151
|
Yan M, Zheng H, Yan R, Lang L, Wang Q, Xiao B, Zhang D, Lin H, Jia Y, Pan S, Chen Q. Vinculin Identified as a Potential Biomarker in Hand-Arm Vibration Syndrome Based on iTRAQ and LC-MS/MS-Based Proteomic Analysis. J Proteome Res 2023; 22:2714-2726. [PMID: 37437295 PMCID: PMC10408646 DOI: 10.1021/acs.jproteome.3c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Indexed: 07/14/2023]
Abstract
Local vibration can induce vascular injuries, one example is the hand-arm vibration syndrome (HAVS) caused by hand-transmitted vibration (HTV). Little is known about the molecular mechanism of HAVS-induced vascular injuries. Herein, the iTRAQ (isobaric tags for relative and absolute quantitation) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was applied to conduct the quantitative proteomic analysis of plasma from specimens with HTV exposure or HAVS diagnosis. Overall, 726 proteins were identified in iTRAQ. 37 proteins upregulated and 43 downregulated in HAVS. Moreover, 37 upregulated and 40 downregulated when comparing severe HAVS and mild HAVS. Among them, Vinculin (VCL) was found to be downregulated in the whole process of HAVS. The concentration of vinculin was further verified by ELISA, and the results suggested that the proteomics data was reliable. Bioinformative analyses were used, and those proteins mainly engaged in specific biological processes like binding, focal adhesion, and integrins. The potential of vinculin application in HAVS diagnosis was validated by the receiver operating characteristic curve.
Collapse
Affiliation(s)
- Maosheng Yan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Hanjun Zheng
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Rong Yan
- The
Centers for Disease Control and Prevention of Haizhu District, Guangzhou, Guangdong 510230, China
| | - Li Lang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Qia Wang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Bin Xiao
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Danying Zhang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Hansheng Lin
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Yanxia Jia
- Department
of Public Health, Shanxi Medical University, Tai Yuan, Shanxi 030000, China
| | - Siyu Pan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
| | - Qingsong Chen
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
| |
Collapse
|
152
|
Imbert B, Kreplak J, Flores RG, Aubert G, Burstin J, Tayeh N. Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes. Front Artif Intell 2023; 6:1191122. [PMID: 37601035 PMCID: PMC10435283 DOI: 10.3389/frai.2023.1191122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
Collapse
Affiliation(s)
- Baptiste Imbert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Raphaël-Gauthier Flores
- Université Paris-Saclay, INRAE, URGI, Versailles, France
- Université Paris-Saclay, INRAE, BioinfOmics, Plant Bioinformatics Facility, Versailles, France
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| |
Collapse
|
153
|
Mark KG, Kolla S, Aguirre JD, Garshott DM, Schmitt S, Haakonsen DL, Xu C, Kater L, Kempf G, Martínez-González B, Akopian D, See SK, Thomä NH, Rapé M. Orphan quality control shapes network dynamics and gene expression. Cell 2023; 186:3460-3475.e23. [PMID: 37478862 DOI: 10.1016/j.cell.2023.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/13/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-Myc oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over unpaired transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers opportunities to modulate gene expression in disease.
Collapse
Affiliation(s)
- Kevin G Mark
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - SriDurgaDevi Kolla
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Danielle M Garshott
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Christina Xu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stephanie K See
- Center for Emerging and Neglected Diseases, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
154
|
Osickova A, Knoblochova S, Bumba L, Man P, Kalaninova Z, Lepesheva A, Jurnecka D, Cizkova M, Biedermannova L, Goldsmith JA, Maynard JA, McLellan JS, Osicka R, Sebo P, Masin J. A conserved tryptophan in the acylated segment of RTX toxins controls their β 2 integrin-independent cell penetration. J Biol Chem 2023; 299:104978. [PMID: 37390987 PMCID: PMC10392135 DOI: 10.1016/j.jbc.2023.104978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
The acylated Repeats in ToXins (RTX) leukotoxins, the adenylate cyclase toxin (CyaA) or α-hemolysin (HlyA), bind β2 integrins of leukocytes but also penetrate cells lacking these receptors. We show that the indoles of conserved tryptophans in the acylated segments, W876 of CyaA and W579 of HlyA, are crucial for β2 integrin-independent membrane penetration. Substitutions of W876 by aliphatic or aromatic residues did not affect acylation, folding, or the activities of CyaA W876L/F/Y variants on cells expressing high amounts of the β2 integrin CR3. However, toxin activity of CyaA W876L/F/Y on cells lacking CR3 was strongly impaired. Similarly, a W579L substitution selectively reduced HlyA W579L cytotoxicity towards cells lacking β2 integrins. Intriguingly, the W876L/F/Y substitutions increased the thermal stability (Tm) of CyaA by 4 to 8 °C but locally enhanced the accessibility to deuteration of the hydrophobic segment and of the interface of the two acylated loops. W876Q substitution (showing no increase in Tm), or combination of W876F with a cavity-filling V822M substitution (this combination decreasing the Tm closer to that of CyaA), yielded a milder defect of toxin activity on erythrocytes lacking CR3. Furthermore, the activity of CyaA on erythrocytes was also selectively impaired when the interaction of the pyrrolidine of P848 with the indole of W876 was ablated. Hence, the bulky indoles of residues W876 of CyaA, or W579 of HlyA, rule the local positioning of the acylated loops and enable a membrane-penetrating conformation in the absence of RTX toxin docking onto the cell membrane by β2 integrins.
Collapse
Affiliation(s)
- Adriana Osickova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sarka Knoblochova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Kalaninova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Anna Lepesheva
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic; Faculty of Sciences, Charles University, Prague, Czech Republic
| | - David Jurnecka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Monika Cizkova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lada Biedermannova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, USA
| | - Jennifer A Maynard
- Department of Chemical Engineering, The University of Texas at Austin, Austin, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, USA
| | - Radim Osicka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Jiri Masin
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| |
Collapse
|
155
|
Gu L, Li X, Zhu W, Shen Y, Wang Q, Liu W, Zhang J, Zhang H, Li J, Li Z, Liu Z, Li C, Wang H. Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition. J Pharm Anal 2023; 13:942-954. [PMID: 37719194 PMCID: PMC10499587 DOI: 10.1016/j.jpha.2023.05.003] [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: 12/29/2022] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 09/19/2023] Open
Abstract
Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development. However, the single-cell or low-input proteomic research in this field is relatively underdeveloped because of the higher threshold of the starting material for mammalian embryo samples and the lack of hypersensitive proteome technology. In this study, a comprehensive solution of ultrasensitive proteome technology (CS-UPT) was developed for single-cell or low-input mouse oocyte/embryo samples. The deep coverage and high-throughput routes significantly reduced the starting material and were selected by investigators based on their demands. Using the deep coverage route, we provided the first large-scale snapshot of the very early stage of mouse maternal-to-zygotic transition, including almost 5,500 protein groups from 20 mouse oocytes or zygotes for each sample. Moreover, significant protein regulatory networks centered on transcription factors and kinases between the MII oocyte and 1-cell embryo provided rich insights into minor zygotic genome activation.
