1
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Jin H, Zhang C, Zwahlen M, von Feilitzen K, Karlsson M, Shi M, Yuan M, Song X, Li X, Yang H, Turkez H, Fagerberg L, Uhlén M, Mardinoglu A. Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation. Nat Commun 2023; 14:5417. [PMID: 37669926 PMCID: PMC10480497 DOI: 10.1038/s41467-023-41132-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/24/2023] [Indexed: 09/07/2023] Open
Abstract
Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-à-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding genes in more than 1,000 human cell lines representing 27 cancer types by a genome-wide transcriptomics analysis. The cell line gene expression is compared with the corresponding profiles in various tissues, organs, single-cell types and cancers. Here, we present the expression for each cell line and give guidance for the most appropriate cell line for a given experimental study. In addition, we explore the cancer-related pathway and cytokine activity of the cell lines to aid human biology studies and drug development projects. All data are presented in an open access cell line section of the Human Protein Atlas to facilitate the exploration of all human protein-coding genes across these cell lines.
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Affiliation(s)
- Han Jin
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Max Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mengnan Shi
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Meng Yuan
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Xiya Song
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Xiangyu Li
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hong Yang
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden.
| | - Adil Mardinoglu
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK.
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2
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Álvez MB, Edfors F, von Feilitzen K, Zwahlen M, Mardinoglu A, Edqvist PH, Sjöblom T, Lundin E, Rameika N, Enblad G, Lindman H, Höglund M, Hesselager G, Stålberg K, Enblad M, Simonson OE, Häggman M, Axelsson T, Åberg M, Nordlund J, Zhong W, Karlsson M, Gyllensten U, Ponten F, Fagerberg L, Uhlén M. Next generation pan-cancer blood proteome profiling using proximity extension assay. Nat Commun 2023; 14:4308. [PMID: 37463882 DOI: 10.1038/s41467-023-39765-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/27/2023] [Indexed: 07/20/2023] Open
Abstract
A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.
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Affiliation(s)
- María Bueno Álvez
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Emma Lundin
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Natallia Rameika
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gunilla Enblad
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Henrik Lindman
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Martin Höglund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Hesselager
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Karin Stålberg
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Malin Enblad
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Oscar E Simonson
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Häggman
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Tomas Axelsson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Mikael Åberg
- Department of Medical Sciences, Clinical Chemistry and SciLifeLab Affinity Proteomics, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Wen Zhong
- Science for Life Laboratory, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden
| | - Max Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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3
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Karlsson M, Sjöstedt E, Oksvold P, Sivertsson Å, Huang J, Álvez MB, Arif M, Li X, Lin L, Yu J, Ma T, Xu F, Han P, Jiang H, Mardinoglu A, Zhang C, von Feilitzen K, Xu X, Wang J, Yang H, Bolund L, Zhong W, Fagerberg L, Lindskog C, Pontén F, Mulder J, Luo Y, Uhlen M. Genome-wide annotation of protein-coding genes in pig. BMC Biol 2022; 20:25. [PMID: 35073880 PMCID: PMC8788080 DOI: 10.1186/s12915-022-01229-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/07/2022] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND There is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here, a new annotation strategy is introduced based on dimensionality reduction and density-based clustering of whole-body co-expression patterns. This strategy has been used to explore the gene expression landscape in pig, and we present a whole-body map of all protein-coding genes in all major pig tissues and organs. RESULTS An open-access pig expression map ( www.rnaatlas.org ) is presented based on the expression of 350 samples across 98 well-defined pig tissues divided into 44 tissue groups. A new UMAP-based classification scheme is introduced, in which all protein-coding genes are stratified into tissue expression clusters based on body-wide expression profiles. The distribution and tissue specificity of all 22,342 protein-coding pig genes are presented. CONCLUSIONS Here, we present a new genome-wide annotation strategy based on dimensionality reduction and density-based clustering. A genome-wide resource of the transcriptome map across all major tissues and organs in pig is presented, and the data is available as an open-access resource ( www.rnaatlas.org ), including a comparison to the expression of human orthologs.
