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Ingelman H, Heffernan JK, Harris A, Brown SD, Shaikh KM, Saqib AY, Pinheiro MJ, de Lima LA, Martinez KR, Gonzalez-Garcia RA, Hawkins G, Daleiden J, Tran L, Zeleznik H, Jensen RO, Reynoso V, Schindel H, Jänes J, Simpson SD, Köpke M, Marcellin E, Valgepea K. Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness. N Biotechnol 2024; 83:1-15. [PMID: 38871051 DOI: 10.1016/j.nbt.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named "LAbrini", exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain "LAbrini" to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
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Affiliation(s)
- Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | - Asfand Yar Saqib
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Marina J Pinheiro
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Karen Rodriguez Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | - Ricardo A Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | | | | | | | | | - Jürgen Jänes
- Institute of Molecular Systems Biology, ETH Zürich, 8049 Zürich, Switzerland
| | | | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia.
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2
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Noore S, Tiwari BK, Wanigasekara J, Amado IR, Fuciños P, McKeever K, Dillon E, Cagney G, Curtin JF, O'Donnell C. Effect of conventional and novel techniques on extraction yield, chemical characterisation and biological activities of proteins from bitter gourd (Momordica charantia). Food Chem 2024; 458:139516. [PMID: 39053391 DOI: 10.1016/j.foodchem.2024.139516] [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: 03/08/2024] [Revised: 04/14/2024] [Accepted: 04/28/2024] [Indexed: 07/27/2024]
Abstract
The study investigates the effect of conventional and novel extraction techniques on the protein extraction yield from bitter gourd seeds (Momordica charantia). Ultrasound assisted-extraction (UAE) treatment for 30 min at 4 °C using a 20 kHz ultrasound probe resulted in the highest extraction yield of crude proteins. After purification, 9.08 ± 0.23 g of protein with 82.69 ± 0.78% purity was obtained from 100 g of M. charantia seeds on a dry basis. Mass spectrometry identified proteins with reported antidiabetic activity. Antidiabetic assays showed significantly higher antidiabetic activity for the purified protein (81.10 ± 2.64%) compared to the crude protein (32.59 ± 2.76%). In vitro cytotoxicity analysis showed minimal cytotoxicity levels at concentrations <200 μg.mL-1. Overall, UAE was effective to obtain crude protein from M. charantia seeds and a subsequent purification step enhanced antidiabetic activity. However, further research is required to demonstrate in-vivo antidiabetic activity.
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Affiliation(s)
- Shaba Noore
- School of Biosystems and Food Engineering, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; Department of Food Chemistry and Technology, Teagasc Food Research Centre, Ashtown, D15 DY05 Dublin, Ireland
| | - Brijesh K Tiwari
- School of Biosystems and Food Engineering, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland; Department of Food Chemistry and Technology, Teagasc Food Research Centre, Ashtown, D15 DY05 Dublin, Ireland
| | - Janith Wanigasekara
- School of Food Science and Environmental Health, College of Sciences and Health, Technological University Dublin, City Campus, Dublin, Ireland; Environmental Sustainability and Health Institute, Technological University Dublin, Dublin, Ireland
| | - Isabel R Amado
- International Iberian Nanotechnology Laboratory, Food Processing, and Nutrition Research Group, Av. Mestre, José Veiga s/n, 4715-330 Braga, Portugal
| | - Pablo Fuciños
- International Iberian Nanotechnology Laboratory, Food Processing, and Nutrition Research Group, Av. Mestre, José Veiga s/n, 4715-330 Braga, Portugal
| | - Kate McKeever
- Mass Spectrometry Resource, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Eugene Dillon
- Mass Spectrometry Resource, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland; BiOrbic, Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - Gerard Cagney
- Mass Spectrometry Resource, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland; BiOrbic, Bioeconomy SFI Research Centre, University College Dublin, Dublin, Ireland
| | - James F Curtin
- School of Food Science and Environmental Health, College of Sciences and Health, Technological University Dublin, City Campus, Dublin, Ireland; Environmental Sustainability and Health Institute, Technological University Dublin, Dublin, Ireland
| | - Colm O'Donnell
- School of Biosystems and Food Engineering, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland.
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3
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Domingos IF, Carvalho LB, Lodeiro C, Gerivaz R, Prag G, Micaglio E, Muchtar E, Santos HM, Capelo JL. Dithiothreitol-based protein equalisation in the context of multiple myeloma: Enhancing proteomic analysis and therapeutic insights. Talanta 2024; 279:126589. [PMID: 39116730 DOI: 10.1016/j.talanta.2024.126589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Abstract
In this study, we employed the dithiothreitol-based protein equalisation technique and analytical proteomics to better understand myeloma diseases by comparing the proteomes of pellets and supernatants formed upon application of DTT on serum samples. The number of unique proteins found in pellets was 252 for healthy individuals and 223 for multiple myeloma patients. The comparison of these proteomes showed 97 dysregulated proteins. The unique proteins found for supernatants were 264 for healthy individuals and 235 for multiple myeloma patients. The comparison of these proteomes showed 87 dysregulated proteins. The analytical proteomic comparison of both groups of dysregulated proteins is translated into parallel dysregulated pathways, including chaperone-mediated autophagy and protein folding, addressing potential therapeutic interventions. Future research endeavours in personalised medicine should prioritize refining analytical proteomic methodologies using serum dithiothreitol-based protein equalisation to explore innovative therapeutic strategies. We highlight the advanced insights gained from this analytical strategy in studying multiple myeloma, emphasising its complex nature and the critical role of personalised, targeted analytical techniques in enhancing therapeutic efficacy in personalised medicine.
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Affiliation(s)
- Ines F Domingos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Luis B Carvalho
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Carlos Lodeiro
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal
| | - Rita Gerivaz
- Serviço de Hematologia, Hospital Garcia de Orta, Almada, Portugal
| | - Gali Prag
- School of Neurobiology, Biochemistry and Biophysics, the George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, Israel
| | - Emanuele Micaglio
- Department of Arrhythmology, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097, Milan, Italy
| | - Eli Muchtar
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Hugo M Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
| | - Jose L Capelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; PROTEOMASS Scientific Society, Praceta Jerónimo Dias, 2825-466., Caparica, Portugal.
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Bhardwaj S, Lee M, O'Carroll D, McDonald J, Osborne K, Khan S, Pickford R, Coleman N, O'Farrell C, Richards S, Manefield MJ. Biotransformation of 6:2/4:2 fluorotelomer alcohols by Dietzia aurantiaca J3: Enzymes and proteomics. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135510. [PMID: 39178776 DOI: 10.1016/j.jhazmat.2024.135510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/12/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are recalcitrant synthetic organohalides known to negatively impact human health. Short-chain fluorotelomer alcohols are considered the precursor of various perfluorocarboxylic acids (PFCAs) in the environment. Their ongoing production and widespread detection motivate investigations of their biological transformation. Dietzia aurantiaca strain J3 was isolated from PFAS-contaminated landfill leachate using 6:2 fluorotelomer sulphonate (6:2 FTS) as a sulphur source. Resting cell experiments were used to test if strain J3 could transform fluorotelomer alcohols (6:2 and 4:2 FTOH). Strain J3 transformed fluorotelomer alcohols into PFCAs, polyfluorocarboxylic acids and transient intermediates. Over 6 days, 80 % and 58 % of 6:2 FTOH (0.1 mM) and 4:2 FTOH (0.12 mM) were degraded with 6.4 % and 14 % fluoride recovery respectively. Fluorotelomer unsaturated carboxylic acid (6:2 FTUCA) was the most abundant metabolite, accounting for 21 to 30 mol% of 6:2 FTOH (0.015 mM) applied on day zero. Glutathione (GSH) conjugates of 6:2/4:2 FTOH and 5:3 FTCA adducts were also structurally identified. Proteomics studies conducted to identify enzymes in the biotransformation pathway have revealed the role of various enzymes involved in β oxidation. This is the first report of 6:2/4:2 FTOH glutathione conjugates and 5:3 FTCA adducts in prokaryotes, and the first study to explore the biotransformation of 4:2 FTOH by pure bacterial strain.
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Affiliation(s)
- Shefali Bhardwaj
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Matthew Lee
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Denis O'Carroll
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - James McDonald
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Keith Osborne
- Environment Protection Science, NSW Department of Climate Change, Energy, the Environment and Water, Lidcombe, NSW 2141, Australia
| | - Stuart Khan
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia
| | - Russell Pickford
- UNSW Mark Wainwright Analytical Centre, UNSW, Sydney, NSW 2052, Australia
| | - Nicholas Coleman
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | | | | | - Michael J Manefield
- UNSW Water Research Centre, School of Civil and Environmental Engineering, UNSW, Sydney, NSW 2052, Australia.
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Stefanakis K, Samiotaki M, Papaevangelou V, Valenzuela-Vallejo L, Giannoukakis N, Mantzoros CS. Longitudinal proteomics of leptin treatment in humans with acute and chronic energy deficiency-induced hypoleptinemia reveal novel, mainly immune-related, pleiotropic effects. Metabolism 2024; 159:155984. [PMID: 39097160 DOI: 10.1016/j.metabol.2024.155984] [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: 05/02/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
BACKGROUND Leptin is known for its metabolic, immunomodulatory and neuroendocrine properties, but the full spectrum of molecules downstream of leptin and relevant underlying mechanisms remain to be fully clarified. Our objective was to identify proteins and pathways influenced by leptin through untargeted proteomics in two clinical trials involving leptin administration in lean individuals. METHODS We performed untargeted liquid chromatography-tandem mass spectrometry serum proteomics across two studies a) Short-term randomized controlled crossover study of lean male and female humans undergoing a 72-h fast with concurrent administration of either placebo or high-dose leptin; b) Long-term (36-week) randomized controlled trial of leptin replacement therapy in human females with acquired relative energy deficiency and hypoleptinemia. We explored longitudinal proteomic changes and run adjusted mixed models followed by post-hoc tests. We further attempted to identify ontological pathways modulated during each experimental condition and/or comparison, through integrated qualitative pathway and enrichment analyses. We also explored dynamic longitudinal relationships between the circulating proteome with clinical and hormonal outcomes. RESULTS 289 and 357 unique proteins were identified per each respective study. Short-term leptin administration during fasting markedly upregulated several proinflammatory molecules, notably C-reactive protein (CRP) and cluster of differentiation (CD) 14, and downregulated lecithin cholesterol acyltransferase and several immunoglobulin variable chains, in contrast with placebo, which produced minimal changes. Quantitative pathway enrichment further indicated an upregulation of the acute phase response and downregulation of immunoglobulin- and B cell-mediated immunity by leptin. These changes were independent of participants' biological sex. In the long term study, leptin likewise robustly and persistently upregulated proteins of the acute phase response, and downregulated immunoglobulin-mediated immunity. Leptin also significantly and differentially affected a wide array of proteins related to immune function, defense response, coagulation, and inflammation compared with placebo. These changes were more notable at the 24-week visit, coinciding with the highest measured levels of serum leptin. We further identified distinct co-regulated clusters of proteins and clinical features during leptin administration indicating robust longitudinal correlations between the regulation of immunoglobulins, immune-related molecules, serpins (including cortisol and thyroxine-binding globulins), lipid transport molecules and growth factors, in contrast with placebo, which did not produce similar associations. CONCLUSIONS These high-throughput longitudinal results provide unique functional insights into leptin physiology, and pave the way for affinity-based proteomic analyses measuring several thousands of molecules, that will confirm these data and may fully delineate underlying mechanisms.
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Affiliation(s)
- Konstantinos Stefanakis
- Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Fleming 34, 166 72 Vari, Greece
| | - Vassiliki Papaevangelou
- Third Department of Paediatrics, Attikon University Hospital, National and Kapodistrian University of Athens, Greece
| | - Laura Valenzuela-Vallejo
- Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nick Giannoukakis
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Christos S Mantzoros
- Department of Internal Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Kabatnik S, Post F, Drici L, Bartels AS, Strauss MT, Zheng X, Madsen GI, Mund A, Rosenberger FA, Moreira J, Mann M. Spatial characterization and stratification of colorectal adenomas by deep visual proteomics. iScience 2024; 27:110620. [PMID: 39252972 PMCID: PMC11381895 DOI: 10.1016/j.isci.2024.110620] [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: 12/22/2023] [Revised: 05/13/2024] [Accepted: 07/26/2024] [Indexed: 09/11/2024] Open
Abstract
Colorectal adenomas (CRAs) are potential precursor lesions to adenocarcinomas, currently classified by morphological features. We aimed to establish a molecular feature-based risk allocation framework toward improved patient stratification. Deep visual proteomics (DVP) is an approach that combines image-based artificial intelligence with automated microdissection and ultra-high sensitive mass spectrometry. Here, we used DVP on formalin-fixed, paraffin-embedded (FFPE) CRA tissues from nine male patients, immunohistologically stained for caudal-type homeobox 2 (CDX2), a protein implicated in colorectal cancer, enabling the characterization of cellular heterogeneity within distinct tissue regions and across patients. DVP identified DMBT1, MARCKS, and CD99 as protein markers linked to recurrence, suggesting their potential for risk assessment. It also detected a metabolic shift to anaerobic glycolysis in cells with high CDX2 expression. Our findings underscore the potential of spatial proteomics to refine early stage detection and contribute to personalized patient management strategies and provided novel insights into metabolic reprogramming.
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Affiliation(s)
- Sonja Kabatnik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Frederik Post
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Lylia Drici
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Annette Snejbjerg Bartels
- Precision Cancer Medicine Laboratory, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maximilian T Strauss
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Xiang Zheng
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Gunvor I Madsen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Andreas Mund
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Florian A Rosenberger
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - José Moreira
- Precision Cancer Medicine Laboratory, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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7
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O'Sullivan PA, Aidarova A, Afonina IS, Manils J, Thurston TLM, Instrell R, Howell M, Boeing S, Ranawana S, Herpels MB, Chetian R, Bassa M, Flynn H, Frith D, Snijders AP, Howes A, Beyaert R, Bowcock AM, Ley SC. CARD14 signalosome formation is associated with its endosomal relocation and mTORC1-induced keratinocyte proliferation. Biochem J 2024; 481:1143-1171. [PMID: 39145956 DOI: 10.1042/bcj20240058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 08/16/2024]
Abstract
Rare mutations in CARD14 promote psoriasis by inducing CARD14-BCL10-MALT1 complexes that activate NF-κB and MAP kinases. Here, the downstream signalling mechanism of the highly penetrant CARD14E138A alteration is described. In addition to BCL10 and MALT1, CARD14E138A associated with several proteins important in innate immune signalling. Interactions with M1-specific ubiquitin E3 ligase HOIP, and K63-specific ubiquitin E3 ligase TRAF6 promoted BCL10 ubiquitination and were essential for NF-κB and MAP kinase activation. In contrast, the ubiquitin binding proteins A20 and ABIN1, both genetically associated with psoriasis development, negatively regulated signalling by inducing CARD14E138A turnover. CARD14E138A localized to early endosomes and was associated with the AP2 adaptor complex. AP2 function was required for CARD14E138A activation of mTOR complex 1 (mTORC1), which stimulated keratinocyte metabolism, but not for NF-κB nor MAP kinase activation. Furthermore, rapamycin ameliorated CARD14E138A-induced keratinocyte proliferation and epidermal acanthosis in mice, suggesting that blocking mTORC1 may be therapeutically beneficial in CARD14-dependent psoriasis.