Collapse
Affiliation(s)
- Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xumiao Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wencheng Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Yi Shen
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenjun Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Junfeng Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Huiping Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziyi Li
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| |
Collapse
|
156
|
Xia W, Wang Q, Lin S, Wang Y, Zhang J, Wang H, Yang X, Hu Y, Liang H, Lu Y, Zhu Z, Liu D. A high-salt diet promotes hypertrophic scarring through TRPC3-mediated mitochondrial Ca 2+ homeostasis dysfunction. Heliyon 2023; 9:e18629. [PMID: 37588604 PMCID: PMC10425910 DOI: 10.1016/j.heliyon.2023.e18629] [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: 05/23/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Diet High in salt content have been associated with cardiovascular disease and chronic inflammation. We recently demonstrated that transient receptor potential canonical 3 (TRPC3) channels regulate myofibroblast transdifferentiation in hypertrophic scars. Here, we examined how high salt activation of TRPC3 participates in hypertrophic scarring during wound healing. In vitro, we confirmed that high salt increased the TRPC3 protein expression and the marker of myofibroblast alpha smooth muscle actin (α-SMA) in wild-type mice (WT) primary cultured dermal fibroblasts but not Trpc3-/- mice. Activation of TRPC3 by high salt elevated cytosolic Ca2+ influx and mitochondrial Ca2+ uptake in dermal fibroblasts in a TRPC3-dependent manner. High salt activation of TRPC3 enhanced mitochondrial respiratory dysfunction and excessive ROS production by inhibiting pyruvate dehydrogenase action, that activated ROS-triggered Ca2+ influx and the Rho kinase/MLC pathway in WT mice but not Trpc3-/- mice. In vivo, a persistent high-salt diet promoted myofibroblast transdifferentiation and collagen deposition in a TRPC3-dependent manner. Therefore, this study demonstrates that high salt enhances myofibroblast transdifferentiation and promotes hypertrophic scar formation through enhanced mitochondrial Ca2+ homeostasis, which activates the ROS-mediated pMLC/pMYPT1 pathway. TRPC3 deficiency antagonizes high salt diet-induced hypertrophic scarring. TRPC3 may be a novel target for hypertrophic scarring during wound healing.
Collapse
Affiliation(s)
- Weijie Xia
- Department of Plastic & Cosmetic Surgery, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Qianran Wang
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Shaoyang Lin
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Yuanyuan Wang
- Department of Plastic & Cosmetic Surgery, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Junbo Zhang
- Department of Plastic & Cosmetic Surgery, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Hailin Wang
- Department of Plastic & Cosmetic Surgery, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Xia Yang
- Department of Wound Infection and Drug, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Yingru Hu
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Huaping Liang
- Department of Wound Infection and Drug, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Yuangang Lu
- Department of Plastic & Cosmetic Surgery, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Zhiming Zhu
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Daoyan Liu
- Department of Hypertension and Endocrinology, Center for Hypertension and Metabolic Diseases, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
- Department of Wound Infection and Drug, State Key Laboratory of Trauma, Burn and Combined Injury, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| |
Collapse
|
157
|
Bowler-Barnett EH, Fan J, Luo J, Magrane M, Martin MJ, Orchard S. UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship. Mol Cell Proteomics 2023; 22:100591. [PMID: 37301379 PMCID: PMC10404557 DOI: 10.1016/j.mcpro.2023.100591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/20/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023] Open
Abstract
The human proteome comprises of all of the proteins produced by the sequences translated from the human genome with additional modifications in both sequence and function caused by nonsynonymous variants and posttranslational modifications including cleavage of the initial transcript into smaller peptides and polypeptides. The UniProtKB database (www.uniprot.org) is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information and presents a summary of experimentally verified, or computationally predicted, functional information added by our expert biocuration team for each protein in the proteome. Researchers in the field of mass spectrometry-based proteomics both consume and add to the body of data available in UniProtKB, and this review highlights the information we provide to this community and the knowledge we in turn obtain from groups via deposition of large-scale datasets in public domain databases.
Collapse
Affiliation(s)
- E H Bowler-Barnett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - J Fan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - J Luo
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - M Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - M J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - S Orchard
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom.
| |
Collapse
|
158
|
McCormick LE, Suarez C, Herring LE, Cannon KS, Kovar DR, Brown NG, Gupton SL. Multi-monoubiquitination controls VASP-mediated actin dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.16.549237. [PMID: 37503134 PMCID: PMC10370145 DOI: 10.1101/2023.07.16.549237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The actin cytoskeleton performs multiple cellular functions, and as such, actin polymerization must be tightly regulated. We previously demonstrated that reversible, non-degradative ubiquitination regulates the function of the actin polymerase VASP in developing neurons. However, the underlying mechanism of how ubiquitination impacts VASP activity was unknown. Here we show that mimicking multi-monoubiquitination of VASP at K240 and K286 negatively regulates VASP interactions with actin. Using in vitro biochemical assays, we demonstrate the reduced ability of multi-monoubiquitinated VASP to bind, bundle, and elongate actin filaments. However, multi-monoubiquitinated VASP maintained the ability to bind and protect barbed ends from capping protein. Lastly, we demonstrate the introduction of recombinant multi-monoubiquitinated VASP protein altered cell spreading morphology. Collectively, these results suggest a mechanism in which ubiquitination controls VASP-mediated actin dynamics.
Collapse
Affiliation(s)
- Laura E McCormick
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Cristian Suarez
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Laura E Herring
- Michael Hooker Proteomics Core, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kevin S Cannon
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - David R Kovar
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Nicholas G Brown
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Stephanie L Gupton
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| |
Collapse
|
159
|
Sartorio MG, Pardue EJ, Scott NE, Feldman MF. Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans. Proc Natl Acad Sci U S A 2023; 120:e2306314120. [PMID: 37364113 PMCID: PMC10319031 DOI: 10.1073/pnas.2306314120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Extracellular vesicles are produced in all three domains of life, and their biogenesis has common ancient origins in eukaryotes and archaea. Although bacterial vesicles were discovered several decades ago and multiple roles have been attributed to them, no mechanism has been established for vesicles biogenesis in bacteria. For this reason, there is a significant level of skepticism about the biological relevance of bacterial vesicles. Bacteroides thetaiotaomicron (Bt), a prominent member of the human intestinal microbiota, produces significant amounts of outer membrane vesicles (OMVs) which have been proposed to play key physiological roles. Here, we employed a dual marker system, consisting of outer membrane- and OMV-specific markers fused to fluorescent proteins to visualize OMV biogenesis by time-lapse microscopy. Furthermore, we performed comparative proteomic analyses to show that, in Bt, the OMV cargo is adapted for the optimal utilization of different polysaccharides. We also show that a negatively charged N-terminal motif acts as a signal for protein sorting into OMVs irrespective of the nutrient availability. Our results demonstrate that OMV production is the result of a highly regulated process in Bt.
