1
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Virág D, Schlosser G, Borbély A, Gellén G, Papp D, Kaleta Z, Dalmadi-Kiss B, Antal I, Ludányi K. A Mass Spectrometry Strategy for Protein Quantification Based on the Differential Alkylation of Cysteines Using Iodoacetamide and Acrylamide. Int J Mol Sci 2024; 25:4656. [PMID: 38731875 PMCID: PMC11083099 DOI: 10.3390/ijms25094656] [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: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
Mass spectrometry has become the most prominent yet evolving technology in quantitative proteomics. Today, a number of label-free and label-based approaches are available for the relative and absolute quantification of proteins and peptides. However, the label-based methods rely solely on the employment of stable isotopes, which are expensive and often limited in availability. Here we propose a label-based quantification strategy, where the mass difference is identified by the differential alkylation of cysteines using iodoacetamide and acrylamide. The alkylation reactions were performed under identical experimental conditions; therefore, the method can be easily integrated into standard proteomic workflows. Using high-resolution mass spectrometry, the feasibility of this approach was assessed with a set of tryptic peptides of human serum albumin. Several critical questions, such as the efficiency of labeling and the effect of the differential alkylation on the peptide retention and fragmentation, were addressed. The concentration of the quality control samples calculated against the calibration curves were within the ±20% acceptance range. It was also demonstrated that heavy labeled peptides exhibit a similar extraction recovery and matrix effect to light ones. Consequently, the approach presented here may be a viable and cost-effective alternative of stable isotope labeling strategies for the quantification of cysteine-containing proteins.
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Affiliation(s)
- Dávid Virág
- Department of Pharmaceutics, Semmelweis University, Hőgyes Endre utca 7., H-1092 Budapest, Hungary; (D.V.); (B.D.-K.); (I.A.)
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (G.S.); (A.B.); (G.G.); (D.P.)
| | - Adina Borbély
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (G.S.); (A.B.); (G.G.); (D.P.)
| | - Gabriella Gellén
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (G.S.); (A.B.); (G.G.); (D.P.)
| | - Dávid Papp
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; (G.S.); (A.B.); (G.G.); (D.P.)
- Hevesy György PhD School of Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Zoltán Kaleta
- Department of Organic Chemistry, Semmelweis University, Hőgyes Endre utca 7., H-1092 Budapest, Hungary;
| | - Borbála Dalmadi-Kiss
- Department of Pharmaceutics, Semmelweis University, Hőgyes Endre utca 7., H-1092 Budapest, Hungary; (D.V.); (B.D.-K.); (I.A.)
| | - István Antal
- Department of Pharmaceutics, Semmelweis University, Hőgyes Endre utca 7., H-1092 Budapest, Hungary; (D.V.); (B.D.-K.); (I.A.)
| | - Krisztina Ludányi
- Department of Pharmaceutics, Semmelweis University, Hőgyes Endre utca 7., H-1092 Budapest, Hungary; (D.V.); (B.D.-K.); (I.A.)
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2
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Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. eLife 2024; 12:RP90579. [PMID: 38517750 PMCID: PMC10959535 DOI: 10.7554/elife.90579] [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] [Indexed: 03/24/2024] Open
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Ludger JE Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Julie Y Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kerry A Pierce
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Clary B Clish
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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3
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Shi M, Evans CA, McQuillan JL, Noirel J, Pandhal J. LFQRatio: A Normalization Method to Decipher Quantitative Proteome Changes in Microbial Coculture Systems. J Proteome Res 2024; 23:999-1013. [PMID: 38354288 PMCID: PMC10913063 DOI: 10.1021/acs.jproteome.3c00714] [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: 02/16/2024]
Abstract
The value of synthetic microbial communities in biotechnology is gaining traction due to their ability to undertake more complex metabolic tasks than monocultures. However, a thorough understanding of strain interactions, productivity, and stability is often required to optimize growth and scale up cultivation. Quantitative proteomics can provide valuable insights into how microbial strains adapt to changing conditions in biomanufacturing. However, current workflows and methodologies are not suitable for simple artificial coculture systems where strain ratios are dynamic. Here, we established a workflow for coculture proteomics using an exemplar system containing two members, Azotobacter vinelandii and Synechococcus elongatus. Factors affecting the quantitative accuracy of coculture proteomics were investigated, including peptide physicochemical characteristics such as molecular weight, isoelectric point, hydrophobicity, and dynamic range as well as factors relating to protein identification such as varying proteome size and shared peptides between species. Different quantification methods based on spectral counts and intensity were evaluated at the protein and cell level. We propose a new normalization method, named "LFQRatio", to reflect the relative contributions of two distinct cell types emerging from cell ratio changes during cocultivation. LFQRatio can be applied to real coculture proteomics experiments, providing accurate insights into quantitative proteome changes in each strain.
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Affiliation(s)
- Mengxun Shi
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Caroline A Evans
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Josie L McQuillan
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Josselin Noirel
- GBCM Laboratory (EA7528), Conservatoire National des Arts et Métiers, HESAM Université, 2 rue Conté, Paris 75003, France
| | - Jagroop Pandhal
- Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
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4
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Zhou C, Wang Y, He S, Lin S, Cheng J, Hu Q, Meng F, Gu T, Cai G, Li Z, Wu Z, Hong L. DIA-based quantitative proteomic analysis of porcine endometrium in the peri-implantation phase. J Proteomics 2024; 293:105065. [PMID: 38158016 DOI: 10.1016/j.jprot.2023.105065] [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: 07/18/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
The 12th day of gestation is a critical period for embryo loss and the beginning of imminent implantation in sows. Data independent acquisition (DIA) technology is one of the high-throughput, high-resolution and reproducible proteomics technologies for large-scale digital qualitative and quantitative research. The aim of this study was to identify and characterize the protein abundance landscape of Yorkshire pig endometrium on the 12th day of pregnancy (P12) and estrous cycle (C12) using DIA proteomics. A total of 1251 differentially abundant proteins (DAPs) were identified, of which 882 were up-regulated and 369 were down-regulated at P12. Functional enrichment analysis showed that the identified proteins were related to metabolism, biosynthesis and signaling pathways. Three proteins were selected for Western blot (WB) validation and the results were consistent with the DIA data. Further combined with transcriptome data, fibrinogen like 2 (FGL2) and S100 calcium binding protein A8 (S100A8) were verified to be highly abundant in the P12 endometrial epithelium. In summary, there were significantly different abundance of proteome profiles in C12 and P12 endometrium, suggesting that DAPs are associated with changes in endometrial receptivity, which laid the foundation for further research on related regulatory mechanisms. SIGNIFICANCE: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation. SIGNIFICANCE OF THE STUDY: The 12th day of gestation is an important point in the peri-implantation period of pigs, when the endometrium presents a receptive state under the stimulation of estrogen. DIA proteomics technology is an emerging protein identification technology in recent years, which can obtain protein information through comprehensive and unbiased scanning. In this study, DIA technology was used to characterize endometrial proteins in pigs during the peri-implantation period. The results showed that higher protein abundance was detected using the DIA technique, and some of these DAPs may be involved in regulating embryo implantation. This study will help to better reveal the related proteins involved in embryo implantation, and lay a foundation for further research on the mechanism of endometrial regulation of embryo implantation.
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Affiliation(s)
- Chen Zhou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yongzhong Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Simin He
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shifei Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Jie Cheng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Qun Hu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Fanming Meng
- Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China; Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, China; Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, China.
| | - Linjun Hong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou, China; National Engineering Research Center for Breeding Swine Industry, Guangzhou, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, China; Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou, China.
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5
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Bouyssié D, Altıner P, Capella-Gutierrez S, Fernández JM, Hagemeijer YP, Horvatovich P, Hubálek M, Levander F, Mauri P, Palmblad M, Raffelsberger W, Rodríguez-Navas L, Di Silvestre D, Kunkli BT, Uszkoreit J, Vandenbrouck Y, Vizcaíno JA, Winkelhardt D, Schwämmle V. WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows. J Proteome Res 2024; 23:418-429. [PMID: 38038272 DOI: 10.1021/acs.jproteome.3c00636] [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: 12/02/2023]
Abstract
The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.
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Affiliation(s)
- David Bouyssié
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III─Paul Sabatier (UT3), 31062 Toulouse, France
- Proteomics French Infrastructure, ProFI, FR 2048 Toulouse, France
| | - Pınar Altıner
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III─Paul Sabatier (UT3), 31062 Toulouse, France
| | | | - José M Fernández
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Yanick Paco Hagemeijer
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, 9712 CP Groningen, The Netherlands
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Peter Horvatovich
- Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, 9712 CP Groningen, The Netherlands
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, CAS, 160 00 Prague, Czech Republic
| | - Fredrik Levander
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Immunotechnology, Lund University, 22100 Lund, Sweden
| | - Pierluigi Mauri
- Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), Segrate, 20054 Milan, Italy
| | - Magnus Palmblad
- Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Wolfgang Raffelsberger
- Wolfgang Raffelsberger: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 1 Rue Laurent Fries, 67404 Illkirch, France
| | - Laura Rodríguez-Navas
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Dario Di Silvestre
- Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), Segrate, 20054 Milan, Italy
| | - Balázs Tibor Kunkli
- Balázs Tibor Kunkli: Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Julian Uszkoreit
- Medical Faculty, Medical Bioinformatics, Ruhr University Bochum, 44801 Bochum, Germany
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany
- Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Yves Vandenbrouck
- Proteomics French Infrastructure, ProFI, FR 2048 Toulouse, France
- CEA, Fundamental Research Division, Proteomics French Infrastructure, 91191 Gif-sur-Yvette, France
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust, Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
| | - Dirk Winkelhardt
- Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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6
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Mitchell W, Goeminne LJ, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.546730. [PMID: 37425825 PMCID: PMC10327104 DOI: 10.1101/2023.06.30.546730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
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Affiliation(s)
- Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Ludger J.E. Goeminne
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Sirui Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Julie Y. Chen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
| | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Kerry A. Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Angelina H. Choy
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 01241 United States
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115 United States
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 United States
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7
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Revell CK, Herrera JA, Lawless C, Lu Y, Kadler KE, Chang J, Jensen OE. Modeling collagen fibril self-assembly from extracellular medium in embryonic tendon. Biophys J 2023; 122:3219-3237. [PMID: 37415335 PMCID: PMC10465709 DOI: 10.1016/j.bpj.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/24/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023] Open
Abstract
Collagen is a key structural component of multicellular organisms and is arranged in a highly organized manner. In structural tissues such as tendons, collagen forms bundles of parallel fibers between cells, which appear within a 24-h window between embryonic day 13.5 (E13.5) and E14.5 during mouse embryonic development. Current models assume that the organized structure of collagen requires direct cellular control, whereby cells actively lay down collagen fibrils from cell surfaces. However, such models appear incompatible with the time and length scales of fibril formation. We propose a phase-transition model to account for the rapid development of ordered fibrils in embryonic tendon, reducing reliance on active cellular processes. We develop phase-field crystal simulations of collagen fibrillogenesis in domains derived from electron micrographs of inter-cellular spaces in embryonic tendon and compare results qualitatively and quantitatively to observed patterns of fibril formation. To test the prediction of this phase-transition model that free protomeric collagen should exist in the inter-cellular spaces before the formation of observable fibrils, we use laser-capture microdissection, coupled with mass spectrometry, which demonstrates steadily increasing free collagen in inter-cellular spaces up to E13.5, followed by a rapid reduction of free collagen that coincides with the appearance of less-soluble collagen fibrils. The model and measurements together provide evidence for extracellular self-assembly of collagen fibrils in embryonic mouse tendon, supporting an additional mechanism for rapid collagen fibril formation during embryonic development.
