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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: 134] [Impact Index Per Article: 33.5] [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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Poverennaya EV, Kopylov AT, Ponomarenko EA, Ilgisonis EV, Zgoda VG, Tikhonova OV, Novikova SE, Farafonova TE, Kiseleva YY, Radko SP, Vakhrushev IV, Yarygin KN, Moshkovskii SA, Kiseleva OI, Lisitsa AV, Sokolov AS, Mazur AM, Prokhortchouk EB, Skryabin KG, Kostrjukova ES, Tyakht AV, Gorbachev AY, Ilina EN, Govorun VM, Archakov AI. State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells. J Proteome Res 2016; 15:4030-4038. [PMID: 27527821 DOI: 10.1021/acs.jproteome.6b00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line and liver tissue proteomes was ∼66%. In total, there were 16 proteins specifically observed in HepG2 cell line, while 15 proteins were found solely in the liver tissue. Comparison between proteome and transcriptome revealed a poor correlation (R2 ≈ 0.1) between corresponding mRNA and protein expression levels. The SRM and shotgun data sets (obtained during 2015-2016) are available in PASSEL (PASS00697) and ProteomeExchange/PRIDE (PXD004407). All measurements were also uploaded into the in-house Chr 18 Knowledgebase at http://kb18.ru/protein/matrix/416126 .
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Affiliation(s)
| | - Arthur T Kopylov
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Elena A Ponomarenko
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | | | - Victor G Zgoda
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Olga V Tikhonova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Svetlana E Novikova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Tatyana E Farafonova
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Yana Yu Kiseleva
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Igor V Vakhrushev
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Konstantin N Yarygin
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia.,Pirogov Russian National Research Medical University , Ostrovitianov Str. 1, Moscow 117997, Russia
| | - Olga I Kiseleva
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Andrey V Lisitsa
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
| | - Alexey S Sokolov
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Alexander M Mazur
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Egor B Prokhortchouk
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Konstantin G Skryabin
- Center "Bioengineering" Russian Academy of Sciences , Prospect 60-let Oktyabrya, 7, Build.1, Moscow 119071, Russia
| | - Elena S Kostrjukova
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexander V Tyakht
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexey Yu Gorbachev
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Elena N Ilina
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Vadim M Govorun
- Scientific Research Institute of Physical-Chemical Medicine , Malaya Pirogovskaya, 1a, Moscow 119435, Russia
| | - Alexander I Archakov
- Institute of Biomedical Chemistry , Pogodinskaya Street, 10, Moscow 119121, Russia
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Breuza L, Poux S, Estreicher A, Famiglietti ML, Magrane M, Tognolli M, Bridge A, Baratin D, Redaschi N. The UniProtKB guide to the human proteome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:bav120. [PMID: 26896845 PMCID: PMC4761109 DOI: 10.1093/database/bav120] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/24/2015] [Indexed: 11/23/2022]
Abstract
Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB. Database URL: www.uniprot.org
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Affiliation(s)
- Lionel Breuza
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
| | - Sylvain Poux
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
| | - Anne Estreicher
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
| | - Maria Livia Famiglietti
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
| | - Michele Magrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Michael Tognolli
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
| | - Alan Bridge
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
| | - Delphine Baratin
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
| | - Nicole Redaschi
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel Servet, Geneva 4, 1211, Switzerland
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