Collapse
Affiliation(s)
- Mariana G. Sartorio
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Evan J. Pardue
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC3000, Australia
| | - Mario F. Feldman
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO63110
| |
Collapse
|
160
|
Hammer L, Moretti D, Abbühl-Eng L, Kandiah P, Hilaj N, Portmann R, Egger L. Mealworm larvae ( Tenebrio molitor) and crickets ( Acheta domesticus) show high total protein in vitro digestibility and can provide good-to-excellent protein quality as determined by in vitro DIAAS. Front Nutr 2023; 10:1150581. [PMID: 37465141 PMCID: PMC10350632 DOI: 10.3389/fnut.2023.1150581] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
Edible insects, such as mealworms (Tenebrio molitor larvae; TM) and crickets (Acheta domesticus; AD), are a sustainable, protein-dense novel food with a favorable amino acid profile, which might be an alternative to animal proteins. To assess the protein quality of TM and AD, we assessed the digestible indispensable amino acid scores (DIAAS), considering individual amino acids and their ileal amino acid digestibility, using an in vitro model based on the INFOGEST digestion protocol. In addition, we evaluated if various processing and food preparation steps influenced the in vitro digestibility of individual amino acids and the in vitro DIAAS values of TM and AD and compared them to chicken breast as a reference of excellent protein quality. The total protein in vitro digestibility ranged from 91 to 99% for TM and from 79 to 93% for AD and was negatively affected by oven-drying and, to a lesser extent, by chitin-reduction. The in vitro DIAAS values were 113, 89, and 92 for chicken, blanched TM, and blanched AD, respectively, when considering the indispensable amino acid (IAA) requirements of young children between 6 months and 3 years. Across different processing and food preparation methods, the in vitro DIAAS values ranged between 59 and 89 for TM and between 40 and 92 for AD, with the lowest values found in chitin-reduced insects. Due to their similarities to chicken regarding protein composition, total protein in vitro digestibility, and in vitro DIAAS values, TM and AD might be an alternative to traditional animal proteins, provided that suitable processing and food preparation methods are applied. Our in vitro DIAAS results suggest that TM and AD can thus be considered good-quality protein sources for children older than 6 months. The DIAAS calculations are currently based on crude protein (total nitrogen × 6.25), resulting in an overestimation of insect protein content, and leading to an underestimation and potential misclassification of protein quality. The in vitro model applied in this study is a valuable tool for product development to optimize the protein quality of edible insects. Further studies are required to assess the in vivo DIAAS of insects in humans.
Collapse
Affiliation(s)
- Laila Hammer
- Agroscope Liebefeld-Posieux, Berne, Switzerland
- Department of Health, Swiss Distant University of Applied Sciences (FFHS), Brig, Switzerland
- Division of Human Nutrition, Wageningen University & Research, Wageningen, Netherlands
| | - Diego Moretti
- Department of Health, Swiss Distant University of Applied Sciences (FFHS), Brig, Switzerland
| | | | | | - Nikolin Hilaj
- Department of Health Sciences and Technology, Human Nutrition Laboratory, ETH Zurich, Zurich, Switzerland
| | | | - Lotti Egger
- Agroscope Liebefeld-Posieux, Berne, Switzerland
| |
Collapse
|
161
|
Brand C, Deschamps-Francoeur G, Bullard-Feibelman KM, Scott MS, Geiss BJ, Bisaillon M. Kunjin Virus, Zika Virus, and Yellow Fever Virus Infections Have Distinct Effects on the Coding Transcriptome and Proteome of Brain-Derived U87 Cells. Viruses 2023; 15:1419. [PMID: 37515107 PMCID: PMC10385720 DOI: 10.3390/v15071419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
As obligate intracellular parasites, viruses rely heavily on host cells for replication, and therefore dysregulate several cellular processes for their benefit. In return, host cells activate multiple signaling pathways to limit viral replication and eradicate viruses. The present study explores the complex interplay between viruses and host cells through next generation RNA sequencing as well as mass spectrometry (SILAC). Both the coding transcriptome and the proteome of human brain-derived U87 cells infected with Kunjin virus, Zika virus, or Yellow Fever virus were compared to the transcriptome and the proteome of mock-infected cells. Changes in the abundance of several hundred mRNAs and proteins were found in each infection. Moreover, the alternative splicing of hundreds of mRNAs was found to be modulated upon viral infection. Interestingly, a significant disconnect between the changes in the transcriptome and those in the proteome of infected cells was observed. These findings provide a global view of the coding transcriptome and the proteome of Flavivirus-infected cells, leading to a better comprehension of Flavivirus-host interactions.
Collapse
Affiliation(s)
- Carolin Brand
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Kristen M Bullard-Feibelman
- Department of Microbiology, Immunology, and Pathology, School of Biomedical Engineering, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | - Michelle S Scott
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Brian J Geiss
- Department of Microbiology, Immunology, and Pathology, School of Biomedical Engineering, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | - Martin Bisaillon
- Département de Biochimie et de Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
| |
Collapse
|
162
|
Man JHK, van Gelder CAGH, Breur M, Molenaar D, Abbink T, Altelaar M, Bugiani M, van der Knaap MS. Regional vulnerability of brain white matter in vanishing white matter. Acta Neuropathol Commun 2023; 11:103. [PMID: 37349783 PMCID: PMC10286497 DOI: 10.1186/s40478-023-01599-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/03/2023] [Indexed: 06/24/2023] Open
Abstract
Vanishing white matter (VWM) is a leukodystrophy that primarily manifests in young children. In this disease, the brain white matter is differentially affected in a predictable pattern with telencephalic brain areas being most severely affected, while others remain allegedly completely spared. Using high-resolution mass spectrometry-based proteomics, we investigated the proteome patterns of the white matter in the severely affected frontal lobe and normal appearing pons in VWM and control cases to identify molecular bases underlying regional vulnerability. By comparing VWM patients to controls, we identified disease-specific proteome patterns. We showed substantial changes in both the VWM frontal and pons white matter at the protein level. Side-by-side comparison of brain region-specific proteome patterns further revealed regional differences. We found that different cell types were affected in the VWM frontal white matter than in the pons. Gene ontology and pathway analyses identified involvement of region specific biological processes, of which pathways involved in cellular respiratory metabolism were overarching features. In the VWM frontal white matter, proteins involved in glycolysis/gluconeogenesis and metabolism of various amino acids were decreased compared to controls. By contrast, in the VWM pons white matter, we found a decrease in proteins involved in oxidative phosphorylation. Taken together, our data show that brain regions are affected in parallel in VWM, but to different degrees. We found region-specific involvement of different cell types and discovered that cellular respiratory metabolism is likely to be differentially affected across white matter regions in VWM. These region-specific changes help explain regional vulnerability to pathology in VWM.