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Affiliation(s)
- Paul A O'Sullivan
- The Francis Crick Institute, London NW1 1AT, U.K
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, U.K
| | - Aigerim Aidarova
- VIB Center for Inflammation Research and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Inna S Afonina
- VIB Center for Inflammation Research and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Joan Manils
- The Francis Crick Institute, London NW1 1AT, U.K
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, U.K
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Teresa L M Thurston
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, U.K
| | | | | | | | - Sashini Ranawana
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, U.K
| | - Melanie B Herpels
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, U.K
| | - Riwia Chetian
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, U.K
| | - Matilda Bassa
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, U.K
| | - Helen Flynn
- The Francis Crick Institute, London NW1 1AT, U.K
| | - David Frith
- The Francis Crick Institute, London NW1 1AT, U.K
| | | | - Ashleigh Howes
- National Heart and Lung Institute, Imperial College London, London W12 0NN, U.K
| | - Rudi Beyaert
- VIB Center for Inflammation Research and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Anne M Bowcock
- Department of Oncological Science, Dermatology, and Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, U.S.A
| | - Steven C Ley
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, U.K
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Rodríguez-Ulloa A, Rosales M, Ramos Y, Guirola O, González LJ, Wiśniewski JR, Perera Y, Perea SE, Besada V. "Phosphoproteomic quantification based on phosphopeptide intensity or occupancy? An evaluation based on casein kinase 2 downstream effects". J Proteomics 2024; 307:105269. [PMID: 39098729 DOI: 10.1016/j.jprot.2024.105269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
Quantitative phosphoproteomic data has mostly been reported from experiments comparing relative phosphopeptides intensities in two or more different conditions, while the ideal parameter to compare is phosphopeptides occupancies. This term is scarcely used and therefore barely implemented in phosphoproteomics studies, and this should be of concern for the scientific journals. In order to demonstrate the relevance of this issue, here we show how the method of choice affects the interpretation of the data. The phosphoproteomic profile modulated in two AML cell lines after CK2 inhibition with CIGB-300 or CX-4945 is shown. Following the downstream action of CK2 the phosphosite intensity and occupancy results were compared to validate the best approach for quantitative phosphoproteomic studies. Even when the total number of quantified phosphopeptides was higher by using the intensity calculation, in all the cases the percent of CK2 consensus sequences which were down-regulated in response to CK2 inhibition was higher using the phosphosite occupancy quantification. To note, a high number of CK2 consensus sequences was found down-regulated with at least a 10% or 15% of phosphosite occupancy variation illustrating that low thresholds of occupancy modulation might be indicative of biological effect. Additionally, several biological processes only appear significantly over-represented in the phosphoproteome quantified by occupancy. The functional enrichment analysis per ranges of occupancy variations also illustrated clear differences among AML cell lines subjected to CK2 inhibition by CX-4945. A low overlap between the phosphoproteomes quantified by intensity and occupancy was obtained illustrating that new developments in proteomics techniques are needed to improve the performance of the occupancy approach. Even in such context, results indicate that occupancy quantification performs better than phosphorylation quantification based on intensity reinforcing the importance of such quantification approach to describe phosphoproteomic data.
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Affiliation(s)
- Arielis Rodríguez-Ulloa
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering& Biotechnology (CIGB), Havana 10600, Cuba.
| | - Mauro Rosales
- Department of Animal and Human Biology, Faculty of Biology, University of Havana, Havana 10600, Cuba; Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering & Biotechnology (CIGB), Havana 10600, Cuba.
| | - Yassel Ramos
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering& Biotechnology (CIGB), Havana 10600, Cuba.
| | - Osmany Guirola
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering& Biotechnology (CIGB), Havana 10600, Cuba.
| | - Luis J González
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering& Biotechnology (CIGB), Havana 10600, Cuba.
| | - Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Munich, Germany.
| | - Yasser Perera
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering & Biotechnology (CIGB), Havana 10600, Cuba; China-Cuba Biotechnology Joint Innovation Center (CCBJIC), Yongzhou Zhong Gu Biotechnology Co., Ltd, Lengshuitan District, Yongzhou City 425000, Hunan Province, China.
| | - Silvio E Perea
- Molecular Oncology Group, Department of Pharmaceuticals, Biomedical Research Division, Center for Genetic Engineering & Biotechnology (CIGB), Havana 10600, Cuba.
| | - Vladimir Besada
- Proteomics Group, Department of System Biology, Biomedical Research Division, Center for Genetic Engineering& Biotechnology (CIGB), Havana 10600, Cuba.
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9
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Stephens KK, Finnerty RM, Grant DG, Winuthayanon S, Martin-DeLeon PA, Winuthayanon W. Proteomic analysis and in vivo visualization of extracellular vesicles from mouse oviducts during pre-implantation embryo development. FASEB J 2024; 38:e70035. [PMID: 39239798 PMCID: PMC11384279 DOI: 10.1096/fj.202400041rr] [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: 01/06/2024] [Revised: 08/11/2024] [Accepted: 08/26/2024] [Indexed: 09/07/2024]
Abstract
Pre-implantation embryonic development occurs in the oviduct during the first few days of pregnancy. The presence of oviductal extracellular vesicles (oEVs, also called oviductosomes) is crucial for pre-implantation embryonic development in vivo as oEVs often contain molecular transmitters such as proteins. Therefore, evaluating oEV cargo during early pregnancy could provide insights into factors required for proper early embryonic development that are missing in the current in vitro embryo culture setting. In this study, we isolated oEVs from the oviductal fluid at estrus and different stages of early embryonic development. The 2306-3066 proteins in oEVs identified at the different time points revealed 58-60 common EV markers identified in exosome databases. Oviductal extracellular vesicle proteins from pregnant samples significantly differed from those in non-pregnant samples. In addition, superovulation changes the protein contents in oEVs compared to natural ovulation at estrus. Importantly, we have identified that embryo-protectant proteins such as high-mobility protein group B1 and serine (or cysteine) peptidase inhibitor were only enriched in the presence of embryos. We also visualized the physical interaction of EVs and the zona pellucida of 4- to 8-cell stage embryos using transmission electron microscopy as well as in vivo live imaging of epithelial cell-derived GFP-tagged CD9 mouse model. All protein data in this study are readily available to the scientific community in a searchable format at https://genes.winuthayanon.com/winuthayanon/oviduct_ev_proteins/. In conclusion, we identified oEVs proteins that could be tested to determine whether they can improve embryonic developmental outcomes in vivo and in vitro setting.
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Affiliation(s)
- Kalli K Stephens
- Division of Animal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | - Ryan M Finnerty
- Department of OB/GYN & Women's Health, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Translational Biosciences Program, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - DeAna G Grant
- Electron Microscopy Core Facility, University of Missouri, Columbia, Missouri, USA
| | - Sarayut Winuthayanon
- Division of Animal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
| | | | - Wipawee Winuthayanon
- Division of Animal Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri, USA
- Department of OB/GYN & Women's Health, School of Medicine, University of Missouri, Columbia, Missouri, USA
- Translational Biosciences Program, School of Medicine, University of Missouri, Columbia, Missouri, USA
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10
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Weiss LM, Warwick T, Zehr S, Günther S, Wolf S, Schmachtel T, Izquierdo Ponce J, Pálfi K, Teichmann T, Schneider A, Stötzel J, Knapp S, Weigert A, Savai R, Rieger MA, Oellerich T, Wittig I, Oo JA, Brandes RP, Leisegang MS. RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions. Commun Biol 2024; 7:1131. [PMID: 39271940 DOI: 10.1038/s42003-024-06794-2] [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: 02/06/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
Monocytes, the circulating macrophage precursors, contribute to diseases like atherosclerosis and asthma. Long non-coding RNAs (lncRNAs) have been shown to modulate the phenotype and inflammatory capacity of monocytes. We previously discovered the lncRNA SMANTIS, which contributes to cellular phenotype expression by controlling BRG1 in mesenchymal cells. Here, we report that SMANTIS is particularly highly expressed in monocytes and lost during differentiation into macrophages. Moreover, different types of myeloid leukemia presented specific SMANTIS expression patterns. Interaction studies revealed that SMANTIS binds RUNX1, a transcription factor frequently mutated in AML, primarily through its Alu-element on the RUNT domain. RNA-seq after CRISPR/Cas9-mediated deletion of SMANTIS or RUNX1 revealed an association with cell adhesion and both limited the monocyte adhesion to endothelial cells. Mechanistically, SMANTIS KO reduced RUNX1 genomic binding and altered the interaction of RUNX1 with EP300 and CBFB. Collectively, SMANTIS interacts with RUNX1 and attenuates monocyte adhesion, which might limit monocyte vascular egress.
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Affiliation(s)
- Lisa M Weiss
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Timothy Warwick
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Simonida Zehr
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sebastian Wolf
- Goethe University Frankfurt, University Hospital, Department of Medicine II, Hematology/Oncology, Frankfurt, Germany
| | - Tessa Schmachtel
- Goethe University Frankfurt, University Hospital, Department of Medicine II, Hematology/Oncology, Frankfurt, Germany
| | - Judit Izquierdo Ponce
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
| | - Katalin Pálfi
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
| | - Tom Teichmann
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Alicia Schneider
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Julia Stötzel
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Stefan Knapp
- Goethe University Frankfurt, Institute for Pharmaceutical Chemistry, Buchman Institute for Life Sciences Campus Riedberg, Frankfurt, Germany
| | - Andreas Weigert
- Goethe University Frankfurt, Institute of Biochemistry I, Frankfurt, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Lung Microenvironmental Niche in Cancerogenesis, Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
| | - Michael A Rieger
- Goethe University Frankfurt, University Hospital, Department of Medicine II, Hematology/Oncology, Frankfurt, Germany
| | - Thomas Oellerich
- Goethe University Frankfurt, University Hospital, Department of Medicine II, Hematology/Oncology, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt, Germany
- University Cancer Center (UCT) Frankfurt, University Hospital, Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt, Germany
| | - Ilka Wittig
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
- Goethe University Frankfurt, Functional Proteomics, Institute for Cardiovascular Physiology, Frankfurt, Germany
| | - James A Oo
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Matthias S Leisegang
- Goethe University Frankfurt, Institute for Cardiovascular Physiology, Frankfurt, Germany.
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany.
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11
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Crissey MAS, Versace A, Bhardwaj M, Jain V, Liu S, Singh A, Beer LA, Tang HY, Villanueva J, Gimotty PA, Xu X, Amaravadi RK. Divergent effects of acute and chronic PPT1 inhibition in melanoma. Autophagy 2024. [PMID: 39265628 DOI: 10.1080/15548627.2024.2403152] [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: 03/22/2024] [Revised: 08/26/2024] [Accepted: 09/07/2024] [Indexed: 09/14/2024] Open
Abstract
Macroautophagy/autophagy-lysosome function promotes growth and survival of cancer cells, making them attractive targets for cancer therapy. One intriguing lysosomal target is PPT1 (palmitoyl-protein thioesterase 1). PPT1 inhibitors derived from chloroquine block autophagy, have significant antitumor activity in preclinical models and are being developed for clinical trials. However, the role of PPT1 in tumorigenesis remains poorly understood. Here we report that in melanoma cells, acute siRNA or pharmacological PPT1 inhibition led to increased ferroptosis sensitivity and significant loss of viability, whereas chronic PPT1 knockout using CRISPR-Cas9 produced blunted ferroptosis that led to sustained viability and growth. Each mode of PPT1 inhibition produced lysosome-autophagy inhibition but distinct proteomic changes, demonstrating the complexity of cellular adaptation mechanisms. To determine whether total genetic loss of Ppt1 would affect tumorigenesis in vivo, we developed a Ppt1 conditional knockout mouse model. We then crossed it into the BrafCA, PtenloxP, Tyr:CreERT2 melanoma mouse model to investigate the impact of Ppt1 loss on tumorigenesis. Loss of Ppt1 had no impact on melanoma histology, time to tumor initiation, or survival of tumor-bearing mice. These results suggest that chemical PPT1 inhibitors produce different adaptations than genetic PPT1 inhibition, and additional studies are warranted to fully understand the mechanism of chloroquine derivatives that target PPT1 in cancer.
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Affiliation(s)
- Mary Ann S Crissey
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Versace
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monika Bhardwaj
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vaibhav Jain
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shujing Liu
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - Arpana Singh
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lynn A Beer
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Hsin-Yao Tang
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Jessie Villanueva
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Phyllis A Gimotty
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, USA
| | - Xiaowei Xu
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravi K Amaravadi
- Abramson Cancer Center and Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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12
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Wong GYM, Li J, McKay M, Castaneda M, Bhimani N, Diakos C, Hugh TJ, Molloy MP. Proteogenomic Characterization of Early Intrahepatic Recurrence after Curative-Intent Treatment of Colorectal Liver Metastases. J Proteome Res 2024. [PMID: 39264718 DOI: 10.1021/acs.jproteome.4c00440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
Clinical and pathological factors are insufficient to accurately identify patients at risk of early recurrence after curative-intent treatment of colorectal liver metastases (CRLM). This study aimed to identify candidate prognostic proteogenomic biomarkers for early intrahepatic recurrence after curative-intent resection of CRLM. Patients diagnosed with intrahepatic recurrence within 6 months of liver resection were categorized as the "early recurrence" group, while those who achieved a recurrence-free status for 10 years were designated as "durable remission". Comprehensive genomic and proteomic profiling of fresh frozen samples from these prognostically distinct groups was performed using the TruSight Oncology 500 assay and label-free data-dependent acquisition liquid chromatography-mass spectrometry. Genetic alterations were identified in 117 of the 523 profiled genes in patients with early recurrence. The most common somatic mutations linked to early recurrence were TP53 (88%), APC (71%), KRAS (38%), and SMAD4 (21%). SMAD4 alterations were absent in samples from patients with a durable remission. Calponin-2, versican core protein, glutathione peroxidase 3, fibulin-5, and amyloid-β precursor protein were upregulated more than 2-fold in early recurrence. Exploratory analysis of these proteogenomic biomarkers suggests that SMAD4, calponin-2, and glutathione peroxidase 3 may have the potential to predict early recurrence, enabling improved prognostication and precision oncology in CRLM.
