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Jotanovic J, Tebani A, Hekmati N, Sivertsson Å, Lindskog C, Uhlèn M, Gudjonsson O, Tsatsaris E, Engström BE, Wikström J, Pontén F, Casar-Borota O. Transcriptome Analysis Reveals Distinct Patterns Between the Invasive and Noninvasive Pituitary Neuroendocrine Tumors. J Endocr Soc 2024; 8:bvae040. [PMID: 38505563 PMCID: PMC10949357 DOI: 10.1210/jendso/bvae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Indexed: 03/21/2024] Open
Abstract
Although most pituitary neuroendocrine tumors (PitNETs)/pituitary adenomas remain intrasellar, a significant proportion of tumors show parasellar invasive growth and 6% to 8% infiltrate the bone structures, thus affecting the prognosis. There is an unmet need to identify novel markers that can predict the parasellar growth of PitNETs. Furthermore, mechanisms that regulate bone invasiveness of PitNETs and factors related to tumor vascularization are largely unknown. We used genome-wide mRNA analysis in a cohort of 77 patients with PitNETs of different types to explore the differences in gene expression patterns between invasive and noninvasive tumors with respect to the parasellar growth and regarding the rare phenomenon of bone invasiveness. Additionally, we studied the genes correlated to the contrast enhancement quotient, a novel radiological parameter of tumor vascularization. Most of the genes differentially expressed related to the parasellar growth were genes involved in tumor invasiveness. Differentially expressed genes associated with bone invasiveness are involved in NF-κB pathway and antitumoral immune response. Lack of clear clustering regarding the parasellar and bone invasiveness may be explained by the influence of the cell lineage-related genes in this heterogeneous cohort of PitNETs. Our transcriptomics analysis revealed differences in the molecular fingerprints between invasive, including bone invasive, and noninvasive PitNETs, although without clear clustering. The contrast enhancement quotient emerged as a radiological parameter of tumor vascularization, correlating with several angiogenesis-related genes. Several of the top genes related to the PitNET invasiveness and vascularization have potential prognostic and therapeutic application requiring further research.
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Affiliation(s)
- Jelena Jotanovic
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, 75185 Uppsala, Sweden
| | - Abdellah Tebani
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, 17121 Solna, Stockholm, Sweden
- Department of Metabolic Biochemistry, UNIROUEN, INSERM U1245, CHU Rouen, Normandie University, 76000 Rouen, France
| | - Neda Hekmati
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, 17121 Solna, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Mathias Uhlèn
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, 17121 Solna, Stockholm, Sweden
| | - Olafur Gudjonsson
- Department of Neuroscience, Uppsala University, 75185 Uppsala, Sweden
| | - Erika Tsatsaris
- Endocrinology and Mineral Metabolism, Department of Medical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | - Britt Edén Engström
- Endocrinology and Mineral Metabolism, Department of Medical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | - Johan Wikström
- Neuroradiology, Department of Surgical Sciences, Uppsala University, 75185 Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Olivera Casar-Borota
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, 75185 Uppsala, Sweden
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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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3
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Tebani A, Jotanovic J, Hekmati N, Sivertsson Å, Gudjonsson O, Edén Engström B, Wikström J, Uhlèn M, Casar-Borota O, Pontén F. Annotation of pituitary neuroendocrine tumors with genome-wide expression analysis. Acta Neuropathol Commun 2021; 9:181. [PMID: 34758873 PMCID: PMC8579660 DOI: 10.1186/s40478-021-01284-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Pituitary neuroendocrine tumors (PitNETs) are common, generally benign tumors with complex clinical characteristics related to hormone hypersecretion and/or growing sellar tumor mass. PitNETs can be classified based on the expression pattern of anterior pituitary hormones and three main transcriptions factors (TF), SF1, PIT1 and TPIT that regulate differentiation of adenohypophysial cells. Here, we have extended this classification based on the global transcriptomics landscape using tumor tissue from a well-defined cohort comprising 51 PitNETs of different clinical and histological types. The molecular profiles were compared with current classification schemes based on immunohistochemistry. Our results identified three main clusters of PitNETs that were aligned with the main pituitary TFs expression patterns. Our analyses enabled further identification of specific genes and expression patterns, including both known and unknown genes, that could distinguish the three different classes of PitNETs. We conclude that the current classification of PitNETs based on the expression of SF1, PIT1 and TPIT reflects three distinct subtypes of PitNETs with different underlying biology and partly independent from the expression of corresponding hormones. The transcriptomic analysis reveals several potentially targetable tumor-driving genes with previously unknown role in pituitary tumorigenesis.
