senescence multi-omic signature in the adult mouse heart and establish its role in neonatal heart regeneration and agrin-mediated cardiac repair in adult mice. We identified early growth response protein 1 (Egr1) as a regulator of regenerative senescence in both models. In the neonatal heart, Egr1 facilitates angiogenesis and cardiomyocyte proliferation. In adult hearts, agrin-induced senescence and repair require Egr1, activated by the integrin-FAK-ERK-Akt1 axis in cardiac fibroblasts. We also identified cathepsins as injury-induced senescence-associated secretory phenotype components that promote extracellular matrix degradation and potentially assist in reducing fibrosis. Altogether, we uncovered the molecular signature and functional benefits of regenerative senescence during heart regeneration, with Egr1 orchestrating the process.
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Affiliation(s)
- Lingling Zhang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob Elkahal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tianzhen Wang
- Department of Bimolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Racheli Rimmer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Genzelinakh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elad Bassat
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Dahlia Perez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Kain
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daria Lendengolts
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Roni Winkler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hanna Bueno-Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Veterinary Resource, Weizmann Institute of Science, Rehovot, Israel
| | - Kfir Baruch Umansky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Mishaly
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Avraham Shakked
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shoval Miyara
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avital Sarusi-Portuguez
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Goldfinger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Prior
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - David Morgenstern
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Baoguo Li
- Department of System Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Uriel Katz
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Valery Krizhanovsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rachel Sarig
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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88
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Silva Medeiros M, Botelho de Carvalho LA, Alves M, Papoila A, Baptista Carreira Dos Santos HM, Capelo-Martínez JL, Viegas de Campos Pinheiro LM. Low Cubilin/Myeloperoxidase ratio as a promising biomarker for prognosis of high-grade T1 bladder cancer. Int Urol Nephrol 2024; 56:2577-2587. [PMID: 38530585 PMCID: PMC11266244 DOI: 10.1007/s11255-024-03971-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/03/2024] [Indexed: 03/28/2024]
Abstract
PURPOSE T1 bladder cancer is known for its high progression and recurrence rates. Identifying aggressive tumours at the non-muscle-invasive stage is crucial to allow early interventions and subsequently increase patient survival. This study aimed to investigate the potential of the cubilin/myeloperoxidase (CUBN/MPO) ratio as a high-grade T1 bladder cancer biomarker. METHODS Urine samples were collected from 30 patients who underwent transurethral resection of the tumour with high-grade T1 bladder cancer (June 2015 to December 2019) before surgery. The urinary proteome was analysed using high-resolution mass spectrometry and the CUBN/MPO ratio was calculated. The primary outcome was the recurrence during the follow-up (around 31.5 months after resection). Univariate Cox regression and Kaplan-Meier curves were used for data analysis. RESULTS Patients with a low CUBN/MPO ratio exhibited upregulated MPO and/or downregulated CUBN. This group of patients had a higher incidence of disease recurrence and progression. Low CUBN/MPO ratio was significantly associated with a higher likelihood of recurrence, progression, and death. It is worth noting that this study was exploratory and conducted on a small sample size, so further research is needed to validate these findings in larger cohorts. CONCLUSION This study highlights the potential of the CUBN/MPO ratio as a prognostic biomarker for high-grade T1 bladder cancer.
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Affiliation(s)
| | | | - Marta Alves
- Epidemiology and Statistics Unit, Research Centre, Central Lisbon University Hospital Centre, Lisbon, Portugal
| | - Ana Papoila
- Epidemiology and Statistics Unit, Research Centre, Central Lisbon University Hospital Centre, Lisbon, Portugal
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89
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Waltho A, Popp O, Lenz C, Pluska L, Lambert M, Dötsch V, Mertins P, Sommer T. K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors. Life Sci Alliance 2024; 7:e202402740. [PMID: 38803224 PMCID: PMC11109483 DOI: 10.26508/lsa.202402740] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different lengths, linkage types, and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying lengths, as well as homotypic and heterotypic branched chains of the two most abundant linkage types-lysine 48-linked (K48) and lysine 63-linked (K63) Ub. We identified some of the first K48/K63-linked branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4, and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50, and p97 adaptor FAF1. Crucially, we compared datasets collected using two common deubiquitinase inhibitors-chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.