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Affiliation(s)
- Geoffrey Yuet Mun Wong
- Department of Upper Gastrointestinal Surgery, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
- Northern Clinical School, The University of Sydney, Sydney, New South Wales 2065, Australia
- Bowel Cancer and Biomarker Research Laboratory, Kolling Institute, St Leonards, New South Wales 2065, Australia
| | - Jun Li
- Bowel Cancer and Biomarker Research Laboratory, Kolling Institute, St Leonards, New South Wales 2065, Australia
| | - Matthew McKay
- Bowel Cancer and Biomarker Research Laboratory, Kolling Institute, St Leonards, New South Wales 2065, Australia
| | - Miguel Castaneda
- Bowel Cancer and Biomarker Research Laboratory, Kolling Institute, St Leonards, New South Wales 2065, Australia
| | - Nazim Bhimani
- Department of Upper Gastrointestinal Surgery, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
- Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Connie Diakos
- Northern Clinical School, The University of Sydney, Sydney, New South Wales 2065, Australia
- Department of Medical Oncology, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
| | - Thomas J Hugh
- Department of Upper Gastrointestinal Surgery, Royal North Shore Hospital, Sydney, New South Wales 2065, Australia
- Northern Clinical School, The University of Sydney, Sydney, New South Wales 2065, Australia
| | - Mark P Molloy
- Bowel Cancer and Biomarker Research Laboratory, Kolling Institute, St Leonards, New South Wales 2065, Australia
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13
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Karpińska K, Mehlich D, Sabbasani VR, Łomiak M, Torres-Ayuso P, Wróbel K, Truong VNP, Serwa R, Swenson RE, Brognard J, Marusiak AA. Selective Degradation of MLK3 by a Novel CEP1347-VHL-02 PROTAC Compound Limits the Oncogenic Potential of TNBC. J Med Chem 2024; 67:15012-15028. [PMID: 39207123 DOI: 10.1021/acs.jmedchem.4c00577] [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: 09/04/2024]
Abstract
Triple-negative breast cancer (TNBC) is associated with poor prognosis because of the lack of effective therapies. Mixed-lineage protein kinase 3 (MLK3) is a protein that is often upregulated in TNBC and involved in driving the tumorigenic potential of cancer cells. Here, we present a selective MLK3 degrader, CEP1347-VHL-02, based on the pan-MLK inhibitor CEP1347 and a ligand for E3 ligase von Hippel-Lindau (VHL) by employing proteolysis-targeting chimera (PROTAC) technology. Our compound effectively targeted MLK3 for degradation via the ubiquitin-proteasome system in several cell line models but did not degrade other MLK family members. Furthermore, we showed that CEP1347-VHL-02 robustly degraded MLK3 and inhibited its oncogenic activity in TNBC, measured as a reduction of clonogenic and migratory potential, cell cycle arrest, and the induction of apoptosis in MDA-MB-468 cells. In conclusion, we present CEP1347-VHL-02 as a novel MLK3 degrader that may be a promising new strategy to target MLK3 in TNBC.
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Affiliation(s)
- Kamila Karpińska
- Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Dawid Mehlich
- Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Venkata R Sabbasani
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michał Łomiak
- Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Pedro Torres-Ayuso
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, United States
| | - Katarzyna Wróbel
- Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Vi Nguyen-Phuong Truong
- Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Remigiusz Serwa
- Proteomic Core Facility, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Rolf E Swenson
- Chemistry and Synthesis Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - John Brognard
- Laboratory of Cell and Developmental Signaling, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Anna A Marusiak
- Laboratory of Molecular OncoSignalling, IMol Polish Academy of Sciences, Warsaw 02-247, Poland
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14
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Weimer A, Pause L, Ries F, Kohlstedt M, Adrian L, Krömer J, Lai B, Wittmann C. Systems biology of electrogenic Pseudomonas putida - multi-omics insights and metabolic engineering for enhanced 2-ketogluconate production. Microb Cell Fact 2024; 23:246. [PMID: 39261865 PMCID: PMC11389600 DOI: 10.1186/s12934-024-02509-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/10/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Pseudomonas putida KT2440 has emerged as a promising host for industrial bioproduction. However, its strictly aerobic nature limits the scope of applications. Remarkably, this microbe exhibits high bioconversion efficiency when cultured in an anoxic bio-electrochemical system (BES), where the anode serves as the terminal electron acceptor instead of oxygen. This environment facilitates the synthesis of commercially attractive chemicals, including 2-ketogluconate (2KG). To better understand this interesting electrogenic phenotype, we studied the BES-cultured strain on a systems level through multi-omics analysis. Inspired by our findings, we constructed novel mutants aimed at improving 2KG production. RESULTS When incubated on glucose, P. putida KT2440 did not grow but produced significant amounts of 2KG, along with minor amounts of gluconate, acetate, pyruvate, succinate, and lactate. 13C tracer studies demonstrated that these products are partially derived from biomass carbon, involving proteins and lipids. Over time, the cells exhibited global changes on both the transcriptomic and proteomic levels, including the shutdown of translation and cell motility, likely to conserve energy. These adaptations enabled the cells to maintain significant metabolic activity for several weeks. Acetate formation was shown to contribute to energy supply. Mutants deficient in acetate production demonstrated superior 2KG production in terms of titer, yield, and productivity. The ∆aldBI ∆aldBII double deletion mutant performed best, accumulating 2KG at twice the rate of the wild type and with an increased yield (0.96 mol/mol). CONCLUSIONS By integrating transcriptomic, proteomic, and metabolomic analyses, this work provides the first systems biology insight into the electrogenic phenotype of P. putida KT2440. Adaptation to anoxic-electrogenic conditions involved coordinated changes in energy metabolism, enabling cells to sustain metabolic activity for extended periods. The metabolically engineered mutants are promising for enhanced 2KG production under these conditions. The attenuation of acetate synthesis represents the first systems biology-informed metabolic engineering strategy for enhanced 2KG production in P. putida. This non-growth anoxic-electrogenic mode expands our understanding of the interplay between growth, glucose phosphorylation, and glucose oxidation into gluconate and 2KG in P. putida.
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Affiliation(s)
- Anna Weimer
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Laura Pause
- Systems Biotechnology Group, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Fabian Ries
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lorenz Adrian
- Department of Molecular Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jens Krömer
- Systems Biotechnology Group, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Bin Lai
- BMBF Junior Research Group Biophotovoltaics, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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15
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Delgado de la Herran H, Vecellio Reane D, Cheng Y, Katona M, Hosp F, Greotti E, Wettmarshausen J, Patron M, Mohr H, Prudente de Mello N, Chudenkova M, Gorza M, Walia S, Feng MSF, Leimpek A, Mielenz D, Pellegata NS, Langer T, Hajnóczky G, Mann M, Murgia M, Perocchi F. Systematic mapping of mitochondrial calcium uniporter channel (MCUC)-mediated calcium signaling networks. EMBO J 2024:10.1038/s44318-024-00219-w. [PMID: 39261663 DOI: 10.1038/s44318-024-00219-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 08/08/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024] Open
Abstract
The mitochondrial calcium uniporter channel (MCUC) mediates mitochondrial calcium entry, regulating energy metabolism and cell death. Although several MCUC components have been identified, the molecular basis of mitochondrial calcium signaling networks and their remodeling upon changes in uniporter activity have not been assessed. Here, we map the MCUC interactome under resting conditions and upon chronic loss or gain of mitochondrial calcium uptake. We identify 89 high-confidence interactors that link MCUC to several mitochondrial complexes and pathways, half of which are associated with human disease. As a proof-of-concept, we validate the mitochondrial intermembrane space protein EFHD1 as a binding partner of the MCUC subunits MCU, EMRE, and MCUB. We further show a MICU1-dependent inhibitory effect of EFHD1 on calcium uptake. Next, we systematically survey compensatory mechanisms and functional consequences of mitochondrial calcium dyshomeostasis by analyzing the MCU interactome upon EMRE, MCUB, MICU1, or MICU2 knockdown. While silencing EMRE reduces MCU interconnectivity, MCUB loss-of-function leads to a wider interaction network. Our study provides a comprehensive and high-confidence resource to gain insights into players and mechanisms regulating mitochondrial calcium signaling and their relevance in human diseases.
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Affiliation(s)
- Hilda Delgado de la Herran
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Denis Vecellio Reane
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Yiming Cheng
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Máté Katona
- Department of Pathology, Anatomy, and Cell Biology, MitoCare Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fabian Hosp
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Roche Pharma Research and Early Development, Large Molecule Research, Mass Spectrometry, Penzberg, Germany
| | - Elisa Greotti
- Neuroscience Institute, National Research Council of Italy, Padua, Italy
- Department of Biomedical Sciences, University of Padova, Padua, Italy
- Padova Neuroscience Center, University of Padova, Padua, Italy
| | - Jennifer Wettmarshausen
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Maria Patron
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Hermine Mohr
- Institute of Diabetes and Cancer, Helmholtz Center Munich, Munich, Germany
| | - Natalia Prudente de Mello
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Margarita Chudenkova
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Matteo Gorza
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Safal Walia
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Michael Sheng-Fu Feng
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Anja Leimpek
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, University of Erlangen, Nikolaus-Fiebiger-Zentrum, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Natalia S Pellegata
- Institute of Diabetes and Cancer, Helmholtz Center Munich, Munich, Germany
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Thomas Langer
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - György Hajnóczky
- Department of Pathology, Anatomy, and Cell Biology, MitoCare Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Marta Murgia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Biomedical Sciences, University of Padova, Padua, Italy.
| | - Fabiana Perocchi
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum Munich, Munich, Germany.
- Institute of Neuronal Cell Biology, Technical University of Munich, Munich, Germany.
- Munich Cluster for Systems Neurology, Munich, Germany.
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16
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. EMBO J 2024:10.1038/s44318-024-00200-7. [PMID: 39256561 DOI: 10.1038/s44318-024-00200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 09/12/2024] Open
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known. Here, we use Saccharomyces cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, the resulting tyrosine phosphorylation is biologically spurious. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3500 proteins. The number of spurious pY sites generated correlates strongly with decreased growth, and we predict over 1000 pY events to be deleterious. However, we also find that many of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with tyrosine kinases. Our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada.
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada.
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada.
- Department of Biology, Université Laval, Québec, QC, Canada.
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17
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Kim JW, Choi SA, Dan K, Koh EJ, Ha S, Phi JH, Kim KH, Han D, Kim SK. Proteomic profiling of cerebrospinal fluid reveals TKT as a potential biomarker for medulloblastoma. Sci Rep 2024; 14:21053. [PMID: 39251709 PMCID: PMC11383936 DOI: 10.1038/s41598-024-71738-z] [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: 02/15/2024] [Accepted: 08/30/2024] [Indexed: 09/11/2024] Open
Abstract
Cerebrospinal fluid (CSF) plays an important role in brain tumors, including medulloblastoma (MBL). Recent advancements in mass spectrometry systems and 'Omics' data analysis methods enable unbiased, high proteome depth research. We conducted proteomic profiling of the total CSF in MBL patients with the purpose of finding a potential diagnostic biomarker for MBL. We quantified 1112 proteins per CSF sample. Feature selection identified four elevated soluble proteins (SPTBN1, HSP90AA1, TKT, and NME1-NME2) in MBL CSF. Validation with ELISA confirmed that TKT was significantly elevated in MBL. Additionally, TKT-positive extracellular vesicles were significantly enriched in MBL CSF and correlated with the burden of leptomeningeal seeding. Our results provide insights into the proteomics data of the total CSF of MBL patients. Furthermore, we identified the significance of TKT within the total CSF and its presence within circulating EVs in the CSF. We suggest that TKT may serve as a biomarker for MBL.
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Affiliation(s)
- Joo Whan Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Kisoon Dan
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Eun Jung Koh
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Saehim Ha
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyung Hyun Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea.
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul, 03082, South Korea.
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, South Korea.
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
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18
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Hsiao Y, Zhang H, Li GX, Deng Y, Yu F, Valipour Kahrood H, Steele JR, Schittenhelm RB, Nesvizhskii AI. Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst. J Proteome Res 2024. [PMID: 39254081 DOI: 10.1021/acs.jproteome.4c00294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
The FragPipe computational proteomics platform is gaining widespread popularity among the proteomics research community because of its fast processing speed and user-friendly graphical interface. Although FragPipe produces well-formatted output tables that are ready for analysis, there is still a need for an easy-to-use and user-friendly downstream statistical analysis and visualization tool. FragPipe-Analyst addresses this need by providing an R shiny web server to assist FragPipe users in conducting downstream analyses of the resulting quantitative proteomics data. It supports major quantification workflows, including label-free quantification, tandem mass tags, and data-independent acquisition. FragPipe-Analyst offers a range of useful functionalities, such as various missing value imputation options, data quality control, unsupervised clustering, differential expression (DE) analysis using Limma, and gene ontology and pathway enrichment analysis using Enrichr. To support advanced analysis and customized visualizations, we also developed FragPipeAnalystR, an R package encompassing all FragPipe-Analyst functionalities that is extended to support site-specific analysis of post-translational modifications (PTMs). FragPipe-Analyst and FragPipeAnalystR are both open-source and freely available.