Collapse
Affiliation(s)
- Jodie H K Man
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, 1081 HV, The Netherlands
- Molecular and Cellular Mechanisms, Amsterdam Neuroscience, Amsterdam, 1081 HV, The Netherlands
| | - Charlotte A G H van Gelder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CS, The Netherlands
- Netherlands Proteomics Center, Utrecht, 3584 CS, The Netherlands
| | - Marjolein Breur
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, 1081 HV, The Netherlands
- Molecular and Cellular Mechanisms, Amsterdam Neuroscience, Amsterdam, 1081 HV, The Netherlands
| | - Douwe Molenaar
- Department of Systems Bioinformatics, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
| | - Truus Abbink
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, 1081 HV, The Netherlands
- Molecular and Cellular Mechanisms, Amsterdam Neuroscience, Amsterdam, 1081 HV, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, 3584 CS, The Netherlands
- Netherlands Proteomics Center, Utrecht, 3584 CS, The Netherlands
| | - Marianna Bugiani
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, 1081 HV, The Netherlands.
- Molecular and Cellular Mechanisms, Amsterdam Neuroscience, Amsterdam, 1081 HV, The Netherlands.
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, 1081 HV, The Netherlands.
| | - Marjo S van der Knaap
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
- Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, 1081 HV, The Netherlands
- Molecular and Cellular Mechanisms, Amsterdam Neuroscience, Amsterdam, 1081 HV, The Netherlands
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, 1081 HV, The Netherlands
| |
Collapse
|
163
|
Mohanty T, Karlsson CAQ, Chao Y, Malmström E, Bratanis E, Grentzmann A, Mørch M, Nizet V, Malmström L, Linder A, Shannon O, Malmström J. A pharmacoproteomic landscape of organotypic intervention responses in Gram-negative sepsis. Nat Commun 2023; 14:3603. [PMID: 37330510 PMCID: PMC10276868 DOI: 10.1038/s41467-023-39269-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/02/2023] [Indexed: 06/19/2023] Open
Abstract
Sepsis is the major cause of mortality across intensive care units globally, yet details of accompanying pathological molecular events remain unclear. This knowledge gap has resulted in ineffective biomarker development and suboptimal treatment regimens to prevent and manage organ dysfunction/damage. Here, we used pharmacoproteomics to score time-dependent treatment impact in a murine Escherichia coli sepsis model after administering beta-lactam antibiotic meropenem (Mem) and/or the immunomodulatory glucocorticoid methylprednisolone (Gcc). Three distinct proteome response patterns were identified, which depended on the underlying proteotype for each organ. Gcc enhanced some positive proteome responses of Mem, including superior reduction of the inflammatory response in kidneys and partial restoration of sepsis-induced metabolic dysfunction. Mem introduced sepsis-independent perturbations in the mitochondrial proteome that Gcc counteracted. We provide a strategy for the quantitative and organotypic assessment of treatment effects of candidate therapies in relationship to dosing, timing, and potential synergistic intervention combinations during sepsis.
Collapse
Affiliation(s)
- Tirthankar Mohanty
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Christofer A Q Karlsson
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Yashuan Chao
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Erik Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
- Emergency Medicine, Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - Eleni Bratanis
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Andrietta Grentzmann
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Martina Mørch
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Victor Nizet
- Department of Pediatrics, Division of Host-Microbe Systems and Therapeutics, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Lars Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Adam Linder
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden
| | - Oonagh Shannon
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden.
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund, Lund University, SE-22184, Lund, Sweden.
| |
Collapse
|
164
|
Yang X, Jiang Z, He J, Shen L. iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions. Life (Basel) 2023; 13:1399. [PMID: 37374181 DOI: 10.3390/life13061399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.
Collapse
Affiliation(s)
- Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jie He
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
165
|
van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW. Mapping the Arabidopsis thaliana proteome in PeptideAtlas and the nature of the unobserved (dark) proteome; strategies towards a complete proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543322. [PMID: 37333403 PMCID: PMC10274743 DOI: 10.1101/2023.06.01.543322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
This study describes a new release of the Arabidopsis thaliana PeptideAtlas proteomics resource providing protein sequence coverage, matched mass spectrometry (MS) spectra, selected PTMs, and metadata. 70 million MS/MS spectra were matched to the Araport11 annotation, identifying ∼0.6 million unique peptides and 18267 proteins at the highest confidence level and 3396 lower confidence proteins, together representing 78.6% of the predicted proteome. Additional identified proteins not predicted in Araport11 should be considered for building the next Arabidopsis genome annotation. This release identified 5198 phosphorylated proteins, 668 ubiquitinated proteins, 3050 N-terminally acetylated proteins and 864 lysine-acetylated proteins and mapped their PTM sites. MS support was lacking for 21.4% (5896 proteins) of the predicted Araport11 proteome - the 'dark' proteome. This dark proteome is highly enriched for certain ( e.g. CLE, CEP, IDA, PSY) but not other ( e.g. THIONIN, CAP,) signaling peptides families, E3 ligases, TFs, and other proteins with unfavorable physicochemical properties. A machine learning model trained on RNA expression data and protein properties predicts the probability for proteins to be detected. The model aids in discovery of proteins with short-half life ( e.g. SIG1,3 and ERF-VII TFs) and completing the proteome. PeptideAtlas is linked to TAIR, JBrowse, PPDB, SUBA, UniProtKB and Plant PTM Viewer.
Collapse
|
166
|
Rešetar Maslov D, Thomas FC, Beletić A, Kuleš J, Rubić I, Benić M, Bačić G, Maćešić N, Eraghi V, Farkaš V, Lenac Roviš T, Lisnić B, Žubčić D, Potočnjak D, Mrljak V. Distinguishing Natural Infections of the Bovine Mammary Gland by Staphylococcus from Streptococcus spp. Using Quantitative Milk Proteomics. Animals (Basel) 2023; 13:1829. [PMID: 37889706 PMCID: PMC10252062 DOI: 10.3390/ani13111829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 10/29/2023] Open
Abstract
Bovine mastitis is the most frequent disease on dairy farms, which leads to a decrease in the health welfare of the animals and great economic losses. This study was aimed at determining the quantitative variations in the milk proteome caused by natural infection by Staphylococcus and Streptococcus species in order to gain further understanding of any discrepancies in pathophysiology and host immune responses, independent of the mastitis level. After identification of Staphylococcus (N = 51) and Streptococcus (N = 67) spp., tandem mass tag (TMT)-labeled quantitative proteomic and liquid chromatography-mass spectrometry (LC-MS/MS) techniques on a modular Ultimate 3000 RSLCnano system coupled to a Q Exactive Plus was applied on aseptically sampled milk from Holstein cows. Proteome Discoverer was used for protein identification and quantitation through the SEQUEST algorithm. Statistical analysis employing R was used to identify differentially abundant proteins between the groups. Protein classes, functions and functional-association networks were determined using the PANTHER and STRING tools and pathway over-representation using the REACTOME. In total, 156 master bovine proteins were identified (two unique peptides, p < 0.05 and FDR < 0.001), and 20 proteins showed significantly discrepant abundance between the genera (p < 0.05 and FDR < 0.5). The most discriminatory proteins per group were odorant-binding protein (higher in staphylococci) and fibrinogen beta chain protein (higher in streptococci). The receiver operating characteristic (ROC) curve showed that protein kinase C-binding protein NELL2, thrombospondin-1, and complement factor I have diagnostic potential for differentiating staphylococci and streptococci intramammary infection and inflammation. Improved understanding of the host response mechanisms and recognition of potential biomarkers of specific-pathogen mastitis, which may aid prompt diagnosis for control implementation, are potential benefits of this study.