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Affiliation(s)
- Anita Waltho
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Christopher Lenz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Lukas Pluska
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
| | - Mahil Lambert
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Volker Dötsch
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Thomas Sommer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Biology, Humboldt-University zu Berlin, Berlin, Germany
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90
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Oliveira D, Assoni AF, Alves LM, Sakugawa A, Melo US, Teles E Silva AL, Sertie AL, Caires LC, Goulart E, Ghirotto B, Carvalho VM, Ferrari MR, Zatz M. ALS-associated VRK1 R321C mutation causes proteostatic imbalance and mitochondrial defects in iPSC-derived motor neurons. Neurobiol Dis 2024; 198:106540. [PMID: 38806131 DOI: 10.1016/j.nbd.2024.106540] [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: 03/20/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
Vaccinia-related kinase 1 (VRK1) is a gene which has been implicated in the pathological process of a broad range of neurodevelopmental disorders as well as neuropathies, such as Amyotrophic Lateral Sclerosis (ALS). Here we report a family presenting ALS in an autosomal recessive mode of inheritance, segregating with a homozygous missense mutation located in VRK1 gene (p.R321C; Arg321Cys). Proteomic analyses from iPSC-derived motor neurons identified 720 proteins eligible for subsequent investigation, and our exploration of protein profiles revealed significant enrichments in pathways such as mTOR signaling, E2F, MYC targets, DNA repair response, cell proliferation and energetic metabolism. Functional studies further validated such alterations, showing that affected motor neurons presented decreased levels of global protein output, ER stress and downregulation of mTOR signaling. Mitochondrial alterations also pointed to decreased reserve capacity and increased non-mitochondrial oxygen consumption. Taken together, our results present the main pathological alterations associated with VRK1 mutation in ALS.
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Affiliation(s)
- D Oliveira
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; School of Medical Sciences Santa Casa and Pathological Sciences Unit, Irmandade Santa Casa de Misericordia de Sao Paulo, Sao Paulo, Brazil.
| | - A F Assoni
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - L M Alves
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - A Sakugawa
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - U S Melo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, Berlin, Germany
| | | | - A L Sertie
- Hospital Albert Einstein, São Paulo, São Paulo, Brazil
| | - L C Caires
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - E Goulart
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - B Ghirotto
- Department of Stem Cell Biology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - V M Carvalho
- Division of Research and Development, Fleury Group, São Paulo, SP 04344-070, Brazil
| | - M R Ferrari
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - M Zatz
- Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.
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91
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Guo Y, Stampoultzis T, Karami P, Nasrollahzadeh N, Rana VK, Pioletti DP. HSP70-A key regulator in chondrocyte homeostasis under naturally coupled hydrostatic pressure-thermal stimuli. Osteoarthritis Cartilage 2024; 32:896-908. [PMID: 38679285 DOI: 10.1016/j.joca.2024.04.008] [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: 12/07/2023] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024]
Abstract
OBJECTIVE During physical activities, chondrocytes experience coupled stimulation of hydrostatic pressure (HP) and a transient increase in temperature (T), with the latter varying within a physiological range from 32.5 °C to 38.7 °C. Previous short-term in vitro studies have demonstrated that the combined hydrostatic pressure-thermal (HP-T) stimuli more significantly enhance chondroinduction and chondroprotection of chondrocytes than isolated applications. Interestingly, this combined benefit is associated with a corresponding increase in HSP70 levels when HP and T are combined. The current study therefore explored the indispensable role of HSP70 in mediating the combined effects of HP-T stimuli on chondrocytes. DESIGN In this mid-long-term study of in vitro engineered cartilage constructs, we assessed chondrocyte responses to HP-T stimuli using customized bioreactor in standard and HSP70-inhibited cultures. RESULTS Surprisingly, under HSP70-inhibited conditions, the usually beneficial HP-T stimuli, especially its thermal component, exerted detrimental effects on chondrocyte homeostasis, showing a distinct and unfavorable shift in gene and protein expression patterns compared to non-HSP70-inhibited settings. Such effects were corroborated through mechanical testing and confirmed using a secondary cell source. A proteomic-based mechanistic analysis revealed a disruption in the balance between biosynthesis and fundamental cellular structural components in HSP70-inhibited conditions under HP-T stimuli. CONCLUSIONS Our results highlight the critical role of sufficient HSP70 induction in mediating the beneficial effects of coupled HP-T stimulation on chondrocytes. These findings help pave the way for new therapeutic approaches to enhance physiotherapy outcomes and potentially shed light on the elusive mechanisms underlying the onset of cartilage degeneration, a long-standing enigma in orthopedics.