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Affiliation(s)
- Christopher K Revell
- Department of Mathematics, University of Manchester, Manchester, United Kingdom; Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jeremy A Herrera
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Yinhui Lu
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Karl E Kadler
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
| | - Joan Chang
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom; Division of Molecular and Cellular Function, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
| | - Oliver E Jensen
- Department of Mathematics, University of Manchester, Manchester, United Kingdom; Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
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8
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Lima TI, Laurila PP, Wohlwend M, Morel JD, Goeminne LJE, Li H, Romani M, Li X, Oh CM, Park D, Rodríguez-López S, Ivanisevic J, Gallart-Ayala H, Crisol B, Delort F, Batonnet-Pichon S, Silveira LR, Sankabattula Pavani Veera Venkata L, Padala AK, Jain S, Auwerx J. Inhibiting de novo ceramide synthesis restores mitochondrial and protein homeostasis in muscle aging. Sci Transl Med 2023; 15:eade6509. [PMID: 37196064 DOI: 10.1126/scitranslmed.ade6509] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023]
Abstract
Disruption of mitochondrial function and protein homeostasis plays a central role in aging. However, how these processes interact and what governs their failure in aging remain poorly understood. Here, we showed that ceramide biosynthesis controls the decline in mitochondrial and protein homeostasis during muscle aging. Analysis of transcriptome datasets derived from muscle biopsies obtained from both aged individuals and patients with a diverse range of muscle disorders revealed that changes in ceramide biosynthesis, as well as disturbances in mitochondrial and protein homeostasis pathways, are prevalent features in these conditions. By performing targeted lipidomics analyses, we found that ceramides accumulated in skeletal muscle with increasing age across Caenorhabditis elegans, mice, and humans. Inhibition of serine palmitoyltransferase (SPT), the rate-limiting enzyme of the ceramide de novo synthesis, by gene silencing or by treatment with myriocin restored proteostasis and mitochondrial function in human myoblasts, in C. elegans, and in the skeletal muscles of mice during aging. Restoration of these age-related processes improved health and life span in the nematode and muscle health and fitness in mice. Collectively, our data implicate pharmacological and genetic suppression of ceramide biosynthesis as potential therapeutic approaches to delay muscle aging and to manage related proteinopathies via mitochondrial and proteostasis remodeling.
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Affiliation(s)
- Tanes I Lima
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Pirkka-Pekka Laurila
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Martin Wohlwend
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Jean David Morel
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Ludger J E Goeminne
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Hao Li
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Mario Romani
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, South Korea
| | - Dohyun Park
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Sandra Rodríguez-López
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne 1005, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne 1005, Switzerland
| | - Barbara Crisol
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Florence Delort
- Laboratoire Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS and Université Paris Cité, Paris 8251, France
| | - Sabrina Batonnet-Pichon
- Laboratoire Biologie Fonctionnelle et Adaptative, UMR 8251, CNRS and Université Paris Cité, Paris 8251, France
| | - Leonardo R Silveira
- Obesity and Comorbidities Research Center, University of Campinas, Campinas 13083-864, Brazil
| | | | - Anil K Padala
- Intonation Research Laboratories, Hyderabad 500076, India
| | - Suresh Jain
- Intonation Research Laboratories, Hyderabad 500076, India
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
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9
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Heazlewood SY, Ahmad T, Cao B, Cao H, Domingues M, Sun X, Heazlewood CK, Li S, Williams B, Fulton M, White JF, Nebl T, Nefzger CM, Polo JM, Kile BT, Kraus F, Ryan MT, Sun YB, Choong PFM, Ellis SL, Anko ML, Nilsson SK. High ploidy large cytoplasmic megakaryocytes are hematopoietic stem cells regulators and essential for platelet production. Nat Commun 2023; 14:2099. [PMID: 37055407 PMCID: PMC10102126 DOI: 10.1038/s41467-023-37780-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
Megakaryocytes (MK) generate platelets. Recently, we and others, have reported MK also regulate hematopoietic stem cells (HSC). Here we show high ploidy large cytoplasmic megakaryocytes (LCM) are critical negative regulators of HSC and critical for platelet formation. Using a mouse knockout model (Pf4-Srsf3Δ/Δ) with normal MK numbers, but essentially devoid of LCM, we demonstrate a pronounced increase in BM HSC concurrent with endogenous mobilization and extramedullary hematopoiesis. Severe thrombocytopenia is observed in animals with diminished LCM, although there is no change in MK ploidy distribution, uncoupling endoreduplication and platelet production. When HSC isolated from a microenvironment essentially devoid of LCM reconstitute hematopoiesis in lethally irradiated mice, the absence of LCM increases HSC in BM, blood and spleen, and the recapitulation of thrombocytopenia. In contrast, following a competitive transplant using minimal numbers of WT HSC together with HSC from a microenvironment with diminished LCM, sufficient WT HSC-generated LCM regulates a normal HSC pool and prevents thrombocytopenia. Importantly, LCM are conserved in humans.
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Affiliation(s)
- Shen Y Heazlewood
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Tanveer Ahmad
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Benjamin Cao
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Huimin Cao
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Melanie Domingues
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Xuan Sun
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Chad K Heazlewood
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Songhui Li
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Brenda Williams
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Madeline Fulton
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
| | - Jacinta F White
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
| | - Tom Nebl
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia
| | - Christian M Nefzger
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Jose M Polo
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
- Monash Biomedicine Discovery Institute, Melbourne, VIC, Australia
| | - Benjamin T Kile
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Felix Kraus
- Monash Biomedicine Discovery Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Michael T Ryan
- Monash Biomedicine Discovery Institute, Melbourne, VIC, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Yu B Sun
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
- Monash Biomedicine Discovery Institute, Melbourne, VIC, Australia
| | - Peter F M Choong
- Department of Surgery, St. Vincent's Hospital, University of Melbourne, Melbourne, VIC, Australia
- Bone and Soft Tissue Sarcoma Service, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Department of Orthopaedics, St. Vincent's Hospital Melbourne, Melbourne, VIC, Australia
| | - Sarah L Ellis
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Minna-Liisa Anko
- Centre for Reproductive Health and Centre for Cancer Research, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Melbourne, VIC, Australia
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Susan K Nilsson
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia.
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC, Australia.
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10
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Herrera JA, Dingle LA, Monetero MA, Venkateswaran RV, Blaikley JF, Granato F, Pearson S, Lawless C, Thornton DJ. Morphologically intact airways in lung fibrosis have an abnormal proteome. Respir Res 2023; 24:99. [PMID: 37005656 PMCID: PMC10066954 DOI: 10.1186/s12931-023-02400-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/16/2023] [Indexed: 04/04/2023] Open
Abstract
Honeycombing is a histological pattern consistent with Usual Interstitial Pneumonia (UIP). Honeycombing refers to cystic airways located at sites of dense fibrosis with marked mucus accumulation. Utilizing laser capture microdissection coupled mass spectrometry (LCM-MS), we interrogated the fibrotic honeycomb airway cells and fibrotic uninvolved airway cells (distant from honeycomb airways and morphologically intact) in specimens from 10 patients with UIP. Non-fibrotic airway cell specimens from 6 patients served as controls. Furthermore, we performed LCM-MS on the mucus plugs found in 6 patients with UIP and 6 patients with mucinous adenocarcinoma. The mass spectrometry data were subject to both qualitative and quantitative analysis and validated by immunohistochemistry. Surprisingly, fibrotic uninvolved airway cells share a similar protein profile to honeycomb airway cells, showing deregulation of the slit and roundabout receptor (Slit and Robo) pathway as the strongest category. We find that (BPI) fold-containing family B member 1 (BPIFB1) is the most significantly increased secretome-associated protein in UIP, whereas Mucin-5AC (MUC5AC) is the most significantly increased in mucinous adenocarcinoma. We conclude that fibrotic uninvolved airway cells share pathological features with fibrotic honeycomb airway cells. In addition, fibrotic honeycomb airway cells are enriched in mucin biogenesis proteins with a marked derangement in proteins essential for ciliogenesis. This unbiased spatial proteomic approach generates novel and testable hypotheses to decipher fibrosis progression.
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Affiliation(s)
- Jeremy A Herrera
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK.
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK.
