1
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Mousseau CB, Hu DD, Schultz SR, Champion MM. Quenching Trypsin Is Unnecessary in Filter-Based Bottom-Up Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2028-2031. [PMID: 38982799 PMCID: PMC11313428 DOI: 10.1021/jasms.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
Quenching digestions in proteomics prior to analysis is routine in order to eliminate residual protease activity. Residual activity leads to overdigestion, nonspecific star-activity, and back-exchange in isotopic 18O quantitation. Chemical and isobaric labeling (e.g., TMT/iTRAQ) of proteins or peptides for mass spectrometry-based proteomics is generally incompatible with ubiquitous postdigestion acidification. This necessitates buffer exchange and pH adjustments. We demonstrate that quenching is unnecessary with peptides generated from protein filter-traps, as trypsin activity and intact trypsin are negligible in the eluate from these preparations. Labeling can be directly performed on enzymatic digests from these methods, improving recovery, throughput, and ease of automation.
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Affiliation(s)
- C. Bruce Mousseau
- Department
of Chemistry and Biochemistry, andBerthiaume Institute for Precision
Health, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Daniel D. Hu
- Department
of Chemistry and Biochemistry, andBerthiaume Institute for Precision
Health, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Sadie R. Schultz
- Department
of Chemistry and Biochemistry, andBerthiaume Institute for Precision
Health, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Matthew M. Champion
- Department
of Chemistry and Biochemistry, andBerthiaume Institute for Precision
Health, University of Notre Dame, Notre Dame, Indiana 46556, United States
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2
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Brough Z, Zhao Z, Duong van Hoa F. From bottom-up to cell surface proteomics: detergents or no detergents, that is the question. Biochem Soc Trans 2024; 52:1253-1263. [PMID: 38666604 PMCID: PMC11346462 DOI: 10.1042/bst20231020] [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: 02/05/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Measuring the expression levels of membrane proteins (MPs) is crucial for understanding cell differentiation and tissue specificity, defining disease characteristics, identifying biomarkers, and developing therapeutics. While bottom-up proteomics addresses the need for accurately surveying the membrane proteome, the lower abundance and hydrophobic nature of MPs pose challenges in sample preparation. As MPs normally reside in the lipid bilayer, conventional extraction methods rely on detergents, introducing here a paradox - detergents prevent aggregation and facilitate protein processing, but themselves become contaminants that interfere with downstream analytical applications. Various detergent removal methods exist to mitigate this issue, including filter-aided sample preparation, SP3, suspension trapping, and membrane mimetics. This review delves into the fundamentals of each strategy, applications, merits, and limitations, providing insights into their effectiveness in MP research.
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Affiliation(s)
- Zora Brough
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Zhiyu Zhao
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Franck Duong van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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3
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Martin KR, Le HT, Abdelgawad A, Yang C, Lu G, Keffer JL, Zhang X, Zhuang Z, Asare-Okai PN, Chan CS, Batish M, Yu Y. Development of an efficient, effective, and economical technology for proteome analysis. CELL REPORTS METHODS 2024; 4:100796. [PMID: 38866007 PMCID: PMC11228373 DOI: 10.1016/j.crmeth.2024.100796] [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: 01/19/2024] [Revised: 03/21/2024] [Accepted: 05/20/2024] [Indexed: 06/14/2024]
Abstract
We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome.
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Affiliation(s)
- Katherine R Martin
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Ahmed Abdelgawad
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Canyuan Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Guotao Lu
- CDS Analytical, LLC, Oxford, PA 19363, USA
| | - Jessica L Keffer
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA
| | | | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Papa Nii Asare-Okai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE 19716, USA; School of Marine Science and Policy, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA.
| | - Yanbao Yu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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4
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Dodd DO, Mechaussier S, Yeyati PL, McPhie F, Anderson JR, Khoo CJ, Shoemark A, Gupta DK, Attard T, Zariwala MA, Legendre M, Bracht D, Wallmeier J, Gui M, Fassad MR, Parry DA, Tennant PA, Meynert A, Wheway G, Fares-Taie L, Black HA, Mitri-Frangieh R, Faucon C, Kaplan J, Patel M, McKie L, Megaw R, Gatsogiannis C, Mohamed MA, Aitken S, Gautier P, Reinholt FR, Hirst RA, O’Callaghan C, Heimdal K, Bottier M, Escudier E, Crowley S, Descartes M, Jabs EW, Kenia P, Amiel J, Bacci GM, Calogero C, Palazzo V, Tiberi L, Blümlein U, Rogers A, Wambach JA, Wegner DJ, Fulton AB, Kenna M, Rosenfeld M, Holm IA, Quigley A, Hall EA, Murphy LC, Cassidy DM, von Kriegsheim A, Papon JF, Pasquier L, Murris MS, Chalmers JD, Hogg C, Macleod KA, Urquhart DS, Unger S, Aitman TJ, Amselem S, Leigh MW, Knowles MR, Omran H, Mitchison HM, Brown A, Marsh JA, Welburn JPI, Ti SC, Horani A, Rozet JM, Perrault I, Mill P. Ciliopathy patient variants reveal organelle-specific functions for TUBB4B in axonemal microtubules. Science 2024; 384:eadf5489. [PMID: 38662826 PMCID: PMC7616230 DOI: 10.1126/science.adf5489] [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: 10/29/2022] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Tubulin, one of the most abundant cytoskeletal building blocks, has numerous isotypes in metazoans encoded by different conserved genes. Whether these distinct isotypes form cell type- and context-specific microtubule structures is poorly understood. Based on a cohort of 12 patients with primary ciliary dyskinesia as well as mouse mutants, we identified and characterized variants in the TUBB4B isotype that specifically perturbed centriole and cilium biogenesis. Distinct TUBB4B variants differentially affected microtubule dynamics and cilia formation in a dominant-negative manner. Structure-function studies revealed that different TUBB4B variants disrupted distinct tubulin interfaces, thereby enabling stratification of patients into three classes of ciliopathic diseases. These findings show that specific tubulin isotypes have distinct and nonredundant subcellular functions and establish a link between tubulinopathies and ciliopathies.
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Affiliation(s)
- Daniel O Dodd
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Sabrina Mechaussier
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris75015, France
| | - Patricia L Yeyati
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Fraser McPhie
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Jacob R Anderson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston 02215, USA
| | - Chen Jing Khoo
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Amelia Shoemark
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, DundeeDD1 9SY, UK
- Royal Brompton Hospital, LondonSW3 6NP, UK
| | - Deepesh K Gupta
- Department of Pediatrics, Washington University School of Medicine, St. Louis 63130, USA
| | - Thomas Attard
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, UK
| | - Maimoona A Zariwala
- Department of Pathology and Laboratory Medicine, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill27599-7248, USA
| | - Marie Legendre
- Molecular Genetics Laboratory, Sorbonne Université, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Armand Trousseau, Paris75012, France
- Sorbonne Université, INSERM, Childhood Genetic Disorders, Paris75012, France
| | - Diana Bracht
- Department of General Pediatrics, University Children’s Hospital Münster, Münster 48149, Germany
| | - Julia Wallmeier
- Department of General Pediatrics, University Children’s Hospital Münster, Münster 48149, Germany
| | - Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston 02215, USA
| | - Mahmoud R Fassad
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, LondonWC1N 1EH, UK
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria21561, Egypt
| | - David A Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Peter A Tennant
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, SouthamptonSO16 6YD, UK
| | - Lucas Fares-Taie
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris75015, France
| | - Holly A Black
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
- South East of Scotland Genetics Service, Western General Hospital, EdinburghEH4 2XU, UK
| | - Rana Mitri-Frangieh
- Department of Anatomy, Cytology and Pathology, Hôpital Intercommuncal de Créteil, Créteil, France
- Biomechanics and Respiratory Apparatus, IMRB, U955 INSERM – Université Paris Est Créteil, CNRS ERL 7000, Créteil 94000, France
| | - Catherine Faucon
- Department of Anatomy, Cytology and Pathology, Hôpital Intercommuncal de Créteil, Créteil, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris75015, France
| | - Mitali Patel
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, LondonWC1N 1EH, UK
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, University College London, LondonW1W 7FF, UK
| | - Lisa McKie
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Roly Megaw
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
- Princess Alexandra Eye Pavilion, EdinburghEH3 9HA, UK
| | - Christos Gatsogiannis
- Center for Soft Nanoscience and Institute of Medical Physics and Biophysics, Münster 48149, Germany
| | - Mai A Mohamed
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, LondonWC1N 1EH, UK
- Biochemistry Division, Chemistry Department, Faculty of Science, Zagazig University, Ash Sharqiyah44519, Egypt
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Finn R Reinholt
- Core Facility for Electron Microscopy, Department of Pathology, Oslo University Hospital-Rikshospitalet, Oslo0372, Norway
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Respiratory Sciences, University of Leicester, LeicesterLE1 9HN, UK
| | - Chris O’Callaghan
- Department of Medical Genetics, Oslo University Hospital, Oslo0407, Norway
| | - Ketil Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo0407, Norway
| | - Mathieu Bottier
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, DundeeDD1 9SY, UK
| | - Estelle Escudier
- Sorbonne Université, INSERM, Childhood Genetic Disorders, Paris75012, France
- Department of Anatomy, Cytology and Pathology, Hôpital Intercommuncal de Créteil, Créteil, France
| | - Suzanne Crowley
- Paediatric Department of Allergy and Lung Diseases, Oslo University Hospital, Oslo0407, Norway
| | - Maria Descartes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, 35294-0024, USA
| | - Ethylin W Jabs
- Icahn School of Medicine at Mount Sinai, New York10029-6504, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester55905, USA
| | - Priti Kenia
- Department of Paediatric Respiratory Medicine, Birmingham Women’s and Children’s Hospital NHS Foundation Trust, BirminghamB15 2TG, UK
| | - Jeanne Amiel
- Département de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), Paris75015, France
- Laboratory of Embryology and Genetics of Human Malformations, INSERM UMR 1163, Institut Imagine, Université de Paris, Paris75015, France
| | - Giacomo Maria Bacci
- Pediatric Ophthalmology Unit, Meyer Children's Hospital IRCCS, Florence50139, Italy
| | - Claudia Calogero
- Pediatric Ophthalmology Unit, Meyer Children's Hospital IRCCS, Florence50139, Italy
| | - Viviana Palazzo
- Pediatric Pulmonary Unit, Meyer Children's Hospital IRCCS, Florence50139, Italy
| | - Lucia Tiberi
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence50139, Italy
| | | | | | - Jennifer A Wambach
- Department of Pediatrics, Washington University School of Medicine, St. Louis 63130, USA
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis 63130, USA
| | - Anne B Fulton
- Department of Ophthalmology, Boston Children’s Hospital; Boston02115, USA
| | - Margaret Kenna
- Department of Otolaryngology, Boston Children’s Hospital; Boston02115, USA
| | - Margaret Rosenfeld
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children’s Research Institute, Seattle 98015, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children’s Hospital, Boston02115, USA
- Department of Pediatrics, Harvard Medical School, Boston 02115, USA
| | - Alan Quigley
- Department of Paediatric Radiology, Royal Hospital for Children and Young People, Edinburgh EH16 4TJ, UK
| | - Emma A Hall
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Diane M Cassidy
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, DundeeDD1 9SY, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Scottish Genomes Partnership
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | | | | | - Jean-François Papon
- ENT Department, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris-Saclay University, Le Kremlin-Bicêtre94270, France
| | - Laurent Pasquier
- Medical Genetics Department, CHU Pontchaillou, Rennes 35033, France
| | - Marlène S Murris
- Department of Pulmonology, Transplantation, and Cystic Fibrosis Centre, Larrey Hospital, Toulouse31400, France
| | - James D Chalmers
- Respiratory Research Group, Molecular and Cellular Medicine, University of Dundee, DundeeDD1 9SY, UK
| | | | | | - Don S Urquhart
- Medical Genetics Department, CHU Pontchaillou, Rennes 35033, France
- Department of Pulmonology, Transplantation, and Cystic Fibrosis Centre, Larrey Hospital, Toulouse31400, France
| | - Stefan Unger
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children and Young People, Edinburgh EH16 4TJ, UK
- Department of Child Life and Health, University of Edinburgh, EdinburghEH16 4TJ, UK
| | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Serge Amselem
- Molecular Genetics Laboratory, Sorbonne Université, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpital Armand Trousseau, Paris75012, France
- Sorbonne Université, INSERM, Childhood Genetic Disorders, Paris75012, France
| | - Margaret W Leigh
- Department of Pediatrics, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill27599-7248, USA
| | - Michael R. Knowles
- Department of Medicine, Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill27599-7248, USA
| | - Heymut Omran
- Department of General Pediatrics, University Children’s Hospital Münster, Münster 48149, Germany
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Department, UCL Institute of Child Health, University College London, LondonWC1N 1EH, UK
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston 02215, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
| | - Julie P I Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3BF, UK
| | - Shih-Chieh Ti
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis 63130, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis 63110, USA
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris75015, France
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology, INSERM UMR_1163, Institute of Genetic Diseases, Institut Imagine, Université de Paris, Paris75015, France
| | - Pleasantine Mill
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, UK
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5
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Kwan R, Das P, Gerrebos N, Li J, Wang XY, DeBoer G, Emnacen-Pankhurst V, Lin S, Feng R, Goodchild S, Sojo LE. Development and application of a multiple reaction monitoring method for the simultaneous quantification of sodium channels Na v 1.1, Na v 1.2, and Na v 1.6 in solubilized membrane proteins from stable HEK293 cell lines, rodents, and human brain tissues. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9672. [PMID: 38211346 DOI: 10.1002/rcm.9672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/13/2023] [Accepted: 10/22/2023] [Indexed: 01/13/2024]
Abstract
RATIONALE Nav 1.1, 1.2, and 1.6 are transmembrane proteins acting as voltage-gated sodium channels implicated in various forms of epilepsy. There is a need for knowing their actual concentration in target tissues during drug development. METHODS Unique peptides for Nav 1.1, Nav 1.2, and Nav 1.6 were selected as quantotropic peptides for each protein and used for their quantification in membranes from stably transfected HEK293 cells and rodent and human brain samples using ultra-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. RESULTS Nav 1.1, 1.2, and 1.6 protein expressions in three stably individually transfected HEK293 cell lines were found to be 2.1 ± 0.2, 6.4 ± 1.2, and 4.0 ± 0.6 fmol/μg membrane protein, respectively. In brains, Nav 1.2 showed the highest expression, with approximately three times higher (P < 0.003) in rodents than in humans at 3.05 ± 0.57, with 3.35 ± 0.56 in mouse and rat brains and 1.09 ± 0.27 fmol/μg in human brain. Both Nav 1.1 and 1.6 expressions were much lower in the brains, with approximately 40% less expression in human Nav 1.1 than rodent Nav 1.1 at 0.49 ± 0.1 (mouse), 0.43 ± 0.3 (rat), and 0.28 ± 0.04 (humans); whereas Nav 1.6 had approximately 60% less expression in humans than rodents at 0.27 ± 0.09 (mouse), 0.26 ± 0.06 (rat), and 0.11 ± 0.02 (humans) fmol/μg membrane proteins. CONCLUSIONS Multiple reaction monitoring was used to quantify sodium channels Nav 1.1, 1.2, and 1.6 expressed in stably transfected HEK293 cells and brain tissues from mice, rats, and humans. We found significant differences in the expression of these channels in mouse, rat, and human brains. Nav expression ranking among the three species was Nav 1.2 ≫ Nav 1.1 > Nav 1.6, with the human brain expressing much lower concentrations overall compared to rodent brain.