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Affiliation(s)
- Yanheng Guo
- Laboratory of Biomechanical Orthopedics, Institute of Bioengineering, EPFL, Switzerland
| | | | - Peyman Karami
- Laboratory of Biomechanical Orthopedics, Institute of Bioengineering, EPFL, Switzerland
| | - Naser Nasrollahzadeh
- Laboratory of Biomechanical Orthopedics, Institute of Bioengineering, EPFL, Switzerland
| | - Vijay K Rana
- Laboratory of Biomechanical Orthopedics, Institute of Bioengineering, EPFL, Switzerland
| | - Dominique P Pioletti
- Laboratory of Biomechanical Orthopedics, Institute of Bioengineering, EPFL, Switzerland.
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92
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Prudhomme N, Pastora R, Thomson S, Zheng E, Sproule A, Krieger JR, Murphy JP, Overy DP, Cossar D, McLean MD, Geddes‐McAlister J. Bacterial growth-mediated systems remodelling of Nicotiana benthamiana defines unique signatures of target protein production in molecular pharming. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2248-2266. [PMID: 38516995 PMCID: PMC11258984 DOI: 10.1111/pbi.14342] [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: 07/01/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
The need for therapeutics to treat a plethora of medical conditions and diseases is on the rise and the demand for alternative approaches to mammalian-based production systems is increasing. Plant-based strategies provide a safe and effective alternative to produce biological drugs but have yet to enter mainstream manufacturing at a competitive level. Limitations associated with batch consistency and target protein production levels are present; however, strategies to overcome these challenges are underway. In this study, we apply state-of-the-art mass spectrometry-based proteomics to define proteome remodelling of the plant following agroinfiltration with bacteria grown under shake flask or bioreactor conditions. We observed distinct signatures of bacterial protein production corresponding to the different growth conditions that directly influence the plant defence responses and target protein production on a temporal axis. Our integration of proteomic profiling with small molecule detection and quantification reveals the fluctuation of secondary metabolite production over time to provide new insight into the complexities of dual system modulation in molecular pharming. Our findings suggest that bioreactor bacterial growth may promote evasion of early plant defence responses towards Agrobacterium tumefaciens (updated nomenclature to Rhizobium radiobacter). Furthermore, we uncover and explore specific targets for genetic manipulation to suppress host defences and increase recombinant protein production in molecular pharming.
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Affiliation(s)
- Nicholas Prudhomme
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| | | | - Sarah Thomson
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| | - Edison Zheng
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphONCanada
| | - Amanda Sproule
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | | | - J. Patrick Murphy
- Department of BiologyUniversity of Prince Edward IslandCharlottetownPECanada
| | - David P. Overy
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
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93
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Yang Z, Chen L, Huang Y, Dong J, Yan Q, Li Y, Qiu J, Li H, Zhao D, Liu F, Tang D, Dai Y. Proteomic profiling of laser capture microdissection kidneys from diabetic nephropathy patients. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1243:124231. [PMID: 38996754 DOI: 10.1016/j.jchromb.2024.124231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/23/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
Diabetic nephropathy (DN) remains the primary cause of end-stage renal disease (ESRD), warranting equal attention and separate analysis of glomerular, tubular, and interstitial lesions in its diagnosis and intervention. This study aims to identify the specific proteomics characteristics of DN, and assess changes in the biological processes associated with DN. 5 patients with DN and 5 healthy kidney transplant donor control individuals were selected for analysis. The proteomic characteristics of glomeruli, renal tubules, and renal interstitial tissue obtained through laser capture microscopy (LCM) were studied using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Significantly, the expression of multiple heat shock proteins (HSPs), tubulins, and heterogeneous nuclear ribonucleoproteins (hnRNPs) in glomeruli and tubules was significantly reduced. Differentially expressed proteins (DEPs) in the glomerulus showed significant enrichment in pathways related to cell junctions and cell movement, including the regulation of actin cytoskeleton and tight junction. DEPs in renal tubules were significantly enriched in glucose metabolism-related pathways, such as glucose metabolism, glycolysis/gluconeogenesis, and the citric acid cycle. Moreover, the glycolysis/gluconeogenesis pathway was a co-enrichment pathway in both DN glomeruli and tubules. Notably, ACTB emerged as the most crucial protein in the protein-protein interaction (PPI) analysis of DEPs in both glomeruli and renal tubules. In this study, we delve into the unique proteomic characteristics of each sub-region of renal tissue. This enhances our understanding of the potential pathophysiological changes in DN, particularly the potential involvement of glycolysis metabolic disorder, glomerular cytoskeleton and cell junctions. These insights are crucial for further research into the identification of disease biomarkers and the pathogenesis of DN.