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Lewis A Dingle
- Blond McIndoe Laboratories, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - M Angeles Monetero
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Rajamiyer V Venkateswaran
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - John F Blaikley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Felice Granato
- Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Stella Pearson
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - Craig Lawless
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
| | - David J Thornton
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, Great Manchester, UK
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11
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Benegiamo G, von Alvensleben GV, Rodríguez-López S, Goeminne LJ, Bachmann AM, Morel JD, Broeckx E, Ma JY, Carreira V, Youssef SA, Azhar N, Reilly DF, D’Aquino K, Mullican S, Bou-Sleiman M, Auwerx J. The genetic background shapes the susceptibility to mitochondrial dysfunction and NASH progression. J Exp Med 2023; 220:213867. [PMID: 36787127 PMCID: PMC9960245 DOI: 10.1084/jem.20221738] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a global health concern without treatment. The challenge in finding effective therapies is due to the lack of good mouse models and the complexity of the disease, characterized by gene-environment interactions. We tested the susceptibility of seven mouse strains to develop NASH. The severity of the clinical phenotypes observed varied widely across strains. PWK/PhJ mice were the most prone to develop hepatic inflammation and the only strain to progress to NASH with extensive fibrosis, while CAST/EiJ mice were completely resistant. Levels of mitochondrial transcripts and proteins as well as mitochondrial function were robustly reduced specifically in the liver of PWK/PhJ mice, suggesting a central role of mitochondrial dysfunction in NASH progression. Importantly, the NASH gene expression profile of PWK/PhJ mice had the highest overlap with the human NASH signature. Our study exposes the limitations of using a single mouse genetic background in metabolic studies and describes a novel NASH mouse model with features of the human NASH.
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Affiliation(s)
- Giorgia Benegiamo
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland,Giorgia Benegiamo:
| | | | - Sandra Rodríguez-López
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Ludger J.E. Goeminne
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Alexis M. Bachmann
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Ellen Broeckx
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | - Jing Ying Ma
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | | | | | - Nabil Azhar
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | | | | | | | - Maroun Bou-Sleiman
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland,Correspondence to Johan Auwerx:
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12
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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13
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Cancer proteomics: Application of case studies in diverse cancers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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14
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Proteomics of the dentate gyrus reveals semantic dementia specific molecular pathology. Acta Neuropathol Commun 2022; 10:190. [PMID: 36578035 PMCID: PMC9795759 DOI: 10.1186/s40478-022-01499-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
Semantic dementia (SD) is a clinical subtype of frontotemporal dementia consistent with the neuropathological diagnosis frontotemporal lobar degeneration (FTLD) TDP type C, with characteristic round TDP-43 protein inclusions in the dentate gyrus. Despite this striking clinicopathological concordance, the pathogenic mechanisms are largely unexplained forestalling the development of targeted therapeutics. To address this, we carried out laser capture microdissection of the dentate gyrus of 15 SD patients and 17 non-demented controls, and assessed relative protein abundance changes by label-free quantitative mass spectrometry. To identify SD specific proteins, we compared our results to eight other FTLD and Alzheimer's disease (AD) proteomic datasets of cortical brain tissue, parallel with functional enrichment analyses and protein-protein interactions (PPI). Of the total 5,354 quantified proteins, 151 showed differential abundance in SD patients (adjusted P-value < 0.01). Seventy-nine proteins were considered potentially SD specific as these were not detected, or demonstrated insignificant or opposite change in FTLD/AD. Functional enrichment indicated an overrepresentation of pathways related to the immune response, metabolic processes, and cell-junction assembly. PPI analysis highlighted a cluster of interacting proteins associated with adherens junction and cadherin binding, the cadherin-catenin complex. Multiple proteins in this complex showed significant upregulation in SD, including β-catenin (CTNNB1), γ-catenin (JUP), and N-cadherin (CDH2), which were not observed in other neurodegenerative proteomic studies, and hence may resemble SD specific involvement. A trend of upregulation of all three proteins was observed by immunoblotting of whole hippocampus tissue, albeit only significant for N-cadherin. In summary, we discovered a specific increase of cell adhesion proteins in SD constituting the cadherin-catenin complex at the synaptic membrane, essential for synaptic signaling. Although further investigation and validation are warranted, we anticipate that these findings will help unravel the disease processes underlying SD.
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15
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Nasseri GG, Matin N, Wild AR, Tosefsky K, Flibotte S, Stacey RG, Hollman RB, Foster LJ, Bamji SX. Synaptic activity-dependent changes in the hippocampal palmitoylome. Sci Signal 2022; 15:eadd2519. [PMID: 36473050 DOI: 10.1126/scisignal.add2519] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dynamic protein S-palmitoylation is critical for neuronal function, development, and synaptic plasticity. Synaptic activity-dependent changes in palmitoylation have been reported for a small number of proteins. Here, we characterized the palmitoylome in the hippocampi of male mice before and after context-dependent fear conditioning. Of the 121 differentially palmitoylated proteins identified, just over half were synaptic proteins, whereas others were associated with metabolic functions, cytoskeletal organization, and signal transduction. The synapse-associated proteins generally exhibited increased palmitoylation after fear conditioning. In contrast, most of the proteins that exhibited decreased palmitoylation were associated with metabolic processes. Similar results were seen in cultured rat hippocampal neurons in response to chemically induced long-term potentiation. Furthermore, we found that the palmitoylation of one of the synaptic proteins, plasticity-related gene-1 (PRG-1), also known as lipid phosphate phosphatase-related protein type 4 (LPPR4), was important for synaptic activity-induced insertion of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) into the postsynaptic membrane. The findings identify proteins whose dynamic palmitoylation may regulate their role in synaptic plasticity, learning, and memory.
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Affiliation(s)
- Glory G Nasseri
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Nusrat Matin
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Angela R Wild
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kira Tosefsky
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Stephane Flibotte
- Life Sciences Institute Bioinformatics Facility, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - R Greg Stacey
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rocio B Hollman
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Shernaz X Bamji
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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16
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Zhang G, Mou Z, Wang H, Liu H. Comprehensive proteomic analysis of the main liver
and attached liver of <i>Glyptosternum maculatum</i> on the basis
of data-independent mass spectrometry acquisition. JOURNAL OF ANIMAL AND FEED SCIENCES 2022. [DOI: 10.22358/jafs/154070/2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Herrera JA, Dingle L, Montero MA, Venkateswaran RV, Blaikley JF, Lawless C, Schwartz MA. The UIP/IPF fibroblastic focus is a collagen biosynthesis factory embedded in a distinct extracellular matrix. JCI Insight 2022; 7:e156115. [PMID: 35852874 PMCID: PMC9462507 DOI: 10.1172/jci.insight.156115] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Usual interstitial pneumonia (UIP) is a histological pattern characteristic of idiopathic pulmonary fibrosis (IPF). The UIP pattern is patchy with histologically normal lung adjacent to dense fibrotic tissue. At this interface, fibroblastic foci (FF) are present and are sites where myofibroblasts and extracellular matrix (ECM) accumulate. Utilizing laser capture microdissection-coupled mass spectrometry, we interrogated the FF, adjacent mature scar, and adjacent alveoli in 6 fibrotic (UIP/IPF) specimens plus 6 nonfibrotic alveolar specimens as controls. The data were subjected to qualitative and quantitative analysis and histologically validated. We found that the fibrotic alveoli protein signature is defined by immune deregulation as the strongest category. The fibrotic mature scar classified as end-stage fibrosis whereas the FF contained an overabundance of a distinctive ECM compared with the nonfibrotic control. Furthermore, FF were positive for both TGFB1 and TGFB3, whereas the aberrant basaloid cell lining of FF was predominantly positive for TGFB2. In conclusion, spatial proteomics demonstrated distinct protein compositions in the histologically defined regions of UIP/IPF tissue. These data revealed that FF are the main site of collagen biosynthesis and that the adjacent alveoli are abnormal. This essential information will inform future mechanistic studies on fibrosis progression.
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Affiliation(s)
| | - Lewis Dingle
- Blond McIndoe Laboratories, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - M. Angeles Montero
- Department of Histopathology, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - Rajamiyer V. Venkateswaran
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Transplant, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | - John F. Blaikley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Transplant, Manchester University National Health Service Foundation Trust, Manchester, United Kingdom
| | | | - Martin A. Schwartz
- The Wellcome Centre for Cell-Matrix Research and
- Yale Cardiovascular Research Center and
- Departments of Internal Medicine (Cardiology) and Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Biomedical Engineering, Yale School of Engineering & Applied Science, New Haven, Connecticut, USA
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18
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Peng M, Wang Z, Sun X, Guo X, Wang H, Li R, Liu Q, Chen M, Chen X. Deep Learning-Based Label-Free Surface-Enhanced Raman Scattering Screening and Recognition of Small-Molecule Binding Sites in Proteins. Anal Chem 2022; 94:11483-11491. [PMID: 35968807 DOI: 10.1021/acs.analchem.2c01158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Identification of small-molecule binding sites in proteins is of great significance in analysis of protein function and drug design. Modified sites can be recognized via proteolytic cleavage followed by liquid chromatography-mass spectrometry (LC-MS); however, this has always been impeded by the complexity of peptide mixtures and the elaborate synthetic design for tags. Here, we demonstrate a novel technique for identifying protein binding sites using a deep learning-based label-free surface-enhanced Raman scattering (SERS) screening (DLSS) strategy. In DLSS, the deep learning model that was trained with large SERS signals could detect signal features of small molecules with high accuracy (>99%). Without any secondary tag, the small molecules are directly complexed with proteins. After proteolysis and LC, SERS signals of all LC fractions are collected and input into the model, whereby the fractions containing the small-molecule-modified peptides can be recognized by the model and sent to MS/MS to identify the binding site(s). By using an automated DLSS system, we successfully identified the modification sites of fomepizole in alcohol dehydrogenase, which is coordinated with zinc along with three peptides. We also showed that the DLSS strategy works for identification of amino-acid residues that covalently bond with ibrutinib in Bruton tyrosine kinase. These results suggest that the DLSS strategy, which provides high molecular recognition capability to LC-MS analysis, has potential in drug discovery, proteomics, and metabolomics.