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Affiliation(s)
- Rainbow Kwan
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Prerna Das
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Neelan Gerrebos
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Jenny Li
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Xin Yin Wang
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Gina DeBoer
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | | | - Sophia Lin
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Raymond Feng
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Sam Goodchild
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
| | - Luis E Sojo
- Xenon Pharmaceuticals Inc., Burnaby, British Columbia, Canada
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6
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Freitas-de-Sousa LA, Colombini M, Souza VC, Silva JPC, Mota-da-Silva A, Almeida MRN, Machado RA, Fonseca WL, Sartim MA, Sachett J, Serrano SMT, Junqueira-de-Azevedo ILM, Grazziotin FG, Monteiro WM, Bernarde PS, Moura-da-Silva AM. Venom Composition of Neglected Bothropoid Snakes from the Amazon Rainforest: Ecological and Toxinological Implications. Toxins (Basel) 2024; 16:83. [PMID: 38393161 PMCID: PMC10891915 DOI: 10.3390/toxins16020083] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Snake venoms have evolved in several families of Caenophidae, and their toxins have been assumed to be biochemical weapons with a role as a trophic adaptation. However, it remains unclear how venom contributes to the success of venomous species for adaptation to different environments. Here we compared the venoms from Bothrocophias hyoprora, Bothrops taeniatus, Bothrops bilineatus smaragdinus, Bothrops brazili, and Bothrops atrox collected in the Amazon Rainforest, aiming to understand the ecological and toxinological consequences of venom composition. Transcriptomic and proteomic analyses indicated that the venoms presented the same toxin groups characteristic from bothropoids, but with distinct isoforms with variable qualitative and quantitative abundances, contributing to distinct enzymatic and toxic effects. Despite the particularities of each venom, commercial Bothrops antivenom recognized the venom components and neutralized the lethality of all species. No clear features could be observed between venoms from arboreal and terrestrial habitats, nor in the dispersion of the species throughout the Amazon habitats, supporting the notion that venom composition may not shape the ecological or toxinological characteristics of these snake species and that other factors influence their foraging or dispersal in different ecological niches.
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Affiliation(s)
| | - Mônica Colombini
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.A.F.-d.-S.); (M.C.)
| | - Vinicius C. Souza
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Joanderson P. C. Silva
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Ageane Mota-da-Silva
- Instituto Federal do Acre, Campus de Cruzeiro do Sul, Cruzeiro do Sul 69980-000, AC, Brazil;
| | - Marllus R. N. Almeida
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Reginaldo A. Machado
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Wirven L. Fonseca
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Marco A. Sartim
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil; (M.A.S.); (J.S.); (W.M.M.)
| | - Jacqueline Sachett
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil; (M.A.S.); (J.S.); (W.M.M.)
| | - Solange M. T. Serrano
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Inácio L. M. Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo 05503-900, SP, Brazil;
| | - Wuelton M. Monteiro
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil; (M.A.S.); (J.S.); (W.M.M.)
| | - Paulo S. Bernarde
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Ana M. Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.A.F.-d.-S.); (M.C.)
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7
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Pade LR, Lombard-Banek C, Li J, Nemes P. Dilute to Enrich for Deeper Proteomics: A Yolk-Depleted Carrier for Limited Populations of Embryonic (Frog) Cells. J Proteome Res 2024; 23:692-703. [PMID: 37994825 PMCID: PMC10872351 DOI: 10.1021/acs.jproteome.3c00541] [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] [Indexed: 11/24/2023]
Abstract
Abundant proteins challenge deep mass spectrometry (MS) analysis of the proteome. Yolk, the source of food in many developing vertebrate embryos, complicates chemical separation and interferes with detection. We report here a strategy that enhances bottom-up proteomics in yolk-laden specimens by diluting the interferences using a yolk-depleted carrier (YODEC) proteome via isobaric multiplexing quantification. This method was tested on embryos of the South African Clawed Frog (Xenopus laevis), where a >90% yolk proteome content challenges deep proteomics. As a proof of concept, we isolated neural and epidermal fated cell clones from the embryo by dissection or fluorescence-activated cell sorting. Compared with the standard multiplexing carrier approach, YODEC more than doubled the detectable X. laevis proteome, identifying 5,218 proteins from D11 cell clones dissected from the embryo. Ca. ∼80% of the proteins were quantified without dropouts in any of the analytical channels. YODEC with high-pH fractionation quantified 3,133 proteins from ∼8,000 V11 cells that were sorted from ca. 2 embryos (1.5 μg total, or 150 ng yolk-free proteome), marking a 15-fold improvement in proteome coverage vs the standard proteomics approach. About 60% of these proteins were only quantifiable by YODEC, including molecular adaptors, transporters, translation, and transcription factors. While this study was tailored to limited populations of Xenopus cells, we anticipate the approach of "dilute to enrich" using a depleted carrier proteome to be adaptable to other biological models in which abundant proteins challenge deep MS proteomics.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Camille Lombard-Banek
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Jie Li
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
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8
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Matveeva A, Watters O, Rukhadze A, Khemka N, Gentile D, Perez IF, Llorente-Folch I, Farrell C, Lo Cacciato E, Jackson J, Piazzesi A, Wischhof L, Woods I, Halang L, Hogg M, Muñoz AG, Dillon ET, Matallanas D, Arijs I, Lambrechts D, Bano D, Connolly NMC, Prehn JHM. Integrated analysis of transcriptomic and proteomic alterations in mouse models of ALS/FTD identify early metabolic adaptions with similarities to mitochondrial dysfunction disorders. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:135-149. [PMID: 37779364 DOI: 10.1080/21678421.2023.2261979] [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: 04/22/2023] [Accepted: 09/10/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE Sporadic and familial amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disease that results in loss of motor neurons and, in some patients, associates with frontotemporal dementia (FTD). Apart from the accumulation of proteinaceous deposits, emerging literature indicates that aberrant mitochondrial bioenergetics may contribute to the onset and progression of ALS/FTD. Here we sought to investigate the pathophysiological signatures of mitochondrial dysfunction associated with ALS/FTD. METHODS By means of label-free mass spectrometry (MS) and mRNA sequencing (mRNA-seq), we report pre-symptomatic changes in the cortices of TDP-43 and FUS mutant mouse models. Using tissues from transgenic mouse models of mitochondrial diseases as a reference, we performed comparative analyses and extracted unique and common mitochondrial signatures that revealed neuroprotective compensatory mechanisms in response to early damage. RESULTS In this regard, upregulation of both Acyl-CoA Synthetase Long-Chain Family Member 3 (ACSL3) and mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) were the most representative change in pre-symptomatic ALS/FTD tissues, suggesting that fatty acid beta-oxidation and mitochondrial protein translation are mechanisms of adaptation in response to ALS/FTD pathology. CONCLUSIONS Together, our unbiased integrative analyses unveil novel molecular components that may influence mitochondrial homeostasis in the earliest phase of ALS.
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Affiliation(s)
- Anna Matveeva
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Orla Watters
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
| | - Ani Rukhadze
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Niraj Khemka
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Debora Gentile
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ivan Fernandez Perez
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Irene Llorente-Folch
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Cliona Farrell
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | | | - Joshua Jackson
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Ina Woods
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Luise Halang
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Marion Hogg
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
- Department of Biosciences, Nottingham Trent University, Clifton Campus, Nottingham, UK
| | - Amaya Garcia Muñoz
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Belfield, Ireland
| | - Eugène T Dillon
- Mass Spectrometry Resource, Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - David Matallanas
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin 4, Belfield, Ireland
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium, and
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Niamh M C Connolly
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Jochen H M Prehn
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
- SFI FutureNeuro Research Centre, Dublin 2, Ireland
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9
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Huang L, Ökmen B, Stolze SC, Kastl M, Khan M, Hilbig D, Nakagami H, Djamei A, Doehlemann G. The fungal pathogen Ustilago maydis targets the maize corepressor RELK2 to modulate host transcription for tumorigenesis. THE NEW PHYTOLOGIST 2024; 241:1747-1762. [PMID: 38037456 DOI: 10.1111/nph.19448] [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: 06/14/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
Ustilago maydis is a biotrophic fungus that causes tumor formation on all aerial parts of maize. U. maydis secretes effector proteins during penetration and colonization to successfully overcome the plant immune response and reprogram host physiology to promote infection. In this study, we functionally characterized the U. maydis effector protein Topless (TPL) interacting protein 6 (Tip6). We found that Tip6 interacts with the N-terminus of RELK2 through its two Ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. We show that the EAR motifs are essential for the virulence function of Tip6 and critical for altering the nuclear distribution pattern of RELK2. We propose that Tip6 mimics the recruitment of RELK2 by plant repressor proteins, thus disrupting host transcriptional regulation. We show that a large group of AP2/ERF B1 subfamily transcription factors are misregulated in the presence of Tip6. Our study suggests a regulatory mechanism where the U. maydis effector Tip6 utilizes repressive domains to recruit the corepressor RELK2 to disrupt the transcriptional networks of the host plant.