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Affiliation(s)
- Max Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jinrong Huang
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - María Bueno Álvez
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xiangyu Li
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jiaying Yu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Tao Ma
- MGI, BGI-Shenzhen, Shenzhen, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | | | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Lars Bolund
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Mathias Uhlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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4
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Hober S, Hellström C, Olofsson J, Andersson E, Bergström S, Jernbom Falk A, Bayati S, Mravinacova S, Sjöberg R, Yousef J, Skoglund L, Kanje S, Berling A, Svensson AS, Jensen G, Enstedt H, Afshari D, Xu LL, Zwahlen M, von Feilitzen K, Hanke L, Murrell B, McInerney G, Karlsson Hedestam GB, Lendel C, Roth RG, Skoog I, Svenungsson E, Olsson T, Fogdell-Hahn A, Lindroth Y, Lundgren M, Maleki KT, Lagerqvist N, Klingström J, Da Silva Rodrigues R, Muschiol S, Bogdanovic G, Arroyo Mühr LS, Eklund C, Lagheden C, Dillner J, Sivertsson Å, Havervall S, Thålin C, Tegel H, Pin E, Månberg A, Hedhammar M, Nilsson P. Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay. Clin Transl Immunology 2021; 10:e1312. [PMID: 34295471 PMCID: PMC8288725 DOI: 10.1002/cti2.1312] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Objective The COVID-19 pandemic poses an immense need for accurate, sensitive and high-throughput clinical tests, and serological assays are needed for both overarching epidemiological studies and evaluating vaccines. Here, we present the development and validation of a high-throughput multiplex bead-based serological assay. Methods More than 100 representations of SARS-CoV-2 proteins were included for initial evaluation, including antigens produced in bacterial and mammalian hosts as well as synthetic peptides. The five best-performing antigens, three representing the spike glycoprotein and two representing the nucleocapsid protein, were further evaluated for detection of IgG antibodies in samples from 331 COVID-19 patients and convalescents, and in 2090 negative controls sampled before 2020. Results Three antigens were finally selected, represented by a soluble trimeric form and the S1-domain of the spike glycoprotein as well as by the C-terminal domain of the nucleocapsid. The sensitivity for these three antigens individually was found to be 99.7%, 99.1% and 99.7%, and the specificity was found to be 98.1%, 98.7% and 95.7%. The best assay performance was although achieved when utilising two antigens in combination, enabling a sensitivity of up to 99.7% combined with a specificity of 100%. Requiring any two of the three antigens resulted in a sensitivity of 99.7% and a specificity of 99.4%. Conclusion These observations demonstrate that a serological test based on a combination of several SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.
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5
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Karlsson M, Zhang C, Méar L, Zhong W, Digre A, Katona B, Sjöstedt E, Butler L, Odeberg J, Dusart P, Edfors F, Oksvold P, von Feilitzen K, Zwahlen M, Arif M, Altay O, Li X, Ozcan M, Mardinoglu A, Fagerberg L, Mulder J, Luo Y, Ponten F, Uhlén M, Lindskog C. A single-cell type transcriptomics map of human tissues. Sci Adv 2021; 7:7/31/eabh2169. [PMID: 34321199 PMCID: PMC8318366 DOI: 10.1126/sciadv.abh2169] [Citation(s) in RCA: 529] [Impact Index Per Article: 176.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/11/2021] [Indexed: 05/09/2023]
Abstract
Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.