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Affiliation(s)
- Mei Peng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Zi Wang
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Xiaotong Sun
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Xiangwei Guo
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Haoyang Wang
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Ruili Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Qi Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Miao Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.,School of Life Sciences, Central South University, Changsha 410013, China
| | - Xiaoqing Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
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Crook OM, Chung CW, Deane CM. Empirical Bayes functional models for hydrogen deuterium exchange mass spectrometry. Commun Biol 2022; 5:588. [PMID: 35705679 PMCID: PMC9200815 DOI: 10.1038/s42003-022-03517-3] [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: 11/04/2021] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a technique to explore differential protein structure by examining the rate of deuterium incorporation for specific peptides. This rate will be altered upon structural perturbation and detecting significant changes to this rate requires a statistical test. To determine rates of incorporation, HDX-MS measurements are frequently made over a time course. However, current statistical testing procedures ignore the correlations in the temporal dimension of the data. Using tools from functional data analysis, we develop a testing procedure that explicitly incorporates a model of hydrogen deuterium exchange. To further improve statistical power, we develop an empirical Bayes version of our method, allowing us to borrow information across peptides and stabilise variance estimates for low sample sizes. Our approach has increased power, reduces false positives and improves interpretation over linear model-based approaches. Due to the improved flexibility of our method, we can apply it to a multi-antibody epitope-mapping experiment where current approaches are inapplicable due insufficient flexibility. Hence, our approach allows HDX-MS to be applied in more experimental scenarios and reduces the burden on experimentalists to produce excessive replicates. Our approach is implemented in the R-package “hdxstats”: https://github.com/ococrook/hdxstats. A statistical analysis approach for HDX-MS time series data incorporates correlations in time, reducing false positives and improving statistical power and data interpretation.
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Affiliation(s)
- Oliver M Crook
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK.
| | - Chun-Wa Chung
- Structural and Biophysical Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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20
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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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21
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Impact of Maternal Feed Restriction at Different Stages of Gestation on the Proteomic Profile of the Newborn Skeletal Muscle. Animals (Basel) 2022; 12:ani12081011. [PMID: 35454257 PMCID: PMC9031497 DOI: 10.3390/ani12081011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
We aimed to investigate the effects of the maternal plane of nutrition during gestation on the proteome profile of the skeletal muscle of the newborn. Pregnant goats were assigned to the following experimental treatments: restriction maintenance (RM) where pregnant dams were fed at 50% of their maintenance requirements from 8−84 days of gestation, and then feed of 100% of the maintenance requirements was supplied from 85—parturition (n = 6); maintenance restriction (MR) where pregnant dams were fed at 100% of their maintenance requirements from 8−84 days of gestation, and then experienced feed restriction of 50% of the maintenance requirements from 85—parturition (n = 8). At birth, newborns were euthanized and samples of the Longissimus dorsi muscle were collected and used to perform HPLC-MS/MS analysis. The network analyses were performed to identify the biological processes and KEGG pathways of the proteins identified as differentially abundant protein and were deemed significant when the adjusted p-value (FDR) < 0.05. Our results suggest that treatment RM affects the energy metabolism of newborns’ skeletal muscle by changing the energy-investment phase of glycolysis, in addition to utilizing glycogen as a carbon source. Moreover, the RM plane of nutrition may contribute to fatty acid oxidation and increases in the cytosolic α-KG and mitochondrial NADH levels in the skeletal muscle of the newborn. On the other hand, treatment MR likely affects the energy-generation phase of glycolysis, contributing to the accumulation of mitochondrial α-KG and the biosynthesis of glutamine.
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22
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Desch K, Schuman EM, Langer JD. Quantifying phosphorylation dynamics in primary neuronal cultures using LC-MS/MS. STAR Protoc 2022; 3:101063. [PMID: 35005645 PMCID: PMC8715330 DOI: 10.1016/j.xpro.2021.101063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cellular processes require tight and coordinated control of protein abundance, localization, and activity. One of the core mechanisms to achieve specific regulation of proteins is protein phosphorylation. Here we present a workflow to monitor protein abundance and phosphorylation in primary cultured neurons using liquid chromatography-coupled mass spectrometry. Our protocol provides a detailed guide on all steps for detection and label-free-quantification of phosphorylated and unmodified proteins of primary cortical neurons, including primary cell culture, phosphoproteomic sample preparation and data-processing, and evaluation. For complete details on the use and execution of this protocol, please refer to Desch et al. (2021).
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Affiliation(s)
- Kristina Desch
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Erin M. Schuman
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Julian D. Langer
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
- Max Planck Institute of Biophysics, Max von Laue Strasse 3, 60438 Frankfurt, Germany
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23
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Chen Y, Huang C, Chen X, Cai Y, Li W, Fang X, Zhang W. Bone protein analysis via label-free quantitative proteomics in patients with periprosthetic joint infection. J Proteomics 2022; 252:104448. [PMID: 34883267 DOI: 10.1016/j.jprot.2021.104448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022]
Abstract
Periprosthetic joint infection (PJI) is a catastrophic complication of arthroplasty. The treatment of PJI often requires multiple operations and long-term use of antibiotics, making PJI a substantial health and economic burden for patients. Therefore, there is an urgent need to elucidate the pathological mechanism of PJI to explore new therapeutic methods. This study aimed to explore proteomics changes in bone tissue around the prosthesis during PJI development, to explain the pathological mechanism and to provide new treatment ideas. Ten patients who underwent revision surgery at our institution were included: 5 patients with Staphylococcus aureus PJI and 5 patients with aseptic failure. The proteomics changes in bone tissues after PJI were investigated by label-free quantitative proteomics, and the pathways affected by the differential proteins were analyzed by GO annotation, GO enrichment analysis, KEGG enrichment analysis and protein-protein interaction network analysis. We identified 435 differentially expressed proteins (DEPs), with 213 upregulated and 222 downregulated proteins. Analysis revealed activation of immune-related pathways, such as complement and coagulation cascades, phagocytosis, and neutrophil activation, and inhibition of energy metabolism pathways represented by the TCA cycle. We also observed an altered balance between osteoblasts and osteoclasts during S. aureus PJI. We hope that these processes will reveal new treatment ideas. SIGNIFICANCE: PJI is a catastrophic complication of arthroplasty. When infection occurs, bacteria may invade periprosthetic bone tissue to escape immunity and cause damage. So far, only few studies focused on the changes of proteomics associated to PJI. This is the first study to describe the proteomics changes of periprosthetic bone tissue of patients with PJI. We found that the pathological process of S. aureus PJI mainly involves activation of the immune system, decreased energy metabolism, and an altered balance of osteoblasts and osteoclasts.
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Affiliation(s)
- Yang Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Changyu Huang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoqing Chen
- Department of Orthopedic Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yuanqing Cai
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Wenbo Li
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xinyu Fang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
| | - Wenming Zhang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.
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24
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Souza MM, Coutinho-Camillo CM, de Paula FM, de Paula F, Bologna SB, Lourenço SV. Relevant proteins for the monitoring of engraftment phases after allogeneic hematopoietic stem cell transplantation. Clinics (Sao Paulo) 2022; 77:100134. [PMID: 36403426 PMCID: PMC9678684 DOI: 10.1016/j.clinsp.2022.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Hematopoietic Stem Cell Transplant (HSCT) has been successfully used as standard therapy for hematological disorders. After conditioning therapy, patients undergoing allogeneic HSCT, present three different phases of engraftment: early pre-engraftment, early post-engraftment, and late engraftment. Severe complications are associated with morbidity, mortality, and malignancies in these phases, which include effects on the oral cavity. OBJECTIVES The changes in the salivary composition after HSCT may contribute to identifying relevant proteins that could map differences among the phases of diseases, driven for personalized diagnostics and therapy. METHODS Unstimulated whole saliva was collected from patients submitted to HSCT. The samples were submitted to trypsin digestion for a Mass spectrometry analysis. MaxQuant processed the Data analysis, and the relevant expressed proteins were subjected to pathway and network analyses. RESULTS Differences were observed in the most identified proteins, specifically in proteins involved with the regulation of body fluid levels and the mucosal immune response. The heatmap showed a list of proteins exclusively expressed during the different phases of HSCT: HBB, KNG1, HSPA, FGB, APOA1, PFN1, PRTN3, TMSB4X, YWHAZ, CAP1, ACTN1, CLU and ALDOA. Bioinformatics analysis implicated pathways involved in protein processing in the endoplasmic reticulum, complement and coagulation cascades, apoptosis signaling, and cholesterol metabolism. CONCLUSION The compositional changes in saliva reflected the three phases of HSCT and demonstrated the usefulness of proteomics and computational approaches as a revolutionary field in diagnostic methods.
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Affiliation(s)
- Milena Monteiro Souza
- Department of Dermatology, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil; Department of General Pathology, Faculdade de Odontologia da Universidade de São Paulo, São Paulo, SP, Brazil; International Research Center, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Fabiana Martins de Paula
- Medical Research Laboratory, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fernanda de Paula
- Department of General Pathology, Faculdade de Odontologia da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Sheyla Batista Bologna
- Department of General Pathology, Faculdade de Odontologia da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Silvia Vanessa Lourenço
- Department of General Pathology, Faculdade de Odontologia da Universidade de São Paulo, São Paulo, SP, Brazil; Medical Research Laboratory, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
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25
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Proteomic analysis of temperature-dependent developmental plasticity within the ventricle of juvenile Atlantic salmon (Salmo salar). Curr Res Physiol 2022; 5:344-354. [PMID: 36035983 PMCID: PMC9403292 DOI: 10.1016/j.crphys.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/20/2022] Open
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26
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Zhu S, Yang C, Wu W. MSPoisDM: A Novel Peptide Identification Algorithm Optimized for Tandem Mass Spectra. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20225501003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Tandem mass spectrometry (MS/MS) plays an extremely important role in proteomics research. Thousands of spectra can be generated in modern experiments, how to interpret the LC-MS/MS is a challenging problem in tandem mass spectra analysis. Our peptide identification algorithm, MSPoisDM, is integrated the intensity information which produced by target-decoy statistics, although intensity information often undervalued. Furthermore, in order to combine the intensity information for better, we propose a novel concept scoring model which based on Poisson distribution. Compared with commonly used commercial software Mascot and Sequest at 1% FDR, the results show MSPoisDM is robust and versatile for various datasets which obtained from different instruments. We expect our algorithm MSPoisDM will be broadly applied in the proteomics studies.