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Affiliation(s)
- Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Haijian Zhang
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yamei Deng
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hossein Valipour Kahrood
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Monash Genomics & Bioinformatics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Joel R Steele
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Platform, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
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19
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Warminski M, Depaix A, Ziemkiewicz K, Spiewla T, Zuberek J, Drazkowska K, Kedzierska H, Popielec A, Baranowski MR, Sklucka M, Bednarczyk M, Smietanski M, Wolosewicz K, Majewski B, Serwa RA, Nowis D, Golab J, Kowalska J, Jemielity J. Trinucleotide cap analogs with triphosphate chain modifications: synthesis, properties, and evaluation as mRNA capping reagents. Nucleic Acids Res 2024:gkae763. [PMID: 39248095 DOI: 10.1093/nar/gkae763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/16/2024] [Accepted: 08/21/2024] [Indexed: 09/10/2024] Open
Abstract
The recent COVID-19 pandemics have demonstrated the great therapeutic potential of in vitro transcribed (IVT) mRNAs, but improvements in their biochemical properties, such as cellular stability, reactogenicity and translational activity, are critical for further practical applications in gene replacement therapy and anticancer immunotherapy. One of the strategies to overcome these limitations is the chemical modification of a unique mRNA 5'-end structure, the 5'-cap, which is responsible for regulating translation at multiple levels. This could be achieved by priming the in vitro transcription reaction with synthetic cap analogs. In this study, we combined a highly efficient trinucleotide IVT capping technology with several modifications of the 5' cap triphosphate bridge to synthesize a series of 16 new cap analogs. We also combined these modifications with epigenetic marks (2'-O-methylation and m6Am) characteristic of mRNA 5'-ends in higher eukaryotes, which was not possible with dinucleotide caps. All analogs were compared for their effect on the interactions with eIF4E protein, IVT priming, susceptibility to decapping, and mRNA translation efficiency in model cell lines. The most promising α-phosphorothiolate modification was also evaluated in an in vivo mouse model. Unexpected differences between some of the analogs were analyzed using a protein cell extract pull-down assay.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Anais Depaix
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Kamil Ziemkiewicz
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Tomasz Spiewla
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Karolina Drazkowska
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Hanna Kedzierska
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Agnieszka Popielec
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Marek R Baranowski
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Marta Sklucka
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | | | - Miroslaw Smietanski
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Karol Wolosewicz
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Bartosz Majewski
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Remigiusz A Serwa
- Proteomics Core Facility, IMol Polish Academy of Sciences, 02-247 Warsaw, Poland
| | - Dominika Nowis
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
- Laboratory of Experimental Medicine, Faculty of Medicine, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland
| | - Jakub Golab
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
- Department of Immunology, Medical University of Warsaw, Nielubowicza 5, 02-097 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
- Explorna Therapeutics sp. z o.o, Zwirki i Wigury 93/2157, 02-089 Warsaw, Poland
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20
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Lobo V, Nowak I, Fernandez C, Correa Muler AI, Westholm JO, Huang HC, Fabrik I, Huynh HT, Shcherbinina E, Poyraz M, Härtlova A, Benhalevy D, Angeletti D, Sarshad AA. Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference. Nucleic Acids Res 2024; 52:9917-9935. [PMID: 38994560 PMCID: PMC11381323 DOI: 10.1093/nar/gkae589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.
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Affiliation(s)
- Vivian Lobo
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Iwona Nowak
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Carola Fernandez
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ana Iris Correa Muler
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Jakub O Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Hsiang-Chi Huang
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Hang T Huynh
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Evgeniia Shcherbinina
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Melis Poyraz
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Anetta Härtlova
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Daniel Benhalevy
- Lab of Cellular RNA Biology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- SciLifeLab, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
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21
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Wu BCH, Zabelina V, Zurovcova M, Zurovec M. Characterization and comparative analysis of sericin protein 150 in Bombyx mori. Sci Rep 2024; 14:20990. [PMID: 39251726 PMCID: PMC11385562 DOI: 10.1038/s41598-024-71503-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 08/28/2024] [Indexed: 09/11/2024] Open
Abstract
Lepidopteran silk is a complex mixture of proteins, consisting mainly of fibroins and sericins. Sericins are a small family of highly divergent proteins that serve as adhesives and coatings for silk fibers. So far, five genes encoding sericin proteins have been identified in Bombyx mori. Having previously identified sericin protein 150 (SP150) as a major sericin-like protein in the cocoons of the pyralid moths Galleria mellonella and Ephestia kuehniella, we describe the identification of its homolog in B. mori. Our refined gene model shows that it consists of four exons and a long open reading frame with a conserved motif, CXCXCX, at the C-terminus, reminiscent of the structure observed in a class of mucin proteins. Notably, despite a similar expression pattern, both mRNA and protein levels of B. mori SP150 were significantly lower than those of its pyralid counterpart. We also discuss the synteny of homologous genes on corresponding chromosomes in different moth species and the possible phylogenetic relationships between SP150 and certain mucin-like proteins. Our results improve our understanding of silk structure and the evolutionary relationships between adhesion proteins in the silk of different lepidopteran species.
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Affiliation(s)
- Bulah Chia-Hsiang Wu
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Valeriya Zabelina
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Martina Zurovcova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Michal Zurovec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic.
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22
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Khoroshkin M, Buyan A, Dodel M, Navickas A, Yu J, Trejo F, Doty A, Baratam R, Zhou S, Lee SB, Joshi T, Garcia K, Choi B, Miglani S, Subramanyam V, Modi H, Carpenter C, Markett D, Corces MR, Mardakheh FK, Kulakovskiy IV, Goodarzi H. Systematic identification of post-transcriptional regulatory modules. Nat Commun 2024; 15:7872. [PMID: 39251607 PMCID: PMC11385195 DOI: 10.1038/s41467-024-52215-7] [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: 03/09/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we perform a systematic annotation of RBP combinatorial interactions via multimodal data integration. We build a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we use CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generate an integrated map of functional RBP interactions. We then use this map to match RBPs to their context-specific functions and validate the predicted functions biochemically for four RBPs. This study provides a detailed map of RBP interactions and deconvolves them into distinct regulatory modules with annotated functions and target regulons. This multimodal and integrative framework provides a principled approach for studying post-transcriptional regulatory processes and enriches our understanding of their underlying mechanisms.
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Affiliation(s)
- Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Andrey Buyan
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Institut Curie, UMR3348 CNRS, Inserm, Orsay, France
| | - Johnny Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Fathima Trejo
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Anthony Doty
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Rithvik Baratam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Shaopu Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sean B Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tanvi Joshi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sohit Miglani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Vishvak Subramanyam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Carpenter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Markett
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
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23
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Watson SS, Zomer A, Fournier N, Lourenco J, Quadroni M, Chryplewicz A, Nassiri S, Aubel P, Avanthay S, Croci D, Abels E, Broekman MLD, Hanahan D, Huse JT, Daniel RT, Hegi ME, Homicsko K, Cossu G, Hottinger AF, Joyce JA. Fibrotic response to anti-CSF-1R therapy potentiates glioblastoma recurrence. Cancer Cell 2024; 42:1507-1527.e11. [PMID: 39255775 DOI: 10.1016/j.ccell.2024.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 06/06/2024] [Accepted: 08/12/2024] [Indexed: 09/12/2024]
Abstract
Glioblastoma recurrence is currently inevitable despite extensive standard-of-care treatment. In preclinical studies, an alternative strategy of targeting tumor-associated macrophages and microglia through CSF-1R inhibition was previously found to regress established tumors and significantly increase overall survival. However, recurrences developed in ∼50% of mice in long-term studies, which were consistently associated with fibrotic scars. This fibrotic response is observed following multiple anti-glioma therapies in different preclinical models herein and in patient recurrence samples. Multi-omics analyses of the post-treatment tumor microenvironment identified fibrotic areas as pro-tumor survival niches that encapsulated surviving glioma cells, promoted dormancy, and inhibited immune surveillance. The fibrotic treatment response was mediated by perivascular-derived fibroblast-like cells via activation by transforming growth factor β (TGF-β) signaling and neuroinflammation. Concordantly, combinatorial inhibition of these pathways inhibited treatment-associated fibrosis, and significantly improved survival in preclinical trials of anti-colony-stimulating factor-1 receptor (CSF-1R) therapy.
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Affiliation(s)
- Spencer S Watson
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Lundin Brain Tumour Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland
| | - Anoek Zomer
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland
| | - Nadine Fournier
- Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Translational Data Science Facility, SIB Swiss Institute of Bioinformatics, Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland
| | - Joao Lourenco
- Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Translational Data Science Facility, SIB Swiss Institute of Bioinformatics, Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland
| | - Manfredo Quadroni
- Proteomics Core Facility, University of Lausanne, 1011 Lausanne, Switzerland
| | - Agnieszka Chryplewicz
- Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sina Nassiri
- Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Translational Data Science Facility, SIB Swiss Institute of Bioinformatics, Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland
| | - Pauline Aubel
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Lundin Brain Tumour Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland
| | - Simona Avanthay
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland
| | - Davide Croci
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland
| | - Erik Abels
- Department of Neurosurgery, Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Neurosurgery, Haaglanden Medical Center, 2597 The Hague, the Netherlands
| | - Marike L D Broekman
- Department of Neurosurgery, Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Neurosurgery, Haaglanden Medical Center, 2597 The Hague, the Netherlands
| | - Douglas Hanahan
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Geneva, Switzerland
| | - Jason T Huse
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roy T Daniel
- Lundin Brain Tumour Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Department of Neurosurgery, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Monika E Hegi
- Lundin Brain Tumour Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Department of Clinical Neurosciences, University Hospital Lausanne, 1011 Lausanne, Switzerland
| | - Krisztian Homicsko
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Giulia Cossu
- Lundin Brain Tumour Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andreas F Hottinger
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Lundin Brain Tumour Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Ludwig Institute for Cancer Research, University of Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Research Center Lausanne, 1011 Lausanne, Switzerland; Agora Cancer Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Lundin Brain Tumour Centre, University Hospital Lausanne, 1011 Lausanne, Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, Geneva, Switzerland.
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24
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Kaplieva-Dudek I, Samak NA, Bormann J, Kaschani F, Kaiser M, Meckenstock RU. Characterization of 2-phenanthroate:CoA ligase from the sulfate-reducing, phenanthrene-degrading enrichment culture TRIP. Appl Environ Microbiol 2024:e0129624. [PMID: 39248461 DOI: 10.1128/aem.01296-24] [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: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are chemically stable pollutants that are poorly degraded by microorganisms in anoxic sediments. The anaerobic degradation pathway of PAHs such as phenanthrene starts with a carboxylation reaction forming phenanthroic acid. In this study, we identified and characterized the next enzyme in the pathway, the 2-phenanthroate:CoA ligase involved in the ATP-dependent formation of 2-phenanthroyl-CoA from cell-free extracts of the sulfate-reducing enrichment culture TRIP grown anaerobically with phenanthrene. The identified gene sequence indicated that 2-phenanthroate:CoA ligase belongs to the phenylacetate:CoA ligase-like enzyme family. Based on the sequence, we predict a two-domain structure of the 2-phenanthroate:CoA ligase with a typical large N-terminal and a smaller C-terminal domain. Partial purification of 2-phenanthroate:CoA ligase allowed us to identify the coding gene in the genome. 2-Phenanthroate:CoA ligase gene was heterologously expressed in Escherichia coli. Characterization of the 2-phenanthroate:CoA ligase was performed using the partially purified enzyme from cell-free extract and the purified recombinant enzyme. Testing all possible phenanthroic acid isomers as substrate for the ligase reaction showed that 2-phenanthroic acid is the preferred substrate and only 3-phenanthroic acid can be utilized to a minor extent. This also suggests that the product of the prior carboxylase reaction is 2-phenanthroic acid. 2-Phenanthroate:CoA ligase has an optimal activity at pH 7.5 and is oxygen-insensitive, analogous to other aryl-CoA ligases. In contrast to aryl-Coenzyme A ligases reported in the literature, which need Mg2+ as cofactor, 2-phenanthroate:CoA ligase showed greatest activity with a combination of 5 mM MgCl2 and 5 mM KCl. Furthermore, a substrate inhibition was observed at ATP concentrations above 1 mM and the enzyme was also active with ADP. IMPORTANCE Polycyclic aromatic hydrocarbons (PAHs) constitute a class of very toxic and persistent pollutants in the environment. However, the anaerobic degradation of three-ring PAHs such as phenanthrene is barely investigated. The initial degradation step starts with a carboxylation followed by a CoA‑thioesterification reaction performed by an aryl-CoA ligase. The formation of a CoA-thioester is an important step in the degradation pathway of aromatic compounds because the CoA-ester is needed for all downstream biochemical reactions in the pathway. Furthermore, we provide biochemical proof for the identification of the first genes for anaerobic phenanthrene degradation. Results presented here provide information about the biochemical and structural properties of the purified 2‑phenanthroate:CoA ligase and expand our knowledge of aryl-CoA ligases.
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Affiliation(s)
- I Kaplieva-Dudek
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbiology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Nadia A Samak
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbiology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Jenny Bormann
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Analytics Core Facility Essen, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Farnusch Kaschani
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
- Analytics Core Facility Essen, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Markus Kaiser
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology (EMB), Aquatic Microbiology, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
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25
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Holendová B, Šalovská B, Benáková Š, Plecitá-Hlavatá L. Beyond glucose: The crucial role of redox signaling in β-cell metabolic adaptation. Metabolism 2024:156027. [PMID: 39260557 DOI: 10.1016/j.metabol.2024.156027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/23/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024]
Abstract
OBJECTIVE Redox signaling mediated by reversible oxidative cysteine thiol modifications is crucial for driving cellular adaptation to dynamic environmental changes, maintaining homeostasis, and ensuring proper function. This is particularly critical in pancreatic β-cells, which are highly metabolically active and play a specialized role in whole organism glucose homeostasis. Glucose stimulation in β-cells triggers signals leading to insulin secretion, including changes in ATP/ADP ratio and intracellular calcium levels. Additionally, lipid metabolism and reactive oxygen species (ROS) signaling are essential for β-cell function and health. METHODS We employed IodoTMT isobaric labeling combined with tandem mass spectrometry to elucidate redox signaling pathways in pancreatic β-cells. RESULTS Glucose stimulation significantly increases ROS levels in β-cells, leading to targeted reversible oxidation of proteins involved in key metabolic pathways such as glycolysis, the tricarboxylic acid (TCA) cycle, pyruvate metabolism, oxidative phosphorylation, protein processing in the endoplasmic reticulum (ER), and insulin secretion. Furthermore, the glucose-induced increase in reversible cysteine oxidation correlates with the presence of other post-translational modifications, including acetylation and phosphorylation. CONCLUSIONS Proper functioning of pancreatic β-cell metabolism relies on fine-tuned regulation, achieved through a sophisticated system of diverse post-translational modifications that modulate protein functions. Our findings demonstrate that glucose induces the production of ROS in pancreatic β-cells, leading to targeted reversible oxidative modifications of proteins. Furthermore, protein activity is modulated by acetylation and phosphorylation, highlighting the complexity of the regulatory mechanisms in β-cell function.
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Affiliation(s)
- Blanka Holendová
- Laboratory of Pancreatic Islet Research, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic.
| | - Barbora Šalovská
- Department of Genome Integrity, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic; Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, USA
| | - Štěpánka Benáková
- Laboratory of Pancreatic Islet Research, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic; First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lydie Plecitá-Hlavatá
- Laboratory of Pancreatic Islet Research, Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic.