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Affiliation(s)
- Luyao Huang
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
| | - Bilal Ökmen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Tübingen, 72076, Germany
| | - Sara Christina Stolze
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Melanie Kastl
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, 53127, Germany
| | - Mamoona Khan
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Daniel Hilbig
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, 53127, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Basic Immune System of Plants, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Armin Djamei
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
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10
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Wilken L, Lasswitz L, Scaturro P, Gerold G. Identification of RVFV Host Factors Using Quantitative Interaction Proteomics. Methods Mol Biol 2024; 2824:189-202. [PMID: 39039414 DOI: 10.1007/978-1-0716-3926-9_13] [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: 07/24/2024]
Abstract
Affinity enrichment coupled with liquid chromatography-tandem mass spectrometry (AE-LC-MS/MS) enables a comprehensive study of virus-host protein-protein interactions in cells and tissues infected with Rift Valley fever virus (RVFV) or ectopically expressing RVFV proteins. Depending on the research question, different experimental setups with carefully chosen controls are needed. Here, we describe the detailed workflow of sample preparation, processing, and cleanup, while also outlining critical points to consider when designing and performing AE-LC-MS/MS experiments.
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Affiliation(s)
- Lucas Wilken
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Lisa Lasswitz
- Institute of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany
| | | | - Gisa Gerold
- Institute of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany.
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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11
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Kato Y, Kuroda H, Ozawa SI, Saito K, Dogra V, Scholz M, Zhang G, de Vitry C, Ishikita H, Kim C, Hippler M, Takahashi Y, Sakamoto W. Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts. eLife 2023; 12:RP88822. [PMID: 37986577 PMCID: PMC10665015 DOI: 10.7554/elife.88822] [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] [Indexed: 11/22/2023] Open
Abstract
Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH.
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Affiliation(s)
- Yusuke Kato
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Faculty of Agriculture, Setsunan UniversityOsakaJapan
| | - Hiroshi Kuroda
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Shin-Ichiro Ozawa
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Keisuke Saito
- Research Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Vivek Dogra
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesShanghaiChina
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampurIndia
| | - Martin Scholz
- Institute of Plant Biology and Biotechnology, University of MünsterMünsterGermany
| | - Guoxian Zhang
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
| | - Catherine de Vitry
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 7141, Centre National de la Recherche Scientifique and Sorbonne Université Pierre et Marie CurieParisFrance
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of SciencesShanghaiChina
| | - Michael Hippler
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
- Institute of Plant Biology and Biotechnology, University of MünsterMünsterGermany
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources (IPSR), Okayama UniversityOkayamaJapan
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12
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Ruffinatti FA, Scarpellino G, Chinigò G, Visentin L, Munaron L. The Emerging Concept of Transportome: State of the Art. Physiology (Bethesda) 2023; 38:0. [PMID: 37668550 DOI: 10.1152/physiol.00010.2023] [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: 04/12/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
The array of ion channels and transporters expressed in cell membranes, collectively referred to as the transportome, is a complex and multifunctional molecular machinery; in particular, at the plasma membrane level it finely tunes the exchange of biomolecules and ions, acting as a functionally adaptive interface that accounts for dynamic plasticity in the response to environmental fluctuations and stressors. The transportome is responsible for the definition of membrane potential and its variations, participates in the transduction of extracellular signals, and acts as a filter for most of the substances entering and leaving the cell, thus enabling the homeostasis of many cellular parameters. For all these reasons, physiologists have long been interested in the expression and functionality of ion channels and transporters, in both physiological and pathological settings and across the different domains of life. Today, thanks to the high-throughput technologies of the postgenomic era, the omics approach to the study of the transportome is becoming increasingly popular in different areas of biomedical research, allowing for a more comprehensive, integrated, and functional perspective of this complex cellular apparatus. This article represents a first effort for a systematic review of the scientific literature on this topic. Here we provide a brief overview of all those studies, both primary and meta-analyses, that looked at the transportome as a whole, regardless of the biological problem or the models they used. A subsequent section is devoted to the methodological aspect by reviewing the most important public databases annotating ion channels and transporters, along with the tools they provide to retrieve such information. Before conclusions, limitations and future perspectives are also discussed.
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Affiliation(s)
- Federico Alessandro Ruffinatti
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Scarpellino
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giorgia Chinigò
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Visentin
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Luca Munaron
- Turin Cell Physiology Laboratory (TCP-Lab), Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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13
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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14
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Stachowicz A, Sadiq A, Walker B, Sundararaman N, Fert-Bober J. Treatment of human cardiac fibroblasts with the protein arginine deiminase inhibitor BB-Cl-amidine activates the Nrf2/HO-1 signaling pathway. Biomed Pharmacother 2023; 167:115443. [PMID: 37703660 DOI: 10.1016/j.biopha.2023.115443] [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: 05/26/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Cardiac fibrosis contributes to end-stage extracellular matrix remodeling and heart failure (HF). Cardiac fibroblasts (CFs) differentiate into myofibroblasts (myoFbs) to preserve the structural integrity of the heart; however, the molecular mechanisms regulating CF transdifferentiation remain poorly understood. Protein arginine deiminase (PAD), which converts arginine to citrulline, has been shown to play a role in myocardial infarction, fibrosis, and HF. This study aimed to investigate the role of PAD in CF differentiation to myoFbs and identify the citrullinated proteins that were associated with phenotypic changes in CFs. RESULTS Gene expression analysis showed that PAD1 and PAD2 isoforms, but not PAD4 isoforms, were abundant in both CFs and myoFbs, and PAD1 was significantly upregulated in myoFbs. The pan-PAD inhibitor BB-Cl-amidine (BB-Cl) downregulated the mRNA expression of PAD1 and PAD2 as well as the protein expression of the fibrosis marker COL1A1 in CFs and myoFbs. Interestingly, a proteomic approach pointed to the activation of the Nrf2/HO-1 signaling pathway upon BB-Cl treatment in CFs and myoFbs. BB-Cl administration resulted in the upregulation of HO-1 at both the gene and protein levels in CFs and myoFbs. Importantly, the protein citrullination landscape of CFs consisting of 86 novel citrullination sites associated with focal adhesion (FN1(R1054)), inflammation (TAGLN(R12)) and DNA replication (EEF2(R767)) pathways was identified. CONCLUSIONS In summary, we revealed that BB-Cl treatment resulted in increased HO-1 expression via the Nrf2 pathway, which could prevent excessive tissue damage, thereby leading to substantial clinical benefits for the treatment of cardiac fibrosis.
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Affiliation(s)
- Aneta Stachowicz
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland; Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alia Sadiq
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brian Walker
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Niveda Sundararaman
- Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Justyna Fert-Bober
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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15
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Wang Y, Liu Y, Cao T, Shi C, Ren Z, Zhao Y. Quantitative proteomics analysis reveals the key proteins related to semen quality in Niangya yaks. Proteome Sci 2023; 21:20. [PMID: 37875878 PMCID: PMC10594827 DOI: 10.1186/s12953-023-00222-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/14/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Proteins related to sperm motility and sperm morphology have an important impact on sperm function such as metabolism, motility and fertilisation etc. An understanding of the key proteins related to semen quality in Niangya yaks would help to provide support for breeding. However, the key proteins that affect semen quality in Niangya yaks remain unclear. METHODS Herein, we applied tandem mass tag (TMT) labeling and liquid chromatography-tandem mass spectrometry (LC‒MS/MS) to analyze the expression levels of sperm proteins in groups of high- and low-quality semen from Niangya yaks. And fifteen differentially expressed proteins (DEPs) were randomly selected for expression level validation by parallel reaction monitoring (PRM). RESULTS Of the 2,092 quantified proteins, 280 were identified as DEPs in the high-quality group versus the low-quality group. Gene Ontology (GO) analysis revealed that in terms of biological pathways, the DEPs were mainly involved in metabolic processes, cell transformation processes, and single organism metabolic processes. In terms of cell composition, the DEPs were mainly located in the cell membrane, organelle, molecular complex. In terms of molecular functions, the most abundant functions of the DEPs were catalytic activity, binding activity, transport activity, and enzyme regulation activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEPs were mainly involved in the cytokine and cytokine receptor interaction, notch signaling pathway, lysine biosynthesis, renal function-related protein and proteasome pathway. From protein-protein interaction (PPI) analysis of DEPs involved in important pathways, 6 related proteins affecting the semen quality of Niangya yaks were identified. And the results of the PRM and TMT analysis were consistent. CONCLUSIONS The differential sperm proteomic analysis of high- and low-quality semen from Niangya yaks, revealed 6 proteins (PSMC5, PSMD8, PSMB3, HSP90AA1, UGP2 and HSPB1), were mainly concentrated in energy production and metabolism, might play important roles in semen quality, which could serve as candidates for the selection and breeding of Niangya yaks.
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Affiliation(s)
- Yaomei Wang
- Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Yuchao Liu
- Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Tingting Cao
- Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Chunyuan Shi
- Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Zili Ren
- Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Yanling Zhao
- Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China.
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Long Q, Zhang Z, Li Y, Zhong Y, Liu H, Chang L, Ying Y, Zuo T, Wang Y, Xu P. Phosphoproteome reveals long-term potentiation deficit following treatment of ultra-low dose soman exposure in mice. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132211. [PMID: 37572605 DOI: 10.1016/j.jhazmat.2023.132211] [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: 05/12/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Soman, a warfare nerve agent, poses a significant threat by inducing severe brain damage that often results in death. Nonetheless, our understanding of the biological changes underlying persistent neurocognitive dysfunction caused by low dosage of soman remains limited. This study used mice to examine the effects of different doses of soman over time. Phosphoproteomic analysis of the mouse brain is the first time to be used to detect toxic effects of soman at such low or ultra-low doses, which were undetectable based on measuring the activity of acetylcholinesterase at the whole-animal level. We also found that phosphoproteome alterations could accurately track the soman dose, irrespective of the sampling time. Moreover, phosphoproteome revealed a rapid and adaptive cellular response to soman exposure, with the points of departure 8-38 times lower than that of acetylcholinesterase activity. Impaired long-term potentiation was identified in phosphoproteomic studies, which was further validated by targeted quantitative proteomics, immunohistochemistry, and immunofluorescence analyses, with significantly increased levels of phosphorylation of protein phosphatase 1 in the hippocampus following soman exposure. This increase in phosphorylation inhibits long-term potentiation, ultimately leading to long-term memory dysfunction in mice.
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Affiliation(s)
- Qi Long
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Yuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang 550025, China
| | - Yuxu Zhong
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Hongyan Liu
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Ying Ying
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China.
| | - Yong'an Wang
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang 550025, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China.
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Pesämaa I, Müller SA, Robinson S, Darcher A, Paquet D, Zetterberg H, Lichtenthaler SF, Haass C. A microglial activity state biomarker panel differentiates FTD-granulin and Alzheimer's disease patients from controls. Mol Neurodegener 2023; 18:70. [PMID: 37775827 PMCID: PMC10543321 DOI: 10.1186/s13024-023-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND With the emergence of microglia-modulating therapies there is an urgent need for reliable biomarkers to evaluate microglial activation states. METHODS Using mouse models and human induced pluripotent stem cell-derived microglia (hiMGL), genetically modified to yield the most opposite homeostatic (TREM2-knockout) and disease-associated (GRN-knockout) states, we identified microglia activity-dependent markers. Non-targeted mass spectrometry was used to identify proteomic changes in microglia and cerebrospinal fluid (CSF) of Grn- and Trem2-knockout mice. Additionally, we analyzed the proteome of GRN- and TREM2-knockout hiMGL and their conditioned media. Candidate marker proteins were tested in two independent patient cohorts, the ALLFTD cohort (GRN mutation carriers versus non-carriers), as well as the proteomic data set available from the EMIF-AD MBD study. RESULTS We identified proteomic changes between the opposite activation states in mouse microglia and CSF, as well as in hiMGL cell lysates and conditioned media. For further verification, we analyzed the CSF proteome of heterozygous GRN mutation carriers suffering from frontotemporal dementia (FTD). We identified a panel of six proteins (FABP3, MDH1, GDI1, CAPG, CD44, GPNMB) as potential indicators for microglial activation. Moreover, we confirmed three of these proteins (FABP3, GDI1, MDH1) to be significantly elevated in the CSF of Alzheimer's (AD) patients. Remarkably, each of these markers differentiated amyloid-positive cases with mild cognitive impairment (MCI) from amyloid-negative individuals. CONCLUSIONS The identified candidate proteins reflect microglia activity and may be relevant for monitoring the microglial response in clinical practice and clinical trials modulating microglial activity and amyloid deposition. Moreover, the finding that three of these markers differentiate amyloid-positive from amyloid-negative MCI cases in the AD cohort suggests that these proteins associate with a very early immune response to seeded amyloid. This is consistent with our previous findings in the Dominantly Inherited Alzheimer's Disease Network (DIAN) cohort, where soluble TREM2 increases as early as 21 years before symptom onset. Moreover, in mouse models for amyloidogenesis, seeding of amyloid is limited by physiologically active microglia further supporting their early protective role. The biological functions of some of our main candidates (FABP3, CD44, GPNMB) also further emphasize that lipid dysmetabolism may be a common feature of neurodegenerative disorders.
