301
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Wen B, Zeng W, Liao Y, Shi Z, Savage SR, Jiang W, Zhang B. Deep Learning in Proteomics. Proteomics 2020; 20:e1900335. [PMID: 32939979 PMCID: PMC7757195 DOI: 10.1002/pmic.201900335] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/14/2020] [Indexed: 12/17/2022]
Abstract
Proteomics, the study of all the proteins in biological systems, is becoming a data-rich science. Protein sequences and structures are comprehensively catalogued in online databases. With recent advancements in tandem mass spectrometry (MS) technology, protein expression and post-translational modifications (PTMs) can be studied in a variety of biological systems at the global scale. Sophisticated computational algorithms are needed to translate the vast amount of data into novel biological insights. Deep learning automatically extracts data representations at high levels of abstraction from data, and it thrives in data-rich scientific research domains. Here, a comprehensive overview of deep learning applications in proteomics, including retention time prediction, MS/MS spectrum prediction, de novo peptide sequencing, PTM prediction, major histocompatibility complex-peptide binding prediction, and protein structure prediction, is provided. Limitations and the future directions of deep learning in proteomics are also discussed. This review will provide readers an overview of deep learning and how it can be used to analyze proteomics data.
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Affiliation(s)
- Bo Wen
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Wen‐Feng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS)Chinese Academy of SciencesInstitute of Computing TechnologyBeijing100190China
| | - Yuxing Liao
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Zhiao Shi
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Sara R. Savage
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Wen Jiang
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Bing Zhang
- Lester and Sue Smith Breast CenterBaylor College of MedicineHoustonTX77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
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302
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Chen DY, Khan N, Close BJ, Goel RK, Blum B, Tavares AH, Kenney D, Conway HL, Ewoldt JK, Kapell S, Chitalia VC, Crossland NA, Chen CS, Kotton DN, Baker SC, Connor JH, Douam F, Emili A, Saeed M. SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33140044 DOI: 10.1101/2020.10.27.358259] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we performed global proteomic analysis of the virus-host interface in a newly established panel of phenotypically diverse, SARS-CoV-2-infectable human cell lines representing different body organs. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cell lines and primary-like cardiomyocytes, and found that several pathway components were targeted by SARS-CoV-2 leading to cellular desensitization to interferon. These findings indicate that the suppression of interferon signaling is a mechanism widely used by SARS-CoV-2 in diverse tissues to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19.
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303
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An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks. Biomedicines 2020; 8:biomedicines8110455. [PMID: 33126421 PMCID: PMC7692261 DOI: 10.3390/biomedicines8110455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Major depressive disorder (MDD) is a leading cause of global disability with a chronic and recurrent course. Recognition of biological markers that could predict and monitor response to drug treatment could personalize clinical decision-making, minimize unnecessary drug exposure, and achieve better outcomes. Four longitudinal plasma samples were collected from each of ten patients with MDD treated with antidepressants for 10 weeks. Plasma proteins were analyzed qualitatively and quantitatively with a nanoflow LC−MS/MS technique. Of 1153 proteins identified in the 40 longitudinal plasma samples, 37 proteins were significantly associated with response/time and clustered into six according to time and response by the linear mixed model. Among them, three early-drug response markers (PHOX2B, SH3BGRL3, and YWHAE) detectable within one week were verified by liquid chromatography-multiple reaction monitoring/mass spectrometry (LC-MRM/MS) in the well-controlled 24 patients. In addition, 11 proteins correlated significantly with two or more psychiatric measurement indices. This pilot study might be useful in finding protein marker candidates that can monitor response to antidepressant treatment during follow-up visits within 10 weeks after the baseline visit.
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304
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Hör J, Di Giorgio S, Gerovac M, Venturini E, Förstner KU, Vogel J. Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. Nucleic Acids Res 2020; 48:9301-9319. [PMID: 32813020 PMCID: PMC7498339 DOI: 10.1093/nar/gkaa676] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ∼85% of all E. coli transcripts and ∼49% of the proteins. These include the majority of small noncoding RNAs (sRNAs) detectable in this bacterium as well as the general sRNA-binding proteins, CsrA, Hfq and ProQ. In presenting use cases for utilization of these RNA and protein maps, we show that a stable association of RyeG with 30S ribosomes gives this seemingly noncoding RNA of prophage origin away as an mRNA of a toxic small protein. Similarly, we show that the broadly conserved uncharacterized protein YggL is a 50S subunit factor in assembled 70S ribosomes. Overall, this study crucially extends our knowledge about the cellular interactome of the primary model bacterium E. coli through providing global RNA/protein complexome information and should facilitate functional discovery in this and related species.
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Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Silvia Di Giorgio
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,ZB MED - Information Centre for Life Sciences, D-50931 Cologne, Germany
| | - Milan Gerovac
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Elisa Venturini
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Konrad U Förstner
- ZB MED - Information Centre for Life Sciences, D-50931 Cologne, Germany.,TH Köln, Faculty of Information Science and Communication Studies, D-50678 Cologne, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), D-97080 Würzburg, Germany
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305
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Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington SR, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res 2020; 19:4735-4746. [PMID: 32931287 DOI: 10.1021/acs.jproteome.0c00485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | | | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | | | | | - Mark S Baker
- Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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306
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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307
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Leblanc S, Brunet MA. Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses. Comput Struct Biotechnol J 2020; 18:2836-2850. [PMID: 33133425 PMCID: PMC7585943 DOI: 10.1016/j.csbj.2020.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/08/2023] Open
Abstract
The Zika virus is a flavivirus that can cause fulminant outbreaks and lead to Guillain-Barré syndrome, microcephaly and fetal demise. Like other flaviviruses, the Zika virus is transmitted by mosquitoes and provokes neurological disorders. Despite its risk to public health, no antiviral nor vaccine are currently available. In the recent years, several studies have set to identify human host proteins interacting with Zika viral proteins to better understand its pathogenicity. Yet these studies used standard human protein sequence databases. Such databases rely on genome annotations, which enforce a minimal open reading frame (ORF) length criterion. An ever-increasing number of studies have demonstrated the shortcomings of such annotation, which overlooks thousands of functional ORFs. Here we show that the use of a customized database including currently non-annotated proteins led to the identification of 4 alternative proteins as interactors of the viral capsid and NS4A proteins. Furthermore, 12 alternative proteins were identified in the proteome profiling of Zika infected monocytes, one of which was significantly up-regulated. This study presents a computational framework for the re-analysis of proteomics datasets to better investigate the viral-host protein interplays upon infection with the Zika virus.