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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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Sjöstedt E, Kolnes AJ, Olarescu NC, Mitsios N, Hikmet F, Sivertsson Å, Lindskog C, Øystese KAB, Jørgensen AP, Bollerslev J, Casar-Borota O. TGFBR3L-An Uncharacterised Pituitary Specific Membrane Protein Detected in the Gonadotroph Cells in Non-Neoplastic and Tumour Tissue. Cancers (Basel) 2020; 13:cancers13010114. [PMID: 33396509 PMCID: PMC7795056 DOI: 10.3390/cancers13010114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/03/2020] [Revised: 12/11/2020] [Accepted: 12/25/2020] [Indexed: 01/23/2023] Open
Abstract
Simple Summary Pituitary neuroendocrine tumours originate from the endocrine cells of the anterior pituitary gland and may develop from any of the cell lineages responsible for producing the different pituitary hormones. The details related to tumour differentiation and hormone production in these tumours are not fully understood. The aim of our study was to investigate an uncharacterised pituitary enriched protein, transforming growth factor beta-receptor 3 like (TGFBR3L). The TGFBR3L protein is highly expressed in the pituitary compared to other organs. We found the protein to be gonadotroph-specific, i.e., detected in the cells that express follicle-stimulating and luteinizing hormones (FSH/LH). The gonadotroph-specific nature of TGFBR3L, a correlation to both FSH and LH as well as an inverse correlation to membranous E-cadherin and oestrogen receptor β suggests a role in gonadotroph cell development and function and, possibly, tumour progression. Abstract Here, we report the investigation of transforming growth factor beta-receptor 3 like (TGFBR3L), an uncharacterised pituitary specific membrane protein, in non-neoplastic anterior pituitary gland and pituitary neuroendocrine tumours. A polyclonal antibody produced within the Human Protein Atlas project (HPA074356) was used for TGFBR3L staining and combined with SF1 and FSH for a 3-plex fluorescent protocol, providing more details about the cell lineage specificity of TGFBR3L expression. A cohort of 230 pituitary neuroendocrine tumours were analysed. In a subgroup of previously characterised gonadotroph tumours, correlation with expression of FSH/LH, E-cadherin, oestrogen (ER) and somatostatin receptors (SSTR) was explored. TGFBR3L showed membranous immunolabeling and was found to be gonadotroph cell lineage-specific, verified by co-expression with SF1 and FSH/LH staining in both tumour and non-neoplastic anterior pituitary tissues. TGFBR3L immunoreactivity was observed in gonadotroph tumours only and demonstrated intra-tumour heterogeneity with a perivascular location. TGFBR3L immunostaining correlated positively to both FSH (R = 0.290) and LH (R = 0.390) immunostaining, and SSTR3 (R = 0.315). TGFBR3L correlated inversely to membranous E-cadherin staining (R = −0.351) and oestrogen receptor β mRNA (R = −0.274). In conclusion, TGFBR3L is a novel pituitary gland specific protein, located in the membrane of gonadotroph cells in non-neoplastic anterior pituitary gland and in a subset of gonadotroph pituitary tumours.
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Affiliation(s)
- Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden;
- Department of Immunology, Genetics and Pathology, Uppsala University, Dag Hammarskjöldsväg 20, 752 37 Uppsala, Sweden; (F.H.); (C.L.); (O.C.-B.)
- Correspondence: ; Tel.: +46-73-956-7077
| | - Anders J. Kolnes
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Rikshospitalet, Pb. 4950 Nydalen, 0424 Oslo, Norway; (A.J.K.); (N.C.O.); (K.A.B.Ø.); (A.P.J.); (J.B.)