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26
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Whitworth IT, Romero S, Kissi-Twum A, Knoener R, Scalf M, Sherer NM, Smith LM. Identification of Host Proteins Involved in Hepatitis B Virus Genome Packaging. J Proteome Res 2024; 23:4128-4138. [PMID: 39078123 DOI: 10.1021/acs.jproteome.4c00505] [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: 07/31/2024]
Abstract
A critical part of the hepatitis B virus (HBV) life cycle is the packaging of the pregenomic RNA (pgRNA) into nucleocapsids. While this process is known to involve several viral elements, much less is known about the identities and roles of host proteins in this process. To better understand the role of host proteins, we isolated pgRNA and characterized its protein interactome in cells expressing either packaging-competent or packaging-incompetent HBV genomes. We identified over 250 host proteins preferentially associated with pgRNA from the packaging-competent version of the virus. These included proteins already known to support capsid formation, enhance viral gene expression, catalyze nucleocapsid dephosphorylation, and bind to the viral genome, demonstrating the ability of the approach to effectively reveal functionally significant host-virus interactors. Three of these host proteins, AURKA, YTHDF2, and ATR, were selected for follow-up analysis. RNA immunoprecipitation qPCR (RIP-qPCR) confirmed pgRNA-protein association in cells, and siRNA knockdown of the proteins showed decreased encapsidation efficiency. This study provides a template for the use of comparative RNA-protein interactome analysis in conjunction with virus engineering to reveal functionally significant host-virus interactions.
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Affiliation(s)
- Isabella T Whitworth
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin 53706, United States
| | - Sofia Romero
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Abena Kissi-Twum
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53705, United States
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rachel Knoener
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin 53706, United States
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin 53706, United States
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin 53705, United States
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison College of Letters and Sciences, Madison, Wisconsin 53706, United States
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27
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Ball B, Sukumaran A, Krieger JR, Geddes-McAlister J. Comparative Cross-Kingdom DDA- and DIA-PASEF Proteomic Profiling Reveals Novel Determinants of Fungal Virulence and a Putative Druggable Target. J Proteome Res 2024; 23:3917-3932. [PMID: 39140824 PMCID: PMC11385706 DOI: 10.1021/acs.jproteome.4c00255] [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: 08/15/2024]
Abstract
Accurate and reliable detection of fungal pathogens presents an important hurdle to manage infections, especially considering that fungal pathogens, including the globally important human pathogen, Cryptococcus neoformans, have adapted diverse mechanisms to survive the hostile host environment and moderate virulence determinant production during coinfections. These pathogen adaptations present an opportunity for improvements (e.g., technological and computational) to better understand the interplay between a host and a pathogen during disease to uncover new strategies to overcome infection. In this study, we performed comparative proteomic profiling of an in vitro coinfection model across a range of fungal and bacterial burden loads in macrophages. Comparing data-dependent acquisition and data-independent acquisition enabled with parallel accumulation serial fragmentation technology, we quantified changes in dual-perspective proteome remodeling. We report enhanced and novel detection of pathogen proteins with data-independent acquisition-parallel accumulation serial fragmentation (DIA-PASEF), especially for fungal proteins during single and dual infection of macrophages. Further characterization of a fungal protein detected only with DIA-PASEF uncovered a novel determinant of fungal virulence, including altered capsule and melanin production, thermotolerance, and macrophage infectivity, supporting proteomics advances for the discovery of a novel putative druggable target to suppress C. neoformans pathogenicity.
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Affiliation(s)
- Brianna Ball
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Arjun Sukumaran
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
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28
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Bourel L, Bray F, Vivier S, Flament S, Guilbert L, Chepy A, Rolando C, Launay D, Dubucquoi S, Sobanski V. Comparative Analysis of Laboratory-Scale Immunoglobulin G Purification Methods from Human Serum. J Proteome Res 2024; 23:3933-3943. [PMID: 39140748 DOI: 10.1021/acs.jproteome.4c00268] [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: 08/15/2024]
Abstract
Immunoglobulin G (IgG) purification is a critical process for evaluating its role in autoimmune diseases, which are defined by the occurrence of autoantibodies. Affinity chromatography with protein G is widely considered to be the optimal technique for laboratory-scale purification. However, this technique has some limitations, including the exposure of IgG to low pH, which can compromise the quality of the purified IgG. Here, we show that alternative methods for IgG purification are possible while maintaining the quality of IgG. Different techniques for IgG purification from serum were evaluated and compared with protein G-based approaches: Melon Gel, caprylic acid-ammonium sulfate (CAAS) precipitation, anion-exchange chromatography with diethylamino ethyl (DEAE) following ammonium sulfate (AS) precipitation, and AS precipitation alone. The results demonstrated that the purification yield of these techniques surpassed that of protein G. However, differences in the purity of IgG were observed using GeLC-MS/MS. The avidity of purified IgG against selected targets (SARS-CoV-2 and topoisomerase-I) was similar between purified IgG obtained using all techniques and unpurified sera. Our work provides valuable insights for future studies of IgG function by recommending alternative purification methods that offer advantages in terms of yield, time efficiency, cost-effectiveness, and milder pH conditions than protein G.
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Affiliation(s)
- Louisa Bourel
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE─Institute for Translational Research in Inflammation, 59000 Lille, France
| | - Fabrice Bray
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, F-59000 Lille, France
| | - Solange Vivier
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE─Institute for Translational Research in Inflammation, 59000 Lille, France
| | - Stéphanie Flament
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, F-59000 Lille, France
| | - Lucile Guilbert
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE─Institute for Translational Research in Inflammation, 59000 Lille, France
- CHU Lille, Institut d'Immunologie, Centre de Biologie Pathologie, 59000 Lille, France
| | - Aurélien Chepy
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE─Institute for Translational Research in Inflammation, 59000 Lille, France
- CHU Lille, Département de Médecine Interne Et Immunologie Clinique, Centre de référence des Maladies Auto-Immunes et Auto-inflammatoires Systémiques rares de l'Adulte du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), 59000 Lille, France
| | - Christian Rolando
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, F-59000 Lille, France
- Shrieking Sixties, 1-3 Allée Lavoisier, F-59650 Villeneuve-d'Ascq, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE─Institute for Translational Research in Inflammation, 59000 Lille, France
- CHU Lille, Département de Médecine Interne Et Immunologie Clinique, Centre de référence des Maladies Auto-Immunes et Auto-inflammatoires Systémiques rares de l'Adulte du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), 59000 Lille, France
| | - Sylvain Dubucquoi
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE─Institute for Translational Research in Inflammation, 59000 Lille, France
- CHU Lille, Institut d'Immunologie, Centre de Biologie Pathologie, 59000 Lille, France
| | - Vincent Sobanski
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE─Institute for Translational Research in Inflammation, 59000 Lille, France
- CHU Lille, Département de Médecine Interne Et Immunologie Clinique, Centre de référence des Maladies Auto-Immunes et Auto-inflammatoires Systémiques rares de l'Adulte du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), 59000 Lille, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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29
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Lascaux P, Hoslett G, Tribble S, Trugenberger C, Antičević I, Otten C, Torrecilla I, Koukouravas S, Zhao Y, Yang H, Aljarbou F, Ruggiano A, Song W, Peron C, Deangeli G, Domingo E, Bancroft J, Carrique L, Johnson E, Vendrell I, Fischer R, Ng AWT, Ngeow J, D'Angiolella V, Raimundo N, Maughan T, Popović M, Milošević I, Ramadan K. TEX264 drives selective autophagy of DNA lesions to promote DNA repair and cell survival. Cell 2024:S0092-8674(24)00911-5. [PMID: 39265577 DOI: 10.1016/j.cell.2024.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 06/04/2024] [Accepted: 08/10/2024] [Indexed: 09/14/2024]
Abstract
DNA repair and autophagy are distinct biological processes vital for cell survival. Although autophagy helps maintain genome stability, there is no evidence of its direct role in the repair of DNA lesions. We discovered that lysosomes process topoisomerase 1 cleavage complexes (TOP1cc) DNA lesions in vertebrates. Selective degradation of TOP1cc by autophagy directs DNA damage repair and cell survival at clinically relevant doses of topoisomerase 1 inhibitors. TOP1cc are exported from the nucleus to lysosomes through a transient alteration of the nuclear envelope and independent of the proteasome. Mechanistically, the autophagy receptor TEX264 acts as a TOP1cc sensor at DNA replication forks, triggering TOP1cc processing by the p97 ATPase and mediating the delivery of TOP1cc to lysosomes in an MRE11-nuclease- and ATR-kinase-dependent manner. We found an evolutionarily conserved role for selective autophagy in DNA repair that enables cell survival, protects genome stability, and is clinically relevant for colorectal cancer patients.
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Affiliation(s)
- Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sara Tribble
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Camilla Trugenberger
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ivan Antičević
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Cecile Otten
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Stelios Koukouravas
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Yichen Zhao
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hongbin Yang
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Cristiano Peron
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Giulio Deangeli
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 2PY, UK
| | - Enric Domingo
- Department of Oncology, Medical Sciences Division, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - James Bancroft
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Loïc Carrique
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK
| | - Errin Johnson
- Dunn School Bioimaging Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7FZ, UK
| | - Alvin Wei Tian Ng
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Vincenzo D'Angiolella
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Edinburgh Cancer Research, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Nuno Raimundo
- Penn State College of Medicine, Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Tim Maughan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7BE, UK
| | - Marta Popović
- DNA Damage Group, Laboratory for Molecular Ecotoxicology, Department for Marine and Environmental Research, Institute Ruđer Bošković, 10000 Zagreb, Croatia
| | - Ira Milošević
- Centre for Human Genetics, Nuffield Department of Medicine (NDM), University of Oxford, Oxford OX3 7BN, UK; Multidisciplinary Institute for Aging, Center for Innovation in Biomedicine and Biotechnology, University of Coimbra, Coimbra 3000-370, Portugal
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Lee Kong Chian School of Medicine (LKCMedicine), Nanyang Technological University, Singapore 636921, Singapore.
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Zhao S, Li X, Yao X, Wan W, Xu L, Guo L, Bai J, Hu C, Yu H. Transformation of antibiotics to non-toxic and non-bactericidal products by laccases ensure the safety of Stropharia rugosoannulata. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135099. [PMID: 38981236 DOI: 10.1016/j.jhazmat.2024.135099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/18/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
The substantial use of antibiotics contributes to the spread and evolution of antibiotic resistance, posing potential risks to food production systems, including mushroom production. In this study, the potential risk of antibiotics to Stropharia rugosoannulata, the third most productive straw-rotting mushroom in China, was assessed, and the underlying mechanisms were investigated. Tetracycline exposure at environmentally relevant concentrations (<500 μg/L) did not influence the growth of S. rugosoannulata mycelia, while high concentrations of tetracycline (>500 mg/L) slightly inhibited its growth. Biodegradation was identified as the main antibiotic removal mechanism in S. rugosoannulata, with a degradation rate reaching 98.31 % at 200 mg/L tetracycline. High antibiotic removal efficiency was observed with secreted proteins of S. rugosoannulata, showing removal efficiency in the order of tetracyclines > sulfadiazines > quinolones. Antibiotic degradation products lost the ability to inhibit the growth of Escherichia coli, and tetracycline degradation products could not confer a growth advantage to antibiotic-resistant strains. Two laccases, SrLAC1 and SrLAC9, responsible for antibiotic degradation were identified based on proteomic analysis. Eleven antibiotics from tetracyclines, sulfonamides, and quinolones families could be transformed by these two laccases with degradation rates of 95.54-99.95 %, 54.43-100 %, and 5.68-57.12 %, respectively. The biosafety of the antibiotic degradation products was evaluated using the Toxicity Estimation Software Tool (TEST), revealing a decreased toxicity or no toxic effect. None of the S. rugosoannulata fruiting bodies from seven provinces in China contained detectable antibiotic-resistance genes (ARGs). This study demonstrated that S. rugosoannulata can degrade antibiotics into non-toxic and non-bactericidal products that do not accelerate the spread of antibiotic resistance, ensuring the safety of S. rugosoannulata production.
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Affiliation(s)
- Shuxue Zhao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, Shandong Province, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, Shandong Province, China
| | - Xiaohang Li
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, Shandong Province, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, Shandong Province, China
| | - Xingdong Yao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, Shandong Province, China
| | - Wei Wan
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, Shandong Province, China
| | - Lili Xu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, Shandong Province, China
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, Shandong Province, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, Shandong Province, China
| | - Chunhui Hu
- Instrumental analysis center of Qingdao Agricultural University, Qingdao 266109, Shandong Province, China.
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, Shandong Province, China.
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Susanto TT, Hung V, Levine AG, Chen Y, Kerr CH, Yoo Y, Oses-Prieto JA, Fromm L, Zhang Z, Lantz TC, Fujii K, Wernig M, Burlingame AL, Ruggero D, Barna M. RAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals composition dynamics in embryonic tissue, cancer cells, and macrophages. Mol Cell 2024:S1097-2765(24)00700-7. [PMID: 39260367 DOI: 10.1016/j.molcel.2024.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/25/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024]
Abstract
Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. We have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including Dhx30 and Llph, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development linked to the translation of genes with long coding sequences. In addition, we showed that RAPIDASH can identify ribosome changes in cancer cells. Finally, we characterized ribosome composition remodeling during immune cell activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs in multiple cell types, tissues, and stimuli and is adaptable to characterize ribosome remodeling in several contexts.
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Affiliation(s)
- Teodorus Theo Susanto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Victoria Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Yuxiang Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yongjin Yoo
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa Fromm
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Zijian Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Travis C Lantz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kotaro Fujii
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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32
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Zheng XF, Sarkar A, Lotana H, Syed A, Nguyen H, Ivey RG, Kennedy JJ, Whiteaker JR, Tomasik B, Huang K, Li F, D'Andrea AD, Paulovich AG, Shah K, Spektor A, Chowdhury D. CDK5-cyclin B1 regulates mitotic fidelity. Nature 2024:10.1038/s41586-024-07888-x. [PMID: 39232161 DOI: 10.1038/s41586-024-07888-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/30/2024] [Indexed: 09/06/2024]
Abstract
CDK1 has been known to be the sole cyclin-dependent kinase (CDK) partner of cyclin B1 to drive mitotic progression1. Here we demonstrate that CDK5 is active during mitosis and is necessary for maintaining mitotic fidelity. CDK5 is an atypical CDK owing to its high expression in post-mitotic neurons and activation by non-cyclin proteins p35 and p392. Here, using independent chemical genetic approaches, we specifically abrogated CDK5 activity during mitosis, and observed mitotic defects, nuclear atypia and substantial alterations in the mitotic phosphoproteome. Notably, cyclin B1 is a mitotic co-factor of CDK5. Computational modelling, comparison with experimentally derived structures of CDK-cyclin complexes and validation with mutational analysis indicate that CDK5-cyclin B1 can form a functional complex. Disruption of the CDK5-cyclin B1 complex phenocopies CDK5 abrogation in mitosis. Together, our results demonstrate that cyclin B1 partners with both CDK5 and CDK1, and CDK5-cyclin B1 functions as a canonical CDK-cyclin complex to ensure mitotic fidelity.