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Key Words
- AP-MS, affinity-purification mass spectrometry
- Alternative ORFs
- DEP, differentially expressed proteins
- FDR, false discovery rate
- FPKM, fragments per kilobase of exon model per million reads mapped
- Flavivirus
- HCIP, highly confident interacting proteins
- HCMV, human cytomegalovirus
- LFQ, label free quantification
- MS, mass spectrometry
- ORF, open reading frame
- PSM, peptide spectrum match
- Protein network
- Proteogenomics
- Proteome profiling
- ZIKV, Zika virus
- Zika
- altProt, alternative protein
- ncRNA, non-coding RNA
- sORF, small open reading frame
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Affiliation(s)
- Sebastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Marie A. Brunet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
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308
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Moore R, Vogt K, Acosta-Martin AE, Shire P, Zeidler M, Smythe E. Integration of JAK/STAT receptor-ligand trafficking, signalling and gene expression in Drosophila melanogaster cells. J Cell Sci 2020; 133:jcs246199. [PMID: 32917740 DOI: 10.1242/jcs.246199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/02/2020] [Indexed: 12/18/2022] Open
Abstract
The JAK/STAT pathway is an essential signalling cascade required for multiple processes during development and for adult homeostasis. A key question in understanding this pathway is how it is regulated in different cell contexts. Here, we have examined how endocytic processing contributes to signalling by the single cytokine receptor in Drosophila melanogaster cells, Domeless. We identify an evolutionarily conserved di-leucine (di-Leu) motif that is required for Domeless internalisation and show that endocytosis is required for activation of a subset of Domeless targets. Our data indicate that endocytosis both qualitatively and quantitatively regulates Domeless signalling. STAT92E, the single STAT transcription factor in Drosophila, appears to be the target of endocytic regulation, and our studies show that phosphorylation of STAT92E on Tyr704, although necessary, is not always sufficient for target transcription. Finally, we identify a conserved residue, Thr702, which is essential for Tyr704 phosphorylation. Taken together, our findings identify previously unknown aspects of JAK/STAT pathway regulation likely to play key roles in the spatial and temporal regulation of signalling in vivo.
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Affiliation(s)
- Rachel Moore
- Centre for Membrane Interactions and Dynamics, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Katja Vogt
- Centre for Membrane Interactions and Dynamics, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Adelina E Acosta-Martin
- biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Patrick Shire
- Centre for Membrane Interactions and Dynamics, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Martin Zeidler
- Centre for Membrane Interactions and Dynamics, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Elizabeth Smythe
- Centre for Membrane Interactions and Dynamics, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
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309
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Guo B, Zhou Q, Jiang J, Chen J, Liang X, Jiaojiao X, Shi D, Ren K, Zhou X, Hassan HM, Li J. Functionalized Vascular Structure in Bioengineered Liver Identified with Proteomics. ACS Biomater Sci Eng 2020; 6:6394-6404. [PMID: 33449649 DOI: 10.1021/acsbiomaterials.0c01353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vascularization has been a major challenge in the development of a bioengineered liver. We aimed to develop a functionalized vascular structure in bioengineered liver and to identify the biological vascularization processes at different time points using proteomics. Decellularized rat liver scaffolds were vascularized with human umbilical vein endothelial cells (HUVECs) for 1, 3, 7, 14, and 21 days. HUVECs adhered to the internal surface and formed a functional barrier structure within 7 days. Vascularized liver scaffolds with biological activity were sustained for more than 21 days in vitro. Proteomics analysis indicated distinct characteristics after 14 days of culture compared with other time points. The biological processes of proteins expressed at days 1, 3, and 7 mainly involved cell adhesion, protein synthesis, and energy metabolism; however, different biological processes associated with muscle contraction and muscle filament sliding were identified at days 14 and 21. Coexpressed proteins at days 14 and 21 participated in 7 biological processes that could be classified as angiogenesis, myogenesis, or vascular function. Furthermore, the validation of related proteins revealed that basement membrane assembly, phenotype plasticity of HUVECs, and the regulation of adherence junctions contribute to the formation of a functionalized vascular structure. The biological vascularization processes at different time points identified with proteomics revealed development characteristics of vascular structure in a bioengineered liver, and at least 14 days of in vitro culture should be recommended for developing a functionalized vascular structure. This study may help to provide a better understanding of the mechanism of vascularization and facilitate the construction of a functional bioengineered liver for future clinical applications.
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Affiliation(s)
- Beibei Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Qian Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jing Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Precision Medicine Center of Taizhou Central Hospital, Taizhou University Medical School, Taizhou 318000, China
| | - Jiaxian Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Xi Liang
- Precision Medicine Center of Taizhou Central Hospital, Taizhou University Medical School, Taizhou 318000, China
| | - Xin Jiaojiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Precision Medicine Center of Taizhou Central Hospital, Taizhou University Medical School, Taizhou 318000, China
| | - Dongyan Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Precision Medicine Center of Taizhou Central Hospital, Taizhou University Medical School, Taizhou 318000, China
| | - Keke Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Xingping Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hozeifa M Hassan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Jun Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.,Precision Medicine Center of Taizhou Central Hospital, Taizhou University Medical School, Taizhou 318000, China
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310
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De Boeck A, Ahn BY, D'Mello C, Lun X, Menon SV, Alshehri MM, Szulzewsky F, Shen Y, Khan L, Dang NH, Reichardt E, Goring KA, King J, Grisdale CJ, Grinshtein N, Hambardzumyan D, Reilly KM, Blough MD, Cairncross JG, Yong VW, Marra MA, Jones SJM, Kaplan DR, McCoy KD, Holland EC, Bose P, Chan JA, Robbins SM, Senger DL. Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression. Nat Commun 2020; 11:4997. [PMID: 33020472 PMCID: PMC7536425 DOI: 10.1038/s41467-020-18569-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Despite a deeper molecular understanding, human glioblastoma remains one of the most treatment refractory and fatal cancers. It is known that the presence of macrophages and microglia impact glioblastoma tumorigenesis and prevent durable response. Herein we identify the dual function cytokine IL-33 as an orchestrator of the glioblastoma microenvironment that contributes to tumorigenesis. We find that IL-33 expression in a large subset of human glioma specimens and murine models correlates with increased tumor-associated macrophages/monocytes/microglia. In addition, nuclear and secreted functions of IL-33 regulate chemokines that collectively recruit and activate circulating and resident innate immune cells creating a pro-tumorigenic environment. Conversely, loss of nuclear IL-33 cripples recruitment, dramatically suppresses glioma growth, and increases survival. Our data supports the paradigm that recruitment and activation of immune cells, when instructed appropriately, offer a therapeutic strategy that switches the focus from the cancer cell alone to one that includes the normal host environment.