Collapse
Affiliation(s)
- Dina Rešetar Maslov
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (F.C.T.); (A.B.); (I.R.); (V.E.); (V.F.); (V.M.)
| | - Funmilola Clara Thomas
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (F.C.T.); (A.B.); (I.R.); (V.E.); (V.F.); (V.M.)
| | - Anđelo Beletić
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (F.C.T.); (A.B.); (I.R.); (V.E.); (V.F.); (V.M.)
| | - Josipa Kuleš
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia;
| | - Ivana Rubić
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (F.C.T.); (A.B.); (I.R.); (V.E.); (V.F.); (V.M.)
| | - Miroslav Benić
- Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Savska Cesta, 143, 10000 Zagreb, Croatia;
| | - Goran Bačić
- Reproduction and Obstetrics Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (G.B.); (N.M.)
| | - Nino Maćešić
- Reproduction and Obstetrics Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (G.B.); (N.M.)
| | - Vida Eraghi
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (F.C.T.); (A.B.); (I.R.); (V.E.); (V.F.); (V.M.)
| | - Vladimir Farkaš
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (F.C.T.); (A.B.); (I.R.); (V.E.); (V.F.); (V.M.)
| | - Tihana Lenac Roviš
- Center for Proteomics University of Rijeka, Faculty of Medicine, Brace Branchetta 20, 51000 Rijeka, Croatia; (T.L.R.); (B.L.)
| | - Berislav Lisnić
- Center for Proteomics University of Rijeka, Faculty of Medicine, Brace Branchetta 20, 51000 Rijeka, Croatia; (T.L.R.); (B.L.)
| | - Damir Žubčić
- Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (D.Ž.); (D.P.)
| | - Dalibor Potočnjak
- Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (D.Ž.); (D.P.)
| | - Vladimir Mrljak
- Laboratory of Proteomics, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (F.C.T.); (A.B.); (I.R.); (V.E.); (V.F.); (V.M.)
- Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova Street 55, 10000 Zagreb, Croatia; (D.Ž.); (D.P.)
| |
Collapse
|
167
|
Ye SB, Cheng YK, Li PS, Zhang L, Zhang LH, Huang Y, Chen P, Wang Y, Wang C, Peng JH, Shi LS, Ling L, Wu XJ, Qin J, Yang ZH, Lan P. High-throughput proteomics profiling-derived signature associated with chemotherapy response and survival for stage II/III colorectal cancer. NPJ Precis Oncol 2023; 7:50. [PMID: 37258779 DOI: 10.1038/s41698-023-00400-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Adjuvant chemotherapy (ACT) is usually used to reduce the risk of disease relapse and improve survival for stage II/III colorectal cancer (CRC). However, only a subset of patients could benefit from ACT. Thus, there is an urgent need to identify improved biomarkers to predict survival and stratify patients to refine the selection of ACT. We used high-throughput proteomics to analyze tumor and adjacent normal tissues of stage II/III CRC patients with /without relapse to identify potential markers for predicting prognosis and benefit from ACT. The machine learning approach was applied to identify relapse-specific markers. Then the artificial intelligence (AI)-assisted multiplex IHC was performed to validate the prognostic value of the relapse-specific markers and construct a proteomic-derived classifier for stage II/III CRC using 3 markers, including FHL3, GGA1, TGFBI. The proteomics profiling-derived signature for stage II/III CRC (PS) not only shows good accuracy to classify patients into high and low risk of relapse and mortality in all three cohorts, but also works independently of clinicopathologic features. ACT was associated with improved disease-free survival (DFS) and overall survival (OS) in stage II (pN0) patients with high PS and pN2 patients with high PS. This study demonstrated the clinical significance of proteomic features, which serve as a valuable source for potential biomarkers. The PS classifier provides prognostic value for identifying patients at high risk of relapse and mortality and optimizes individualized treatment strategy by detecting patients who may benefit from ACT for survival.
Collapse
Affiliation(s)
- Shu-Biao Ye
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Yi-Kan Cheng
- Department of Radiation Oncology; The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Pei-Si Li
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
- Sun Yat-sen University School of Medicine, Sun Yat-sen University, Guangzhou, PR China
| | - Lin Zhang
- Department of Clinical Laboratory, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Lian-Hai Zhang
- Department of Surgery, Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Yan Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Ping Chen
- Department of VIP, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Yi Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing, China
| | - Chao Wang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China
| | - Jian-Hong Peng
- Department of Colorectal Surgery, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, PR China
| | - Li-Shuo Shi
- Department of Probability and Statistics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Li Ling
- Department of Probability and Statistics, School of Public Health, Sun Yat-sen University, Guangzhou, PR China
| | - Xiao-Jian Wu
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
| | - Jun Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing, China.
| | - Zi-Huan Yang
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
| | - Ping Lan
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
- Department of Colorectal Surgery, Department of General Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, PR China.
| |
Collapse
|
168
|
Völkel S, Tarawneh TS, Sacher L, Bhagwat AM, Karim I, Mack HID, Wiesmann T, Beutel B, Hoyer J, Keller C, Renz H, Burchert A, Neubauer A, Graumann J, Skevaki C, Mack EKM. Serum proteomics hint at an early T-cell response and modulation of SARS-CoV-2-related pathogenic pathways in COVID-19-ARDS treated with Ruxolitinib. Front Med (Lausanne) 2023; 10:1176427. [PMID: 37293294 PMCID: PMC10244732 DOI: 10.3389/fmed.2023.1176427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 06/10/2023] Open
Abstract
Background Acute respiratory distress syndrome (ARDS) in corona virus disease 19 (COVID-19) is triggered by hyperinflammation, thus providing a rationale for immunosuppressive treatments. The Janus kinase inhibitor Ruxolitinib (Ruxo) has shown efficacy in severe and critical COVID-19. In this study, we hypothesized that Ruxo's mode of action in this condition is reflected by changes in the peripheral blood proteome. Methods This study included 11 COVID-19 patients, who were treated at our center's Intensive Care Unit (ICU). All patients received standard-of-care treatment and n = 8 patients with ARDS received Ruxo in addition. Blood samples were collected before (day 0) and on days 1, 6, and 10 of Ruxo treatment or, respectively, ICU admission. Serum proteomes were analyzed by mass spectrometry (MS) and cytometric bead array. Results Linear modeling of MS data yielded 27 significantly differentially regulated proteins on day 1, 69 on day 6 and 72 on day 10. Only five factors (IGLV10-54, PSMB1, PGLYRP1, APOA5, WARS1) were regulated both concordantly and significantly over time. Overrepresentation analysis revealed biological processes involving T-cells only on day 1, while a humoral immune response and complement activation were detected at day 6 and day 10. Pathway enrichment analysis identified the NRF2-pathway early under Ruxo treatment and Network map of SARS-CoV-2 signaling and Statin inhibition of cholesterol production at later time points. Conclusion Our results indicate that the mechanism of action of Ruxo in COVID-19-ARDS can be related to both known effects of this drug as a modulator of T-cells and the SARS-CoV-2-infection.