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Affiliation(s)
- Zhiqian Yang
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China; Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Liangmei Chen
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Yingxin Huang
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China; Department of Nephrology, Xiaolan People's Hospital of Zhongshan, 528400, China
| | - Jingjing Dong
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China; Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Qiang Yan
- Department of Organ Transplantation, 924 Hospital, Guilin 541002, China
| | - Ya Li
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Jing Qiu
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Haitao Li
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China
| | - Da Zhao
- The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan 232001, Anhui, China
| | - Fanna Liu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China.
| | - Donge Tang
- Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People' s Hospital, The Second Clinical Medical College, Jinan University, Shenzhen 518020, China.
| | - Yong Dai
- Comprehensive Health Industry Research Center, Taizhou Research Institute, Southern University of Science and Technology, Taizhou 317000, China; The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan 232001, Anhui, China.
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94
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Dhulkifle H, Therachiyil L, Hasan MH, Sayed TS, Younis SM, Korashy HM, Yalcin HC, Maayah ZH. Inhibition of cytochrome P450 epoxygenase promotes endothelium-to-mesenchymal transition and exacerbates doxorubicin-induced cardiovascular toxicity. Mol Biol Rep 2024; 51:859. [PMID: 39066934 PMCID: PMC11283412 DOI: 10.1007/s11033-024-09803-z] [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: 05/15/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Doxorubicin (DOX) is a potent chemotherapy widely used in treating various neoplastic diseases. However, the clinical use of DOX is limited due to its potential toxic effect on the cardiovascular system. Thus, identifying the pathway involved in this toxicity may help minimize chemotherapy risk and improve cancer patients' quality of life. Recent studies suggest that Endothelial-to-Mesenchymal transition (EndMT) and endothelial toxicity contribute to the pathogenesis of DOX-induced cardiovascular toxicity. However, the molecular mechanism is yet unknown. Given that arachidonic acid and associated cytochrome P450 (CYP) epoxygenase have been involved in endothelial and cardiovascular function, we aimed to examine the effect of suppressing CYP epoxygenases on DOX-induced EndMT and cardiovascular toxicity in vitro and in vivo. METHODS AND RESULTS To test this, human endothelial cells were treated with DOX, with or without CYP epoxygenase inhibitor, MSPPOH. We also investigated the effect of MSPPOH on the cardiovascular system in our zebrafish model of DOX-induced cardiotoxicity. Our results showed that MSPPOH exacerbated DOX-induced EndMT, inflammation, oxidative stress, and apoptosis in our endothelial cells. Furthermore, we also show that MSPPOH increased cardiac edema, lowered vascular blood flow velocity, and worsened the expression of EndMT and cardiac injury markers in our zebrafish model of DOX-induced cardiotoxicity. CONCLUSION Our data indicate that a selective CYP epoxygenase inhibitor, MSPPOH, induces EndMT and endothelial toxicity to contribute to DOX-induced cardiovascular toxicity.
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Affiliation(s)
- Hevna Dhulkifle
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health Sector, Qatar University, 2713, Doha, Qatar
| | - Lubna Therachiyil
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health Sector, Qatar University, 2713, Doha, Qatar
- Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Maram H Hasan
- Biomedical Research Center, QU Health Sector, Qatar University, 2713, Doha, Qatar
| | - Tahseen S Sayed
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health Sector, Qatar University, 2713, Doha, Qatar
| | - Shahd M Younis
- Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Hesham M Korashy
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health Sector, Qatar University, 2713, Doha, Qatar
| | - Huseyin C Yalcin
- Biomedical Research Center, QU Health Sector, Qatar University, 2713, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences, QU Health Sector, Qatar University, 2713, Doha, Qatar
| | - Zaid H Maayah
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health Sector, Qatar University, 2713, Doha, Qatar.