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Affiliation(s)
- Xiao-Feng Zheng
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aniruddha Sarkar
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Humphrey Lotana
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Aleem Syed
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Huy Nguyen
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bartłomiej Tomasik
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Faculty of Medicine, Gdańsk, Poland
| | - Kaimeng Huang
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Feng Li
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kavita Shah
- Department of Chemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Alexander Spektor
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Dipanjan Chowdhury
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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Davin ME, Thompson RA, Giannone RJ, Mendelson LW, Carper DL, Martin MZ, Martin ME, Engle NL, Tschaplinski TJ, Brown SD, Hettich RL. Clostridium autoethanogenum alters cofactor synthesis, redox metabolism, and lysine-acetylation in response to elevated H 2:CO feedstock ratios for enhancing carbon capture efficiency. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:119. [PMID: 39227857 PMCID: PMC11370222 DOI: 10.1186/s13068-024-02554-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/10/2024] [Indexed: 09/05/2024]
Abstract
BACKGROUND Clostridium autoethanogenum is an acetogenic bacterium that autotrophically converts carbon monoxide (CO) and carbon dioxide (CO2) gases into bioproducts and fuels via the Wood-Ljungdahl pathway (WLP). To facilitate overall carbon capture efficiency, the reaction stoichiometry requires supplementation of hydrogen at an increased ratio of H2:CO to maximize CO2 utilization; however, the molecular details and thus the ability to understand the mechanism of this supplementation are largely unknown. RESULTS In order to elucidate the microbial physiology and fermentation where at least 75% of the carbon in ethanol comes from CO2, we established controlled chemostats that facilitated a novel and high (11:1) H2:CO uptake ratio. We compared and contrasted proteomic and metabolomics profiles to replicate continuous stirred tank reactors (CSTRs) at the same growth rate from a lower (5:1) H2:CO condition where ~ 50% of the carbon in ethanol is derived from CO2. Our hypothesis was that major changes would be observed in the hydrogenases and/or redox-related proteins and the WLP to compensate for the elevated hydrogen feed gas. Our analyses did reveal protein abundance differences between the two conditions largely related to reduction-oxidation (redox) pathways and cofactor biosynthesis, but the changes were more minor than we would have expected. While the Wood-Ljungdahl pathway proteins remained consistent across the conditions, other post-translational regulatory processes, such as lysine-acetylation, were observed and appeared to be more important for fine-tuning this carbon metabolism pathway. Metabolomic analyses showed that the increase in H2:CO ratio drives the organism to higher carbon dioxide utilization resulting in lower carbon storages and accumulated fatty acid metabolite levels. CONCLUSIONS This research delves into the intricate dynamics of carbon fixation in C. autoethanogenum, examining the influence of highly elevated H2:CO ratios on metabolic processes and product outcomes. The study underscores the significance of optimizing gas feed composition for enhanced industrial efficiency, shedding light on potential mechanisms, such as post-translational modifications (PTMs), to fine-tune enzymatic activities and improve desired product yields.
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Affiliation(s)
- Megan E Davin
- Bredesen Center for Interdisciplinary Research, Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
- Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | | | | | | | - Dana L Carper
- Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | | | | | - Nancy L Engle
- Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Vivier S, Bray F, Flament S, Guilbert L, Renaud F, Rolando C, Launay D, Dubucquoi S, Sobanski V. Analysis of Unfolded Protein Response Activation in Colon Adenocarcinoma Epithelial Cells: A Proteomic Study. Proteomics Clin Appl 2024:e202400008. [PMID: 39226110 DOI: 10.1002/prca.202400008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 07/26/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024]
Abstract
PURPOSE High throughput technologies have identified molecular patterns in colorectal cancer (CRC) cells, aiding in modeling responses to anti-cancer treatments. The different responses observed depend on the type of cancer, the tumour grade and the functional programme of the cancer cells. Recent studies suggest that the unfolded protein response (UPR), autophagy and apoptosis could be involved in treatment resistance mechanisms by interacting with the tumour microenvironment (TME). EXPERIMENTAL DESIGN We analysed by LC-MS/MS the proteome of two representative colon adenocarcinoma epithelial cell lines from different tumour grades (CCL-233 and CCL-221) at the basal state or after the UPR induction. RESULTS Cell lines expressed a different proteome on about 10% of their total proteins identified, especially on UPR, autophagy and apoptosis pathways proteins at basal state. After UPR induction, the proteome of the cells was modified with a greater adaptive response to cellular stress in CCL-221 cells where the UPR was strongly activated at the basal state. CONCLUSIONS AND CLINICAL RELEVANCE CRC cell lines at different tumour grades expressed different functional programmes at the proteomic level and were characterised by different responses to the UPR induction. This study suggests that baseline cancer cell stress status could have an impact on the efficiency of cancer therapies.
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Affiliation(s)
- Solange Vivier
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
| | - Fabrice Bray
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Stéphanie Flament
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Lucile Guilbert
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- Institut d'Immunologie, Centre de Biologie Pathologie, CHU Lille, Lille, Hauts-de-France, France
| | - Florence Renaud
- Sorbonne Université, INSERM, Unité Mixte de Recherche Scientifique 938 and SIRIC CURAMUS, Centre de Recherche Saint-Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Christian Rolando
- Univ. Lille, CNRS, UAR 3290 - MSAP - Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - David Launay
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes et Auto-inflammatoires Systémiques Rares du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), Lille, Hauts-de-France, France
| | - Sylvain Dubucquoi
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- Institut d'Immunologie, Centre de Biologie Pathologie, CHU Lille, Lille, Hauts-de-France, France
| | - Vincent Sobanski
- Univ. Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, Lille, France
- CHU Lille, Département de Médecine Interne et Immunologie Clinique, Centre de Référence des Maladies Auto-immunes et Auto-inflammatoires Systémiques Rares du Nord, Nord-Ouest, Méditerranée et Guadeloupe (CeRAINOM), Lille, Hauts-de-France, France
- Institut Universitaire de France (IUF), Paris, France
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35
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Sicairos B, Zhou J, Hu Z, Zhang Q, Shi WQ, Du Y. Proteomic analysis reveals the dominant effect of ipomoeassin F on the synthesis of membrane and secretory proteins in triple-negative breast cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.605505. [PMID: 39131350 PMCID: PMC11312459 DOI: 10.1101/2024.07.28.605505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Ipomoeassin F (Ipom-F) is a natural compound with embedded carbohydrates that exhibits a potent cytotoxic effect on triple-negative breast cancer (TNBC) cells. The mechanism behind this selective potency remains unclear. To elucidate this mechanism, we analyzed the proteome profiles of the TNBC MDA-MB-231 cells after exposure to Ipom-F at different time points and increasing doses using a quantitative proteomic method. Our proteomic data demonstrate that the major effect of Ipom-F on MDA-MB-231 cells is the inhibition of membrane and secreted protein expression. Our proteomic data are consistent with the recently uncovered molecular mechanism of action of Ipom-F, which binds to Sec61-α and inhibits the co-translational import of proteins into the endoplasmic reticulum. We have defined a subset of membrane and secreted proteins particularly sensitive to Ipom-F. Analysis of the expression of these Ipom-F-sensitive proteins in cancer cell lines and breast cancer tissues demonstrates that some of these proteins are upregulated in TNBC cells. Thus, it is likely that TNBC cells may have adapted to the elevated levels of some proteins identified as sensitive to Ipom-F in this study; inhibition of the expression of these proteins leads to a crisis in proliferation and/or survival for the cells.
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36
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Mass S, Cohen H, Podicheti R, Rusch DB, Gerlic M, Ushijima B, van Kessel JC, Bosis E, Salomon D. The coral pathogen Vibrio coralliilyticus uses a T6SS to secrete a group of novel anti-eukaryotic effectors that contribute to virulence. PLoS Biol 2024; 22:e3002734. [PMID: 39226241 PMCID: PMC11371242 DOI: 10.1371/journal.pbio.3002734] [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: 03/20/2024] [Accepted: 07/03/2024] [Indexed: 09/05/2024] Open
Abstract
Vibrio coralliilyticus is a pathogen of coral and shellfish, leading to devastating economic and ecological consequences worldwide. Although rising ocean temperatures correlate with increased V. coralliilyticus pathogenicity, the specific molecular mechanisms and determinants contributing to virulence remain poorly understood. Here, we systematically analyzed the type VI secretion system (T6SS), a contact-dependent toxin delivery apparatus, in V. coralliilyticus. We identified 2 omnipresent T6SSs that are activated at temperatures in which V. coralliilyticus becomes virulent; T6SS1 is an antibacterial system mediating interbacterial competition, whereas T6SS2 mediates anti-eukaryotic toxicity and contributes to mortality during infection of an aquatic model organism, Artemia salina. Using comparative proteomics, we identified the T6SS1 and T6SS2 toxin arsenals of 3 V. coralliilyticus strains with distinct disease etiologies. Remarkably, T6SS2 secretes at least 9 novel anti-eukaryotic toxins comprising core and accessory repertoires. We propose that T6SSs differently contribute to V. coralliilyticus's virulence: T6SS2 plays a direct role by targeting the host, while T6SS1 plays an indirect role by eliminating competitors.
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Affiliation(s)
- Shir Mass
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hadar Cohen
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ram Podicheti
- Center for Genomics and Bioinformatics Indiana University, Bloomington, Indiana, United States of America
| | - Douglas B. Rusch
- Center for Genomics and Bioinformatics Indiana University, Bloomington, Indiana, United States of America
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina, United States of America
| | - Julia C. van Kessel
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Eran Bosis
- Department of Biotechnology Engineering, Braude College of Engineering, Karmiel, Israel
| | - Dor Salomon
- Department of Clinical Microbiology and Immunology, School of Medicine, Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
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Senesi G, Guerricchio L, Ghelardoni M, Bertola N, Rebellato S, Grinovero N, Bartolucci M, Costa A, Raimondi A, Grange C, Bolis S, Massa V, Paladini D, Coviello D, Pandolfi A, Bussolati B, Petretto A, Fazio G, Ravera S, Barile L, Balbi C, Bollini S. Extracellular vesicles from II trimester human amniotic fluid as paracrine conveyors counteracting oxidative stress. Redox Biol 2024; 75:103241. [PMID: 38901103 PMCID: PMC11253147 DOI: 10.1016/j.redox.2024.103241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/07/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND We previously demonstrated that the human amniotic fluid (hAF) from II trimester of gestation is a feasible source of stromal progenitors (human amniotic fluid stem cells, hAFSC), with significant paracrine potential for regenerative medicine. Extracellular vesicles (EVs) separated and concentrated from hAFSC secretome can deliver pro-survival, proliferative, anti-fibrotic and cardioprotective effects in preclinical models of skeletal and cardiac muscle injury. While hAFSC-EVs isolation can be significantly influenced by in vitro cell culture, here we profiled EVs directly concentrated from hAF as an alternative option and investigated their paracrine potential against oxidative stress. METHODS II trimester hAF samples were obtained as leftover material from prenatal diagnostic amniocentesis following written informed consent. EVs were separated by size exclusion chromatography and concentrated by ultracentrifugation. hAF-EVs were assessed by nanoparticle tracking analysis, transmission electron microscopy, Western Blot, and flow cytometry; their metabolic activity was evaluated by oximetric and luminometric analyses and their cargo profiled by proteomics and RNA sequencing. hAF-EV paracrine potential was tested in preclinical in vitro models of oxidative stress and dysfunction on murine C2C12 cells and on 3D human cardiac microtissue. RESULTS Our protocol resulted in a yield of 6.31 ± 0.98 × 109 EVs particles per hAF milliliter showing round cup-shaped morphology and 209.63 ± 6.10 nm average size, with relevant expression of CD81, CD63 and CD9 tetraspanin markers. hAF-EVs were enriched in CD133/1, CD326, CD24, CD29, and SSEA4 and able to produce ATP by oxygen consumption. While oxidative stress significantly reduced C2C12 survival, hAF-EV priming resulted in significant rescue of cell viability, with notable recovery of ATP synthesis and concomitant reduction of cell damage and lipid peroxidation activity. 3D human cardiac microtissues treated with hAF-EVs and experiencing H2O2 stress and TGFβ stimulation showed improved survival with a remarkable decrease in the onset of fibrosis. CONCLUSIONS Our results suggest that leftover samples of II trimester human amniotic fluid can represent a feasible source of EVs to counteract oxidative damage on target cells, thus offering a novel candidate therapeutic option to counteract skeletal and cardiac muscle injury.
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Affiliation(s)
- Giorgia Senesi
- Cardiovascular Theranostics, Istituto Cardiocentro Ticino and Laboratories for Traslational Research Ente Ospedaliero Cantonale, CH-6500, Bellinzona, Switzerland; Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera Italiana, CH-6900, Lugano, Switzerland
| | - Laura Guerricchio
- Department of Experimental Medicine (DIMES), University of Genova, 16132, Genova, Italy
| | | | - Nadia Bertola
- IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy
| | - Stefano Rebellato
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, 20900, Monza, Italy; School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Nicole Grinovero
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147, Genova, Italy
| | - Martina Bartolucci
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147, Genova, Italy
| | - Ambra Costa
- IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy
| | - Andrea Raimondi
- Institute for Research in Biomedicine, Università della Svizzera Italiana, CH-6500, Bellinzona, Switzerland
| | - Cristina Grange
- VEXTRA Facility and Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Sara Bolis
- Cardiovascular Theranostics, Istituto Cardiocentro Ticino and Laboratories for Traslational Research Ente Ospedaliero Cantonale, CH-6500, Bellinzona, Switzerland
| | - Valentina Massa
- Department of Health Sciences, University of Milan, 20146, Milan, Italy
| | - Dario Paladini
- Fetal Medicine and Surgery Unit, IRCCS Istituto Giannina Gaslini, 16147, Genova, Italy
| | - Domenico Coviello
- Human Genetics Laboratory, IRCCS Istituto Giannina Gaslini, 16147, Genova, Italy
| | - Assunta Pandolfi
- Department of Medical, Oral and Biotechnological Sciences, University "G. d'Annunzio" Chieti-Pescara and Center for Advanced Studies and Technology - CAST, 66100, Chieti, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126, Turin, Italy
| | - Andrea Petretto
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, 16147, Genova, Italy
| | - Grazia Fazio
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, 20900, Monza, Italy; School of Medicine and Surgery, University of Milano-Bicocca, 20900, Monza, Italy
| | - Silvia Ravera
- Department of Experimental Medicine (DIMES), University of Genova, 16132, Genova, Italy
| | - Lucio Barile
- Cardiovascular Theranostics, Istituto Cardiocentro Ticino and Laboratories for Traslational Research Ente Ospedaliero Cantonale, CH-6500, Bellinzona, Switzerland; Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera Italiana, CH-6900, Lugano, Switzerland.
| | - Carolina Balbi
- Center for Molecular Cardiology, University of Zurich, 8952, Schlieren, Switzerland; Department of Internal Medicine, Cantonal Hospital Baden, Baden, Switzerland.
| | - Sveva Bollini
- Department of Experimental Medicine (DIMES), University of Genova, 16132, Genova, Italy; IRCCS Ospedale Policlinico San Martino, 16132, Genova, Italy.