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27
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Quast JP, Schuster D, Picotti P. protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data. BIOINFORMATICS ADVANCES 2021; 2:vbab041. [PMID: 36699412 PMCID: PMC9710675 DOI: 10.1093/bioadv/vbab041] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/28/2021] [Accepted: 12/06/2021] [Indexed: 01/28/2023]
Abstract
Summary We present a flexible, user-friendly R package called protti for comprehensive quality control, analysis and interpretation of quantitative bottom-up proteomics data. protti supports the analysis of protein-centric data such as those associated with protein expression analyses, as well as peptide-centric data such as those resulting from limited proteolysis-coupled mass spectrometry analysis. Due to its flexible design, it supports analysis of label-free, data-dependent, data-independent and targeted proteomics datasets. protti can be run on the output of any search engine and software package commonly used for bottom-up proteomics experiments such as Spectronaut, Skyline, MaxQuant or Proteome Discoverer, adequately exported to table format. Availability and implementation protti is implemented as an open-source R package. Release versions are available via CRAN (https://CRAN.R-project.org/package=protti) and work on all major operating systems. The development version is maintained on GitHub (https://github.com/jpquast/protti). Full documentation including examples is provided in the form of vignettes on our package website (jpquast.github.io/protti/).
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Affiliation(s)
- Jan-Philipp Quast
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Dina Schuster
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland,Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Paola Picotti
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland,To whom correspondence should be addressed.
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28
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Song Y, Jiang CY, Liang ZL, Zhu HZ, Jiang Y, Yin Y, Qin YL, Huang HJ, Wang BJ, Wei ZY, Cheng RX, Liu ZP, Liu Y, Jin T, Wang AJ, Liu SJ. Candidatus Kaistella beijingensis sp. nov., Isolated from a Municipal Wastewater Treatment Plant, Is Involved in Sludge Foaming. Appl Environ Microbiol 2021; 87:e0153421. [PMID: 34586909 PMCID: PMC8612268 DOI: 10.1128/aem.01534-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 12/30/2022] Open
Abstract
Biological foaming (or biofoaming) is a frequently occurring problem in wastewater treatment plants (WWTPs) and is attributed to the overwhelming growth of filamentous bulking and foaming bacteria (BFB). Biological foaming has been intensively investigated, with BFB like Microthrix and Skermania having been identified from WWTPs and implicated in foaming. Nevertheless, studies are still needed to improve our understanding of the microbial diversity of WWTP biofoams and how microbial activities contribute to foaming. In this study, sludge foaming at the Qinghe WWTP of China was monitored, and sludge foams were investigated using culture-dependent and culture-independent microbiological methods. The foam microbiomes exhibited high abundances of Skermania, Mycobacterium, Flavobacteriales, and Kaistella. A previously unknown bacterium, Candidatus Kaistella beijingensis, was cultivated from foams, its genome was sequenced, and it was phenotypically characterized. Ca. K. beijingensis exhibits hydrophobic cell surfaces, produces extracellular polymeric substances (EPS), and metabolizes lipids. Ca. K. beijingensis abundances were proportional to EPS levels in foams. Several proteins encoded by the Ca. K. beijingensis genome were identified from EPS that was extracted from sludge foams. Ca. K. beijingensis populations accounted for 4 to 6% of the total bacterial populations in sludge foam samples within the Qinghe WWTP, although their abundances were higher in spring than in other seasons. Cooccurrence analysis indicated that Ca. K. beijingensis was not a core node among the WWTP community network, but its abundances were negatively correlated with those of the well-studied BFB Skermania piniformis among cross-season Qinghe WWTP communities. IMPORTANCE Biological foaming, also known as scumming, is a sludge separation problem that has become the subject of major concern for long-term stable activated sludge operation in decades. Biological foaming was considered induced by foaming bacteria. However, the occurrence and deterioration of foaming in many WWTPs are still not completely understood. Cultivation and characterization of the enriched bacteria in foaming are critical to understand their genetic, physiological, phylogenetic, and ecological traits, as well as to improve the understanding of their relationships with foaming and performance of WWTPs.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- The Ecology and Environment Branch of State Center for Research and Development of Oil Shale Exploitation, PetroChina Planning and Engineering Institute, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, China
| | - Ye Yin
- BGI-Qingdao, Qingdao, China
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zi-Yan Wei
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rui-Xue Cheng
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, China
| | | | - Ai-Jie Wang
- CAS Key Laboratory of Environmental Biotechnology and RCEES-IMCAS-UCAS Joint Laboratory for Environmental Microbial Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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Zhang G, Mou Z, Xue W, Liu H. Phosphorylated protein modification analysis on normal liver and Exo-celiac liver of Glyptosternum maculatum. JOURNAL OF FISH BIOLOGY 2021; 99:1696-1707. [PMID: 34392541 DOI: 10.1111/jfb.14877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND This study aimed to reveal the biological function and molecular mechanism of phosphorylated proteins in the normal liver (NG) and Exo-celiac liver (WG) of Glyptosternum maculatum and potential plateau-adaption mechanisms of G. maculatum. METHODS A multivariate analysis was performed on proteomic quantitative data (label-free group) and phosphorylated proteome data (phosphorylation group) to reveal protein characteristics. The differentially expressed proteins (DEPs) between NG and WG in the two groups were analysed. Enrichment analysis of these DEPs was performed prior to the protein-protein interaction (PPI) analysis. Finally, an integrated interaction network was constructed to reveal the biological mechanism of the DEP-mediated signal transduction process. RESULT The NG and WG samples in the phosphorylation group were well distinguished compared to the label-free group. A total of 49 and 313 DEPs were identified in the label-free and phosphorylation groups, respectively. These DEPs, including LIM and calponin homology domains-containing protein 1 (LIMCH1) and DEAD(Asp-Glu-Ala-Asp)-Box Helicase 51 (DDX51), were mainly assembled in functions such as cell adhesion. Two PPI networks were constructed using DEPs in the two groups. Finally, an integrated interaction network was constructed using co-DEP Ferredoxin 1 (FDX1) and associated pathways, including RNA transport. CONCLUSION LIMCH1 and DDX51 might play important roles in the organogenesis of normal liver and Exo-celiac liver in G. maculatum via the cell adhesion function. Moreover, FXD1 might be associated with the plateau-adaption mechanisms of G. maculatum via participation in the RNA transport pathway.
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Affiliation(s)
- Guoqiang Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Zhenbo Mou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Wenhua Xue
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Haiping Liu
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
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30
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Fusco CM, Desch K, Dörrbaum AR, Wang M, Staab A, Chan ICW, Vail E, Villeri V, Langer JD, Schuman EM. Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins. Nat Commun 2021; 12:6127. [PMID: 34675203 PMCID: PMC8531293 DOI: 10.1038/s41467-021-26365-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs rapidly associated with translating ribosomes in the cytoplasm and that this incorporation was independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (following oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing neuronal synapses a rapid means to regulate local protein synthesis.
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Affiliation(s)
- Claudia M. Fusco
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Kristina Desch
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Aline R. Dörrbaum
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,Present Address: MOS, Center for Mass Spectrometry and Optical Spectroscopy, Mannheim, Germany
| | - Mantian Wang
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.508836.0Present Address: Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Anja Staab
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Ivy C. W. Chan
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.424247.30000 0004 0438 0426Present Address: German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Eleanor Vail
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Veronica Villeri
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.412041.20000 0001 2106 639XPresent Address: Department of Neuroscience, University of Bordeaux, Bordeaux, France
| | - Julian D. Langer
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.419494.50000 0001 1018 9466Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Erin M. Schuman
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
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Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021; 8:747333. [PMID: 34631760 PMCID: PMC8492935 DOI: 10.3389/fmed.2021.747333] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins. For example, cancer proteomics unraveled key information in mechanistic studies on tumor growth and metastasis, which has contributed to the identification of clinically applicable biomarkers as well as therapeutic targets. Several cancer proteome databases have been established and are being shared worldwide. Importantly, the integration of proteomics studies with other omics is providing extensive data related to molecular mechanisms and target modulators. These data may be analyzed and processed through bioinformatic pipelines to obtain useful information. The purpose of this review is to provide an overview of cancer proteomics and recent advances in proteomic techniques. In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage. This review covers applications of proteomics from the discovery of biomarkers to the characterization of molecular mechanisms through advances in technology. Moreover, it addresses global trends in proteomics approaches for translational research. As a core method in translational research, the continued development of this field is expected to provide valuable information at a scale beyond that previously seen.