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Affiliation(s)
- Max Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Loren Méar
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Wen Zhong
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Digre
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Borbala Katona
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lynn Butler
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
- Clinical Chemistry, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
| | - Philip Dusart
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Per Oksvold
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Ozlem Altay
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Xiangyu Li
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mehmet Ozcan
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine and Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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6
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Sivertsson Å, Lindström E, Oksvold P, Katona B, Hikmet F, Vuu J, Gustavsson J, Sjöstedt E, von Feilitzen K, Kampf C, Schwenk JM, Uhlén M, Lindskog C. Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins. J Proteome Res 2020; 19:4766-4781. [PMID: 33170010 PMCID: PMC7723238 DOI: 10.1021/acs.jproteome.0c00486] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The localization of proteins at a
tissue- or cell-type-specific
level is tightly linked to the protein function. To better understand
each
protein’s role in cellular systems, spatial information constitutes
an important complement to quantitative data. The standard methods
for determining the spatial distribution of proteins in single cells
of complex tissue samples make use of antibodies. For a stringent
analysis of the human proteome, we used orthogonal methods and independent
antibodies to validate 5981 antibodies that show the expression of
3775 human proteins across all major human tissues. This enhanced
validation uncovered 56 proteins corresponding to the group of “missing
proteins” and 171 proteins of unknown function. The presented
strategy will facilitate further discussions around criteria for evidence
of protein existence based on immunohistochemistry and serves as a
useful guide to identify candidate proteins for integrative studies
with quantitative proteomics methods.
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Affiliation(s)
- Åsa Sivertsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Emil Lindström
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Borbala Katona
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jimmy Vuu
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jonas Gustavsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden.,Atlas Antibodies AB, 16869 Bromma, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
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7
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Tebani A, Gummesson A, Zhong W, Koistinen IS, Lakshmikanth T, Olsson LM, Boulund F, Neiman M, Stenlund H, Hellström C, Karlsson MJ, Arif M, Dodig-Crnković T, Mardinoglu A, Lee S, Zhang C, Chen Y, Olin A, Mikes J, Danielsson H, von Feilitzen K, Jansson PA, Angerås O, Huss M, Kjellqvist S, Odeberg J, Edfors F, Tremaroli V, Forsström B, Schwenk JM, Nilsson P, Moritz T, Bäckhed F, Engstrand L, Brodin P, Bergström G, Uhlen M, Fagerberg L. Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat Commun 2020; 11:4487. [PMID: 32900998 PMCID: PMC7479148 DOI: 10.1038/s41467-020-18148-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/03/2020] [Indexed: 12/19/2022] Open
Abstract
An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, we sample a longitudinal wellness cohort with 100 healthy individuals and analyze blood molecular profiles including proteomics, transcriptomics, lipidomics, metabolomics, autoantibodies and immune cell profiling, complemented with gut microbiota composition and routine clinical chemistry. Overall, our results show high variation between individuals across different molecular readouts, while the intra-individual baseline variation is low. The analyses show that each individual has a unique and stable plasma protein profile throughout the study period and that many individuals also show distinct profiles with regards to the other omics datasets, with strong underlying connections between the blood proteome and the clinical chemistry parameters. In conclusion, the results support an individual-based definition of health and show that comprehensive omics profiling in a longitudinal manner is a path forward for precision medicine. An important aspect of precision medicine is to probe the stability in molecular profiles among healthy individuals over time. Here, the authors sample a longitudinal wellness cohort and analyse blood molecular profiles as well as gut microbiota composition.
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Affiliation(s)
- Abdellah Tebani
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders Gummesson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Wen Zhong
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ina Schuppe Koistinen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Lisa M Olsson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Boulund
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maja Neiman
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hans Stenlund
- Swedish Metabolomics Centre, Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Cecilia Hellström
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Max J Karlsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Sunjae Lee
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yang Chen
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Axel Olin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Hanna Danielsson
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Per-Anders Jansson
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Internal Medicine, Gothenburg, Sweden
| | - Oskar Angerås
- Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Cardiology, Gothenburg, Sweden
| | - Mikael Huss
- Codon Consulting, 118 26, Stockholm, Sweden.,Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden
| | - Sanela Kjellqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Björn Forsström
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Thomas Moritz
- Swedish Metabolomics Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 907 36, Umeå, Sweden
| | - Fredrik Bäckhed
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Engstrand
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Göran Bergström
- Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Center for Biosustainability, Danish Technical University, Copenhagen, Denmark
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.