Collapse
Affiliation(s)
- Sara Völkel
- Institute of Laboratory Medicine, Philipps-University Marburg, Marburg, Germany
| | - Thomas S. Tarawneh
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
| | - Laura Sacher
- Institute of Laboratory Medicine, Philipps-University Marburg, Marburg, Germany
| | - Aditya M. Bhagwat
- Institute of Translational Proteomics, Philipps-University Marburg, Marburg, Germany
| | - Ihab Karim
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
| | - Hildegard I. D. Mack
- Institute for Biomedical Aging Research, Leopold-Franzens-Universität Innsbruck, Innsbruck, Austria
| | - Thomas Wiesmann
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, Diakonie-Klinikum Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Björn Beutel
- Department of Pulmonary and Critical Care Medicine, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Member of the Universities of Gießen and Marburg Lung Center, Gießen, Germany
| | - Joachim Hoyer
- Department of Nephrology, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
| | - Christian Keller
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine, Philipps-University Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Member of the Universities of Gießen and Marburg Lung Center, Gießen, Germany
| | - Andreas Burchert
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
| | - Johannes Graumann
- Institute of Translational Proteomics, Philipps-University Marburg, Marburg, Germany
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Philipps-University Marburg, Marburg, Germany
- German Center for Lung Research (DZL), Member of the Universities of Gießen and Marburg Lung Center, Gießen, Germany
| | - Elisabeth K. M. Mack
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg, Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
169
|
Bader JM, Albrecht V, Mann M. MS-based proteomics of body fluids: The end of the beginning. Mol Cell Proteomics 2023:100577. [PMID: 37209816 PMCID: PMC10388585 DOI: 10.1016/j.mcpro.2023.100577] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones are often unspecific and new ones have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification and quantification making it an ideal technology for biomarker discovery and routine measurement. It has unique attributes compared to affinity binder technologies, such as OLINK Proximity Extension Assay and SOMAscan. In a previous review we described technological and conceptual limitations that had held back success (Geyer et al., 2017). We proposed a 'rectangular strategy' to better separate true biomarkers by minimizing cohort-specific effects. Today, this has converged with advances in MS-based proteomics technology, such as increased sample throughput, depth of identification and quantification. As a result, biomarker discovery studies have become more successful, producing biomarker candidates that withstand independent verification and, in some cases, already outperform state-of-the-art clinical assays. We summarize developments over the last years, including the benefits of large and independent cohorts, which are necessary for clinical acceptance. They are also required for machine learning or deep learning. Shorter gradients, new scan modes and multiplexing are about to drastically increase throughput, cross-study integration, and quantification, including proxies for absolute levels. We have found that multi-protein panels are inherently more robust than current single analyte tests and better capture the complexity of human phenotypes. Routine MS measurement in the clinic is fast becoming a viable option. The full set of proteins in a body fluid (global proteome) is the most important reference and the best process control. Additionally, it increasingly has all the information that could be obtained from targeted analysis although the latter may be the most straightforward way to enter into regular use. Many challenges remain, not least of a regulatory and ethical nature, but the outlook for MS-based clinical applications has never been brighter.
Collapse
Affiliation(s)
- Jakob M Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Vincent Albrecht
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| |
Collapse
|
170
|
Vaparanta K, Jokilammi A, Paatero I, Merilahti JA, Heliste J, Hemanthakumar KA, Kivelä R, Alitalo K, Taimen P, Elenius K. STAT5b is a key effector of NRG-1/ERBB4-mediated myocardial growth. EMBO Rep 2023; 24:e56689. [PMID: 37009825 PMCID: PMC10157316 DOI: 10.15252/embr.202256689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 04/04/2023] Open
Abstract
The growth factor Neuregulin-1 (NRG-1) regulates myocardial growth and is currently under clinical investigation as a treatment for heart failure. Here, we demonstrate in several in vitro and in vivo models that STAT5b mediates NRG-1/EBBB4-stimulated cardiomyocyte growth. Genetic and chemical disruption of the NRG-1/ERBB4 pathway reduces STAT5b activation and transcription of STAT5b target genes Igf1, Myc, and Cdkn1a in murine cardiomyocytes. Loss of Stat5b also ablates NRG-1-induced cardiomyocyte hypertrophy. Dynamin-2 is shown to control the cell surface localization of ERBB4 and chemical inhibition of Dynamin-2 downregulates STAT5b activation and cardiomyocyte hypertrophy. In zebrafish embryos, Stat5 is activated during NRG-1-induced hyperplastic myocardial growth, and chemical inhibition of the Nrg-1/Erbb4 pathway or Dynamin-2 leads to loss of myocardial growth and Stat5 activation. Moreover, CRISPR/Cas9-mediated knockdown of stat5b results in reduced myocardial growth and cardiac function. Finally, the NRG-1/ERBB4/STAT5b signaling pathway is differentially regulated at mRNA and protein levels in the myocardium of patients with pathological cardiac hypertrophy as compared to control human subjects, consistent with a role of the NRG-1/ERBB4/STAT5b pathway in myocardial growth.