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95
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Ousalem F, Ngo S, Oïffer T, Omairi-Nasser A, Hamon M, Monlezun L, Boël G. Global regulation via modulation of ribosome pausing by the ABC-F protein EttA. Nat Commun 2024; 15:6314. [PMID: 39060293 PMCID: PMC11282234 DOI: 10.1038/s41467-024-50627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Having multiple rounds of translation of the same mRNA creates dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences. Yet, mechanisms controlling these critical processes and the principles guiding their evolution remain poorly understood. Through genetic, genomic, physiological, and biochemical approaches, we demonstrate that regulating ribosome pausing at specific amino acid sequences can produce ~2-fold changes in protein expression levels which strongly influence cell growth and therefore evolutionary fitness. We demonstrate, both in vivo and in vitro, that the ABC-F protein EttA directly controls the translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle and its glyoxylate shunt, which modulates growth in some chemical environments. EttA also modulates expression of specific proteins involved in metabolically related physiological and stress-response pathways. These regulatory activities are mediated by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within the first 30 amino acids of nascent proteins. We thus establish a unique global regulatory paradigm based on sequence-specific modulation of translational pausing.
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Affiliation(s)
- Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
- Biomarqueurs et nouvelles cibles thérapeutiques en oncologie, INSERM U981, Université Paris Saclay, Institut de Cancérologie Gustave Roussy, Villejuif Cedex, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Thomas Oïffer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Amin Omairi-Nasser
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Marion Hamon
- CNRS, Institut de Biologie Physico-Chimique, Plateforme de Protéomique, FR550, Paris, France
| | - Laura Monlezun
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.
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96
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Fernandes EFA, Palner M, Raval NR, Jeppesen TE, Danková D, Bærentzen SL, Werner C, Eilts J, Maric HM, Doose S, Aripaka SS, Kaalund SS, Aznar S, Kjaer A, Schlosser A, Haugaard-Kedström LM, Knudsen GM, Herth MM, Stro Mgaard K. Development of Peptide-Based Probes for Molecular Imaging of the Postsynaptic Density in the Brain. J Med Chem 2024; 67:11975-11988. [PMID: 38981131 DOI: 10.1021/acs.jmedchem.4c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The postsynaptic density (PSD) comprises numerous scaffolding proteins, receptors, and signaling molecules that coordinate synaptic transmission in the brain. Postsynaptic density protein 95 (PSD-95) is a master scaffold protein within the PSD and one of its most abundant proteins and therefore constitutes a very attractive biomarker of PSD function and its pathological changes. Here, we exploit a high-affinity inhibitor of PSD-95, AVLX-144, as a template for developing probes for molecular imaging of the PSD. AVLX-144-based probes were labeled with the radioisotopes fluorine-18 and tritium, as well as a fluorescent tag. Tracer binding showed saturable, displaceable, and uneven distribution in rat brain slices, proving effective in quantitative autoradiography and cell imaging studies. Notably, we observed diminished tracer binding in human post-mortem Parkinson's disease (PD) brain slices, suggesting postsynaptic impairment in PD. We thus offer a suite of translational probes for visualizing and understanding PSD-related pathologies.