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Affiliation(s)
- Astrid De Boeck
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bo Young Ahn
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Charlotte D'Mello
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Xueqing Lun
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Shyam V Menon
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mana M Alshehri
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Frank Szulzewsky
- Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Lubaba Khan
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ngoc Ha Dang
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Elliott Reichardt
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kimberly-Ann Goring
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer King
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Natalie Grinshtein
- Department of Molecular Genetics, University of Toronto and Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute and the Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Karlyne M Reilly
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Michael D Blough
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - J Gregory Cairncross
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - David R Kaplan
- Department of Molecular Genetics, University of Toronto and Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Eric C Holland
- Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Pinaki Bose
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Chan
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Stephen M Robbins
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Donna L Senger
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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311
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Cerciello F, Choi M, Sinicropi-Yao SL, Lomeo K, Amann JM, Felley-Bosco E, Stahel RA, Robinson BWS, Creaney J, Pass HI, Vitek O, Carbone DP. Verification of a Blood-Based Targeted Proteomics Signature for Malignant Pleural Mesothelioma. Cancer Epidemiol Biomarkers Prev 2020; 29:1973-1982. [PMID: 32732250 PMCID: PMC7541795 DOI: 10.1158/1055-9965.epi-20-0543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/18/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND We have verified a mass spectrometry (MS)-based targeted proteomics signature for the detection of malignant pleural mesothelioma (MPM) from the blood. METHODS A seven-peptide biomarker MPM signature by targeted proteomics in serum was identified in a previous independent study. Here, we have verified the predictive accuracy of a reduced version of that signature, now composed of six-peptide biomarkers. We have applied liquid chromatography-selected reaction monitoring (LC-SRM), also known as multiple-reaction monitoring (MRM), for the investigation of 402 serum samples from 213 patients with MPM and 189 cancer-free asbestos-exposed donors from the United States, Australia, and Europe. RESULTS Each of the biomarkers composing the signature was independently informative, with no apparent functional or physical relation to each other. The multiplexing possibility offered by MS proteomics allowed their integration into a single signature with a higher discriminating capacity than that of the single biomarkers alone. The strategy allowed in this way to increase their potential utility for clinical decisions. The signature discriminated patients with MPM and asbestos-exposed donors with AUC of 0.738. For early-stage MPM, AUC was 0.765. This signature was also prognostic, and Kaplan-Meier analysis showed a significant difference between high- and low-risk groups with an HR of 1.659 (95% CI, 1.075-2.562; P = 0.021). CONCLUSIONS Targeted proteomics allowed the development of a multianalyte signature with diagnostic and prognostic potential for MPM from the blood. IMPACT The proteomic signature represents an additional diagnostic approach for informing clinical decisions for patients at risk for MPM.
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Affiliation(s)
- Ferdinando Cerciello
- James Thoracic Center, James Cancer Center, The Ohio State University Medical Center, Columbus, Ohio.
| | - Meena Choi
- College of Computer and Information Science, Northeastern University, Boston, Massachusetts
| | - Sara L Sinicropi-Yao
- James Thoracic Center, James Cancer Center, The Ohio State University Medical Center, Columbus, Ohio
| | - Katie Lomeo
- James Thoracic Center, James Cancer Center, The Ohio State University Medical Center, Columbus, Ohio
| | - Joseph M Amann
- James Thoracic Center, James Cancer Center, The Ohio State University Medical Center, Columbus, Ohio
| | - Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Division of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Rolf A Stahel
- Department of Oncology, Center of Hematology and Oncology, Comprehensive Cancer Center Zürich, University Hospital Zürich, Zürich, Switzerland
| | - Bruce W S Robinson
- National Centre for Asbestos Related Disease, University of Western Australia, School of Medicine and Pharmacology, Nedlands, Western Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Disease, University of Western Australia, School of Medicine and Pharmacology, Nedlands, Western Australia
| | - Harvey I Pass
- New York University, Langone Medical Center, New York, New York
| | - Olga Vitek
- College of Computer and Information Science, Northeastern University, Boston, Massachusetts
| | - David P Carbone
- James Thoracic Center, James Cancer Center, The Ohio State University Medical Center, Columbus, Ohio.
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312
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Dost AFM, Moye AL, Vedaie M, Tran LM, Fung E, Heinze D, Villacorta-Martin C, Huang J, Hekman R, Kwan JH, Blum BC, Louie SM, Rowbotham SP, Sainz de Aja J, Piper ME, Bhetariya PJ, Bronson RT, Emili A, Mostoslavsky G, Fishbein GA, Wallace WD, Krysan K, Dubinett SM, Yanagawa J, Kotton DN, Kim CF. Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells. Cell Stem Cell 2020; 27:663-678.e8. [PMID: 32891189 PMCID: PMC7541765 DOI: 10.1016/j.stem.2020.07.022] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
Abstract
Mutant KRAS is a common driver in epithelial cancers. Nevertheless, molecular changes occurring early after activation of oncogenic KRAS in epithelial cells remain poorly understood. We compared transcriptional changes at single-cell resolution after KRAS activation in four sample sets. In addition to patient samples and genetically engineered mouse models, we developed organoid systems from primary mouse and human induced pluripotent stem cell-derived lung epithelial cells to model early-stage lung adenocarcinoma. In all four settings, alveolar epithelial progenitor (AT2) cells expressing oncogenic KRAS had reduced expression of mature lineage identity genes. These findings demonstrate the utility of our in vitro organoid approaches for uncovering the early consequences of oncogenic KRAS expression. This resource provides an extensive collection of datasets and describes organoid tools to study the transcriptional and proteomic changes that distinguish normal epithelial progenitor cells from early-stage lung cancer, facilitating the search for targets for KRAS-driven tumors.