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Affiliation(s)
- Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
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Zhang Y, Zhang Z, Chen Y. Biochar Mitigates N 2O Emission of Microbial Denitrification through Modulating Carbon Metabolism and Allocation of Reducing Power. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8068-8078. [PMID: 34029075 DOI: 10.1021/acs.est.1c01976] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To elucidate the direct effects of biochar on denitrification metabolism at the cellular level, the global response of model denitrifying soil bacterium (Paracoccus denitrificans) to biochar addition was investigated by physiological, proteomic, and metabolomics analyses. The enhancement effect on denitrification was positively correlated with its pyrolysis temperatures (300-500 °C) and dosages (0.1-1%), regardless of precursors [corn straw (CS) or wheat straw). Moreover, the stimulating effect of CS biochar made at 500 °C (CS-500) was mainly attributed to the bulk particles rather than the released soluble compounds. Without direct contact with cells, bulk CS-500 particles might directly modulate the carbon metabolism by the adsorption of extracellular metabolites. Since carbon flux to storage was shifted to oxidative catabolism and growth assimilation, more share of the produced reducing power was used for nitrogen reduction. Meanwhile, except for nitrate reductase, both protein expressions and enzyme activities of nitrite reductase, nitric oxide reductase, and nitrous oxide reductase were up-regulated. Accordingly, the accumulation of N2O was reduced by 98% due to the optimized electron distribution among denitrifying enzymes. Eventually, the growth rate of Pc. denitrificans enhanced because of the improved energy utilization efficiency. These results updated the regulation mechanism of biochar on denitrification metabolism and N2O mitigation.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Zhengzhe Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Chenery AL, Rosini S, Parkinson JE, Ajendra J, Herrera JA, Lawless C, Chan BHK, Loke P, MacDonald AS, Kadler KE, Sutherland TE, Allen JE. IL-13 deficiency exacerbates lung damage and impairs epithelial-derived type 2 molecules during nematode infection. Life Sci Alliance 2021; 4:4/8/e202001000. [PMID: 34127548 PMCID: PMC8321663 DOI: 10.26508/lsa.202001000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 02/06/2023] Open
Abstract
IL-13 is implicated in effective repair after acute lung injury and the pathogenesis of chronic diseases such as allergic asthma. Both these processes involve matrix remodelling, but understanding the specific contribution of IL-13 has been challenging because IL-13 shares receptors and signalling pathways with IL-4. Here, we used Nippostrongylus brasiliensis infection as a model of acute lung damage comparing responses between WT and IL-13-deficient mice, in which IL-4 signalling is intact. We found that IL-13 played a critical role in limiting tissue injury and haemorrhaging in the lung, and through proteomic and transcriptomic profiling, identified IL-13-dependent changes in matrix and associated regulators. We further showed a requirement for IL-13 in the induction of epithelial-derived type 2 effector molecules such as RELM-α and surfactant protein D. Pathway analyses predicted that IL-13 induced cellular stress responses and regulated lung epithelial cell differentiation by suppression of Foxa2 pathways. Thus, in the context of acute lung damage, IL-13 has tissue-protective functions and regulates epithelial cell responses during type 2 immunity.
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Affiliation(s)
- Alistair L Chenery
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK,Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Silvia Rosini
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK,Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - James E Parkinson
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK,Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Jesuthas Ajendra
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK,Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Jeremy A Herrera
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Brian HK Chan
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK,Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - P’ng Loke
- Department of Microbiology, NYU Langone Health, New York, NY, USA
| | - Andrew S MacDonald
- Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Karl E Kadler
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK,Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Tara E Sutherland
- Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Judith E Allen
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK .,Lydia Becker Institute for Immunology and Infection, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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Escobar EE, Venkat Ramani MK, Zhang Y, Brodbelt JS. Evaluating Spatiotemporal Dynamics of Phosphorylation of RNA Polymerase II Carboxy-Terminal Domain by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2021; 143:8488-8498. [PMID: 34053220 DOI: 10.1021/jacs.1c03321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The critical role of site-specific phosphorylation in eukaryotic transcription has motivated efforts to decipher the complex phosphorylation patterns exhibited by the carboxyl-terminal domain (CTD) of RNA polymerase II. Phosphorylation remains a challenging post-translational modification to characterize by mass spectrometry owing to the labile phosphate ester linkage and low stoichiometric prevalence, two features that complicate analysis by high-throughput MS/MS methods. Identifying phosphorylation sites represents one significant hurdle in decrypting the CTD phosphorylation, a problem exaggerated by a large number of potential phosphorylation sites. An even greater obstacle is decoding the dynamic phosphorylation pattern along the length of the periodic CTD sequence. Ultraviolet photodissociation (UVPD) is a high-energy ion activation method that provides ample backbone cleavages of peptides while preserving labile post-translational modifications that facilitate their confident localization. Herein, we report a quantitative parallel reaction monitoring (PRM) method developed to monitor spatiotemporal changes in site-specific Ser5 phosphorylation of the CTD by cyclin-dependent kinase 7 (CDK7) using UVPD for sequence identification, phosphosite localization, and differentiation of phosphopeptide isomers. We capitalize on the series of phospho-retaining fragment ions produced by UVPD to create unique transition lists that are pivotal for distinguishing the array of phosphopeptides generated from the CTD.
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35
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Hondius DC, Koopmans F, Leistner C, Pita-Illobre D, Peferoen-Baert RM, Marbus F, Paliukhovich I, Li KW, Rozemuller AJM, Hoozemans JJM, Smit AB. The proteome of granulovacuolar degeneration and neurofibrillary tangles in Alzheimer's disease. Acta Neuropathol 2021; 141:341-358. [PMID: 33492460 PMCID: PMC7882576 DOI: 10.1007/s00401-020-02261-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/12/2022]
Abstract
Granulovacuolar degeneration (GVD) is a common feature in Alzheimer's disease (AD). The occurrence of GVD is closely associated with that of neurofibrillary tangles (NFTs) and GVD is even considered to be a pre-NFT stage in the disease process of AD. Currently, the composition of GVD bodies, the mechanisms associated with GVD and how GVD exactly relates to NFTs is not well understood. By combining immunohistochemistry (IHC) and laser microdissection (LMD) we isolated neurons with GVD and those bearing tangles separately from human post-mortem AD hippocampus (n = 12) using their typical markers casein kinase (CK)1δ and phosphorylated tau (AT8). Control neurons were isolated from cognitively healthy cases (n = 12). 3000 neurons per sample were used for proteome analysis by label free LC-MS/MS. In total 2596 proteins were quantified across samples and a significant change in abundance of 115 proteins in GVD and 197 in tangle bearing neurons was observed compared to control neurons. With IHC the presence of PPIA, TOMM34, HSP70, CHMP1A, TPPP and VXN was confirmed in GVD containing neurons. We found multiple proteins localizing specifically to the GVD bodies, with VXN and TOMM34 being the most prominent new protein markers for GVD bodies. In general, protein groups related to protein folding, proteasomal function, the endolysosomal pathway, microtubule and cytoskeletal related function, RNA processing and glycolysis were found to be changed in GVD neurons. In addition to these protein groups, tangle bearing neurons show a decrease in ribosomal proteins, as well as in various proteins related to protein folding. This study, for the first time, provides a comprehensive human based quantitative assessment of protein abundances in GVD and tangle bearing neurons. In line with previous functional data showing that tau pathology induces GVD, our data support the model that GVD is part of a pre-NFT stage representing a phase in which proteostasis and cellular homeostasis is disrupted. Elucidating the molecular mechanisms and cellular processes affected in GVD and its relation to the presence of tau pathology is highly relevant for the identification of new drug targets for therapy.
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Affiliation(s)
- David C Hondius
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, PO Box 7057, Amsterdam, 1007 MB, The Netherlands.
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands.
| | - Frank Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands
| | - Conny Leistner
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands
| | - Débora Pita-Illobre
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands
| | - Regina M Peferoen-Baert
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, PO Box 7057, Amsterdam, 1007 MB, The Netherlands
| | - Fenna Marbus
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, PO Box 7057, Amsterdam, 1007 MB, The Netherlands
| | - Iryna Paliukhovich
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, PO Box 7057, Amsterdam, 1007 MB, The Netherlands
| | - Jeroen J M Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location VUmc, PO Box 7057, Amsterdam, 1007 MB, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands
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Dowell JA, Wright LJ, Armstrong EA, Denu JM. Benchmarking Quantitative Performance in Label-Free Proteomics. ACS OMEGA 2021; 6:2494-2504. [PMID: 33553868 PMCID: PMC7859943 DOI: 10.1021/acsomega.0c04030] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/11/2021] [Indexed: 05/07/2023]
Abstract
Previous benchmarking studies have demonstrated the importance of instrument acquisition methodology and statistical analysis on quantitative performance in label-free proteomics. However, the effects of these parameters in combination with replicate number and false discovery rate (FDR) corrections are not known. Using a benchmarking standard, we systematically evaluated the combined impact of acquisition methodology, replicate number, statistical approach, and FDR corrections. These analyses reveal a complex interaction between these parameters that greatly impacts the quantitative fidelity of protein- and peptide-level quantification. At a high replicate number (n = 8), both data-dependent acquisition (DDA) and data-independent acquisition (DIA) methodologies yield accurate protein quantification across statistical approaches. However, at a low replicate number (n = 4), only DIA in combination with linear models for microarrays (LIMMA) and reproducibility-optimized test statistic (ROTS) produced a high level of quantitative fidelity. Quantitative accuracy at low replicates is also greatly impacted by FDR corrections, with Benjamini-Hochberg and Storey corrections yielding variable true positive rates for DDA workflows. For peptide quantification, replicate number and acquisition methodology are even more critical. A higher number of replicates in combination with DIA and LIMMA produce high quantitative fidelity, while DDA performs poorly regardless of replicate number or statistical approach. These results underscore the importance of pairing instrument acquisition methodology with the appropriate replicate number and statistical approach for optimal quantification performance.
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Affiliation(s)
- James A. Dowell
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
| | - Logan J. Wright
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
| | - Eric A. Armstrong
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin−Madison, 420 Henry Mall Room 1135 Biochemistry Building, Madison, Wisconsin 53706, United States
- .
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37
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Abstract
Metadata is essential in proteomics data repositories and is crucial to interpret and reanalyze the deposited data sets. For every proteomics data set, we should capture at least three levels of metadata: (i) data set description, (ii) the sample to data files related information, and (iii) standard data file formats (e.g., mzIdentML, mzML, or mzTab). While the data set description and standard data file formats are supported by all ProteomeXchange partners, the information regarding the sample to data files is mostly missing. Recently, members of the European Bioinformatics Community for Mass Spectrometry (EuBIC) have created an open-source project called Sample to Data file format for Proteomics (https://github.com/bigbio/proteomics-metadata-standard/) to enable the standardization of sample metadata of public proteomics data sets. Here, the project is presented to the proteomics community, and we call for contributors, including researchers, journals, and consortiums to provide feedback about the format. We believe this work will improve reproducibility and facilitate the development of new tools dedicated to proteomics data analysis.