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Affiliation(s)
- Eduardo F A Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Mikael Palner
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Nakul Ravi Raval
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, Connecticut 06520, United States
| | - Troels E Jeppesen
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Daniela Danková
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Simone L Bærentzen
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Christian Werner
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Janna Eilts
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Hans M Maric
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Julius-Maximilians-University, Josef-Schneider-Str. 2, Würzburg 97080, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Sanjay Sagar Aripaka
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Sanne Simone Kaalund
- Center for Neuroscience and Stereology, Bispebjerg University Hospital, Nielsine Nielsens Vej 6B, Copenhagen DK-2400, Denmark
| | - Susana Aznar
- Center for Neuroscience and Stereology, Bispebjerg University Hospital, Nielsine Nielsens Vej 6B, Copenhagen DK-2400, Denmark
- Center for Translational Research, Bispebjerg University Hospital, Nielsine Nielsens Vej 4B, Copenhagen DK-2400, Denmark
| | - Andreas Kjaer
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Andreas Schlosser
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-University, Am Hubland, Würzburg D-97074, Germany
| | - Linda M Haugaard-Kedström
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
| | - Gitte M Knudsen
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Matthias M Herth
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
- Neurobiology Research Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen DK-2100, Denmark
- Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital - Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen DK-2200, Denmark
| | - Kristian Stro Mgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100, Denmark
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97
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Wang C, Zhang X, Wu K, Liu S, Li X, Zhu C, Xiao Y, Fang Z, Liu J. Two Zn 2Cys 6-type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta. Appl Environ Microbiol 2024; 90:e0054524. [PMID: 38899887 PMCID: PMC11267944 DOI: 10.1128/aem.00545-24] [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: 03/22/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
White-rot fungi differentially express laccases when they encounter aromatic compounds. However, the underlying mechanisms are still being explored. Here, proteomics analysis revealed that in addition to increased laccase activity, proteins involved in sphingolipid metabolism and toluene degradation as well as some cytochrome P450s (CYP450s) were differentially expressed and significantly enriched during 48 h of o-toluidine exposure, in Trametes hirsuta AH28-2. Two Zn2Cys6-type transcription factors (TFs), TH8421 and TH4300, were upregulated. Bioinformatics docking and isothermal titration calorimetry assays showed that each of them could bind directly to o-toluidine and another aromatic monomer, guaiacol. Binding to aromatic compounds promoted the formation of TH8421/TH4300 heterodimers. TH8421 and TH4300 silencing in T. hirsuta AH28-2 led to decreased transcriptional levels and activities of LacA and LacB upon o-toluidine and guaiacol exposure. EMSA and ChIP-qPCR analysis further showed that TH8421 and TH4300 bound directly with the promoter regions of lacA and lacB containing CGG or CCG motifs. Furthermore, the two TFs were involved in direct and positive regulation of the transcription of some CYP450s. Together, TH8421 and TH4300, two key regulators found in T. hirsuta AH28-2, function as heterodimers to simultaneously trigger the expression of downstream laccases and intracellular enzymes. Monomeric aromatic compounds act as ligands to promote heterodimer formation and enhance the transcriptional activities of the two TFs.IMPORTANCEWhite-rot fungi differentially express laccase isoenzymes when exposed to aromatic compounds. Clarification of the molecular mechanisms underlying differential laccase expression is essential to elucidate how white-rot fungi respond to the environment. Our study shows that two Zn2Cys6-type transcription factors form heterodimers, interact with the promoters of laccase genes, and positively regulate laccase transcription in Trametes hirsuta AH28-2. Aromatic monomer addition induces faster heterodimer formation and rate of activity. These findings not only identify two new transcription factors involved in fungal laccase transcription but also deepen our understanding of the mechanisms underlying the response to aromatics exposure in white-rot fungi.
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Affiliation(s)
- Chenkai Wang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xinlei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Kun Wu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Shenglong Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Xiang Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Chaona Zhu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, China
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98
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Phongbunchoo Y, Braikia FZ, Pessoa-Rodrigues C, Ramamoorthy S, Ramachandran H, Grosschedl A, Ma F, Cauchy P, Akhtar A, Sen R, Mittler G, Grosschedl R. YY1-mediated enhancer-promoter communication in the immunoglobulin μ locus is regulated by MSL/MOF recruitment. Cell Rep 2024; 43:114456. [PMID: 38990722 DOI: 10.1016/j.celrep.2024.114456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/02/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The rearrangement and expression of the immunoglobulin μ heavy chain (Igh) gene require communication of the intragenic Eμ and 3' regulatory region (RR) enhancers with the variable (VH) gene promoter. Eμ binding of the transcription factor YY1 has been implicated in enhancer-promoter communication, but the YY1 protein network remains obscure. By analyzing the comprehensive proteome of the 1-kb Eμ wild-type enhancer and that of Eμ lacking the YY1 binding site, we identified the male-specific lethal (MSL)/MOF complex as a component of the YY1 protein network. We found that MSL2 recruitment depends on YY1 and that gene knockout of Msl2 in primary pre-B cells reduces μ gene expression and chromatin looping of Eμ to the 3' RR enhancer and VH promoter. Moreover, Mof heterozygosity in mice impaired μ expression and early B cell differentiation. Together, these data suggest that the MSL/MOF complex regulates Igh gene expression by augmenting YY1-mediated enhancer-promoter communication.