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Affiliation(s)
- Antonella F M Dost
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron L Moye
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Marall Vedaie
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Linh M Tran
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eileen Fung
- Department of Surgery, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dar Heinze
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; Section of Gastroenterology and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ryan Hekman
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Julian H Kwan
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sharon M Louie
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel P Rowbotham
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Julio Sainz de Aja
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mary E Piper
- Harvard T.H. Chan School of Public Health, Department of Biostatistics, Boston, MA 02115, USA
| | - Preetida J Bhetariya
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard T.H. Chan School of Public Health, Department of Biostatistics, Boston, MA 02115, USA
| | - Roderick T Bronson
- Rodent Histopathology Core, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; Department of Biology, Boston University, Boston, MA 02215, USA
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; Section of Gastroenterology and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Gregory A Fishbein
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William D Wallace
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - Kostyantyn Krysan
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Steven M Dubinett
- Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jane Yanagawa
- Department of Surgery, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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313
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Characterization of Local and Systemic Impact of Whitefly ( Bemisia tabaci) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteomics. Int J Mol Sci 2020; 21:ijms21197241. [PMID: 33008056 PMCID: PMC7583044 DOI: 10.3390/ijms21197241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 11/23/2022] Open
Abstract
Tomato mottle virus (ToMoV) is a single-stranded DNA (ssDNA) begomovirus transmitted to solanaceous crops by the whitefly species complex (Bemisia tabaci), causing stunted growth, leaf mottling, and reduced yield. Using a genetic repertoire of seven genes, ToMoV pathogenesis includes the manipulation of multiple plant biological processes to circumvent antiviral defenses. To further understand the effects of whitefly feeding and whitefly-transmitted ToMoV infection on tomato plants (Solanum lycopersicum ‘Florida Lanai’), we generated comprehensive protein profiles of leaves subjected to feeding by either viruliferous whiteflies harboring ToMoV, or non-viruliferous whiteflies, or a no-feeding control. The effects of whitefly feeding and ToMoV infection were measured both locally and systemically by sampling either a mature leaf directly from the site of clip-cage confined whitefly feeding, or from a newly formed leaf 10 days post feeding (dpf). At 3 dpf, tomato’s response to ToMoV included proteins associated with translation initiation and elongation as well as plasmodesmata dynamics. In contrast, systemic impacts of ToMoV on younger leaves 10 dpf were more pronounced and included a virus-specific change in plant proteins associated with mRNA maturation and export, RNA-dependent DNA methylation, and other antiviral plant processes. Our analysis supports previous findings and provides novel insight into tomato’s local and systemic response to whitefly feeding and ToMoV infection.
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314
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Li Y, Ivica NA, Dong T, Papageorgiou DP, He Y, Brown DR, Kleyman M, Hu G, Chen WW, Sullivan LB, Del Rosario A, Hammond PT, Vander Heiden MG, Chen J. MFSD7C switches mitochondrial ATP synthesis to thermogenesis in response to heme. Nat Commun 2020; 11:4837. [PMID: 32973183 PMCID: PMC7515921 DOI: 10.1038/s41467-020-18607-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 08/31/2020] [Indexed: 12/18/2022] Open
Abstract
ATP synthesis and thermogenesis are two critical outputs of mitochondrial respiration. How these outputs are regulated to balance the cellular requirement for energy and heat is largely unknown. Here we show that major facilitator superfamily domain containing 7C (MFSD7C) uncouples mitochondrial respiration to switch ATP synthesis to thermogenesis in response to heme. When heme levels are low, MSFD7C promotes ATP synthesis by interacting with components of the electron transport chain (ETC) complexes III, IV, and V, and destabilizing sarcoendoplasmic reticulum Ca2+-ATPase 2b (SERCA2b). Upon heme binding to the N-terminal domain, MFSD7C dissociates from ETC components and SERCA2b, resulting in SERCA2b stabilization and thermogenesis. The heme-regulated switch between ATP synthesis and thermogenesis enables cells to match outputs of mitochondrial respiration to their metabolic state and nutrient supply, and represents a cell intrinsic mechanism to regulate mitochondrial energy metabolism.
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Affiliation(s)
- Yingzhong Li
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nikola A Ivica
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ting Dong
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Dimitrios P Papageorgiou
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Yanpu He
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Douglas R Brown
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Marianna Kleyman
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Guangan Hu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Walter W Chen
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Boston Combined Residency Program, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Lucas B Sullivan
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Amanda Del Rosario
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Paula T Hammond
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Jianzhu Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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315
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Nabet B, Ferguson FM, Seong BKA, Kuljanin M, Leggett AL, Mohardt ML, Robichaud A, Conway AS, Buckley DL, Mancias JD, Bradner JE, Stegmaier K, Gray NS. Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules. Nat Commun 2020; 11:4687. [PMID: 32948771 PMCID: PMC7501296 DOI: 10.1038/s41467-020-18377-w] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Chemical biology strategies for directly perturbing protein homeostasis including the degradation tag (dTAG) system provide temporal advantages over genetic approaches and improved selectivity over small molecule inhibitors. We describe dTAGV-1, an exclusively selective VHL-recruiting dTAG molecule, to rapidly degrade FKBP12F36V-tagged proteins. dTAGV-1 overcomes a limitation of previously reported CRBN-recruiting dTAG molecules to degrade recalcitrant oncogenes, supports combination degrader studies and facilitates investigations of protein function in cells and mice.