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Affiliation(s)
- Ida Pesämaa
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Ludwig-Maximilians-University Munich, Munich, Germany
- Department of Psychiatry & Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Sophie Robinson
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Ludwig-Maximilians-University Munich, Munich, Germany
- Institute for Stroke and Dementia Research, University Hospital Munich, Ludwig-Maximilians- University Munich, Munich, Germany
| | - Alana Darcher
- Epileptology, University Hospital Bonn, Bonn, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, University Hospital Munich, Ludwig-Maximilians- University Munich, Munich, Germany
- Munich Cluster for Systems Neurology (Synergy), Munich, Germany
| | - Henrik Zetterberg
- Department of Psychiatry & Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (Synergy), Munich, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany.
- Munich Cluster for Systems Neurology (Synergy), Munich, Germany.
- Biomedical Centre (BMC), Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany.
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Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules 2023; 13:1108. [PMID: 37509144 PMCID: PMC10377647 DOI: 10.3390/biom13071108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The progressive degeneration of the skeletal musculature in Duchenne muscular dystrophy is accompanied by reactive myofibrosis, fat substitution, and chronic inflammation. Fibrotic changes and reduced tissue elasticity correlate with the loss in motor function in this X-chromosomal disorder. Thus, although dystrophinopathies are due to primary abnormalities in the DMD gene causing the almost-complete absence of the cytoskeletal Dp427-M isoform of dystrophin in voluntary muscles, the excessive accumulation of extracellular matrix proteins presents a key histopathological hallmark of muscular dystrophy. Animal model research has been instrumental in the characterization of dystrophic muscles and has contributed to a better understanding of the complex pathogenesis of dystrophinopathies, the discovery of new disease biomarkers, and the testing of novel therapeutic strategies. In this article, we review how mass-spectrometry-based proteomics can be used to study changes in key components of the endomysium, perimysium, and epimysium, such as collagens, proteoglycans, matricellular proteins, and adhesion receptors. The mdx-4cv mouse diaphragm displays severe myofibrosis, making it an ideal model system for large-scale surveys of systematic alterations in the matrisome of dystrophic fibers. Novel biomarkers of myofibrosis can now be tested for their appropriateness in the preclinical and clinical setting as diagnostic, pharmacodynamic, prognostic, and/or therapeutic monitoring indicators.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
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19
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McNeilly AD, Gallagher JR, Evans ML, de Galan BE, Pedersen-Bjergaard U, Thorens B, Dinkova-Kostova AT, Huang JT, Ashford MLJ, McCrimmon RJ. Chronic hyperglycaemia increases the vulnerability of the hippocampus to oxidative damage induced during post-hypoglycaemic hyperglycaemia in a mouse model of chemically induced type 1 diabetes. Diabetologia 2023; 66:1340-1352. [PMID: 37015997 PMCID: PMC10244284 DOI: 10.1007/s00125-023-05907-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/26/2023] [Indexed: 04/06/2023]
Abstract
AIMS/HYPOTHESIS Chronic hyperglycaemia and recurrent hypoglycaemia are independently associated with accelerated cognitive decline in type 1 diabetes. Recurrent hypoglycaemia in rodent models of chemically induced (streptozotocin [STZ]) diabetes leads to cognitive impairment in memory-related tasks associated with hippocampal oxidative damage. This study examined the hypothesis that post-hypoglycaemic hyperglycaemia in STZ-diabetes exacerbates hippocampal oxidative stress and explored potential contributory mechanisms. METHODS The hyperinsulinaemic glucose clamp technique was used to induce equivalent hypoglycaemia and to control post-hypoglycaemic glucose levels in mice with and without STZ-diabetes and Nrf2-/- mice (lacking Nrf2 [also known as Nfe2l2]). Subsequently, quantitative proteomics based on stable isotope labelling by amino acids in cell culture and biochemical approaches were used to assess oxidative damage and explore contributory pathways. RESULTS Evidence of hippocampal oxidative damage was most marked in mice with STZ-diabetes exposed to post-hypoglycaemic hyperglycaemia; these mice also showed induction of Nrf2 and the Nrf2 transcriptional targets Sod2 and Hmox-1. In this group, hypoglycaemia induced a significant upregulation of proteins involved in alternative fuel provision, reductive biosynthesis and degradation of damaged proteins, and a significant downregulation of proteins mediating the stress response. Key differences emerged between mice with and without STZ-diabetes following recovery from hypoglycaemia in proteins mediating the stress response and reductive biosynthesis. CONCLUSIONS/INTERPRETATION There is a disruption of the cellular response to a hypoglycaemic challenge in mice with STZ-induced diabetes that is not seen in wild-type non-diabetic animals. The chronic hyperglycaemia of diabetes and post-hypoglycaemic hyperglycaemia act synergistically to induce oxidative stress and damage in the hippocampus, possibly leading to irreversible damage/modification to proteins or synapses between cells. In conclusion, recurrent hypoglycaemia in sub-optimally controlled diabetes may contribute, at least in part, to accelerated cognitive decline through amplifying oxidative damage in key brain regions, such as the hippocampus. DATA AVAILABILITY The datasets generated during and/or analysed during the current study are available in ProteomeXchange, accession no. 1-20220824-173727 ( www.proteomexchange.org ). Additional datasets generated during and/or analysed during the present study are available from the corresponding author upon reasonable request.
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Affiliation(s)
- Alison D McNeilly
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Jennifer R Gallagher
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Mark L Evans
- Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Bastiaan E de Galan
- Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands
- CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, the Netherlands
| | | | - Bernard Thorens
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Albena T Dinkova-Kostova
- Division of Cancer Research, School of Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Jeffrey-T Huang
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, Dundee, UK
- Biomarker and Drug Analysis Core Facility, School of Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Michael L J Ashford
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - Rory J McCrimmon
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, Dundee, UK.
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20
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Pesämaa I, Müller SA, Robinson S, Darcher A, Paquet D, Zetterberg H, Lichtenthaler SF, Haass C. A MICROGLIAL ACTIVITY STATE BIOMARKER PANEL DIFFERENTIATES FTD-GRANULIN AND ALZHEIMER'S DISEASE PATIENTS FROM CONTROLS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545187. [PMID: 37398209 PMCID: PMC10312678 DOI: 10.1101/2023.06.15.545187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background With the emergence of microglia-modulating therapies there is an urgent need for reliable biomarkers to evaluate microglial activation states. Methods Using mouse models and human induced pluripotent stem cell-derived microglia (hiMGL), which were genetically modified to yield the most opposite homeostatic ( TREM2- knockout) and disease-associated ( GRN -knockout) states, we identified microglia activity-dependent markers. Non-targeted mass spectrometry was used to identify changes in microglial and cerebrospinal (CSF) proteome of Grn - and Trem2 -knockout mice. Additionally, we analyzed the proteome of GRN - and TREM2 -knockout hiMGL and their conditioned media. Candidate marker proteins were tested in two independent patient cohorts, the ALLFTD cohort with 11 GRN mutation carriers and 12 non-carriers, as well as the proteomic data set available from the European Medical Information Framework Alzheimer's Disease Multimodal Biomarker Discovery (EMIF-AD MBD). Findings We identified proteomic changes between the opposite activation states in mouse microglia and cerebrospinal fluid (CSF), as well as in hiMGL cell lysates and conditioned media. For further verification, we analyzed the CSF proteome of heterozygous GRN mutation carriers suffering from frontotemporal dementia (FTD). We identified a panel of six proteins (FABP3, MDH1, GDI1, CAPG, CD44, GPNMB) as potential indicators for microglial activation. Moreover, we confirmed three of these proteins (FABP3, GDI1, MDH1) to be significantly elevated in the CSF of AD patients. In AD, these markers differentiated amyloid-positive cases with mild cognitive impairment (MCI) from amyloid-negative individuals. Interpretation The identified candidate proteins reflect microglia activity and may be relevant for monitoring the microglial response in clinical practice and clinical trials modulating microglial activity and amyloid deposition. Moreover, the finding that three of these markers differentiate amyloid-positive from amyloid-negative MCI cases in the AD cohort suggests that these marker proteins associate with a very early immune response to seeded amyloid. This is consistent with our previous findings in the DIAN (Dominantly Inherited Alzheimer's Disease Network) cohort, where soluble TREM2 increases as early as 21 years before symptom onset. Moreover, in mouse models for amyloidogenesis, seeding of amyloid is limited by physiologically active microglia further supporting their early protective role. The biological functions of some of our main candidates (FABP3, CD44, GPNMB) also further emphasize that lipid dysmetabolism may be a common feature of neurodegenerative disorders. Funding This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy within the framework of the Munich Cluster for Systems Neurology (EXC 2145 SyNergy - ID 390857198 to CH, SFL and DP) and a Koselleck Project HA1737/16-1 (to CH).
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Ramgopal A, Braverman EL, Sun LK, Monlish D, Wittmann C, Ramsey MJ, Caitley R, Hawse W, Byersdorfer CA. AMPK Drives Both Glycolytic and Oxidative Metabolism in T Cells During Graft-versus-host Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544686. [PMID: 37398326 PMCID: PMC10312647 DOI: 10.1101/2023.06.12.544686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Allogeneic T cells reprogram their metabolism during acute graft-versus-host disease (GVHD) in a process reliant on the cellular energy sensor AMP-activated protein kinase (AMPK). Deletion of AMPK in donor T cells limits GVHD but still preserves homeostatic reconstitution and graft-versus-leukemia (GVL) effects. In the current studies, murine T cells lacking AMPK decreased oxidative metabolism at early timepoints post-transplant and were also unable to mediate a compensatory increase in glycolysis following inhibition of the electron transport chain. Human T cells lacking AMPK gave similar results, with glycolytic compensation impaired both in vitro and following expansion in vivo in a modified model of GVHD. Immunoprecipitation of proteins from day 7 allogeneic T cells, using an antibody specific to phosphorylated AMPK targets, recovered lower levels of multiple glycolysis-related proteins including the glycolytic enzymes aldolase, enolase, pyruvate kinase M (PKM), and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Functionally, murine T cells lacking AMPK exhibited impaired aldolase activity following anti-CD3/CD28 stimulation and a decrease in GAPDH activity on day 7 post-transplant. Importantly, these changes in glycolysis correlated with an impaired ability of AMPK KO T cells to produce significant amounts of interferon gamma (IFNγ) upon antigenic re-stimulation. Together these data highlight a significant role for AMPK in controlling oxidative and glycolytic metabolism in both murine and human T cells during GVHD and endorse further study of AMPK inhibition as a potential target for future clinical therapies. KEY POINTS AMPK plays a key role in driving both and oxidative and glycolytic metabolism in T cells during graft-versus-host disease (GVHD)Absence of AMPK simultaneously impairs both glycolytic enzyme activity, most notably by aldolase, and interferon gamma (IFNγ) production.