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8
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Tegel H, Dannemeyer M, Kanje S, Sivertsson Å, Berling A, Svensson AS, Hober A, Enstedt H, Volk AL, Lundqvist M, Moradi M, Afshari D, Ekblad S, Xu L, Westin M, Bidad F, Schiavone LH, Davies R, Mayr LM, Knight S, Göpel SO, Voldborg BG, Edfors F, Forsström B, von Feilitzen K, Zwahlen M, Rockberg J, Takanen JO, Uhlén M, Hober S. High throughput generation of a resource of the human secretome in mammalian cells. N Biotechnol 2020; 58:45-54. [DOI: 10.1016/j.nbt.2020.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/04/2020] [Accepted: 05/30/2020] [Indexed: 02/07/2023]
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9
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Sjöstedt E, Zhong W, Fagerberg L, Karlsson M, Mitsios N, Adori C, Oksvold P, Edfors F, Limiszewska A, Hikmet F, Huang J, Du Y, Lin L, Dong Z, Yang L, Liu X, Jiang H, Xu X, Wang J, Yang H, Bolund L, Mardinoglu A, Zhang C, von Feilitzen K, Lindskog C, Pontén F, Luo Y, Hökfelt T, Uhlén M, Mulder J. An atlas of the protein-coding genes in the human, pig, and mouse brain. Science 2020; 367:367/6482/eaay5947. [PMID: 32139519 DOI: 10.1126/science.aay5947] [Citation(s) in RCA: 429] [Impact Index Per Article: 107.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022]
Abstract
The brain, with its diverse physiology and intricate cellular organization, is the most complex organ of the mammalian body. To expand our basic understanding of the neurobiology of the brain and its diseases, we performed a comprehensive molecular dissection of 10 major brain regions and multiple subregions using a variety of transcriptomics methods and antibody-based mapping. This analysis was carried out in the human, pig, and mouse brain to allow the identification of regional expression profiles, as well as to study similarities and differences in expression levels between the three species. The resulting data have been made available in an open-access Brain Atlas resource, part of the Human Protein Atlas, to allow exploration and comparison of the expression of individual protein-coding genes in various parts of the mammalian brain.
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Affiliation(s)
- Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.,Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Max Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Nicholas Mitsios
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Csaba Adori
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | | | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Jinrong Huang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark.,Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Yutao Du
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Lin Lin
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Zhanying Dong
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Ling Yang
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Hui Jiang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Cheng Zhang
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85 Uppsala, Sweden
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,Department of Biomedicine, Aarhus University, 80000 Aarhus, Denmark
| | - Tomas Hökfelt
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mathias Uhlén
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden. .,Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institutet, 171 77 Stockholm, Sweden.
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10
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Uhlen M, Karlsson MJ, Zhong W, Tebani A, Pou C, Mikes J, Lakshmikanth T, Forsström B, Edfors F, Odeberg J, Mardinoglu A, Zhang C, von Feilitzen K, Mulder J, Sjöstedt E, Hober A, Oksvold P, Zwahlen M, Ponten F, Lindskog C, Sivertsson Å, Fagerberg L, Brodin P. A genome-wide transcriptomic analysis of protein-coding genes in human blood cells. Science 2019; 366:366/6472/eaax9198. [DOI: 10.1126/science.aax9198] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022]
Abstract
Blood is the predominant source for molecular analyses in humans, both in clinical and research settings. It is the target for many therapeutic strategies, emphasizing the need for comprehensive molecular maps of the cells constituting human blood. In this study, we performed a genome-wide transcriptomic analysis of protein-coding genes in sorted blood immune cell populations to characterize the expression levels of each individual gene across the blood cell types. All data are presented in an interactive, open-access Blood Atlas as part of the Human Protein Atlas and are integrated with expression profiles across all major tissues to provide spatial classification of all protein-coding genes. This allows for a genome-wide exploration of the expression profiles across human immune cell populations and all major human tissues and organs.