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Karlström V, Sagredo EA, Planells J, Welinder C, Jungfleisch J, Barrera-Conde A, Engfors L, Daniel C, Gebauer F, Visa N, Öhman M. ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation. Nucleic Acids Res 2024:gkae753. [PMID: 39217468 DOI: 10.1093/nar/gkae753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
ADAR3 is a catalytically inactive member of the family of adenosine deaminases acting on RNA (ADARs). Here we have investigated its function in the context of the developing mouse brain. The expression of ADAR3 gradually increases throughout embryogenesis and drops after birth. Using primary cortical neurons, we show that ADAR3 is only expressed in a subpopulation of in vitro differentiated neurons, which suggests specific functions rather than being a general regulator of ADAR editing in the brain. The analysis of the ADAR3 interactome suggested a role in mRNA stability and translation, and we show that expression of ADAR3 in a neuronal cell line that is otherwise ADAR3-negative changes the expression and stability of a large number of mRNAs. Notably, we show that ADAR3 associates with polysomes and inhibits translation. We propose that ADAR3 binds to target mRNAs and stabilizes them in non-productive polysome complexes. Interestingly, the expression of ADAR3 downregulates genes related to neuronal differentiation and inhibits neurofilament outgrowth in vitro. In summary, we propose that ADAR3 negatively regulates neuronal differentiation, and that it does so by regulating mRNA stability and translation in an editing-independent manner.
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Affiliation(s)
- Victor Karlström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Eduardo A Sagredo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Jordi Planells
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Charlotte Welinder
- Mass Spectrometry, Clinical Sciences, Lund University, Lund SE-221 84, Sweden
| | - Jennifer Jungfleisch
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, ES-08003 Barcelona, Spain
| | - Andrea Barrera-Conde
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, ES-08003 Barcelona, Spain
| | - Linus Engfors
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Chammiran Daniel
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, ES-08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), ES-08003 Barcelona, Spain
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
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Vorri SC, Holl NJ, Leeming M, Apostolova P, Marple A, Ravich JW, Canbaz A, Rahnama R, Choe J, Modi A, Fearnow AD, Walsh STR, Pearce EL, Varadhan R, Bonifant CL. Activation of Cell-Intrinsic Signaling in CAR-T Cells via a Chimeric IL7R Domain. CANCER RESEARCH COMMUNICATIONS 2024; 4:2359-2373. [PMID: 39186002 PMCID: PMC11382189 DOI: 10.1158/2767-9764.crc-24-0286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/01/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Chimeric antigen receptor (CAR) T cells can effectively treat leukemias, but sustained antitumor responses can be hindered by a lack of CAR T-cell persistence. Cytotoxic effector T cells are short-lived, and establishment of CAR-T cells with memory to ensure immune surveillance is important. Memory T cells depend on cytokine support, with IL7 activation of the IL7 receptor (IL7R) being critical. However, IL7R surface expression is negatively regulated by exposure to IL7. We aimed to support CAR T-cell persistence by equipping CAR-T cells with a sustained IL7Rα signal. We engineered T cells to constitutively secrete IL7 or to express an anti-acute myeloid leukemia-targeted IL7Rα-chimeric cytokine receptor (CCR) and characterized the phenotype of these cell types. Canonical downstream signaling was activated in CCR-T cells with IL7R activation. When coexpressed with a cytotoxic CAR, functionality of both the CCR and CAR was maintained. We designed hybrid CAR-CCR and noted membrane proximity of the intracellular domains as vital for signaling. These data show cell-intrinsic cytokine support with canonical signaling, and functionality can be provided via expression of an IL7Rα domain whether independently expressed or incorporated into a cytotoxic CAR for use in anticancer therapy. SIGNIFICANCE To improve the phenotype of tumor-directed T-cell therapy, we show that provision of cell-intrinsic IL7R-mediated signaling is preferable to activation of cells with exogenous IL7. We engineer this signaling via independent receptor engineering and incorporation into a CAR and validate maintained antigen-specific cytotoxic activity.
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MESH Headings
- Humans
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/metabolism
- Signal Transduction
- Immunotherapy, Adoptive/methods
- Interleukin-7/metabolism
- Interleukin-7/genetics
- Receptors, Interleukin-7/metabolism
- Receptors, Interleukin-7/genetics
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Cell Line, Tumor
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Interleukin-7 Receptor alpha Subunit
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Affiliation(s)
- Stamatia C Vorri
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Natalie J Holl
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael Leeming
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Petya Apostolova
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Division of Hematology, University Hospital Basel, Basel, Switzerland
| | - Andrew Marple
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonas W Ravich
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ata Canbaz
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ruyan Rahnama
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jun Choe
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Arjun Modi
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Adam D Fearnow
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Scott T R Walsh
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Erika L Pearce
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ravi Varadhan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Challice L Bonifant
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
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40
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Feehan J, Tripodi N, Kondrikov D, Wijeratne T, Gimble J, Hill W, Apostolopoulos V, Duque G. Differential Responses to Aging Among the Transcriptome and Proteome of Mesenchymal Progenitor Populations. J Gerontol A Biol Sci Med Sci 2024; 79:glae147. [PMID: 38837176 PMCID: PMC11369222 DOI: 10.1093/gerona/glae147] [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: 12/29/2023] [Indexed: 06/06/2024] Open
Abstract
The biological aging of stem cells (exhaustion) is proposed to contribute to the development of a variety of age-related conditions. Despite this, little is understood about the specific mechanisms which drive this process. In this study, we assess the transcriptomic and proteomic changes in 3 different populations of mesenchymal progenitor cells from older (50-70 years) and younger (20-40 years) individuals to uncover potential mechanisms driving stem cell exhaustion in mesenchymal tissues. To do this, we harvested primary bone marrow mesenchymal stem and progenitor cells (MPCs), circulating osteoprogenitors (COP), and adipose-derived stem cells (ADSCs) from younger and older donors, with an equal number of samples from men and women. These samples underwent RNA sequencing and label-free proteomic analysis, comparing the younger samples to the older ones. There was a distinct transcriptomic phenotype in the analysis of pooled older stem cells, suggestive of suppressed proliferation and differentiation; however, these changes were not reflected in the proteome of the cells. Analyzed independently, older MPCs had a distinct phenotype in both the transcriptome and proteome consistent with altered differentiation and proliferation with a proinflammatory immune shift in older adults. COP cells showed a transcriptomic shift to proinflammatory signaling but no consistent proteomic phenotype. Similarly, ADSCs displayed transcriptomic shifts in physiologies associated with cell migration, adherence, and immune activation but no proteomic change with age. These results show that there are underlying transcriptomic changes with stem cell aging that may contribute to a decline in tissue regeneration. However, the proteome of the cells was inconsistently regulated.
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Affiliation(s)
- Jack Feehan
- Department of Medicine—Western Health, University of Melbourne, Melbourne, Victoria, Australia
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Nicholas Tripodi
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Western Health, Victoria University and University of Melbourne, Melbourne, Victoria, Australia
| | - Dmitry Kondrikov
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Tissa Wijeratne
- Department of Medicine—Western Health, University of Melbourne, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Western Health, Victoria University and University of Melbourne, Melbourne, Victoria, Australia
| | - Jeffrey Gimble
- Center for Stem Cell Research and Regenerative Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - William Hill
- Department of Veterans Affairs, Ralph H Johnson VA Medical Center, Charleston, South Carolina, USA
- Center for Healthy Aging, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Western Health, Victoria University and University of Melbourne, Melbourne, Victoria, Australia
| | - Gustavo Duque
- Bone, Muscle & Geroscience Research Group, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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41
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Kulkarni A, Mohan V, Tang TT, Post L, Chan YC, Manning M, Thio N, Parker BL, Dawson MA, Rosenbluh J, Vissers JH, Harvey KF. Identification of resistance mechanisms to small-molecule inhibition of TEAD-regulated transcription. EMBO Rep 2024; 25:3944-3969. [PMID: 39103676 PMCID: PMC11387499 DOI: 10.1038/s44319-024-00217-3] [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: 06/27/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 08/07/2024] Open
Abstract
The Hippo tumor suppressor pathway controls transcription by regulating nuclear abundance of YAP and TAZ, which activate transcription with the TEAD1-TEAD4 DNA-binding proteins. Recently, several small-molecule inhibitors of YAP and TEADs have been reported, with some entering clinical trials for different cancers with Hippo pathway deregulation, most notably, mesothelioma. Using genome-wide CRISPR/Cas9 screens we reveal that mutations in genes from the Hippo, MAPK, and JAK-STAT signaling pathways all modulate the response of mesothelioma cell lines to TEAD palmitoylation inhibitors. By exploring gene expression programs of mutant cells, we find that MAPK pathway hyperactivation confers resistance to TEAD inhibition by reinstating expression of a subset of YAP/TAZ target genes. Consistent with this, combined inhibition of TEAD and the MAPK kinase MEK, synergistically blocks proliferation of multiple mesothelioma and lung cancer cell lines and more potently reduces the growth of patient-derived lung cancer xenografts in vivo. Collectively, we reveal mechanisms by which cells can overcome small-molecule inhibition of TEAD palmitoylation and potential strategies to enhance the anti-tumor activity of emerging Hippo pathway targeted therapies.
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Affiliation(s)
- Aishwarya Kulkarni
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Varshini Mohan
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Tracy T Tang
- Vivace Therapeutics Inc., San Mateo, CA, 94404, USA
| | - Leonard Post
- Vivace Therapeutics Inc., San Mateo, CA, 94404, USA
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Murray Manning
- Department of Biochemistry, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Functional Genomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joseph Rosenbluh
- Department of Biochemistry, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Functional Genomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Joseph Ha Vissers
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Anatomy and Developmental Biology, and Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.
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42
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Pinto G, Gelzo M, Cernera G, Esposito M, Illiano A, Serpico S, Pinchera B, Gentile I, Castaldo G, Amoresano A. Molecular fingerprint by omics-based approaches in saliva from patients affected by SARS-CoV-2 infection. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5082. [PMID: 39228271 DOI: 10.1002/jms.5082] [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: 11/13/2023] [Revised: 06/10/2024] [Accepted: 08/02/2024] [Indexed: 09/05/2024]
Abstract
Clinical expression of coronavirus disease 2019 (COVID-19) infectionis widely variable including fatal cases and patients with mild symptoms and a rapid resolution. We studied saliva from 63 hospitalized COVID-19 patients and from 30 healthy controls by integrating large-scale proteomics, peptidomics and targeted metabolomics to assess the biochemical alterations following the infection and to obtain a set of putative biomarkers useful for noninvasive diagnosis. We used an untargeted approach by using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for proteomics and peptidomics analysis and targeted LC-multiple reaction monitoring/MS for the analysis of amino acids. The levels of 77 proteins were significantly different in COVID-19 patients. Among these, seven proteins were found only in saliva from patients with COVID-19, four were up-regulated and three were down-regulated at least five-folds in saliva from COVID-19 patients in comparison to controls. The analysis of proteins revealed a complex balance between pro-inflammatory and anti-inflammatory proteins and a reduced amount of several proteins with immune activity that possibly favours the spreading of the virus. Such reduction could be related to the enhanced activity of endopeptidases induced by the infection that in turn caused an altered balance of free peptides. In fact, on a total of 28 peptides, 22 (80%) were differently expressed in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and control subjects. The multivariate analysis of such peptides permits to obtain a diagnostic algorithm that discriminate the two populations with a high diagnostic efficiency. Among amino acids, only threonine resulted significantly different between COVID-19 patients and controls, while alanine levels were significantly different between COVID-19 patients with different severity. In conclusion, the present study defined a set of molecules to be detected with a quick and easy method based on mass spectrometry tandem useful to reveal biochemical alterations involved in the pathogenesis of such a complex disease. Data are available via ProteomeXchange with identifier PXD045612.
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Affiliation(s)
- Gabriella Pinto
- Dipartimento di Scienze Chimiche, University of Naples Federico II, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Rome, Italy
| | - Monica Gelzo
- CEINGE-Biotecnologie avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, University of Naples Federico II, Naples, Italy
| | - Gustavo Cernera
- CEINGE-Biotecnologie avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, University of Naples Federico II, Naples, Italy
| | - Mariapia Esposito
- Dipartimento di Scienze Chimiche, University of Naples Federico II, Naples, Italy
| | - Anna Illiano
- Dipartimento di Scienze Chimiche, University of Naples Federico II, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Rome, Italy
| | - Stefania Serpico
- Dipartimento di Scienze Chimiche, University of Naples Federico II, Naples, Italy
| | - Biagio Pinchera
- Dipartimento di Medicina Clinica e Chirurgia, University of Naples Federico II, Naples, Italy
| | - Ivan Gentile
- Dipartimento di Medicina Clinica e Chirurgia, University of Naples Federico II, Naples, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie avanzate Franco Salvatore, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, University of Naples Federico II, Naples, Italy
| | - Angela Amoresano
- Dipartimento di Scienze Chimiche, University of Naples Federico II, Naples, Italy
- Istituto Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Rome, Italy
- CEINGE-Biotecnologie avanzate Franco Salvatore, Naples, Italy
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43
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Aumer T, Däther M, Bergmayr L, Kartika S, Zeng T, Ge Q, Giorgio G, Hess AJ, Michalakis S, Traube FR. The type of DNA damage response after decitabine treatment depends on the level of DNMT activity. Life Sci Alliance 2024; 7:e202302437. [PMID: 38906675 PMCID: PMC11192838 DOI: 10.26508/lsa.202302437] [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: 10/15/2023] [Revised: 06/08/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Decitabine and azacytidine are considered as epigenetic drugs that induce DNA methyltransferase (DNMT)-DNA crosslinks, resulting in DNA hypomethylation and damage. Although they are already applied against myeloid cancers, important aspects of their mode of action remain unknown, highly limiting their clinical potential. Using a combinatorial approach, we reveal that the efficacy profile of both compounds primarily depends on the level of induced DNA damage. Under low DNMT activity, only decitabine has a substantial impact. Conversely, when DNMT activity is high, toxicity and cellular response to both compounds are dramatically increased, but do not primarily depend on DNA hypomethylation or RNA-associated processes. By investigating proteome dynamics on chromatin, we show that decitabine induces a strictly DNMT-dependent multifaceted DNA damage response based on chromatin recruitment, but not expression-level changes of repair-associated proteins. The choice of DNA repair pathway hereby depends on the severity of decitabine-induced DNA lesions. Although under moderate DNMT activity, mismatch (MMR), base excision (BER), and Fanconi anaemia-dependent DNA repair combined with homologous recombination are activated in response to decitabine, high DNMT activity and therefore immense replication stress induce activation of MMR and BER followed by non-homologous end joining.