Collapse
Affiliation(s)
- Katri Vaparanta
- Turku Bioscience CentreUniversity of Turku and Åbo Akademi UniversityTurkuFinland
- Medicity Research LaboratoriesUniversity of TurkuTurkuFinland
- Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Anne Jokilammi
- Turku Bioscience CentreUniversity of Turku and Åbo Akademi UniversityTurkuFinland
- Medicity Research LaboratoriesUniversity of TurkuTurkuFinland
- Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Ilkka Paatero
- Turku Bioscience CentreUniversity of Turku and Åbo Akademi UniversityTurkuFinland
| | - Johannes A Merilahti
- Turku Bioscience CentreUniversity of Turku and Åbo Akademi UniversityTurkuFinland
| | - Juho Heliste
- Turku Bioscience CentreUniversity of Turku and Åbo Akademi UniversityTurkuFinland
- Medicity Research LaboratoriesUniversity of TurkuTurkuFinland
- Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Karthik Amudhala Hemanthakumar
- Wihuri Research InstituteHelsinkiFinland
- Translational Cancer Biology Program, Research Programs Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Riikka Kivelä
- Wihuri Research InstituteHelsinkiFinland
- Translational Cancer Biology Program, Research Programs Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Kari Alitalo
- Wihuri Research InstituteHelsinkiFinland
- Translational Cancer Biology Program, Research Programs Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Pekka Taimen
- Institute of Biomedicine and FICAN West Cancer CentreUniversity of TurkuTurkuFinland
- Department of PathologyTurku University HospitalTurkuFinland
| | - Klaus Elenius
- Turku Bioscience CentreUniversity of Turku and Åbo Akademi UniversityTurkuFinland
- Medicity Research LaboratoriesUniversity of TurkuTurkuFinland
- Institute of BiomedicineUniversity of TurkuTurkuFinland
- Department of OncologyTurku University HospitalTurkuFinland
| |
Collapse
|
171
|
Kurland AP, Bonaventure B, Johnson JR. A Chemical Proteomics Approach to Discover Regulators of Innate Immune Signaling. Viruses 2023; 15:v15051112. [PMID: 37243198 DOI: 10.3390/v15051112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Innate immune pathways are tightly regulated to balance an appropriate response to infectious agents and tolerable levels of inflammation. Dysregulation of innate immune pathways can lead to severe autoinflammatory disorders or susceptibility to infections. Here, we aimed to identify kinases in common cellular pathways that regulate innate immune pathways by combining small-scale kinase inhibitor screening with quantitative proteomics. We found that inhibitors of kinases ATM, ATR, AMPK, and PLK1 reduced the induction of interferon-stimulated gene expression in response to innate immune pathway activation by poly(I:C) transfection. However, siRNA depletion of these kinases did not validate findings with kinase inhibitors, suggesting that off-target effects may explain their activities. We mapped the effects of kinase inhibitors to various stages in innate immune pathways. Determining the mechanisms by which kinase inhibitors antagonize these pathways may illuminate novel mechanisms of innate immune pathway control.
Collapse
Affiliation(s)
- Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
172
|
Wang R, Kumar B, Bhat-Nakshatri P, Khatpe AS, Murphy MP, Wanczyk KE, Simpson E, Chen D, Gao H, Liu Y, Doud EH, Mosley AL, Nakshatri H. A human skeletal muscle stem/myotube model reveals multiple signaling targets of cancer secretome in skeletal muscle. iScience 2023; 26:106541. [PMID: 37102148 PMCID: PMC10123345 DOI: 10.1016/j.isci.2023.106541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/16/2022] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Skeletal muscle dysfunction or reprogramming due to the effects of the cancer secretome is observed in multiple malignancies. Although mouse models are routinely used to study skeletal muscle defects in cancer, because of species specificity of certain cytokines/chemokines in the secretome, a human model system is required. Here, we establish simplified multiple skeletal muscle stem cell lines (hMuSCs), which can be differentiated into myotubes. Using single nuclei ATAC-seq (snATAC-seq) and RNA-seq (snRNA-seq), we document chromatin accessibility and transcriptomic changes associated with the transition of hMuSCs to myotubes. Cancer secretome accelerated stem to myotube differentiation, altered the alternative splicing machinery and increased inflammatory, glucocorticoid receptor, and wound healing pathways in hMuSCs. Additionally, cancer secretome reduced metabolic and survival pathway associated miR-486, AKT, and p53 signaling in hMuSCs. hMuSCs underwent myotube differentiation when engrafted into NSG mice and thus providing a humanized in vivo skeletal muscle model system to study cancer cachexia.
Collapse
Affiliation(s)
- Ruizhong Wang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brijesh Kumar
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Aditi S. Khatpe
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael P. Murphy
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Kristen E. Wanczyk
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| | - Edward Simpson
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Duojiao Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma H. Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- VA Roudebush Medical Center, Indianapolis, IN 46202, USA
| |
Collapse
|
173
|
Tossounian MA, Baczynska M, Dalton W, Peak-Chew SY, Undzenas K, Korza G, Filonenko V, Skehel M, Setlow P, Gout I. Bacillus subtilis YtpP and Thioredoxin A Are New Players in the Coenzyme-A-Mediated Defense Mechanism against Cellular Stress. Antioxidants (Basel) 2023; 12:antiox12040938. [PMID: 37107313 PMCID: PMC10136147 DOI: 10.3390/antiox12040938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Coenzyme A (CoA) is an important cellular metabolite that is critical for metabolic processes and the regulation of gene expression. Recent discovery of the antioxidant function of CoA has highlighted its protective role that leads to the formation of a mixed disulfide bond with protein cysteines, which is termed protein CoAlation. To date, more than 2000 CoAlated bacterial and mammalian proteins have been identified in cellular responses to oxidative stress, with the majority being involved in metabolic pathways (60%). Studies have shown that protein CoAlation is a widespread post-translational modification which modulates the activity and conformation of the modified proteins. The induction of protein CoAlation by oxidative stress was found to be rapidly reversed after the removal of oxidizing agents from the medium of cultured cells. In this study, we developed an enzyme-linked immunosorbent assay (ELISA)-based deCoAlation assay to detect deCoAlation activity from Bacillus subtilis and Bacillus megaterium lysates. We then used a combination of ELISA-based assay and purification strategies to show that deCoAlation is an enzyme-driven mechanism. Using mass-spectrometry and deCoAlation assays, we identified B. subtilis YtpP (thioredoxin-like protein) and thioredoxin A (TrxA) as enzymes that can remove CoA from different substrates. With mutagenesis studies, we identified YtpP and TrxA catalytic cysteine residues and proposed a possible deCoAlation mechanism for CoAlated methionine sulfoxide reducatse A (MsrA) and peroxiredoxin 5 (PRDX5) proteins, which results in the release of both CoA and the reduced form of MsrA or PRDX5. Overall, this paper reveals the deCoAlation activity of YtpP and TrxA and opens doors to future studies on the CoA-mediated redox regulation of CoAlated proteins under various cellular stress conditions.