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Affiliation(s)
- Yutthaphong Phongbunchoo
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fatima-Zohra Braikia
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cecilia Pessoa-Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Haribaskar Ramachandran
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Anna Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fei Ma
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Pierre Cauchy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Ranjan Sen
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA.
| | - Gerhard Mittler
- Proteomics Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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99
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Schmidt L, Saynisch M, Hoegsbjerg C, Schmidt A, Mackey A, Lackmann JW, Müller S, Koch M, Brachvogel B, Kjaer M, Antczak P, Krüger M. Spatial proteomics of skeletal muscle using thin cryosections reveals metabolic adaptation at the muscle-tendon transition zone. Cell Rep 2024; 43:114374. [PMID: 38900641 DOI: 10.1016/j.celrep.2024.114374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/05/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Morphological studies of skeletal muscle tissue provide insights into the architecture of muscle fibers, the surrounding cells, and the extracellular matrix (ECM). However, a spatial proteomics analysis of the skeletal muscle including the muscle-tendon transition zone is lacking. Here, we prepare cryotome muscle sections of the mouse soleus muscle and measure each slice using short liquid chromatography-mass spectrometry (LC-MS) gradients. We generate 3,000 high-resolution protein profiles that serve as the basis for a network analysis to reveal the complex architecture of the muscle-tendon junction. Among the protein profiles that increase from muscle to tendon, we find proteins related to neuronal activity, fatty acid biosynthesis, and the renin-angiotensin system (RAS). Blocking the RAS in cultured mouse tenocytes using losartan reduces the ECM synthesis. Overall, our analysis of thin cryotome sections provides a spatial proteome of skeletal muscle and reveals that the RAS acts as an additional regulator of the matrix within muscle-tendon junctions.
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Affiliation(s)
- Luisa Schmidt
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Michael Saynisch
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Christian Hoegsbjerg
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Abigail Mackey
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan-Wilm Lackmann
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Stefan Müller
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty, University of Cologne, Cologne, Germany; Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Michael Kjaer
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark; Part of IOC Research Center Copenhagen and Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philipp Antczak
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
| | - Marcus Krüger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Center for Molecular Medicine (CMMC), University of Cologne, 50931 Cologne, Germany.
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Anagho HA, Mullari M, Prósz AG, Buch-Larsen SC, Cho H, Locard-Paulet M, Szallasi Z, Nielsen ML. ADP-ribosylome analysis reveals homogeneous DNA-damage-induced serine ADP-ribosylation across wild-type and BRCA-mutant breast cancer cell lines. Cell Rep 2024; 43:114433. [PMID: 38985679 DOI: 10.1016/j.celrep.2024.114433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/24/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
ADP-ribosylation (ADPr) signaling plays a crucial role in DNA damage response. Inhibitors against the main enzyme catalyzing ADPr after DNA damage, poly(ADP-ribose) polymerase 1 (PARP1), are used to treat patients with breast cancer harboring BRCA1/2 mutations. However, resistance to PARP inhibitors (PARPi) is a major obstacle in treating patients. To understand the role of ADPr in PARPi sensitivity, we use liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze ADPr in six breast cancer cell lines exhibiting different PARPi sensitivities. We identify 1,632 sites on 777 proteins across all cell lines, primarily on serine residues, with site-specific overlap of targeted residues across DNA-damage-related proteins across all cell lines, demonstrating high conservation of serine ADPr-signaling networks upon DNA damage. Furthermore, we observe site-specific differences in ADPr intensities in PARPi-sensitive BRCA mutants and unique ADPr sites in PARPi-resistant BRCA-mutant HCC1937 cells, which have low poly(ADP-ribose) glycohydrolase (PARG) levels and longer ADPr chains on PARP1.
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Affiliation(s)
- Holda Awah Anagho
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Meeli Mullari
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | | | - Sara Charlotte Buch-Larsen
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Hayoung Cho
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark; Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Michael Lund Nielsen
- Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, 2200 Copenhagen, Denmark.
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