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Musiał N, Bogucka A, Tretiakow D, Skorek A, Ryl J, Czaplewska P. Proteomic analysis of sialoliths from calcified, lipid and mixed groups as a source of potential biomarkers of deposit formation in the salivary glands. Clin Proteomics 2023; 20:11. [PMID: 36949424 PMCID: PMC10035263 DOI: 10.1186/s12014-023-09402-3] [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: 01/12/2023] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Salivary stones, also known as sialoliths, are formed in a pathological situation in the salivary glands. So far, neither the mechanism of their formation nor the factors predisposing to their formation are known despite several hypotheses. While they do not directly threaten human life, they significantly deteriorate the patient's quality of life. Although this is not a typical research material, attempts are made to apply various analytical tools to characterise sialoliths and search for the biomarkers in their proteomes. In this work, we used mass spectrometry and SWATH-MS qualitative and quantitative analysis to investigate the composition and select proteins that may contribute to solid deposits in the salivary glands. Twenty sialoliths, previously characterized spectroscopically and divided into the following groups: calcified (CAL), lipid (LIP) and mixed (MIX), were used for the study. Proteins unique for each of the groups were found, including: for the CAL group among them, e.g. proteins from the S100 group (S100 A8/A12 and P), mucin 7 (MUC7), keratins (KRT1/2/4/5/13), elastase (ELANE) or stomatin (STOM); proteins for the LIP group-transthyretin (TTR), lactotransferrin (LTF), matrix Gla protein (MPG), submandibular gland androgen-regulated protein 3 (SMR3A); mixed stones had the fewest unique proteins. Bacterial proteins present in sialoliths have also been identified. The analysis of the results indicates the possible role of bacterial infections, disturbances in calcium metabolism and neutrophil extracellular traps (NETs) in the formation of sialoliths.
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Affiliation(s)
- Natalia Musiał
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
| | - Aleksandra Bogucka
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland
- Institute of Biochemistry, Medical Faculty, Justus Liebig University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Dmitry Tretiakow
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Andrzej Skorek
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Jacek Ryl
- Division of Electrochemistry and Surface Physical Chemistry, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
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Screening of Candidate Effectors from Magnaporthe oryzae by In Vitro Secretomic Analysis. Int J Mol Sci 2023; 24:ijms24043189. [PMID: 36834598 PMCID: PMC9962664 DOI: 10.3390/ijms24043189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Magnaporthe oryzae is the causal agent of rice blast, one of the most serious diseases of rice worldwide. Secreted proteins play essential roles during a M. oryzae-rice interaction. Although much progress has been made in recent decades, it is still necessary to systematically explore M. oryzae-secreted proteins and to analyze their functions. This study employs a shotgun-based proteomic analysis to investigate the in vitro secretome of M. oryzae by spraying fungus conidia onto the PVDF membrane to mimic the early stages of infection, during which 3315 non-redundant secreted proteins were identified. Among these proteins, 9.6% (319) and 24.7% (818) are classified as classically or non-classically secreted proteins, while the remaining 1988 proteins (60.0%) are secreted through currently unknown secretory pathway. Functional characteristics analysis show that 257 (7.8%) and 90 (2.7%) secreted proteins are annotated as CAZymes and candidate effectors, respectively. Eighteen candidate effectors are selected for further experimental validation. All 18 genes encoding candidate effectors are significantly up- or down-regulated during the early infection process. Sixteen of the eighteen candidate effectors cause the suppression of BAX-mediated cell death in Nicotiana benthamiana by using an Agrobacterium-mediated transient expression assay, suggesting their involvement in pathogenicity related to secretion effectors. Our results provide high-quality experimental secretome data of M. oryzae and will expand our knowledge on the molecular mechanisms of M. oryzae pathogenesis.
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:2415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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Carrillo-Rodriguez P, Selheim F, Hernandez-Valladares M. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers (Basel) 2023; 15:555. [PMID: 36672506 PMCID: PMC9856946 DOI: 10.3390/cancers15020555] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
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Affiliation(s)
- Paula Carrillo-Rodriguez
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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Dijkstra J, Neikes HK, Rezaeifard S, Ma X, Voest EE, Tauriello DVF, Vermeulen M. Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation. J Proteome Res 2023; 22:138-151. [PMID: 36450103 PMCID: PMC9830641 DOI: 10.1021/acs.jproteome.2c00551] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The development of metastasis severely reduces the life expectancy of patients with colorectal cancer (CRC). Although loss of SMAD4 is a key event in CRC progression, the resulting changes in biological processes in advanced disease and metastasis are not fully understood. Here, we applied a multiomics approach to a CRC organoid model that faithfully reflects the metastasis-supporting effects of SMAD4 inactivation. We show that loss of SMAD4 results in decreased differentiation and activation of pro-migratory and cell proliferation processes, which is accompanied by the disruption of several key oncogenic pathways, including the TGFβ, WNT, and VEGF pathways. In addition, SMAD4 inactivation leads to increased secretion of proteins that are known to be involved in a variety of pro-metastatic processes. Finally, we show that one of the factors that is specifically secreted by SMAD4-mutant organoids─DKK3─reduces the antitumor effects of natural killer cells (NK cells). Altogether, our data provide new insights into the role of SMAD4 perturbation in advanced CRC.
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Affiliation(s)
- Jelmer
J. Dijkstra
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Hannah K. Neikes
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Somayeh Rezaeifard
- Department
of Cell Biology, Radboud University Medical Center/Radboud Institute
for Molecular Life Sciences (RIMLS), Radboud
University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Xuhui Ma
- Department
of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Antoni van Leeuwenhoek
Hospital, 1066 CX Amsterdam, The Netherlands
| | - Emile E. Voest
- Department
of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Antoni van Leeuwenhoek
Hospital, 1066 CX Amsterdam, The Netherlands
| | - Daniele V. F. Tauriello
- Department
of Cell Biology, Radboud University Medical Center/Radboud Institute
for Molecular Life Sciences (RIMLS), Radboud
University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands,
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Oliveira CAB, Isaakova E, Beli P, Xirodimas DP. A Mass Spectrometry-Based Strategy for Mapping Modification Sites for the Ubiquitin-Like Modifier NEDD8. Methods Mol Biol 2023; 2602:137-149. [PMID: 36446972 DOI: 10.1007/978-1-0716-2859-1_10] [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: 06/16/2023]
Abstract
The identification of modification sites for ubiquitin and ubiquitin-like modifiers is an essential step in the elucidation of controlled processes. The ubiquitin-like modifier NEDD8 is an important regulator of plethora of biological processes both under homeostatic and proteotoxic stress conditions. Here, we describe a detailed protocol for proteome-wide identification of NEDDylation sites. The approach is based on the use of cell lines stably expressing the NEDD8R74K mutant. Digestion of samples with Lysyl endopeptidase generates peptides with a di-glycine remnant only from proteins modified with NEDD8R74K but not with ubiquitin or ISG15. The isolation of these peptides with anti-di-glycine antibodies (K-ε-GG) allows the identification of NEDDylation sites by liquid chromatography tandem mass spectrometry (LC-MS/MS).
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Affiliation(s)
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany.
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany.
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Martin KR, Day JA, Hansen JA, D'Silva DB, Wong HL, Garnham A, Sandow JJ, Nijagal B, Wilson N, Wicks IP. CD98 defines a metabolically flexible, proinflammatory subset of low-density neutrophils in systemic lupus erythematosus. Clin Transl Med 2023; 13:e1150. [PMID: 36653319 PMCID: PMC9849148 DOI: 10.1002/ctm2.1150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Low-density neutrophils (LDN) are a distinct subset of neutrophils rarely detected in healthy people but appear in the blood of patients with autoimmune diseases, including systemic lupus erythematosus (SLE), and are mobilised in response to granulocyte colony-stimulating factor (G-CSF). The aim of this study was to identify novel mechanisms responsible for the pathogenic capacity of LDN in SLE. METHODS Neutrophils were isolated from donors treated with G-CSF, and whole-cell proteomic analysis was performed on LDN and normal-density neutrophils. RESULTS CD98 is significantly upregulated in LDN from G-CSF donors and defines a subset of LDN within the blood of SLE patients. CD98 is a transmembrane protein that dimerises with L-type amino acid transporters. We show that CD98 is responsible for the increased bioenergetic capacity of LDN. CD98 on LDN mediates the uptake of essential amino acids that are used by mitochondria to produce adenosine triphosphate, especially in the absence of glucose. Inhibition of CD98 reduces the metabolic flexibility of this population, which may limit their pathogenic capacity. CD98+ LDN produce more proinflammatory cytokines and chemokines than their normal density counterparts and are resistant to apoptosis, which may also contribute to tissue inflammation and end organ damage in SLE. CONCLUSIONS CD98 provides a phenotypic marker for LDN that facilitates identification of this population without density-gradient separation and represents a novel therapeutic target to limit its pathogenic capacity.
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Affiliation(s)
- Katherine R. Martin
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Jessica A. Day
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVictoriaAustralia
- Department of RheumatologyRoyal Melbourne HospitalParkvilleVictoriaAustralia
| | - Jacinta A. Hansen
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
| | - Damian B. D'Silva
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
| | - Huon L. Wong
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
| | - Alexandra Garnham
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Jarrod J. Sandow
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Brunda Nijagal
- Metabolomics AustraliaBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVictoriaAustralia
| | | | - Ian P. Wicks
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneParkvilleVictoriaAustralia
- Department of RheumatologyRoyal Melbourne HospitalParkvilleVictoriaAustralia
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Kondethimmanahalli C, Ganta RR. Proteome analysis of Ehrlichia chaffeensis containing phagosome membranes revealed the presence of numerous bacterial and host proteins. Front Cell Infect Microbiol 2022; 12:1070356. [PMID: 36619760 PMCID: PMC9816426 DOI: 10.3389/fcimb.2022.1070356] [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: 10/14/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Tick-transmitted Ehrlichia chaffeensis, the causative agent for human monocytic ehrlichiosis, resides and multiplies within a host cell phagosome. Infection progression of E. chaffeensis includes internalization into a host cell by host cell membrane fusion events following engulfment leading to the formation of E. chaffeensis containing vacuole (ECV). Revealing the molecular composition of ECV is important in understanding the host cellular processes, evasion of host defense pathways and in defining host-pathogen interactions. ECVs purified from infected host cells were analyzed to define both host and bacterial proteomes associated with the phagosome membranes. About 160 bacterial proteins and 2,683 host proteins were identified in the ECV membranes. The host proteins included predominantly known phagosome proteins involved in phagocytic trafficking, fusion of vesicles, protein transport, Ras signaling pathway and pathogenic infection. Many highly expressed proteins were similar to the previously documented proteins of phagosome vacuole membranes containing other obligate pathogenic bacteria. The finding of many bacterial membrane proteins is novel; they included multiple outer membrane proteins, such as the p28-Omps, the 120 kDa protein, preprotein translocases, lipoproteins, metal binding proteins, and chaperonins, although the presence of ankyrin repeat proteins, several Type I and IV secretion system proteins is anticipated. This study demonstrates that ECV membrane is extensively modified by the pathogen. This study represents the first and the most comprehensive description of ECV membrane proteome. The identity of many host and Ehrlichia proteins in the ECV membrane will be a valuable to define pathogenic mechanisms critical for the replication of the pathogen within macrophages.
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Affiliation(s)
| | - Roman R. Ganta
- Center of Excellence for Vector-Borne Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
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30
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Ciancone AM, Hosseinibarkooie S, Bai DL, Borne AL, Ferris HA, Hsu KL. Global profiling identifies a stress-responsive tyrosine site on EDC3 regulating biomolecular condensate formation. Cell Chem Biol 2022; 29:1709-1720.e7. [PMID: 36476517 PMCID: PMC9779741 DOI: 10.1016/j.chembiol.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
RNA granules are cytoplasmic condensates that organize biochemical and signaling complexes in response to cellular stress. Functional proteomic investigations under RNA-granule-inducing conditions are needed to identify protein sites involved in coupling stress response with ribonucleoprotein regulation. Here, we apply chemical proteomics using sulfonyl-triazole (SuTEx) probes to capture cellular responses to oxidative and nutrient stress. The stress-responsive tyrosine and lysine sites detected mapped to known proteins involved in processing body (PB) and stress granule (SG) pathways, including LSM14A, FUS, and Enhancer of mRNA-decapping protein 3 (EDC3). Notably, disruption of EDC3 tyrosine 475 (Y475) resulted in hypo-phosphorylation at S161 and S131 and altered protein-protein interactions (PPIs) with decapping complex components (DDX6, DCP1A/B) and 14-3-3 proteins. This resulting mutant form of EDC3 was capable of rescuing the PB-deficient phenotype of EDC3 knockout cells. Taken together, our findings identify Y475 as an arsenic-responsive site that regulates RNA granule formation by coupling EDC3 post-translational modification and PPI states.