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Affiliation(s)
- Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Miljan Kuljanin
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alan L Leggett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikaela L Mohardt
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy S Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dennis L Buckley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Joseph D Mancias
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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316
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Lindhout FW, Kooistra R, Portegies S, Herstel LJ, Stucchi R, Snoek BL, Altelaar AFM, MacGillavry HD, Wierenga CJ, Hoogenraad CC. Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons. eLife 2020; 9:e58124. [PMID: 32940601 PMCID: PMC7498259 DOI: 10.7554/elife.58124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
The differentiation of neuronal stem cells into polarized neurons is a well-coordinated process which has mostly been studied in classical non-human model systems, but to what extent these findings are recapitulated in human neurons remains unclear. To study neuronal polarization in human neurons, we cultured hiPSC-derived neurons, characterized early developmental stages, measured electrophysiological responses, and systematically profiled transcriptomic and proteomic dynamics during these steps. The neuron transcriptome and proteome shows extensive remodeling, with differential expression profiles of ~1100 transcripts and ~2200 proteins during neuronal differentiation and polarization. We also identified a distinct axon developmental stage marked by the relocation of axon initial segment proteins and increased microtubule remodeling from the distal (stage 3a) to the proximal (stage 3b) axon. This developmental transition coincides with action potential maturation. Our comprehensive characterization and quantitative map of transcriptome and proteome dynamics provides a solid framework for studying polarization in human neurons.
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Affiliation(s)
- Feline W Lindhout
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Robbelien Kooistra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Sybren Portegies
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Lotte J Herstel
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Riccardo Stucchi
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht UniversityUtrechtNetherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht UniversityUtrechtNetherlands
| | - Harold D MacGillavry
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Corette J Wierenga
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Casper C Hoogenraad
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
- Department of Neuroscience, Genentech, IncSan FranciscoUnited States
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317
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Wang Y, Tian Y, Liu X, Dong J, Wang L, Ye M. A New Workflow for the Analysis of Phosphosite Occupancy in Paired Samples by Integration of Proteomics and Phosphoproteomics Data Sets. J Proteome Res 2020; 19:3807-3816. [PMID: 32786891 DOI: 10.1021/acs.jproteome.0c00345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Knowledge of phosphosite occupancy is important to explain biological functions for phosphoproteomics studies. Determination of occupancy using three ratios, i.e., protein ratio, phosphopeptide ratio, and its unmodified peptide counterpart ratio between a pair of samples, is straightforward but suffers from large variances. Here, an optimized protocol of offline fractionation and LC-MS analysis combined with an integrated data processing approach was developed to improve the reliability of the phosphosite occupancy determination. An outlier score S was introduced to evaluate the deviation between the ratio of absolute occupancy and relative occupancy and was further used to define the bounds of a credible interval of absolute occupancy. For a preset product-moment correlation coefficient, the credible interval can be resolved through the S value. Using this strategy, more than 176k unique peptide sequences covering 11k protein groups and 32k phosphosites were identified from one paired hepatocellular carcinoma (HCC) sample and about 3000 reliable phosphosite occupancies were finally determined. By bioinformatics analysis, we characterized the biological properties associated with phosphorylation sites with different quantified occupancies from the paired HCC sample. Data are available via ProteomeXchange with identifier PXD019045.
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Affiliation(s)
- Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Tian
- Department of Vascular Surgery, The Second Hospital of Dalian Medical University, Dalian 116023, China.,Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Liming Wang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The Second Hospital of Dalian Medical University, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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318
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Hofsetz E, Demir F, Szczepanowska K, Kukat A, Kizhakkedathu JN, Trifunovic A, Huesgen PF. The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis. Mol Cell Proteomics 2020; 19:1330-1345. [PMID: 32467259 PMCID: PMC8014998 DOI: 10.1074/mcp.ra120.002082] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Indexed: 12/29/2022] Open
Abstract
The mammalian mitochondrial proteome consists of more than 1100 annotated proteins and their proteostasis is regulated by only a few ATP-dependent protease complexes. Technical advances in protein mass spectrometry allowed for detailed description of the mitoproteome from different species and tissues and their changes under specific conditions. However, protease-substrate relations within mitochondria are still poorly understood. Here, we combined Terminal Amine Isotope Labeling of Substrates (TAILS) N termini profiling of heart mitochondria proteomes isolated from wild type and Clpp-/- mice with a classical substrate-trapping screen using FLAG-tagged proteolytically active and inactive CLPP variants to identify new ClpXP substrates in mammalian mitochondria. Using TAILS, we identified N termini of more than 200 mitochondrial proteins. Expected N termini confirmed sequence determinants for mitochondrial targeting signal (MTS) cleavage and subsequent N-terminal processing after import, but the majority were protease-generated neo-N termini mapping to positions within the proteins. Quantitative comparison revealed widespread changes in protein processing patterns, including both strong increases or decreases in the abundance of specific neo-N termini, as well as an overall increase in the abundance of protease-generated neo-N termini in CLPP-deficient mitochondria that indicated altered mitochondrial proteostasis. Based on the combination of altered processing patterns, protein accumulation and stabilization in CLPP-deficient mice and interaction with CLPP, we identified OAT, HSPA9 and POLDIP2 and as novel bona fide ClpXP substrates. Finally, we propose that ClpXP participates in the cooperative degradation of UQCRC1. Together, our data provide the first landscape of the heart mitochondria N terminome and give further insights into regulatory and assisted proteolysis mediated by ClpXP.