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Affiliation(s)
- Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
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38
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Schäpe SS, Krause JL, Masanetz RK, Riesbeck S, Starke R, Rolle-Kampczyk U, Eberlein C, Heipieper HJ, Herberth G, von Bergen M, Jehmlich N. Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx. Microorganisms 2020; 8:microorganisms8091436. [PMID: 32961728 PMCID: PMC7564734 DOI: 10.3390/microorganisms8091436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 11/29/2022] Open
Abstract
Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS. By determining biomass, growth of SIHUMIx was followed but no differences during BPS exposure were observed. To validate if the membrane composition was affected, fatty acid methyl esters (FAMEs) profiles were compared. Changes in the individual membrane fatty acid composition could not been described; however, the saturation level of the membranes slightly increased during BPS exposure. By applying targeted metabolomics to quantify short-chain fatty acids (SCFA), it was shown that the activity of SIHUMIx was unaffected. Metaproteomics revealed temporal effect on the community structure and function, showing that BPS has minor effects on the structure or functionality of SIHUMIx.
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Affiliation(s)
- Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Jannike Lea Krause
- Department of Environmental Immunology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (J.L.K.); (G.H.)
| | - Rebecca Katharina Masanetz
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Sarah Riesbeck
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (C.E.); (H.-J.H.)
| | - Hermann-Josef Heipieper
- Department of Environmental Biotechnology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (C.E.); (H.-J.H.)
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (J.L.K.); (G.H.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
- Correspondence: ; Tel.: +49-341-235-4767
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Schwämmle V, Hagensen CE, Rogowska-Wrzesinska A, Jensen ON. PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features. Mol Cell Proteomics 2020; 19:1396-1408. [PMID: 32424025 PMCID: PMC8015005 DOI: 10.1074/mcp.ra119.001777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/1919] [Revised: 04/18/2020] [Indexed: 12/11/2022] Open
Abstract
Statistical testing remains one of the main challenges for high-confidence detection of differentially regulated proteins or peptides in large-scale quantitative proteomics experiments by mass spectrometry. Statistical tests need to be sufficiently robust to deal with experiment intrinsic data structures and variations and often also reduced feature coverage across different biological samples due to ubiquitous missing values. A robust statistical test provides accurate confidence scores of large-scale proteomics results, regardless of instrument platform, experimental protocol and software tools. However, the multitude of different combinations of experimental strategies, mass spectrometry techniques and informatics methods complicate the decision of choosing appropriate statistical approaches. We address this challenge by introducing PolySTest, a user-friendly web service for statistical testing, data browsing and data visualization. We introduce a new method, Miss test, that simultaneously tests for missingness and feature abundance, thereby complementing common statistical tests by rescuing otherwise discarded data features. We demonstrate that PolySTest with integrated Miss test achieves higher confidence and higher sensitivity for artificial and experimental proteomics data sets with known ground truth. Application of PolySTest to mass spectrometry based large-scale proteomics data obtained from differentiating muscle cells resulted in the rescue of 10-20% additional proteins in the identified molecular networks relevant to muscle differentiation. We conclude that PolySTest is a valuable addition to existing tools and instrument enhancements that improve coverage and depth of large-scale proteomics experiments. A fully functional demo version of PolySTest and Miss test is available via http://computproteomics.bmb.sdu.dk/Apps/PolySTest.
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Affiliation(s)
- Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark.
| | - Christina E Hagensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark; VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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40
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Xinqiang S, Erqin D, Yu Z, Hongtao D, Lei W, Ningning Y. Potential mechanisms of action of celastrol against rheumatoid arthritis: Transcriptomic and proteomic analysis. PLoS One 2020; 15:e0233814. [PMID: 32726313 PMCID: PMC7390347 DOI: 10.1371/journal.pone.0233814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/06/2020] [Indexed: 12/25/2022] Open
Abstract
The clinical efficacy for treating of celastrol rheumatoid arthritis (RA) has been well-documented, but its mechanism of action remains unclear. Here we explored through what proteins and processes celastrol may act in activated fibroblast-like synoviocytes (FLS) from RA patients. Differential expression of genes and proteins after celastrol treatment of FLS was examined using RNA sequencing, label-free relatively quantitative proteomics and molecular docking. In this paper, expression of 26,565 genes and 3,372 proteins was analyzed. Celastrol was associated with significant changes in genes that respond to oxidative stress and oxygen levels, as well as genes that stabilize or synthesize components of the extracellular matrix. These results identify several potential mechanisms through which celastrol may inhibit inflammation in RA.
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MESH Headings
- Anti-Inflammatory Agents/pharmacology
- Anti-Inflammatory Agents/therapeutic use
- Arthritis, Rheumatoid/drug therapy
- Arthritis, Rheumatoid/genetics
- Arthritis, Rheumatoid/pathology
- Cells, Cultured
- Chromatography, Liquid
- Gene Expression Regulation/drug effects
- Gene Ontology
- High-Throughput Nucleotide Sequencing
- Humans
- Models, Molecular
- Molecular Docking Simulation
- Pentacyclic Triterpenes
- Proteomics/methods
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Spectrometry, Mass, Electrospray Ionization
- Synoviocytes/drug effects
- Synoviocytes/metabolism
- Tandem Mass Spectrometry
- Transcriptome/drug effects
- Triterpenes/pharmacology
- Triterpenes/therapeutic use
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Affiliation(s)
- Song Xinqiang
- Department of Biological Sciences, Xinyang Normal University, Xinyang, China
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, China
- * E-mail: (SX); (YN)
| | - Dai Erqin
- Department of Biological Sciences, Xinyang Normal University, Xinyang, China
| | - Zhang Yu
- Department of Biological Sciences, Xinyang Normal University, Xinyang, China
| | - Du Hongtao
- Department of Biological Sciences, Xinyang Normal University, Xinyang, China
| | - Wang Lei
- Department of Biological Sciences, Xinyang Normal University, Xinyang, China
| | - Yang Ningning
- Department of Biological Sciences, Xinyang Normal University, Xinyang, China
- * E-mail: (SX); (YN)
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Sticker A, Goeminne L, Martens L, Clement L. Robust Summarization and Inference in Proteome-wide Label-free Quantification. Mol Cell Proteomics 2020; 19:1209-1219. [PMID: 32321741 PMCID: PMC7338080 DOI: 10.1074/mcp.ra119.001624] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 04/20/2020] [Indexed: 12/27/2022] Open
Abstract
Label-Free Quantitative mass spectrometry based workflows for differential expression (DE) analysis of proteins impose important challenges on the data analysis because of peptide-specific effects and context dependent missingness of peptide intensities. Peptide-based workflows, like MSqRob, test for DE directly from peptide intensities and outperform summarization methods which first aggregate MS1 peptide intensities to protein intensities before DE analysis. However, these methods are computationally expensive, often hard to understand for the non-specialized end-user, and do not provide protein summaries, which are important for visualization or downstream processing. In this work, we therefore evaluate state-of-the-art summarization strategies using a benchmark spike-in dataset and discuss why and when these fail compared with the state-of-the-art peptide based model, MSqRob. Based on this evaluation, we propose a novel summarization strategy, MSqRobSum, which estimates MSqRob's model parameters in a two-stage procedure circumventing the drawbacks of peptide-based workflows. MSqRobSum maintains MSqRob's superior performance, while providing useful protein expression summaries for plotting and downstream analysis. Summarizing peptide to protein intensities considerably reduces the computational complexity, the memory footprint and the model complexity, and makes it easier to disseminate DE inferred on protein summaries. Moreover, MSqRobSum provides a highly modular analysis framework, which provides researchers with full flexibility to develop data analysis workflows tailored toward their specific applications.
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Affiliation(s)
- Adriaan Sticker
- Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Ludger Goeminne
- Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Belgium; VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science & Statistics, Ghent University, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
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Tarazona S, Balzano-Nogueira L, Gómez-Cabrero D, Schmidt A, Imhof A, Hankemeier T, Tegnér J, Westerhuis JA, Conesa A. Harmonization of quality metrics and power calculation in multi-omic studies. Nat Commun 2020; 11:3092. [PMID: 32555183 PMCID: PMC7303201 DOI: 10.1038/s41467-020-16937-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Multi-omic studies combine measurements at different molecular levels to build comprehensive models of cellular systems. The success of a multi-omic data analysis strategy depends largely on the adoption of adequate experimental designs, and on the quality of the measurements provided by the different omic platforms. However, the field lacks a comparative description of performance parameters across omic technologies and a formulation for experimental design in multi-omic data scenarios. Here, we propose a set of harmonized Figures of Merit (FoM) as quality descriptors applicable to different omic data types. Employing this information, we formulate the MultiPower method to estimate and assess the optimal sample size in a multi-omics experiment. MultiPower supports different experimental settings, data types and sample sizes, and includes graphical for experimental design decision-making. MultiPower is complemented with MultiML, an algorithm to estimate sample size for machine learning classification problems based on multi-omic data.
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Affiliation(s)
- Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia, Spain
| | - Leandro Balzano-Nogueira
- Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida, Gainesville, FL, USA
| | - David Gómez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
- Mucosal & Salivary Biology Division, King's College London Dental Institute, London, UK
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Andreas Schmidt
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Munich Center of Integrated Protein Science LMU Munich, Planegg-Martinsried, Germany
| | - Thomas Hankemeier
- Division Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
- Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Johan A Westerhuis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Department of Statistics, Faculty of Natural Sciences, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - Ana Conesa
- Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
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43
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Mallikarjun V, Richardson SM, Swift J. BayesENproteomics: Bayesian Elastic Nets for Quantification of Peptidoforms in Complex Samples. J Proteome Res 2020; 19:2167-2184. [PMID: 32319298 DOI: 10.1021/acs.jproteome.9b00468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Multivariate regression modelling provides a statistically powerful means of quantifying the effects of a given treatment while compensating for sources of variation and noise, such as variability between human donors and the behavior of different peptides during mass spectrometry. However, methods to quantify endogenous post-translational modifications (PTMs) are typically reliant on summary statistical methods that fail to consider sources of variability such as changes in the levels of the parent protein. Here, we compare three multivariate regression methods, including a novel Bayesian elastic net algorithm (BayesENproteomics) that enables assessment of relative protein abundances while also quantifying identified PTMs for each protein. We tested the ability of these methods to accurately quantify expression of proteins in a mixed-species benchmark experiment and to quantify synthetic PTMs induced by stable isotope labelling. Finally, we extended our regression pipeline to calculate fold changes at the pathway level, providing a complement to commonly used enrichment analysis. Our results show that BayesENproteomics can quantify changes to protein levels across a broad dynamic range while also accurately quantifying PTM and pathway-level fold changes.