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Affiliation(s)
- Anthony M Ciancone
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Heather A Ferris
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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Stachowicz A, Pandey R, Sundararaman N, Venkatraman V, Van Eyk JE, Fert-Bober J. Protein arginine deiminase 2 (PAD2) modulates the polarization of THP-1 macrophages to the anti-inflammatory M2 phenotype. J Inflamm (Lond) 2022; 19:20. [DOI: 10.1186/s12950-022-00317-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
Abstract
Background
Macrophages are effector cells of the innate immune system that undergo phenotypical changes in response to organ injury and repair. These cells are most often classified as proinflammatory M1 and anti-inflammatory M2 macrophages. Protein arginine deiminase (PAD), which catalyses the irreversible conversion of protein-bound arginine into citrulline, is expressed in macrophages. However, the substrates of PAD and its role in immune cells remain unclear. This study aimed to investigate the role of PAD in THP-1 macrophage polarization to the M1 and M2 phenotypes and identify the citrullinated proteins and modified arginines that are associated with this biological switch using mass spectrometry.
Results
Our study showed that PAD2 and, to a lesser extent, PAD1 and PAD4 were predominantly expressed in M1 macrophages. We showed that inhibiting PAD expression with BB-Cl-amidine decreased macrophage polarization to the M1 phenotype (TNF-α, IL-6) and increased macrophage polarization to the M2 phenotype (MRC1, ALOX15). This process was mediated by the downregulation of proteins involved in the NF-κβ pathway. Silencing PAD2 confirmed the activation of M2 macrophages by increasing the antiviral innate immune response and interferon signalling. A total of 192 novel citrullination sites associated with inflammation, cell death and DNA/RNA processing pathways were identified in M1 and M2 macrophages.
Conclusions
We showed that inhibiting PAD activity using a pharmacological inhibitor or silencing PAD2 with PAD2 siRNA shifted the activation of macrophages towards the M2 phenotype, which can be crucial for designing novel macrophage-mediated therapeutic strategies. We revealed a major citrullinated proteome and its rearrangement following macrophage polarization, which after further validation could lead to significant clinical benefits for the treatment of inflammation and autoimmune diseases.
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Zhang Y, Xu B. Involvement of testicular N-glycoproteome heterogeneity in seasonal spermatogenesis of the American mink (Neovison vison). Front Vet Sci 2022; 9:1001431. [PMID: 36406079 PMCID: PMC9672844 DOI: 10.3389/fvets.2022.1001431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Spermatogenesis in the American mink is characterized by an annual cycle of transition involving completely inactive and fully activated stages. N-glycosylation of proteins has emerged as an important regulator as it affects protein folding, secretion, degradation, and activity. However, the function of protein N-glycosylation in seasonal spermatogenesis of the American mink remains unclear. In the present study, we established a proteome-wide stoichiometry of N-glycosylation in mink testes at various phases of spermatogenesis using N-linked glycosylated-peptide enrichment in combination with liquid chromatography-tandem mass spectrometry analysis. A total of 532 N-glycosylated sites matching the canonical Asn-X-Ser/Thr motif were identified in 357 testicular proteins. Both the number of glycoproteins and the sites of N-glycosylated proteins in mink testes were highly dynamic at different stages. Functional analyses showed that testicular proteins with different N-glycosylation might play a vital role in spermatogenesis by affecting their folding, distribution, stability, and activity. Overall, our data suggest that the dynamics of N-glycosylation of testicular proteins are involved in seasonal spermatogenesis in the American mink.
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de Abreu Pereira D, Sandim V, Fernandes TFB, Almeida VH, Rocha MR, do Amaral RJFC, Rossi MID, Kalume DE, Zingali RB. Proteomic Analysis of HCC-1954 and MCF-7 Cell Lines Highlights Crosstalk between αv and β1 Integrins, E-Cadherin and HER-2. Int J Mol Sci 2022; 23:ijms231710194. [PMID: 36077593 PMCID: PMC9456615 DOI: 10.3390/ijms231710194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 08/04/2022] [Accepted: 08/28/2022] [Indexed: 01/13/2023] Open
Abstract
Overexpression of human epidermal growth factor receptor-2 (HER-2) occurs in 20% of all breast cancer subtypes, especially those that present the worst prognostic outcome through a very invasive and aggressive tumour. HCC-1954 (HER-2+) is a highly invasive, metastatic cell line, whereas MCF-7 is mildly aggressive and non-invasive. We investigated membrane proteins from both cell lines that could have a pivotal biological significance in metastasis. Membrane protein enrichment for HCC-1954 and MCF-7 proteomic analysis was performed. The samples were analysed and quantified by mass spectrometry. High abundance membrane proteins were confirmed by Western blot, immunofluorescence, and flow cytometry. Protein interaction prediction and correlations with the Cancer Genome Atlas (TCGA) patient data were conducted by bioinformatic analysis. In addition, β1 integrin expression was analysed by Western blot in cells upon trastuzumab treatment. The comparison between HCC-1954 and MCF-7 membrane-enriched proteins revealed that proteins involved in cytoskeleton organisation, such as HER-2, αv and β1 integrins, E-cadherin, and CD166 were more abundant in HCC-1954. β1 integrin membrane expression was higher in the HCC-1954 cell line resistant after trastuzumab treatment. TCGA data analysis showed a trend toward a positive correlation between HER-2 and β1 integrin in HER-2+ breast cancer patients. Differences in protein profile and abundance reflected distinctive capabilities for aggressiveness and invasiveness between HCC-1954 and MCF-7 cell line phenotypes. The higher membrane β1 integrin expression after trastuzumab treatment in the HCC-1954 cell line emphasised the need for investigating the contribution of β1 integrin modulation and its effect on the mechanism of trastuzumab resistance.
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Affiliation(s)
- Denise de Abreu Pereira
- Programa de Oncobiologia Celular e Molecular (POCM), Coordenação de Pesquisa, Instituto Nacional do Câncer, Rio de Janeiro 20231-050, Brazil
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Vanessa Sandim
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Laboratório de Hemostase e Venenos (LABHEMOVEN), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Thais F. B. Fernandes
- Programa de Oncobiologia Celular e Molecular (POCM), Coordenação de Pesquisa, Instituto Nacional do Câncer, Rio de Janeiro 20231-050, Brazil
| | - Vitor Hugo Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Murilo Ramos Rocha
- Programa de Oncobiologia Celular e Molecular (POCM), Coordenação de Pesquisa, Instituto Nacional do Câncer, Rio de Janeiro 20231-050, Brazil
| | - Ronaldo J. F. C. do Amaral
- Laboratório de Proliferação e Diferenciação Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Maria Isabel D. Rossi
- Instituto de Ciências Biomédicas e Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Dário Eluan Kalume
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMed), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Russolina B. Zingali
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Laboratório de Hemostase e Venenos (LABHEMOVEN), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Correspondence:
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Beller NC, Hummon AB. Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis. Mol Omics 2022; 18:579-590. [PMID: 35723214 PMCID: PMC9378559 DOI: 10.1039/d2mo00077f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The field of proteomics is continually improving, requiring the development of new quantitative methods. Stable isotope labeling in cell culture (SILAC) is a metabolic labeling technique originating in the early 2000s. By incorporating isotopically labeled amino acids into the media used for cell culture, unlabeled versus labeled cells can be differentiated by the mass spectrometer. Traditional SILAC labeling has been expanded to pulsed applications allowing for a new quantitative dimension of proteomics - temporal analysis. The complete introduction of Heavy SILAC labeling chased with surplus unlabeled medium mimics traditional pulse-chase experiments and allows for the loss of heavy signal to track proteomic changes over time. In a similar fashion, pulsed SILAC (pSILAC) monitors the initial incorporation of a heavy label across a period of time, which allows for the rate of protein label integration to be assessed. These innovative techniques have aided in inspiring numerous SILAC-based temporal and spatial labeling applications, including super SILAC, spike-in SILAC, spatial SILAC, and a revival in label multiplexing. This review reflects upon the evolution of SILAC and the pulsed SILAC application, introduces advances in SILAC labeling, and proposes future perspectives for this novel and exciting field.
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Affiliation(s)
- Nicole C Beller
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA, 43210.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA, 43210.
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA, 43210
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Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle. THE ISME JOURNAL 2022; 16:1883-1895. [PMID: 35444262 PMCID: PMC9296628 DOI: 10.1038/s41396-022-01226-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 12/11/2022]
Abstract
Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.
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36
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Lee D, Lee KH, Kim DW, Yoon S, Cho JY. CXCL5 inhibits excessive oxidative stress by regulating white adipocyte differentiation. Redox Biol 2022; 54:102359. [PMID: 35696764 PMCID: PMC9194457 DOI: 10.1016/j.redox.2022.102359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 10/31/2022] Open
Abstract
Chemokines have been well-documented as a major factor in immune cell migration and the regulation of immune responses. However, recent studies have reported that chemokines have diverse roles, both in immune cells and other cell types, including adipocytes. This study investigated the molecular functions of C-X-C motif chemokine ligand 5 (CXCL5) in white adipose cells using Cxcl5 knock-out (KO) mice fed a high-fat diet (HFD). The expression of Cxcl5 decreased by 90% during adipocyte differentiation and remained at a low level in mature adipocytes. Moreover, adipogenesis was enhanced when adipocytes were differentiated from the stromal vascular fraction (SFV) of Cxcl5 KO mice. Feeding an HFD increased the generation of reactive oxygen species (ROS) and promoted abnormal adipogenesis in Cxcl5 KO mice. Oxidative stress and insulin resistance occurred in Cxcl5 KO mice due to decreased antioxidant enzymes and failure to remove ROS. These results indicate the principal roles of CXCL5 in adipogenesis and ROS regulation in adipose tissue, further suggesting that CXCL5 is a valuable chemokine for metabolic disease research.
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Affiliation(s)
- Dabin Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea; Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong Wook Kim
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sanghyuk Yoon
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea; Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
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37
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Bravo-Miana RDC, Soler MF, Ceschin DG, Royo F, Negretti-Borga DM, Azkargorta M, Elortza F, Montesinos MDM, Pellizas CG, Falcón-Pérez JM, Donadio AC. Extracellular vesicles from thyroid cancer harbor a functional machinery involved in extracellular matrix remodeling. Eur J Cell Biol 2022; 101:151254. [PMID: 35849996 DOI: 10.1016/j.ejcb.2022.151254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 12/18/2022] Open
Abstract
Extracellular vesicles (EVs) participate in cell-stroma crosstalk within the tumor microenvironment and fibroblasts (Fb) contribute to tumor promotion in thyroid cancer. However, the role of tumor-stroma derived EVs still needs to be deciphered. We hypothesized that the interaction of thyroid tumor cells with Fb would liberate EVs with a specific proteomic profile, which would have an impact on EV-functionality in thyroid tumor progression-related events. Tumor (TPC-1, 8505c) and non-tumor (NThyOri) thyroid cells were co-cultured with human Fb. EVs, obtained by ultracentrifugation of conditioned media, were characterized by nanoparticle tracking analysis and western blotting. EV-proteomic analysis was performed by mass-spectrometry, and metalloproteinases (MMPs) were studied by zymography. EV-exchange was evaluated using immunofluorescence, confocal microscopy and FACS. EVs expressed classical exosome markers, with EVs from thyroid tumor cell-Fb co-cultures showing a proteomic profile related to extracellular matrix (ECM) remodeling. Bidirectional crosstalk between Fb and TPC-1 cells produced significantly more EVs than their isolated cells, and potentiated EV-functionality. In line with this, Fb-TPC-1 derived EVs induced MMP2 activation in NThyOri supernatants, and MMP2 activity could be evidenced in Fb and TPC-1 contact-independent co-cultures. Besides, MMP2 interactors allowed us to discriminate between EVs from thyroid tumoral and non-tumoral milieus. Interestingly, Fb internalized more EVs from TPC-1 than from NThyOri producing cells. Fb and thyroid tumor cell crosstalk produces specialized EVs with an ECM remodeling proteomic profile, enabling activation of MMP2 and possibly facilitating ECM-degradation, which is potentially linked with thyroid tumor progression.