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Affiliation(s)
- Mathias Uhlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Max J. Karlsson
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Wen Zhong
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Abdellah Tebani
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Christian Pou
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Jaromir Mikes
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Tadepally Lakshmikanth
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Björn Forsström
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Jacob Odeberg
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
- Coagulation Unit, Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King’s College London, London, UK
| | - Cheng Zhang
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Andreas Hober
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Per Oksvold
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden
| | - Petter Brodin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- Unit of Pediatric Rheumatology, Karolinska University Hospital, Stockholm, Sweden
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11
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Uhlén M, Karlsson MJ, Hober A, Svensson AS, Scheffel J, Kotol D, Zhong W, Tebani A, Strandberg L, Edfors F, Sjöstedt E, Mulder J, Mardinoglu A, Berling A, Ekblad S, Dannemeyer M, Kanje S, Rockberg J, Lundqvist M, Malm M, Volk AL, Nilsson P, Månberg A, Dodig-Crnkovic T, Pin E, Zwahlen M, Oksvold P, von Feilitzen K, Häussler RS, Hong MG, Lindskog C, Ponten F, Katona B, Vuu J, Lindström E, Nielsen J, Robinson J, Ayoglu B, Mahdessian D, Sullivan D, Thul P, Danielsson F, Stadler C, Lundberg E, Bergström G, Gummesson A, Voldborg BG, Tegel H, Hober S, Forsström B, Schwenk JM, Fagerberg L, Sivertsson Å. The human secretome. Sci Signal 2019; 12:12/609/eaaz0274. [PMID: 31772123 DOI: 10.1126/scisignal.aaz0274] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The proteins secreted by human cells (collectively referred to as the secretome) are important not only for the basic understanding of human biology but also for the identification of potential targets for future diagnostics and therapies. Here, we present a comprehensive analysis of proteins predicted to be secreted in human cells, which provides information about their final localization in the human body, including the proteins actively secreted to peripheral blood. The analysis suggests that a large number of the proteins of the secretome are not secreted out of the cell, but instead are retained intracellularly, whereas another large group of proteins were identified that are predicted to be retained locally at the tissue of expression and not secreted into the blood. Proteins detected in the human blood by mass spectrometry-based proteomics and antibody-based immunoassays are also presented with estimates of their concentrations in the blood. The results are presented in an updated version 19 of the Human Protein Atlas in which each gene encoding a secretome protein is annotated to provide an open-access knowledge resource of the human secretome, including body-wide expression data, spatial localization data down to the single-cell and subcellular levels, and data about the presence of proteins that are detectable in the blood.
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Affiliation(s)
- Mathias Uhlén
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. .,Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Max J Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Hober
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anne-Sophie Svensson
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Julia Scheffel
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - David Kotol
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Wen Zhong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Abdellah Tebani
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linnéa Strandberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Jan Mulder
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Berling
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Siri Ekblad
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Melanie Dannemeyer
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sara Kanje
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Johan Rockberg
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Magnus Lundqvist
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Magdalena Malm
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna-Luisa Volk
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Anna Månberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Tea Dodig-Crnkovic
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Elisa Pin
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Martin Zwahlen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Per Oksvold
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Ragna S Häussler
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mun-Gwan Hong
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Fredrik Ponten
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Borbala Katona
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Jimmy Vuu
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Emil Lindström
- Department of Pathology, Uppsala University, Uppsala, Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jonathan Robinson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Burcu Ayoglu
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Diana Mahdessian
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Devin Sullivan
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Peter Thul
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Frida Danielsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Charlotte Stadler
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bjørn G Voldborg
- Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Hanna Tegel
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Björn Forsström
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
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12
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Uhlen M, Zhang C, Lee S, Sjöstedt E, Fagerberg L, Bidkhori G, Benfeitas R, Arif M, Liu Z, Edfors F, Sanli K, von Feilitzen K, Oksvold P, Lundberg E, Hober S, Nilsson P, Mattsson J, Schwenk JM, Brunnström H, Glimelius B, Sjöblom T, Edqvist PH, Djureinovic D, Micke P, Lindskog C, Mardinoglu A, Ponten F. A pathology atlas of the human cancer transcriptome. Science 2017; 357:357/6352/eaan2507. [PMID: 28818916 DOI: 10.1126/science.aan2507] [Citation(s) in RCA: 2030] [Impact Index Per Article: 290.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/02/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022]
Abstract
Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes of 17 major cancer types with respect to clinical outcome. A general pattern emerged: Shorter patient survival was associated with up-regulation of genes involved in cell growth and with down-regulation of genes involved in cellular differentiation. Using genome-scale metabolic models, we show that cancer patients have widespread metabolic heterogeneity, highlighting the need for precise and personalized medicine for cancer treatment. All data are presented in an interactive open-access database (www.proteinatlas.org/pathology) to allow genome-wide exploration of the impact of individual proteins on clinical outcomes.