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Affiliation(s)
- Eduard Hofsetz
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany
| | - Karolina Szczepanowska
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Alexandra Kukat
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, School of Biomedical Engineering, Department of Pathology & Laboratory Medicine, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aleksandra Trifunovic
- Institute for Mitochondrial Diseases and Aging at CECAD Research Centre, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
| | - Pitter F Huesgen
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), Cologne, Germany, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
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319
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Petkovic M, Oses-Prieto J, Burlingame A, Jan LY, Jan YN. TMEM16K is an interorganelle regulator of endosomal sorting. Nat Commun 2020; 11:3298. [PMID: 32620747 PMCID: PMC7335067 DOI: 10.1038/s41467-020-17016-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
Communication between organelles is essential for their cellular homeostasis. Neurodegeneration reflects the declining ability of neurons to maintain cellular homeostasis over a lifetime, where the endolysosomal pathway plays a prominent role by regulating protein and lipid sorting and degradation. Here we report that TMEM16K, an endoplasmic reticulum lipid scramblase causative for spinocerebellar ataxia (SCAR10), is an interorganelle regulator of the endolysosomal pathway. We identify endosomal transport as a major functional cluster of TMEM16K in proximity biotinylation proteomics analyses. TMEM16K forms contact sites with endosomes, reconstituting split-GFP with the small GTPase RAB7. Our study further implicates TMEM16K lipid scrambling activity in endosomal sorting at these sites. Loss of TMEM16K function led to impaired endosomal retrograde transport and neuromuscular function, one of the symptoms of SCAR10. Thus, TMEM16K-containing ER-endosome contact sites represent clinically relevant platforms for regulating endosomal sorting.
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Affiliation(s)
- Maja Petkovic
- Departments of Physiology, Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, 94158, USA.
| | - Juan Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Alma Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Lily Yeh Jan
- Departments of Physiology, Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Yuh Nung Jan
- Departments of Physiology, Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, 94158, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
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320
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Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, Smith L, Stefan MI, Wittig U, Myers CJ. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J Integr Bioinform 2020; 17:jib-2020-0005. [PMID: 32598315 PMCID: PMC7756615 DOI: 10.1515/jib-2020-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 01/23/2023] Open
Abstract
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.
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Affiliation(s)
- Dagmar Waltemath
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Michael Hucka
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Esther Thea Inau
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Olga Krebs
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Ernst Oberortner
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Labs, Berkeley, CA, USA
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Falk Schreiber
- Department of Computer and Information Science, University ofKonstanz, Germany.,Faculty of IT, Monash University, Melbourne, VIC, Australia
| | - Lucian Smith
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Melanie I Stefan
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK.,ZJU-UoE Institute, Zhejiang University, Haining, China.,University of Utah, Salt Lake City, UT, USA
| | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Chris J Myers
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
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321
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Ogden AJ, Bhatt JJ, Brewer HM, Kintigh J, Kariuki SM, Rudrabhatla S, Adkins JN, Curtis WR. Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature. Int J Mol Sci 2020; 21:E4461. [PMID: 32586033 PMCID: PMC7352395 DOI: 10.3390/ijms21124461] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 11/17/2022] Open
Abstract
Drought is the leading cause of agricultural yield loss among all abiotic stresses, and the link between water deficit and phloem protein contents is relatively unexplored. Here we collected phloem exudates from Solanum lycopersicum leaves during periods of drought stress and recovery. Our analysis identified 2558 proteins, the most abundant of which were previously localized to the phloem. Independent of drought, enrichment analysis of the total phloem exudate protein profiles from all samples suggests that the protein content of phloem sap is complex, and includes proteins that function in chaperone systems, branched-chain amino acid synthesis, trehalose metabolism, and RNA silencing. We observed 169 proteins whose abundance changed significantly within the phloem sap, either during drought or recovery. Proteins that became significantly more abundant during drought include members of lipid metabolism, chaperone-mediated protein folding, carboxylic acid metabolism, abscisic acid signaling, cytokinin biosynthesis, and amino acid metabolism. Conversely, proteins involved in lipid signaling, sphingolipid metabolism, cell wall organization, carbohydrate metabolism, and a mitogen-activated protein kinase are decreased during drought. Our experiment has achieved an in-depth profiling of phloem sap protein contents during drought stress and recovery that supports previous findings and provides new evidence that multiple biological processes are involved in drought adaptation.
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Affiliation(s)
- Aaron J. Ogden
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, 902 Battelle Blvd, Richland, WA 99301, USA; (A.J.O.); (H.M.B.); (J.N.A.)
| | - Jishnu J. Bhatt
- Plant Biology Graduate Program, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Heather M. Brewer
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, 902 Battelle Blvd, Richland, WA 99301, USA; (A.J.O.); (H.M.B.); (J.N.A.)
| | - Jack Kintigh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (J.K.); (S.M.K.)
| | - Samwel M. Kariuki
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (J.K.); (S.M.K.)
| | - Sairam Rudrabhatla
- School of Science, Engineering, and Technology, The Pennsylvania State University, Harrisburg Campus, 777 W Harrisburg Pike, Middletown, PA 17057, USA;
| | - Joshua N. Adkins
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, 902 Battelle Blvd, Richland, WA 99301, USA; (A.J.O.); (H.M.B.); (J.N.A.)
| | - Wayne R. Curtis
- Plant Biology Graduate Program, The Pennsylvania State University, University Park, PA 16802, USA;
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (J.K.); (S.M.K.)
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322
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Kim HR, Xu J, Maeda S, Duc NM, Ahn D, Du Y, Chung KY. Structural mechanism underlying primary and secondary coupling between GPCRs and the Gi/o family. Nat Commun 2020; 11:3160. [PMID: 32572026 PMCID: PMC7308389 DOI: 10.1038/s41467-020-16975-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Heterotrimeric G proteins are categorized into four main families based on their function and sequence, Gs, Gi/o, Gq/11, and G12/13. One receptor can couple to more than one G protein subtype, and the coupling efficiency varies depending on the GPCR-G protein pair. However, the precise mechanism underlying different coupling efficiencies is unknown. Here, we study the structural mechanism underlying primary and secondary Gi/o coupling, using the muscarinic acetylcholine receptor type 2 (M2R) as the primary Gi/o-coupling receptor and the β2-adrenergic receptor (β2AR, which primarily couples to Gs) as the secondary Gi/o-coupling receptor. Hydrogen/deuterium exchange mass spectrometry and mutagenesis studies reveal that the engagement of the distal C-terminus of Gαi/o with the receptor differentiates primary and secondary Gi/o couplings. This study suggests that the conserved hydrophobic residue within the intracellular loop 2 of the receptor (residue 34.51) is not critical for primary Gi/o-coupling; however, it might be important for secondary Gi/o-coupling. G protein-coupled receptors (GPCRs) can couple to more than one G protein subtype, and the coupling efficiency varies depending on the GPCR-G protein pair. Here authors use hydrogen/deuterium exchange mass spectrometry and mutagenesis to study the structural mechanism underlying primary and secondary Gi/o coupling.