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Affiliation(s)
- Tina Aumer
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Maike Däther
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Linda Bergmayr
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Stephanie Kartika
- Department of Biochemistry, University of Munich (LMU), München, Germany
| | - Theodor Zeng
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Qingyi Ge
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | - Grazia Giorgio
- Department of Ophthalmology, University Hospital LMU Munich, München, Germany
| | - Alexander J Hess
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
| | | | - Franziska R Traube
- Institute of Chemical Epigenetics Munich, Department of Chemistry, University of Munich (LMU), München, Germany
- https://ror.org/02kkvpp62 TUM School of Natural Sciences, Technical University of Munich (TUM), München, Germany
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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Sinpru P, Suwanvichanee C, Bunnom R, Kubota S, Yongsawatdigul J, Molee W, Thumanu K, Molee A. Revealing the global mechanism related to carnosine synthesis in the pectoralis major of slow-growing Korat chickens using a proteomic approach. Anim Biosci 2024; 37:1692-1701. [PMID: 39139081 PMCID: PMC11366509 DOI: 10.5713/ab.24.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/30/2024] [Accepted: 05/15/2024] [Indexed: 08/15/2024] Open
Abstract
OBJECTIVE This study aimed to find global mechanisms related to carnosine synthesis in slow-growing Korat chickens (KRC) using a proteomic approach. METHODS M. pectoralis major samples were collected from 10-week-old female KRC including low-carnosine (LC, 2,756.6±82.88 μg/g; n = 5) and high-carnosine (HC, 4,212.5 ±82.88 μg/g; n = 5). RESULTS We identified 152 common proteins, and 8 of these proteins showed differential expression between the LC and HC groups (p<0.05). Heat shock 70 kDa protein 8, Heat shock 70 kDa protein 2, protein disulfide isomerase family A, member 6, and endoplasmic reticulum resident protein 29 were significantly involved in protein processing in the endoplasmic reticulum pathway (false discovery rate<0.05), suggesting that the pathway is related to differential carnosine concentration in the M. pectoralis major of KRC. A high concentration of carnosine in the meat is mainly involved in low abundances of Titin isoform Ch12 and Connectin and high abundances of M-protein to maintain homeostasis during muscle contraction. These consequences improve meat characteristics, which were confirmed by the principal component analysis. CONCLUSION Carnosine synthesis may occur when muscle cells need to recover homeostasis after being interfered with carnosine synthesis precursors, leading to improved muscle function. To the best of our knowledge, this is the first study to describe in detail the global molecular mechanisms in divergent carnosine contents in meat based on the proteomic approach.
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Affiliation(s)
- Panpradub Sinpru
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000,
Thailand
| | - Chanadda Suwanvichanee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000,
Thailand
| | - Rujjira Bunnom
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000,
Thailand
| | - Satoshi Kubota
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000,
Thailand
| | - Jirawat Yongsawatdigul
- School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000,
Thailand
| | - Wittawat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000,
Thailand
| | - Kanjana Thumanu
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, 30000,
Thailand
| | - Amonrat Molee
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000,
Thailand
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45
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Zou J, McNair E, DeCastro S, Lyons SP, Mordant A, Herring LE, Vetreno RP, Coleman LG. Microglia either promote or restrain TRAIL-mediated excitotoxicity caused by Aβ 1-42 oligomers. J Neuroinflammation 2024; 21:215. [PMID: 39218898 PMCID: PMC11367981 DOI: 10.1186/s12974-024-03208-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) features progressive neurodegeneration and microglial activation that results in dementia and cognitive decline. The release of soluble amyloid (Aβ) oligomers into the extracellular space is an early feature of AD pathology. This can promote excitotoxicity and microglial activation. Microglia can adopt several activation states with various functional outcomes. Protective microglial activation states have been identified in response to Aβ plaque pathology in vivo. However, the role of microglia and immune mediators in neurotoxicity induced by soluble Aβ oligomers is unclear. Further, there remains a need to identify druggable molecular targets that promote protective microglial states to slow or prevent the progression of AD. METHODS Hippocampal entorhinal brain slice culture (HEBSC) was employed to study mechanisms of Aβ1-42 oligomer-induced neurotoxicity as well as the role of microglia. The roles of glutamate hyperexcitation and immune signaling in Aβ-induced neurotoxicity were assessed using MK801 and neutralizing antibodies to the TNF-related apoptosis-inducing ligand (TRAIL) respectively. Microglial activation state was manipulated using Gi-hM4di designer receptor exclusively activated by designer drugs (DREADDs), microglial depletion with the colony-stimulating factor 1 receptor (CSF1R) antagonist PLX3397, and microglial repopulation (PLX3397 withdrawal). Proteomic changes were assessed by LC-MS/MS in microglia isolated from control, repopulated, or Aβ-treated HEBSCs. RESULTS Neurotoxicity induced by soluble Aβ1-42 oligomers involves glutamatergic hyperexcitation caused by the proinflammatory mediator and death receptor ligand TRAIL. Microglia were found to have the ability to both promote and restrain Aβ-induced toxicity. Induction of microglial Gi-signaling with hM4di to prevent pro-inflammatory activation blunted Aβ neurotoxicity, while microglial depletion with CSF1R antagonism worsened neurotoxicity caused by Aβ as well as TRAIL. HEBSCs with repopulated microglia, however, showed a near complete resistance to Aβ-induced neurotoxicity. Comparison of microglial proteomes revealed that repopulated microglia have a baseline anti-inflammatory and trophic phenotype with a predicted pathway activation that is nearly opposite that of Aβ-exposed microglia. mTORC2 and IRF7 were identified as potential targets for intervention. CONCLUSION Microglia are key mediators of both protection and neurodegeneration in response to Aβ. Polarizing microglia toward a protective state could be used as a preventative strategy against Aβ-induced neurotoxicity.
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Affiliation(s)
- Jian Zou
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Elizabeth McNair
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Sagan DeCastro
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Scott P Lyons
- Department of Pharmacology, UNC Proteomics Core, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Angie Mordant
- Department of Pharmacology, UNC Proteomics Core, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Laura E Herring
- Department of Pharmacology, UNC Proteomics Core, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ryan P Vetreno
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Leon G Coleman
- Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
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46
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Fleischer S, Nash TR, Tamargo MA, Lock RI, Venturini G, Morsink M, Graney PL, Li V, Lamberti MJ, Liberman M, Kim Y, Tavakol DN, Zhuang RZ, Whitehead J, Friedman RA, Soni RK, Seidman JG, Seidman CE, Geraldino-Pardilla L, Winchester R, Vunjak-Novakovic G. An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury. NATURE CARDIOVASCULAR RESEARCH 2024; 3:1123-1139. [PMID: 39195859 DOI: 10.1038/s44161-024-00525-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/18/2024] [Indexed: 08/29/2024]
Abstract
Systemic lupus erythematosus (SLE) is a heterogenous autoimmune disease that affects multiple organs, including the heart. The mechanisms of myocardial injury in SLE remain poorly understood. In this study, we engineered human cardiac tissues and cultured them with IgG from patients with SLE, with and without myocardial involvement. IgG from patients with elevated myocardial inflammation exhibited increased binding to apoptotic cells within cardiac tissues subjected to stress, whereas IgG from patients with systolic dysfunction exhibited enhanced binding to the surface of live cardiomyocytes. Functional assays and RNA sequencing revealed that, in the absence of immune cells, IgG from patients with systolic dysfunction altered cellular composition, respiration and calcium handling. Phage immunoprecipitation sequencing (PhIP-seq) confirmed distinctive IgG profiles between patient subgroups. Coupling IgG profiling with cell surfaceome analysis identified four potential pathogenic autoantibodies that may directly affect the myocardium. Overall, these insights may improve patient risk stratification and inform the development of new therapeutic strategies.
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Affiliation(s)
- Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Roberta I Lock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Margaretha Morsink
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Vanessa Li
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Morgan J Lamberti
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Daniel N Tavakol
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jaron Whitehead
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Robert Winchester
- Department of Medicine, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
- College of Dental Medicine, Columbia University, New York, NY, USA.
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47
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Welch LG, Muschalik N, Munro S. The FAM114A proteins are adaptors for the recycling of Golgi enzymes. J Cell Sci 2024; 137:jcs262160. [PMID: 39129673 DOI: 10.1242/jcs.262160] [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: 03/27/2024] [Accepted: 08/01/2024] [Indexed: 08/13/2024] Open
Abstract
Golgi-resident enzymes remain in place while their substrates flow through from the endoplasmic reticulum to elsewhere in the cell. COPI-coated vesicles bud from the Golgi to recycle Golgi residents to earlier cisternae. Different enzymes are present in different parts of the stack, and one COPI adaptor protein, GOLPH3, acts to recruit enzymes into vesicles in part of the stack. Here, we used proximity biotinylation to identify further components of intra-Golgi vesicles and found FAM114A2, a cytosolic protein. Affinity chromatography with FAM114A2, and its paralogue FAM114A1, showed that they bind to Golgi-resident membrane proteins, with membrane-proximal basic residues in the cytoplasmic tail being sufficient for the interaction. Deletion of both proteins from U2OS cells did not cause substantial defects in Golgi function. However, a Drosophila orthologue of these proteins (CG9590/FAM114A) is also localised to the Golgi and binds directly to COPI. Drosophila mutants lacking FAM114A have defects in glycosylation of glue proteins in the salivary gland. Thus, the FAM114A proteins bind Golgi enzymes and are candidate adaptors to contribute specificity to COPI vesicle recycling in the Golgi stack.
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Affiliation(s)
- Lawrence G Welch
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Nadine Muschalik
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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48
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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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49
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Gomes FA, Souza Junior DR, Massafera MP, Ronsein GE. Robust assessment of sample preparation protocols for proteomics of cells and tissues. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141030. [PMID: 38944097 DOI: 10.1016/j.bbapap.2024.141030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
In proteomic studies, the reliability and reproducibility of results hinge on well-executed protein extraction and digestion protocols. Here, we systematically compared three established digestion methods for macrophages, namely filter-assisted sample preparation (FASP), in-solution, and in-gel digestion protocols. We also compared lyophilization and manual lysis for liver tissue protein extraction, each of them tested using either sodium deoxycholate (SDC)- or RIPA-based lysis buffer. For the macrophage cell line, FASP using passivated filter units outperformed the other tested methods regarding the number of identified peptides and proteins. However, a careful standardization has shown that all three methods can yield robust results across a wide range of starting material (even starting with 1 μg of proteins). Importantly, inter and intra-day coefficients of variance (CVs) were determined for all sample preparation protocols. Thus, the median inter-day CVs for in-solution, in-gel and FASP protocols were respectively 10, 8 and 9%, very similar to the median CVs obtained for the intra-day analysis (9, 8 and 8%, respectively). Moreover, FASP digestion presented 80% of proteins with a CV lower than 25%, followed closely by in-gel digestion (78%) and in-solution sample preparation (72%) protocols. For tissue proteomics, both manual lysis and lyophilization presented similar proteome coverage and reproducibility, but the efficiency of protein extraction depended on the lysis buffer used, with RIPA buffer showing better results. In conclusion, although each sample preparation method has its own particularity, they are all suited for successful proteomic experiments if a careful standardization of the sample preparation workflow is carried out.
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Affiliation(s)
- Francielle Aguiar Gomes
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | | | - Graziella Eliza Ronsein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
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50
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Cao L, Zhou Y, Lin S, Yang C, Guan Z, Li X, Yang S, Gao T, Zhao J, Fan N, Song Y, Li D, Li X, Li Z, Guan F, Tan Z. The trajectory of vesicular proteomic signatures from HBV-HCC by chitosan-magnetic bead-based separation and DIA-proteomic analysis. J Extracell Vesicles 2024; 13:e12499. [PMID: 39207047 PMCID: PMC11359709 DOI: 10.1002/jev2.12499] [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] [Received: 03/11/2024] [Revised: 07/04/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a prevalent primary liver cancer often associated with chronic hepatitis B virus infection (CHB) and liver cirrhosis (LC), underscoring the critical need for biomarker discovery to improve patient outcomes. Emerging as a promising avenue for biomarker development, proteomic technology leveraging liquid biopsy from small extracellular vesicles (sEV) offers new insights. Here, we evaluated various methods for sEV isolation and identified polysaccharide chitosan (CS) as an optimal approach. Subsequently, we employed optimized CS-based magnetic beads (Mag-CS) for sEV separation from serum samples of healthy controls, CHB, LC, and HBV-HCC patients. Leveraging data-independent acquisition mass spectrometry coupled with machine learning, we uncovered potential vesicular protein biomarker signatures (KNG1, F11, KLKB1, CAPNS1, CDH1, CPN2, NME2) capable of distinguishing HBV-HCC from CHB, LC, and non-HCC conditions. Collectively, our findings highlight the utility of Mag-CS-based sEV isolation for identifying early detection biomarkers in HBV-HCC.
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Affiliation(s)
- Lin Cao
- Institute of HematologyProvincial Key Laboratory of Biotechnology, School of MedicineNorthwest UniversityXi'anShaanxiChina
| | - Yue Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Shuai Lin
- Department of OncologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShaanxiChina
| | - Chunyan Yang
- Institute of Basic and Translational MedicineXi'an Medical UniversityXi'anShaanxiChina
| | - Zixuan Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Xiaofan Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Shujie Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Tong Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Jiazhen Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Ning Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Yanan Song
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Dongmin Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesXi'an Jiaotong University Health Science CenterXi'anShaanxiP.R. China
| | - Xiang Li
- Institute of HematologyProvincial Key Laboratory of Biotechnology, School of MedicineNorthwest UniversityXi'anShaanxiChina
| | - Zhuo Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
- Department of Laboratory MedicineThe First Affiliated Hospital of Xi'an Medical UniversityXi'anShaanxiP.R. China
| | - Feng Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Provincial Key Laboratory of Biotechnology, College of Life SciencesNorthwest UniversityXi'anShaanxiChina
| | - Zengqi Tan
- Institute of HematologyProvincial Key Laboratory of Biotechnology, School of MedicineNorthwest UniversityXi'anShaanxiChina
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