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Affiliation(s)
- Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. .,Center for Biosustainability, Danish Technical University, Copenhagen, Denmark.,School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sunjae Lee
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Evelina Sjöstedt
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Gholamreza Bidkhori
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Rui Benfeitas
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Muhammad Arif
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Zhengtao Liu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kemal Sanli
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Per Oksvold
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Johanna Mattsson
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Hans Brunnström
- Division of Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Bengt Glimelius
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Dijana Djureinovic
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,School of Biotechnology, AlbaNova University Center, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Ponten
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
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13
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Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM, Bäckström A, Danielsson F, Fagerberg L, Fall J, Gatto L, Gnann C, Hober S, Hjelmare M, Johansson F, Lee S, Lindskog C, Mulder J, Mulvey CM, Nilsson P, Oksvold P, Rockberg J, Schutten R, Schwenk JM, Sivertsson Å, Sjöstedt E, Skogs M, Stadler C, Sullivan DP, Tegel H, Winsnes C, Zhang C, Zwahlen M, Mardinoglu A, Pontén F, von Feilitzen K, Lilley KS, Uhlén M, Lundberg E. A subcellular map of the human proteome. Science 2017; 356:science.aal3321. [PMID: 28495876 DOI: 10.1126/science.aal3321] [Citation(s) in RCA: 1619] [Impact Index Per Article: 231.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/31/2017] [Indexed: 12/13/2022]
Abstract
Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.
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Affiliation(s)
- Peter J Thul
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lovisa Åkesson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Mikaela Wiking
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Diana Mahdessian
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Hammou Ait Blal
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Tove Alm
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Lars Björk
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Anna Bäckström
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Frida Danielsson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jenny Fall
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Christian Gnann
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Sophia Hober
- Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Martin Hjelmare
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Sunjae Lee
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Claire M Mulvey
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Peter Nilsson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Johan Rockberg
- Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Rutger Schutten
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Marie Skogs
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Charlotte Stadler
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Devin P Sullivan
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Hanna Tegel
- Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Casper Winsnes
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Mathias Uhlén
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden.
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden.
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14
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Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CAK, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Proteomics. Tissue-based map of the human proteome. Science 2015. [PMID: 25613900 DOI: 10.1126/science.1260419.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.
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Affiliation(s)
- Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Per Oksvold
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Evelina Sjöstedt
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - IngMarie Olsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at Dortmund TU, D-44139 Dortmund, Germany
| | - Emma Lundberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | | | | | - Jacob Odeberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Jenny Ottosson Takanen
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Tove Alm
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Holger Berling
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Hanna Tegel
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Johan Rockberg
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Marica Hamsten
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Mattias Forsberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lukas Persson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark. Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
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15
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Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CAK, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Proteomics. Tissue-based map of the human proteome. Science 2015. [PMID: 25613900 DOI: 10.1126/science.1260419/suppl_file/1260419_uhlen.sm.pdf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in all major tissues and organs in the human body.