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Affiliation(s)
- Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Jun Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.,Division of Precision Medicine, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
| | - Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Yang Du
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, 2001 Longxiang Ave, Shenzhen, Guangdong, 518172, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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323
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Drozdova P, Saranchina A, Morgunova M, Kizenko A, Lubyaga Y, Baduev B, Timofeyev M. The level of putative carotenoid-binding proteins determines the body color in two species of endemic Lake Baikal amphipods. PeerJ 2020; 8:e9387. [PMID: 32596057 PMCID: PMC7307558 DOI: 10.7717/peerj.9387] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023] Open
Abstract
Color is an essential clue for intra- and interspecies communication, playing a role in selection and speciation. Coloration can be based on nanostructures and pigments; carotenoids and carotenoproteins are among the most widespread pigments in animals. Over 350 species and subspecies of amphipods (Crustacea: Amphipoda) endemic to Lake Baikal exhibit an impressive variability of colors and coloration patterns, including intraspecific color morphs. However, the mechanisms forming this diversity are underexplored, as while the carotenoid composition of several transparent, green, and red species was investigated, there have been no reports on the corresponding carotenoid-binding proteins. In this work, we analyze the coloration of two brightly colored Baikal amphipods characterized by intraspecific color variability, Eulimnogammarus cyaneus and E. vittatus. We showed that the color of either species is defined by the level of putative carotenoid-binding proteins similar to the pheromone/odorant-binding protein family, as the concentration of these putative crustacyanin analogs was higher in blue or teal-colored animals than in the orange- or yellow-colored ones. At the same time, the color did not depend on the total carotenoid content, as it was similar between animals of contrasting color morphs. By exploring the diversity of these sequences within a larger phylogeny of invertebrate crustacyanins, we show that amphipods lack orthologs of the well-studied crustacyanins A and C, even though they possess some crustacyanin-like sequences. The analysis of expression levels in E. cyaneus showed that the transcripts encoding crustacyanin analogs had much higher expression than the crustacyanin-like sequences, suggesting that the former indeed contribute to the color of these brightly colored animals. The crustacyanin analogs seem to act in a similar way to the well-studied crustacyanins in body color formation, but the details of their action are still to be revealed.
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Affiliation(s)
- Polina Drozdova
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | | | | | - Alena Kizenko
- Institute of Cytology RAS, St. Petersburg, Russia.,Bioinformatics Institute, St. Petersburg, Russia
| | - Yulia Lubyaga
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
| | - Boris Baduev
- Institute of Biology, Irkutsk State University, Irkutsk, Russia
| | - Maxim Timofeyev
- Institute of Biology, Irkutsk State University, Irkutsk, Russia.,Baikal Research Centre, Irkutsk, Russia
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324
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Ahn HS, Kim JH, Jeong H, Yu J, Yeom J, Song SH, Kim SS, Kim IJ, Kim K. Differential Urinary Proteome Analysis for Predicting Prognosis in Type 2 Diabetes Patients with and without Renal Dysfunction. Int J Mol Sci 2020; 21:ijms21124236. [PMID: 32545899 PMCID: PMC7352871 DOI: 10.3390/ijms21124236] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/28/2022] Open
Abstract
Renal dysfunction, a major complication of type 2 diabetes, can be predicted from estimated glomerular filtration rate (eGFR) and protein markers such as albumin concentration. Urinary protein biomarkers may be used to monitor or predict patient status. Urine samples were selected from patients enrolled in the retrospective diabetic kidney disease (DKD) study, including 35 with good and 19 with poor prognosis. After removal of albumin and immunoglobulin, the remaining proteins were reduced, alkylated, digested, and analyzed qualitatively and quantitatively with a nano LC-MS platform. Each protein was identified, and its concentration normalized to that of creatinine. A prognostic model of DKD was formulated based on the adjusted quantities of each protein in the two groups. Of 1296 proteins identified in the 54 urine samples, 66 were differentially abundant in the two groups (area under the curve (AUC): p-value < 0.05), but none showed significantly better performance than albumin. To improve the predictive power by multivariate analysis, five proteins (ACP2, CTSA, GM2A, MUC1, and SPARCL1) were selected as significant by an AUC-based random forest method. The application of two classifiers—support vector machine and random forest—showed that the multivariate model performed better than univariate analysis of mucin-1 (AUC: 0.935 vs. 0.791) and albumin (AUC: 1.0 vs. 0.722). The urinary proteome can reflect kidney function directly and can predict the prognosis of patients with chronic kidney dysfunction. Classification based on five urinary proteins may better predict the prognosis of DKD patients than urinary albumin concentration or eGFR.
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Affiliation(s)
- Hee-Sung Ahn
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea; (H.-S.A.); (J.Y.)
| | - Jong Ho Kim
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Korea; (J.H.K.); (S.H.S.); (S.S.K.)
| | - Hwangkyo Jeong
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Jiyoung Yu
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea; (H.-S.A.); (J.Y.)
| | - Jeonghun Yeom
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Seoul 05505, Korea;
| | - Sang Heon Song
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Korea; (J.H.K.); (S.H.S.); (S.S.K.)
| | - Sang Soo Kim
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Korea; (J.H.K.); (S.H.S.); (S.S.K.)
| | - In Joo Kim
- Department of Internal Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan 49241, Korea; (J.H.K.); (S.H.S.); (S.S.K.)
- Correspondence: (I.J.K.); (K.K.); Tel.: +82-51-240-7224 (I.J.K.); +82-2-1688-7575 (K.K.)
| | - Kyunggon Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea; (H.-S.A.); (J.Y.)
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 05505, Korea;
- Clinical Proteomics Core Laboratory, Convergence Medicine Research Center, Asan Medical Center, Seoul 05505, Korea
- Bio-Medical Institute of Technology, Asan Medical Center, Seoul 05505, Korea
- Correspondence: (I.J.K.); (K.K.); Tel.: +82-51-240-7224 (I.J.K.); +82-2-1688-7575 (K.K.)