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Box 1072 Blindern, 0316 Oslo, Norway
| | - Nicoleta C. Olarescu
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Rikshospitalet, Pb. 4950 Nydalen, 0424 Oslo, Norway; (A.J.K.); (N.C.O.); (K.A.B.Ø.); (A.P.J.); (J.B.)
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Box 1072 Blindern, 0316 Oslo, Norway
| | - Nicholas Mitsios
- Department of Neuroscience, Karolinska Institutet, Solnavägen 1, 171 77 Solna, Sweden;
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Uppsala University, Dag Hammarskjöldsväg 20, 752 37 Uppsala, Sweden; (F.H.); (C.L.); (O.C.-B.)
| | - Åsa Sivertsson
- Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, Tomtebodavägen 23a, 171 65 Solna, Sweden;
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Dag Hammarskjöldsväg 20, 752 37 Uppsala, Sweden; (F.H.); (C.L.); (O.C.-B.)
| | - Kristin A. B. Øystese
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Rikshospitalet, Pb. 4950 Nydalen, 0424 Oslo, Norway; (A.J.K.); (N.C.O.); (K.A.B.Ø.); (A.P.J.); (J.B.)
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Box 1072 Blindern, 0316 Oslo, Norway
| | - Anders P. Jørgensen
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Rikshospitalet, Pb. 4950 Nydalen, 0424 Oslo, Norway; (A.J.K.); (N.C.O.); (K.A.B.Ø.); (A.P.J.); (J.B.)
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Box 1072 Blindern, 0316 Oslo, Norway
| | - Jens Bollerslev
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Rikshospitalet, Pb. 4950 Nydalen, 0424 Oslo, Norway; (A.J.K.); (N.C.O.); (K.A.B.Ø.); (A.P.J.); (J.B.)
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Box 1072 Blindern, 0316 Oslo, Norway
| | - Olivera Casar-Borota
- Department of Immunology, Genetics and Pathology, Uppsala University, Dag Hammarskjöldsväg 20, 752 37 Uppsala, Sweden; (F.H.); (C.L.); (O.C.-B.)
- Department of Clinical Pathology, Uppsala University Hospital, 75185 Uppsala, Sweden
- Department of Pathology, Oslo University Hospital, Oslo University Hospital, Rikshospitalet, Pb. 4950 Nydalen, 0424 Oslo, Norway
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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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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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Ding M, Tegel H, Sivertsson Å, Hober S, Snijder A, Ormö M, Strömstedt PE, Davies R, Holmberg Schiavone L. Secretome-Based Screening in Target Discovery. SLAS Discov 2020; 25:535-551. [PMID: 32425085 PMCID: PMC7309359 DOI: 10.1177/2472555220917113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Mats Ormö
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rick Davies
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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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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10
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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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11
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Sjöstedt E, Sivertsson Å, Hikmet Noraddin F, Katona B, Näsström Å, Vuu J, Kesti D, Oksvold P, Edqvist PH, Olsson I, Uhlén M, Lindskog C. Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues. J Proteome Res 2018; 17:4127-4137. [DOI: 10.1021/acs.jproteome.8b00406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Evelina Sjöstedt
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
| | - Feria Hikmet Noraddin
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Borbala Katona
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Åsa Näsström
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Jimmy Vuu
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Dennis Kesti
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
| | - Per-Henrik Edqvist
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Ingmarie Olsson
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm SE 171 21, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE 752 37, Sweden
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12
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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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13
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Gremel G, Djureinovic D, Niinivirta M, Laird A, Ljungqvist O, Johannesson H, Bergman J, Edqvist PH, Navani S, Khan N, Patil T, Sivertsson Å, Uhlén M, Harrison DJ, Ullenhag GJ, Stewart GD, Pontén F. A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma. BMC Cancer 2017; 17:9. [PMID: 28052770 PMCID: PMC5215231 DOI: 10.1186/s12885-016-3030-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 10/14/2015] [Accepted: 12/23/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND There is an unmet clinical need for better prognostic and diagnostic tools for renal cell carcinoma (RCC). METHODS Human Protein Atlas data resources, including the transcriptomes and proteomes of normal and malignant human tissues, were searched for RCC-specific proteins and cubilin (CUBN) identified as a candidate. Patient tissue representing various cancer types was constructed into a tissue microarray (n = 940) and immunohistochemistry used to investigate