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Affiliation(s)
- Rocío Del Carmen Bravo-Miana
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina
| | - María Florencia Soler
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina
| | - Danilo Guillermo Ceschin
- Centro de Investigación en Medicina Traslacional Severo Amuchástegui, Instituto Universitario de Ciencias Biomédicas de Córdoba, Naciones Unidas 420, Parque Velez Sarsfield, Córdoba, Argentina
| | - Félix Royo
- Exosomes Laboratory, CIC bioGUNE-BRTA, CIBERehd, Bizkaia Technology Park, Derio 48160, Spain
| | - Dana María Negretti-Borga
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina
| | - Mikel Azkargorta
- Proteomics Unit, CICbioGUNE-BRTA, CIBERehd, ProteoRed, Bizkaia Technology Park, Derio 48160, Bizkaia, Spain
| | - Félix Elortza
- Proteomics Unit, CICbioGUNE-BRTA, CIBERehd, ProteoRed, Bizkaia Technology Park, Derio 48160, Bizkaia, Spain
| | - María Del Mar Montesinos
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina
| | - Claudia Gabriela Pellizas
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina
| | - Juan Manuel Falcón-Pérez
- Exosomes Laboratory, CIC bioGUNE-BRTA, CIBERehd, Bizkaia Technology Park, Derio 48160, Spain; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain.
| | - Ana Carolina Donadio
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica, Córdoba, Argentina; Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI-CONICET), Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina.
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Yang W, Ma L, Hai DM, Liu N, Yang JM, Lan XB, Du J, Yang LS, Sun T, Yu JQ. Hippocampal Proteomic Analysis in Male Mice Following Aggressive Behavior Induced by Long-Term Administration of Perampanel. ACS OMEGA 2022; 7:19388-19400. [PMID: 35721950 PMCID: PMC9202264 DOI: 10.1021/acsomega.2c01008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 05/03/2023]
Abstract
Antiepileptic drugs have been shown to be associated with inducing or exacerbating adverse psychotropic reaction, including aggressive behavior. Perampanel, the first pharmacological compound approved by the FDA in 2012, is an effective antiepileptic drug for intractable epilepsy but induces severe aggression. So far, the underlying molecular mechanisms of aggression induced by perampanel remain incompletely understood. In the present study, a model of aggressive behavior based on the clinical use of perampanel was established and resident-intruder test and open field test were performed. Changes in hippocampal protein profiles were detected by tandem mass tag (TMT) proteomics. The behavioral results indicated that long-term use of perampanel increased the aggressive behavior of C57BL/6J mice. Proteomic analysis revealed that 93 proteins were significantly altered in the hippocampus of the perampanel-treated group (corrected p < 0.05), which were divided into multiple functional groups, mainly related to synaptic function, synaptogenesis, postsynaptic density protein, neurite outgrowth, AMPA-type glutamate receptor immobilization, and others. Bioinformatic analysis showed that differentially expressed proteins were involved in synaptic plasticity and the Ras signaling pathway. Furthermore, validation results by western blot demonstrated that glutamate receptor 1 (GluA1) and phosphorylation of mitogen-activated protein kinase (ERK1/2) were notably up-regulated, and synaptophysin (Syn) and postsynaptic density 95 (PSD95) were down-regulated in perampanel-treated mice. Therefore, our results provide valuable insight into the molecular mechanisms of aggressive behavior induced by perampanel, as well as potential options for safety treatment of perampanel in the future.
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Affiliation(s)
- Wu Yang
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
- Department
of Emergency, General Hospital of Ningxia
Medical University, Yinchuan 750004, Ningxia, PR China
| | - Lin Ma
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
| | - Dong-Mei Hai
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
| | - Ning Liu
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
| | - Jia-Mei Yang
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
| | - Xiao-Bing Lan
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
| | - Juan Du
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
| | - Li-Shan Yang
- Department
of Emergency, General Hospital of Ningxia
Medical University, Yinchuan 750004, Ningxia, PR China
| | - Tao Sun
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
- Ningxia Key Laboratory of Cerebrocranial
Disease, The Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
| | - Jian Qiang Yu
- Department of Pharmacology, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
- Ningxia
Hui Medicine Modern Engineering Research Center and Collaborative
Innovation Center, Ningxia Medical University, Yinchuan 750004, Ningxia, PR China
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Long Q, Feng L, Li Y, Zuo T, Chang L, Zhang Z, Xu P. Time-resolved quantitative phosphoproteomics reveals cellular responses induced by caffeine and coumarin. Toxicol Appl Pharmacol 2022; 449:116115. [PMID: 35691368 DOI: 10.1016/j.taap.2022.116115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
Protein phosphorylation is a critical way that cells respond to external signals and environmental stresses. However, the patterns of cellular response to chemicals at different times were largely unknown. Here, we used quantitative phosphoproteomics to analyze the cellular response of kinases and signaling pathways, as well as pattern change of phosphorylated substrates in HepG2 cells that were exposed to caffeine and coumarin for 10 min and 24 h. Comparing the 10 min and 24 h groups, 33 kinases were co-responded and 32 signaling pathways were co-enriched in caffeine treated samples, while 48 kinases and 34 signaling pathways were co-identified in coumarin treated samples. Instead, the percentage of co-identified phosphorylated substrates only accounted for 4.31% and 9.57% between 10 min and 24 h in caffeine and coumarin treated samples, respectively. The results showed that specific chemical exposure led to a bunch of the same kinases and signaling pathways changed in HepG2 cells, while the phosphorylated substrates were different. In addition, it was found that insulin signaling pathway was significantly enriched by both the caffeine and coumarin treatment. The pattern changes in phosphorylation of protein substrates, kinases and signaling pathways with varied chemicals and different time course shed light on the potential mechanism of cellular responses to endless chemical stimulation.
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Affiliation(s)
- Qi Long
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Lijie Feng
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Medicine, Guizhou University, Guiyang 550025, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China.
| | - Ping Xu
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Medicine, Guizhou University, Guiyang 550025, China; School of Public Health, China Medical University, Shenyang 110122, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China.
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40
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Integrated multi-omics reveal polycomb repressive complex 2 restricts human trophoblast induction. Nat Cell Biol 2022; 24:858-871. [PMID: 35697783 PMCID: PMC9203278 DOI: 10.1038/s41556-022-00932-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here we define the chromatin-associated proteome, histone post-translational modifications and transcriptome of human naive and primed pluripotent stem cells. Our integrated analysis reveals differences in the relative abundance and activities of distinct chromatin modules. We identify a strong enrichment of polycomb repressive complex 2 (PRC2)-associated H3K27me3 in the chromatin of naive pluripotent stem cells and H3K27me3 enrichment at promoters of lineage-determining genes, including trophoblast regulators. PRC2 activity acts as a chromatin barrier restricting the differentiation of naive cells towards the trophoblast lineage, whereas inhibition of PRC2 promotes trophoblast-fate induction and cavity formation in human blastoids. Together, our results establish that human naive pluripotent stem cells are not epigenetically unrestricted, but instead possess chromatin mechanisms that oppose the induction of alternative cell fates. Two side-by-side papers report that H3K27me3 deposited by polycomb repressive complex 2 represents an epigenetic barrier that restricts naive human pluripotent cell differentiation into alternative lineages including trophoblasts.
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41
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Zhang Z, Zhang Y, Li Y, Jiang S, Xu F, Li K, Chang L, Gao H, Kukic P, Carmichael P, Liddell M, Li J, Zhang Q, Lyu Z, Peng S, Zuo T, Tulum L, Xu P. Quantitative phosphoproteomics reveal cellular responses from caffeine, coumarin and quercetin in treated HepG2 cells. Toxicol Appl Pharmacol 2022; 449:116110. [DOI: 10.1016/j.taap.2022.116110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 11/15/2022]
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Zou J, Yang L, Li Y, Piao M, Li Y, Yao N, Zhang X, Zhang Q, Hu G, Yang D, Zuo Z. Comparative Proteomics Combined with Morphophysiological Analysis Revealed Chilling Response Patterns in Two Contrasting Maize Genotypes. Cells 2022; 11:cells11081321. [PMID: 35456000 PMCID: PMC9024610 DOI: 10.3390/cells11081321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 02/04/2023] Open
Abstract
Maize yield is significantly influenced by low temperature, particularly chilling stress at the maize seedling stage. Various physiological approaches have been established to resist chilling stress; however, the detailed proteins change patterns underlying the maize chilling stress response at the seedling stage remain unknown, preventing the development of breeding-based methods to resist chilling stress in maize. Thus, we performed comprehensive physiological, comparative proteomics and specific phytohormone abscisic acid (ABA) assay on different maize inbred lines (tolerant-line KR701 and sensitive-line hei8834) at different seedling stages (the first leaf stage and third leaf stage) under chilling stress. The results revealed several signalling proteins and pathways in response to chilling stress at the maize seedling stage. Meanwhile, we found ABA pathway was important for chilling resistance of tolerant-line KR701 at the first leaf stage. Related chilling-responsive proteins were further catalogued and analysed, providing a resource for further investigation and maize breeding.
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Affiliation(s)
- Jinpeng Zou
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (J.Z.); (Q.Z.)
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Y.); (M.P.)
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
| | - Liang Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Y.); (M.P.)
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
| | - Yuhong Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
| | - Mingxin Piao
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Y.); (M.P.)
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
| | - Yaxing Li
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
| | - Nan Yao
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
| | - Xiaohong Zhang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
| | - Qian Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (J.Z.); (Q.Z.)
| | - Guanghui Hu
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150030, China;
| | - Deguang Yang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (J.Z.); (Q.Z.)
- Correspondence: (D.Y.); (Z.Z.)
| | - Zecheng Zuo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China; (L.Y.); (M.P.)
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Y.L.); (N.Y.); (X.Z.)
- Correspondence: (D.Y.); (Z.Z.)
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Georgiou M, Ntavelou P, Stokes W, Roy R, Maher GJ, Stoilova T, Rakhit CP, Martins M, Ajuh P, Horowitz N, Berkowitz RS, Elias K, Seckl MJ, Pardo OE. ATR and CDK4/6 inhibition target the growth of methotrexate-resistant choriocarcinoma. Oncogene 2022; 41:2540-2554. [PMID: 35301407 PMCID: PMC9054653 DOI: 10.1038/s41388-022-02251-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/12/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022]
Abstract
Low-risk gestational trophoblastic neoplasia including choriocarcinoma is often effectively treated with Methotrexate (MTX) as a first line therapy. However, MTX resistance (MTX-R) occurs in at least ≈33% of cases. This can sometimes be salvaged with actinomycin-D but often requires more toxic combination chemotherapy. Moreover, additional therapy may be needed and, for high-risk patients, 5% still die from the multidrug-resistant disease. Consequently, new treatments that are less toxic and could reverse MTX-R are needed. Here, we compared the proteome/phosphoproteome of MTX-resistant and sensitive choriocarcinoma cells using quantitative mass-spectrometry to identify therapeutically actionable molecular changes associated with MTX-R. Bioinformatics analysis of the proteomic data identified cell cycle and DNA damage repair as major pathways associated with MTX-R. MTX-R choriocarcinoma cells undergo cell cycle delay in G1 phase that enables them to repair DNA damage more efficiently through non-homologous end joining in an ATR-dependent manner. Increased expression of cyclin-dependent kinase 4 (CDK4) and loss of p16Ink4a in resistant cells suggested that CDK4 inhibition may be a strategy to treat MTX-R choriocarcinoma. Indeed, inhibition of CDK4/6 using genetic silencing or the clinically relevant inhibitor, Palbociclib, induced growth inhibition both in vitro and in an orthotopic in vivo mouse model. Finally, targeting the ATR pathway, genetically or pharmacologically, re-sensitised resistant cells to MTX in vitro and potently prevented the growth of MTX-R tumours in vivo. In short, we identified two novel therapeutic strategies to tackle MTX-R choriocarcinoma that could rapidly be translated into the clinic.
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Affiliation(s)
- Marina Georgiou
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Panagiota Ntavelou
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - William Stokes
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Rajat Roy
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Geoffrey J Maher
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | - Tsvetana Stoilova
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
| | | | - Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | | | - Neil Horowitz
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ross S Berkowitz
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kevin Elias
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Michael J Seckl
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK.
| | - Olivier E Pardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK.