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325
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Ultrasonic-Based Filter Aided Sample Preparation as the General Method to Sample Preparation in Proteomics. Anal Chem 2020; 92:9164-9171. [PMID: 32484334 DOI: 10.1021/acs.analchem.0c01470] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We propose a new high-throughput ultrafast method for large-scale proteomics approaches by speeding up the classic filter aided sample preparation protocol, FASP, from overnight to 2.5 h. Thirty-six samples can be treated in 2.5 h, and the method is scalable to 96-well plate-based pipelines. After a modification of the FASP-tube, the steps of protein reduction, protein alkylation, and protein digestion of complex proteomes are done in just 5.25 min, each one under the effects of an ultrasonic field (7 cycles: 30 s on and 15 s off). The new method was compared to the standard overnight digestion FASP protocol, and no statistical differences were found for more than 92.4%, 92%, and 93.3% of the proteins identified by studying the proteome of E. coli, mouse brain, and mouse liver tissue samples, respectively. Furthermore, the successful relative label-free quantification of four spiked proteins in E. coli samples, BSA, β-lactoglobulin, α-casein, and α-lactalbumin, was achieved, using either the ultrasonic-based FASP protocol or the classic overnight one. The new US-FASP method matches the analytical minimalism rules as time, cost, sample requirement, reagent consumption, energy requirements, and production of waste products are reduced to a minimum while maintaining high sample throughput in a robust manner as all of the advantages of the filter aided sample preparation protocol are maintained.
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326
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Sinsky J, Majerova P, Kovac A, Kotlyar M, Jurisica I, Hanes J. Physiological Tau Interactome in Brain and Its Link to Tauopathies. J Proteome Res 2020; 19:2429-2442. [PMID: 32357304 DOI: 10.1021/acs.jproteome.0c00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Alzheimer's disease (AD) and most of the other tauopathies are incurable neurodegenerative diseases with unpleasant symptoms and consequences. The common hallmark of all of these diseases is tau pathology, but its connection with disease progress has not been completely understood so far. Therefore, uncovering novel tau-interacting partners and pathology affected molecular pathways can reveal the causes of diseases as well as potential targets for the development of AD treatment. Despite the large number of known tau-interacting partners, a limited number of studies focused on in vivo tau interactions in disease or healthy conditions are available. Here, we applied an in vivo cross-linking approach, capable of capturing weak and transient protein-protein interactions, to a unique transgenic rat model of progressive tau pathology similar to human AD. We have identified 175 potential novel and known tau-interacting proteins by MALDI-TOF mass spectrometry. Several of the most promising candidates for possible drug development were selected for validation by coimmunoprecipitation and colocalization experiments in animal and cellular models. Three proteins, Baiap2, Gpr37l1, and Nptx1, were confirmed as novel tau-interacting partners, and on the basis of their known functions and implications in neurodegenerative or psychiatric disorders, we proposed their potential role in tau pathology.
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Affiliation(s)
- Jakub Sinsky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,AXON Neuroscience R&D Services SE, Dvorakovo nabrezie 10, Bratislava 811 02, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,AXON Neuroscience R&D Services SE, Dvorakovo nabrezie 10, Bratislava 811 02, Slovakia
| | - Max Kotlyar
- Krembil Research Institute, UHN, 60 Leonard Avenue, Toronto, Ontario M5T 0S8, Canada
| | - Igor Jurisica
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,Krembil Research Institute, UHN, 60 Leonard Avenue, Toronto, Ontario M5T 0S8, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, 27 King's College Circle, Toronto, Ontario ON M5S, Canada
| | - Jozef Hanes
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, Bratislava 84510, Slovakia.,AXON Neuroscience R&D Services SE, Dvorakovo nabrezie 10, Bratislava 811 02, Slovakia
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327
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Chiapello M, Zampieri E, Mello A. A Small Effort for Researchers, a Big Gain for Soil Metaproteomics. Front Microbiol 2020; 11:88. [PMID: 32117118 PMCID: PMC7010931 DOI: 10.3389/fmicb.2020.00088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/15/2020] [Indexed: 11/23/2022] Open
Affiliation(s)
- Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Elisa Zampieri
- Council for Agricultural Research and Economics Research Centre for Cereal and Industrial Crops (CREA-CI), Vercelli, Italy
| | - Antonietta Mello
- Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
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328
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Rigden DJ, Fernández XM. The 27th annual Nucleic Acids Research database issue and molecular biology database collection. Nucleic Acids Res 2020; 48:D1-D8. [PMID: 31906604 PMCID: PMC6943072 DOI: 10.1093/nar/gkz1161] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 2020 Nucleic Acids Research Database Issue contains 148 papers spanning molecular biology. They include 59 papers reporting on new databases and 79 covering recent changes to resources previously published in the issue. A further ten papers are updates on databases most recently published elsewhere. This issue contains three breakthrough articles: AntiBodies Chemically Defined (ABCD) curates antibody sequences and their cognate antigens; SCOP returns with a new schema and breaks away from a purely hierarchical structure; while the new Alliance of Genome Resources brings together a number of Model Organism databases to pool knowledge and tools. Major returning nucleic acid databases include miRDB and miRTarBase. Databases for protein sequence analysis include CDD, DisProt and ELM, alongside no fewer than four newcomers covering proteins involved in liquid-liquid phase separation. In metabolism and signaling, Pathway Commons, Reactome and Metabolights all contribute papers. PATRIC and MicroScope update in microbial genomes while human and model organism genomics resources include Ensembl, Ensembl genomes and UCSC Genome Browser. Immune-related proteins are covered by updates from IPD-IMGT/HLA and AFND, as well as newcomers VDJbase and OGRDB. Drug design is catered for by updates from the IUPHAR/BPS Guide to Pharmacology and the Therapeutic Target Database. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been revised, updating 305 entries, adding 65 new resources and eliminating 125 discontinued URLs; so bringing the current total to 1637 databases. It is available at http://www.oxfordjournals.org/nar/database/c/.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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