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Affiliation(s)
- Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Per Oksvold
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Evelina Sjöstedt
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - IngMarie Olsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at Dortmund TU, D-44139 Dortmund, Germany
| | - Emma Lundberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | | | | | - Jacob Odeberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Jenny Ottosson Takanen
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Tove Alm
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Holger Berling
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Hanna Tegel
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Johan Rockberg
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Marica Hamsten
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Mattias Forsberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lukas Persson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark. Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
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16
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Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CAK, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Tissue-based map of the human proteome. Science 2015; 347:1260419. [PMID: 25613900 DOI: 10.1126/science.1260419] [Citation(s) in RCA: 8900] [Impact Index Per Article: 988.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mathias Uhlén
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden. Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
| | - Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Björn M Hallström
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Per Oksvold
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Adil Mardinoglu
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Evelina Sjöstedt
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - IngMarie Olsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) at Dortmund TU, D-44139 Dortmund, Germany
| | - Emma Lundberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | | | | | - Jacob Odeberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Jenny Ottosson Takanen
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Tove Alm
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
| | - Holger Berling
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Hanna Tegel
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Johan Rockberg
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Marica Hamsten
- Department of Proteomics, KTH-Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Mattias Forsberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lukas Persson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Gunnar von Heijne
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark. Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden·
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Alm T, von Feilitzen K, Lundberg E, Sivertsson Å, Uhlén M. A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia. J Proteome Res 2014; 13:1669-76. [PMID: 24533432 DOI: 10.1021/pr4011525] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Antibodies are crucial for the study of human proteins and have been defined as one of the three pillars in the human chromosome-centric Human Proteome Project (C-HPP). In this article the chromosome-centric structure has been used to analyze the availability of antibodies as judged by the presence within the portal Antibodypedia, a database designed to allow comparisons and scoring of publicly available antibodies toward human protein targets. This public database displays antibody data from more than one million antibodies toward human protein targets. A summary of the content in this knowledge resource reveals that there exist more than 10 antibodies to over 70% of all the putative human genes, evenly distributed over the 24 human chromosomes. The analysis also shows that at present, less than 10% of the putative human protein-coding genes (n = 1882) predicted from the genome sequence lack antibodies, suggesting that focused efforts from the antibody-based and mass spectrometry-based proteomic communities should be encouraged to pursue the analysis of these missing proteins. We show that Antibodypedia may be used to track the development of available and validated antibodies to the individual chromosomes, and thus the database is an attractive tool to identify proteins with no or few antibodies yet generated.
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Affiliation(s)
- Tove Alm
- Science for Life Laboratory, KTH-Royal Institute of Technology , SE-171 21 Stockholm, Sweden
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Fagerberg L, Hallström BM, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto CAK, Skogs M, Takanen JO, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk JM, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson A, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics 2013; 13:397-406. [PMID: 24309898 DOI: 10.1074/mcp.m113.035600] [Citation(s) in RCA: 2361] [Impact Index Per Article: 214.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.
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Affiliation(s)
- Linn Fagerberg
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
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Fagerberg L, Oksvold P, Skogs M, Algenäs C, Lundberg E, Pontén F, Sivertsson A, Odeberg J, Klevebring D, Kampf C, Asplund A, Sjöstedt E, Al-Khalili Szigyarto C, Edqvist PH, Olsson I, Rydberg U, Hudson P, Ottosson Takanen J, Berling H, Björling L, Tegel H, Rockberg J, Nilsson P, Navani S, Jirström K, Mulder J, Schwenk JM, Zwahlen M, Hober S, Forsberg M, von Feilitzen K, Uhlén M. Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP). J Proteome Res 2012; 12:2439-48. [PMID: 23276153 DOI: 10.1021/pr300924j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A gene-centric Human Proteome Project has been proposed to characterize the human protein-coding genes in a chromosome-centered manner to understand human biology and disease. Here, we report on the protein evidence for all genes predicted from the genome sequence based on manual annotation from literature (UniProt), antibody-based profiling in cells, tissues and organs and analysis of the transcript profiles using next generation sequencing in human cell lines of different origins. We estimate that there is good evidence for protein existence for 69% (n = 13985) of the human protein-coding genes, while 23% have only evidence on the RNA level and 7% still lack experimental evidence. Analysis of the expression patterns shows few tissue-specific proteins and approximately half of the genes expressed in all the analyzed cells. The status for each gene with regards to protein evidence is visualized in a chromosome-centric manner as part of a new version of the Human Protein Atlas ( www.proteinatlas.org ).
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Affiliation(s)
- Linn Fagerberg
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
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