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Abstract
INTRODUCTION Due to its excellent sensitivity, nano-flow liquid chromatography tandem mass spectrometry (LC-MS/MS) is the mainstay in proteome research; however, this comes at the expense of limited throughput and robustness. In contrast, micro-flow LC-MS/MS enables high-throughput, robustness, quantitative reproducibility, and precision while retaining a moderate degree of sensitivity. Such features make it an attractive technology for a wide range of proteomic applications. In particular, large-scale projects involving the analysis of hundreds to thousands of samples. AREAS COVERED This review summarizes the history of chromatographic separation in discovery proteomics with a focus on micro-flow LC-MS/MS, discusses the current state-of-the-art, highlights advances in column development and instrumentation, and provides guidance on which LC flow best supports different types of proteomic applications. EXPERT OPINION Micro-flow LC-MS/MS will replace nano-flow LC-MS/MS in many proteomic applications, particularly when sample quantities are not limited and sample cohorts are large. Examples include clinical analyses of body fluids, tissues, drug discovery and chemical biology investigations, plus systems biology projects across all kingdoms of life. When combined with rapid and sensitive MS, intelligent data acquisition, and informatics approaches, it will soon become possible to analyze large cohorts of more than 10,000 samples in a comprehensive and fully quantitative fashion.
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Affiliation(s)
- Yangyang Bian
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Chunli Gao
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
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Li H, Nian J, Fang S, Guo M, Huang X, Zhang F, Wang Q, Zhang J, Bai J, Dong G, Xin P, Xie X, Chen F, Wang G, Wang Y, Qian Q, Zuo J, Chu J, Ma X. Regulation of nitrogen starvation responses by the alarmone (p)ppGpp in rice. J Genet Genomics 2022; 49:469-480. [DOI: 10.1016/j.jgg.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 12/20/2022]
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Martinez R, Huang W, Buck H, Rea S, Defnet AE, Kane MA, Shapiro P. Proteomic Changes in the Monolayer and Spheroid Melanoma Cell Models of Acquired Resistance to BRAF and MEK1/2 Inhibitors. ACS OMEGA 2022; 7:3293-3311. [PMID: 35128241 PMCID: PMC8811929 DOI: 10.1021/acsomega.1c05361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Extracellular signal-regulated kinase-1/2 (ERK1/2) pathway inhibitors are important therapies for treating many cancers. However, acquired resistance to most protein kinase inhibitors limits their ability to provide durable responses. Approximately 50% of malignant melanomas contain activating mutations in BRAF, which promotes cancer cell survival through the direct phosphorylation of the mitogen-activated protein kinase MAPK/ERK 1/2 (MEK1/2) and the activation of ERK1/2. Although the combination treatment with BRAF and MEK1/2 inhibitors is a recommended approach to treat melanoma, the development of drug resistance remains a barrier to achieving long-term patient benefits. Few studies have compared the global proteomic changes in BRAF/MEK1/2 inhibitor-resistant melanoma cells under different growth conditions. The current study uses high-resolution label-free mass spectrometry to compare relative protein changes in BRAF/MEK1/2 inhibitor-resistant A375 melanoma cells grown as monolayers or spheroids. While approximately 66% of proteins identified were common in the monolayer and spheroid cultures, only 6.2 or 3.6% of proteins that significantly increased or decreased, respectively, were common between the drug-resistant monolayer and spheroid cells. Drug-resistant monolayers showed upregulation of ERK-independent signaling pathways, whereas drug-resistant spheroids showed primarily elevated catabolic metabolism to support oxidative phosphorylation. These studies highlight the similarities and differences between monolayer and spheroid cell models in identifying actionable targets to overcome drug resistance.
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Affiliation(s)
- Ramon Martinez
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Weiliang Huang
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Heather Buck
- Nathan
Schnaper Internship Program in Translational Cancer Research, Marlene
and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 22S. Greene Street, Baltimore, Maryland 21201, United States
| | - Samantha Rea
- Nathan
Schnaper Internship Program in Translational Cancer Research, Marlene
and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 22S. Greene Street, Baltimore, Maryland 21201, United States
| | - Amy E. Defnet
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Maureen A. Kane
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Paul Shapiro
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
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Savchenko A, Müller C, Lubec J, Leo D, Korz V, Afjehi-Sadat L, Malikovic J, Sialana FJ, Lubec G, Sukhanov I. The Lack of Dopamine Transporter Is Associated With Conditional Associative Learning Impairments and Striatal Proteomic Changes. Front Psychiatry 2022; 13:799433. [PMID: 35370807 PMCID: PMC8971526 DOI: 10.3389/fpsyt.2022.799433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/04/2022] [Indexed: 11/14/2022] Open
Abstract
Dopamine (DA) is critically involved in different functions of the central nervous system (CNS) including control of voluntary movement, affect, reward, sleep, and cognition. One of the key components of DA neurotransmission is DA reuptake by the DA transporter (DAT), ensuring rapid clearance of DA from the synaptic cleft. Thus, lack of DAT leads to persistent high extracellular DA levels. While there is strong evidence for a role of striatal dopaminergic activity in learning and memory processes, little is known about the contribution of DAT deficiency to conditional learning impairments and underlying molecular processes. DAT-knockout (DAT-KO) rats were tested in a set of behavioral experiments evaluating conditional associative learning, which requires unaltered striatal function. In parallel, a large-scale proteomic analysis of the striatum was performed to identify molecular factors probably underlying behavioral patterns. DAT-KO rats were incapable to acquire a new operant skill in Pavlovian/instrumental autoshaping, although the conditional stimulus-unconditional stimulus (CS-US) association seems to be unaffected. These findings suggest that DAT directly or indirectly contributes to the reduction of transference of incentive salience from the reward to the CS. We propose that specific impairment of conditional learning might be caused by molecular adaptations to the hyperdopaminergic state, presumably by dopamine receptor 1 (DRD1) hypofunction, as proposed by proteomic analysis. Whether DRD1 downregulation can cause cognitive deficits in the hyperdopaminergic state is the subject of discussion, and further studies are needed to answer this question. This study may be useful for the interpretation of previous and the design of future studies in the dopamine field.
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Affiliation(s)
- Artem Savchenko
- Institute of Pharmacology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Carina Müller
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Jana Lubec
- Programme for Proteomics, Paracelsus Medical University, Salzburg, Austria
| | - Damiana Leo
- Department of Neurosciences, University of Mons, Mons, Belgium
| | - Volker Korz
- Programme for Proteomics, Paracelsus Medical University, Salzburg, Austria
| | - Leila Afjehi-Sadat
- Programme for Proteomics, Paracelsus Medical University, Salzburg, Austria
| | - Jovana Malikovic
- Programme for Proteomics, Paracelsus Medical University, Salzburg, Austria
| | - Fernando J Sialana
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Gert Lubec
- Programme for Proteomics, Paracelsus Medical University, Salzburg, Austria
| | - Ilya Sukhanov
- Institute of Pharmacology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
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Kongpracha P, Wiriyasermkul P, Isozumi N, Moriyama S, Kanai Y, Nagamori S. Simple but efficacious enrichment of integral membrane proteins and their interactions for in-depth membrane proteomics. Mol Cell Proteomics 2022; 21:100206. [PMID: 35085786 PMCID: PMC9062332 DOI: 10.1016/j.mcpro.2022.100206] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/13/2021] [Accepted: 01/20/2022] [Indexed: 12/19/2022] Open
Abstract
Membrane proteins play essential roles in various cellular processes, such as nutrient transport, bioenergetic processes, cell adhesion, and signal transduction. Proteomics is one of the key approaches to exploring membrane proteins comprehensively. Bottom–up proteomics using LC–MS/MS has been widely used in membrane proteomics. However, the low abundance and hydrophobic features of membrane proteins, especially integral membrane proteins, make it difficult to handle the proteins and are the bottleneck for identification by LC–MS/MS. Herein, to improve the identification and quantification of membrane proteins, we have stepwisely evaluated methods of membrane enrichment for the sample preparation. The enrichment methods of membranes consisted of precipitation by ultracentrifugation and treatment by urea or alkaline solutions. The best enrichment method in the study, washing with urea after isolation of the membranes, resulted in the identification of almost twice as many membrane proteins compared with samples without the enrichment. Notably, the method significantly enhances the identified numbers of multispanning transmembrane proteins, such as solute carrier transporters, ABC transporters, and G-protein–coupled receptors, by almost sixfold. Using this method, we revealed the profiles of amino acid transport systems with the validation by functional assays and found more protein–protein interactions, including membrane protein complexes and clusters. Our protocol uses standard procedures in biochemistry, but the method was efficient for the in-depth analysis of membrane proteome in a wide range of samples. Fractionation of membranes improves the identification of membrane proteins. Membranes washed with urea or alkaline increase identified transmembrane proteins. Urea wash increases the detection of multispanning transmembrane proteins. Proteomics of urea-washed membranes keeps more protein–protein interactions.
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Affiliation(s)
- Pornparn Kongpracha
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan; Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan
| | - Pattama Wiriyasermkul
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan; Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan
| | - Noriyoshi Isozumi
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Satomi Moriyama
- Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shushi Nagamori
- Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo, Japan; Department of Collaborative Research for Biomolecular Dynamics, Nara Medical University, Nara, Japan.
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49
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Halkoum R, Salnot V, Capallere C, Plaza C, L'Honoré A, Pays K, Friguet B, Nizard C, Petropoulos I. Glyoxal induces senescence in human keratinocytes through oxidative stress and activation of the AKT/FOXO3a/p27 KIP1 pathway. J Invest Dermatol 2021; 142:2068-2078.e7. [PMID: 34971698 DOI: 10.1016/j.jid.2021.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 11/08/2021] [Accepted: 12/07/2021] [Indexed: 01/10/2023]
Abstract
Senescence is a well-characterized cellular state associated with specific markers such as permanent cell proliferation arrest, and the secretion of messenger molecules by cells expressing the Senescence-Associated Secretory Phenotype (SASP). The SASP composition depends on many factors such as the cell type or the nature of the stress that induces senescence. Since the skin constitutes a barrier with the external environment, it is particularly subjected to different types of stresses, and consequently prone to premature cellular aging. The dicarbonyl compounds glyoxal and methylglyoxal are precursors of Advanced Glycation End-products (AGEs), whose presence marks normal and pathological aging. In this study, we demonstrate that glyoxal treatment provokes oxidative stress by increasing reactive oxygen species and AGEs levels and induces senescence in human keratinocytes. Furthermore, glyoxal-induced senescence bears a unique molecular progression profile: an "early-stage" when AKT-FOXO3a-p27KIP1 pathway mediates cell-cycle arrest, and a "late-stage" senescence maintained by the p16INK4/pRb pathway. Moreover, we characterized the resulting secretory phenotype during early senescence by mass spectrometry. Our study provides evidence that glyoxal can affect keratinocyte functions and act as a driver of human skin aging. Hence, senotherapeutics aimed at modulating glyoxal-associated senescence phenotype hold promising potential.
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Affiliation(s)
- Rym Halkoum
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005 Paris, France; LVMH Recherche. Life Science Department, 185 Avenue de Verdun, 45800, Saint Jean de Braye, France
| | - Virginie Salnot
- 3P5 proteom'IC facility, Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France
| | - Christophe Capallere
- Ashland, Global Skin Research Center, Advanced Skin Research & Bioengineering Dept., Sophia Antipolis, France
| | - Christelle Plaza
- Ashland, Global Skin Research Center, Advanced Skin Research & Bioengineering Dept., Sophia Antipolis, France
| | - Aurore L'Honoré
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005 Paris, France
| | - Karl Pays
- LVMH Recherche. Life Science Department, 185 Avenue de Verdun, 45800, Saint Jean de Braye, France
| | - Bertrand Friguet
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005 Paris, France
| | - Carine Nizard
- LVMH Recherche. Life Science Department, 185 Avenue de Verdun, 45800, Saint Jean de Braye, France
| | - Isabelle Petropoulos
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, Biological Adaptation and Ageing, B2A-IBPS, 75005 Paris, France.
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50
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Advances in sample preparation for membrane proteome quantification. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:23-29. [PMID: 34906323 DOI: 10.1016/j.ddtec.2021.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022]
Abstract
Membrane proteins mediate various biological processes. Most drugs commercially available target proteins on the cell surface. Therefore, proteomics of plasma membrane proteins provides useful information for drug discovery. However, membrane proteins are one of the most difficult biological groups to quantify by proteomics because of their hydrophobicity and low protein content. To obtain unbiased quantitative membrane proteomics data, specific strategies should be followed during sample preparation. This review explores the most recent advances in sample preparation for the quantitative analysis of the membrane proteome, including enrichment by subcellular fractionation and trypsin digestion.
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