Collapse
Affiliation(s)
| | - Maria Baczynska
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - William Dalton
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Sew Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Kipras Undzenas
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - George Korza
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Valeriy Filonenko
- Department of Cell Signaling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Ivan Gout
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
- Department of Cell Signaling, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680 Kyiv, Ukraine
| |
Collapse
|
174
|
Prioretti L, D’Ermo G, Infossi P, Kpebe A, Lebrun R, Bauzan M, Lojou E, Guigliarelli B, Giudici-Orticoni MT, Guiral M. Carbon Fixation in the Chemolithoautotrophic Bacterium Aquifex aeolicus Involves Two Low-Potential Ferredoxins as Partners of the PFOR and OGOR Enzymes. Life (Basel) 2023; 13:life13030627. [PMID: 36983784 PMCID: PMC10052474 DOI: 10.3390/life13030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Aquifex aeolicus is a microaerophilic hydrogen- and sulfur -oxidizing bacterium that assimilates CO2 via the reverse tricarboxylic acid cycle (rTCA). Key enzymes of this pathway are pyruvate:ferredoxin oxidoreductase (PFOR) and 2-oxoglutarate:ferredoxin oxidoreductase (OGOR), which are responsible, respectively, for the reductive carboxylation of acetyl-CoA to pyruvate and of succinyl-CoA to 2-oxoglutarate, two energetically unfavorable reactions that require a strong reduction potential. We have confirmed, by biochemistry and proteomics, that A. aeolicus possesses a pentameric version of these enzyme complexes ((αβγδε)2) and that they are highly abundant in the cell. In addition, we have purified and characterized, from the soluble fraction of A. aeolicus, two low redox potential and oxygen-stable [4Fe-4S] ferredoxins (Fd6 and Fd7, E0 = −440 and −460 mV, respectively) and shown that they can physically interact and exchange electrons with both PFOR and OGOR, suggesting that they could be the physiological electron donors of the system in vivo. Shotgun proteomics indicated that all the enzymes assumed to be involved in the rTCA cycle are produced in the A. aeolicus cells. A number of additional enzymes, previously suggested to be part of a putative partial Wood-Ljungdahl pathway used for the synthesis of serine and glycine from CO2 were identified by mass spectrometry, but their abundance in the cell seems to be much lower than that of the rTCA cycle. Their possible involvement in carbon assimilation is discussed.
Collapse
Affiliation(s)
- Laura Prioretti
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Giulia D’Ermo
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Pascale Infossi
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Arlette Kpebe
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Marielle Bauzan
- CNRS, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Elisabeth Lojou
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | - Bruno Guigliarelli
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
| | | | - Marianne Guiral
- CNRS, Bioénergétique et Ingénierie des Protéines, Aix Marseille Université, IMM, 13009 Marseille, France
- Correspondence:
| |
Collapse
|
175
|
Kamens JL, Nance S, Koss C, Xu B, Cotton A, Lam JW, Garfinkle EAR, Nallagatla P, Smith AMR, Mitchell S, Ma J, Currier D, Wright WC, Kavdia K, Pagala VR, Kim W, Wallace LM, Cho JH, Fan Y, Seth A, Twarog N, Choi JK, Obeng EA, Hatley ME, Metzger ML, Inaba H, Jeha S, Rubnitz JE, Peng J, Chen T, Shelat AA, Guy RK, Gruber TA. Proteasome inhibition targets the KMT2A transcriptional complex in acute lymphoblastic leukemia. Nat Commun 2023; 14:809. [PMID: 36781850 PMCID: PMC9925443 DOI: 10.1038/s41467-023-36370-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Rearrangments in Histone-lysine-N-methyltransferase 2A (KMT2Ar) are associated with pediatric, adult and therapy-induced acute leukemias. Infants with KMT2Ar acute lymphoblastic leukemia (ALL) have a poor prognosis with an event-free-survival of 38%. Herein we evaluate 1116 FDA approved compounds in primary KMT2Ar infant ALL specimens and identify a sensitivity to proteasome inhibition. Upon exposure to this class of agents, cells demonstrate a depletion of histone H2B monoubiquitination (H2Bub1) and histone H3 lysine 79 dimethylation (H3K79me2) at KMT2A target genes in addition to a downregulation of the KMT2A gene expression signature, providing evidence that it targets the KMT2A transcriptional complex and alters the epigenome. A cohort of relapsed/refractory KMT2Ar patients treated with this approach on a compassionate basis had an overall response rate of 90%. In conclusion, we report on a high throughput drug screen in primary pediatric leukemia specimens whose results translate into clinically meaningful responses. This innovative treatment approach is now being evaluated in a multi-institutional upfront trial for infants with newly diagnosed ALL.
Collapse
Affiliation(s)
- Jennifer L Kamens
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephanie Nance
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cary Koss
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anitria Cotton
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeannie W Lam
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pratima Nallagatla
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Amelia M R Smith
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharnise Mitchell
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Duane Currier
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William C Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Vishwajeeth R Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wonil Kim
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - LaShanale M Wallace
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aman Seth
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nathaniel Twarog
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John K Choi
- Department of Pathology, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Monika L Metzger
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sima Jeha
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey E Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - R Kiplin Guy
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
176
|
Deutsch EW, Mendoza L, Shteynberg DD, Hoopmann MR, Sun Z, Eng JK, Moritz RL. Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. J Proteome Res 2023; 22:615-624. [PMID: 36648445 PMCID: PMC10166710 DOI: 10.1021/acs.jproteome.2c00624] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. Many of the tools include machine-learning modeling to extract the most information from data sets and build robust statistical models to compute the probabilities that derived information is correct. Here we present the latest information on the many TPP tools, and how TPP can be deployed on various platforms from personal Windows laptops to Linux clusters and expansive cloud computing environments. We describe tutorials on how to use TPP in a variety of ways and describe synergistic projects that leverage TPP. We conclude with plans for continued development of TPP.
Collapse
Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | | | | | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jimmy K Eng
- Proteomics Resource, University of Washington, Seattle, Washington 98195, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| |
Collapse
|
177
|
Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh E, Orchard S, Papatheodorou I, Velankar S, Vizcaino J, Witham R, Zdrazil B, McEntyre J. EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022. Nucleic Acids Res 2023; 51:D9-D17. [PMID: 36477213 PMCID: PMC9825486 DOI: 10.1093/nar/gkac1098] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/21/2022] [Accepted: 10/31/2022] [Indexed: 12/13/2022] Open
Abstract
The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe's only intergovernmental life sciences organisation. This overview summarises the status of services that EMBL-EBI data resources provide to scientific communities globally. The scale, openness, rich metadata and extensive curation of EMBL-EBI added-value databases makes them particularly well-suited as training sets for deep learning, machine learning and artificial intelligence applications, a selection of which are described here. The data resources at EMBL-EBI can catalyse such developments because they offer sustainable, high-quality data, collected in some cases over decades and made openly availability to any researcher, globally. Our aim is for EMBL-EBI data resources to keep providing the foundations for tools and research insights that transform fields across the life sciences.
Collapse
Affiliation(s)
| | - Alex Bateman
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Cath Brooksbank
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Mallory Freeberg
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Melissa Harrison
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Matthew Hartley
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Thomas Keane
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Gerard Kleywegt
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Andrew Leach
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Mariia Levchenko
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Sarah Morgan
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Ellen M McDonagh
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
- OpenTargets, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Sandra Orchard
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Irene Papatheodorou
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Sameer Velankar
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Juan Antonio Vizcaino
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Rick Witham
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Barbara Zdrazil
- Data Services Teams, EMBL’s European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | | |
Collapse
|