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Affiliation(s)
- Venkatesh Mallikarjun
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Stephen M Richardson
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Joe Swift
- Wellcome Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, U.K.,Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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44
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Xiao Y, Huang S, Qiu F, Ding X, Sun Y, Wei C, Hu X, Wei K, Long S, Xie L, Xun Y, Chen W, Zhang Z, Liu N, Xiang S. Tumor necrosis factor α-induced protein 1 as a novel tumor suppressor through selective downregulation of CSNK2B blocks nuclear factor-κB activation in hepatocellular carcinoma. EBioMedicine 2020; 51:102603. [PMID: 31901862 PMCID: PMC6950786 DOI: 10.1016/j.ebiom.2019.102603] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
Background Tumor necrosis factor α-induced protein 1 (TNFAIP1) is frequently downregulated in cancer cell lines and promotes cancer cell apoptosis. However, its role, clinical significance and molecular mechanisms in hepatocellular carcinoma (HCC) are unknown. Methods The expression of TNFAIP1 in HCC tumor tissues and cell lines was measured by Western blot and immunohistochemistry. The effects of TNFAIP1 on HCC proliferation, apoptosis, metastasis, angiogenesis and tumor formation were evaluated by Cell Counting Kit-8 (CCK8), Terminal deoxynucleotidyl transferase dUTP Nick-End Labeling (TUNEL), transwell, tube formation assay in vitro and nude mice experiments in vivo. The interaction between TNFAIP1 and CSNK2B was validated by liquid chromatography-tandem mass spectrometry (LC-MS/MS), Co-immunoprecipitation and Western blot. The mechanism of how TNFAIP1 regulated nuclear factor-kappaB (NF-κB) pathway was analyzed by dual-luciferase reporter, immunofluorescence, quantitative Real-time polymerase chain reaction (RT-qPCR) and Western blot. Findings The TNFAIP1 expression is significantly decreased in HCC tissues and cell lines, and negatively correlated with the increased HCC histological grade. Overexpression of TNFAIP1 inhibits HCC cell proliferation, metastasis, angiogenesis and promotes cancer cell apoptosis both in vitro and in vivo, whereas the knockdown of TNFAIP1 in HCC cell displays opposite effects. Mechanistically, TNFAIP1 interacts with CSNK2B and promotes its ubiquitin-mediated degradation with Cul3, causing attenuation of CSNK2B-dependent NF-κB trans-activation in HCC cell. Moreover, the enforced expression of CSNK2B counteracts the inhibitory effects of TNFAIP1 on HCC cell proliferation, migration, and angiogenesis in vitro and in vivo. Interpretation Our results support that TNFAIP1 can act as a tumor suppressor of HCC by modulating TNFAIP1/CSNK2B/NF-κB pathway, implying that TNFAIP1 may represent a potential marker and a promising therapeutic target for HCC.
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Affiliation(s)
- Ye Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China; Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Shulan Huang
- Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Feng Qiu
- Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaofeng Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yi Sun
- Department of Pathology, Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Chenxi Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ke Wei
- Medical school, Hunan University of Traditional Chinese Medicine, Changsha, 410208, China
| | - Shengwen Long
- Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Lina Xie
- Department of Stomatology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Yu Xun
- Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Wen Chen
- Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Zhijian Zhang
- Department of Pathology, Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Ning Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China; Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, School of Medicine, Hunan Normal University, Changsha, 410013, China.
| | - Shuanglin Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Key Laboratory of Protein Chemistry and Development Biology of State Education Ministry of China, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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Matthiesen R, Carvalho AS. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. Methods Mol Biol 2020; 2051:161-197. [PMID: 31552629 DOI: 10.1007/978-1-4939-9744-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
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Affiliation(s)
- Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.
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46
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Yao K, Zhou QX, Liu DM, Chen SM, Yuan K. Comparative proteomics of the metabolic pathways involved in l-lactic acid production in Bacillus coagulans BCS13002 using different carbon sources. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108445] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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47
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Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019; 20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
Abstract
Yeasts are one of the mostly used microorganisms as models in several studies. A wide range of applications in different processes can be attributed to their intrinsic characteristics. They are eukaryotes and therefore valuable expression hosts that require elaborate post-translational modifications. Their arsenal of proteins has become a valuable biochemical tool for the catalysis of several reactions of great value to the food (beverages), pharmaceutical and energy industries. Currently, the main challenge in systemic yeast biology is the understanding of the expression, function and regulation of the protein pool encoded by such microorganisms. In this review, we will provide an overview of the proteomic methodologies used in the analysis of yeasts. This research focuses on the advantages and improvements in their most recent applications with an understanding of the functionality of the proteins of these microorganisms, as well as an update of the advances of methodologies employed in mass spectrometry.
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Affiliation(s)
- Maria Priscila F Lacerda
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Mônica Yonashiro Marcelino
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Natália M S Lourencetti
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Álvaro Baptista Neto
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | - Edwil A Gattas
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | | | - Ana Marisa Fusco-Almeida
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
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48
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He Y, Mohamedali A, Huang C, Baker MS, Nice EC. Oncoproteomics: Current status and future opportunities. Clin Chim Acta 2019; 495:611-624. [PMID: 31176645 DOI: 10.1016/j.cca.2019.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early clinical stage cancer detection, targeted molecular therapies, disease monitoring, and drug development. Such information will lead to new understandings of cancer biology and impact dramatically on the future care of cancer patients. In this review, we will summarize the advantages and limitations of the key technologies used in (onco)proteogenomics, (the Omics Pipeline), explain how they can assist us in understanding the biology behind the overarching "Hallmarks of Cancer", discuss how they can advance the development of precision/personalised medicine and the future directions in the field.
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Affiliation(s)
- Yujia He
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Canhua Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia.
| | - Edouard C Nice
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
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49
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Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma. Sci Rep 2019; 9:895. [PMID: 30696890 PMCID: PMC6351558 DOI: 10.1038/s41598-018-37273-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/30/2018] [Indexed: 11/30/2022] Open
Abstract
The prognosis of patients with relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL) remains unsatisfactory and, despite major advances in genomic studies, the biological mechanisms underlying chemoresistance are still poorly understood. We conducted for the first time a large-scale differential multi-omics investigation on DLBCL patient’s samples in order to identify new biomarkers that could early identify patients at risk of R/R disease and to identify new targets that could determine chemorefractoriness. We compared a well-characterized cohort of R/R versus chemosensitive DLBCL patients by combining label-free quantitative proteomics and targeted RNA sequencing performed on the same tissues samples. The cross-section of both data levels allowed extracting a sub-list of 22 transcripts/proteins pairs whose expression levels significantly differed between the two groups of patients. In particular, we identified significant targets related to tumor metabolism (Hexokinase 3), microenvironment (IDO1, CXCL13), cancer cells proliferation, migration and invasion (S100 proteins) or BCR signaling pathway (CD79B). Overall, this study revealed several extremely promising biomarker candidates related to DLBCL chemorefractoriness and highlighted some new potential therapeutic drug targets. The complete datasets have been made publically available and should constitute a valuable resource for the future research.
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50
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Guo W, Cheng J, Song Y, Kumar S, Ali KA, Guo C, Qiao Z. Developing a CO2 bicarbonation absorber for promoting microalgal growth rates with an improved photosynthesis pathway. RSC Adv 2019; 9:2746-2755. [PMID: 35520536 PMCID: PMC9059880 DOI: 10.1039/c8ra09538h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/02/2019] [Indexed: 12/16/2022] Open
Abstract
In order to solve the problems of the short residence time and low utilization efficiency of carbon dioxide (CO2) gas added directly to a raceway pond, a CO2 bicarbonation absorber (CBA) was proposed to efficiently convert CO2 gas and sodium carbonate (Na2CO3) solution to sodium bicarbonate (NaHCO3), which was dissolved easily in the culture medium and left to promote the microalgal growth rate. The CO2 gas reacted with the Na2CO3 solution (initial concentration = 200 mM L−1 and volume ratio in CBA = 60%) for 90 min at 0.3 MPa to give the optimized molar proportion (92%) of NaHCO3 product in total inorganic carbon and increase the microalgal growth rate by 5.0 times. Quantitative label-free protein analysis showed that the expression levels of the photosystem II (PSII) reaction centre protein (PsbH) and PSII cytochrome (PsbV2) in the photosynthesis pathway increased by 4.8 and 3.4 times, respectively, while that of the RuBisCO enzyme (rbcL) in the carbon fixation pathway increased by 3.5 times in Arthrospira platensis cells cultivated with the NaHCO3 product in the CBA at 0.3 MPa. To increase the residence time of CO2 gas added directly to the raceway pond, a CO2 bicarbonation absorber was proposed to convert CO2 gas and Na2CO3 to NaHCO3, which was dissolved easily in the solution and left to promote the biomass growth rate.![]()
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Affiliation(s)
- Wangbiao Guo
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Jun Cheng
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Yanmei Song
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Santosh Kumar
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Kubar Ameer Ali
- State Key Laboratory of Clean Energy Utilization
- Zhejiang University
- Hangzhou 310027
- China
| | - Caifeng Guo
- Ordos Jiali Spirulina Co., Ltd
- Ordos 016199
- China
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