the specificity of CUBN expression in RCC as compared to other cancers. Two independent RCC cohorts (n = 181; n = 114) were analyzed to further establish the sensitivity of CUBN as RCC-specific marker and to explore if the fraction of RCCs lacking CUBN expression could predict differences in patient survival. RESULTS CUBN was identified as highly RCC-specific protein with 58% of all primary RCCs staining positive for CUBN using immunohistochemistry. In venous tumor thrombi and metastatic lesions, the frequency of CUBN expression was increasingly lost. Clear cell RCC (ccRCC) patients with CUBN positive tumors had a significantly better prognosis compared to patients with CUBN negative tumors, independent of T-stage, Fuhrman grade and nodal status (HR 0.382, CI 0.203-0.719, P = 0.003). CONCLUSIONS CUBN expression is highly specific to RCC and loss of the protein is significantly and independently associated with poor prognosis. CUBN expression in ccRCC provides a promising positive prognostic indicator for patients with ccRCC. The high specificity of CUBN expression in RCC also suggests a role as a new diagnostic marker in clinical cancer differential diagnostics to confirm or rule out RCC.
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Affiliation(s)
- Gabriela Gremel
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marjut Niinivirta
- Department of Oncology, Radiology and Radiation Science, Uppsala University, Uppsala, Sweden
| | - Alexander Laird
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK.,Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | | | - Julia Bergman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | - Åsa Sivertsson
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | | | - Gustav J Ullenhag
- Department of Oncology, Radiology and Radiation Science, Uppsala University, Uppsala, Sweden
| | - Grant D Stewart
- Edinburgh Urological Cancer Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Academic Urology Group, University of Cambridge, Box 43, Addenbrooke's Hospital, Cambridge Biomedical Campus, Hill's Road, CB2 0QQ, Cambridge, UK
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, SE-751 85, Uppsala, 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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Lundqvist M, Edfors F, Sivertsson Å, Hallström BM, Hudson EP, Tegel H, Holmberg A, Uhlén M, Rockberg J. Solid-phase cloning for high-throughput assembly of single and multiple DNA parts. Nucleic Acids Res 2015; 43:e49. [PMID: 25618848 PMCID: PMC4402512 DOI: 10.1093/nar/gkv036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 09/26/2014] [Accepted: 01/12/2015] [Indexed: 11/14/2022] Open
Abstract
We describe solid-phase cloning (SPC) for high-throughput assembly of expression plasmids. Our method allows PCR products to be put directly into a liquid handler for capture and purification using paramagnetic streptavidin beads and conversion into constructs by subsequent cloning reactions. We present a robust automated protocol for restriction enzyme based SPC and its performance for the cloning of >60 000 unique human gene fragments into expression vectors. In addition, we report on SPC-based single-strand assembly for applications where exact control of the sequence between fragments is needed or where multiple inserts are to be assembled. In this approach, the solid support allows for head-to-tail assembly of DNA fragments based on hybridization and polymerase fill-in. The usefulness of head-to-tail SPC was demonstrated by assembly of >150 constructs with up to four DNA parts at an average success rate above 80%. We report on several applications for SPC and we suggest it to be particularly suitable for high-throughput efforts using laboratory workstations.
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Affiliation(s)
- Magnus Lundqvist
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Fredrik Edfors
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Åsa Sivertsson
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Björn M Hallström
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Elton P Hudson
- KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm 17165, Sweden
| | - Hanna Tegel
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Anders Holmberg
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Mathias Uhlén
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, Sweden KTH - Royal Institute of Technology, Science for Life Laboratory, Stockholm 17165, Sweden Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark
| | - Johan Rockberg
- KTH-Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, Stockholm 10691, 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. 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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17
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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: 8863] [Impact Index Per Article: 984.8] [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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18
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Habuka M, Fagerberg L, Hallström BM, Kampf C, Edlund K, Sivertsson Å, Yamamoto T, Pontén F, Uhlén M, Odeberg J. The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling. PLoS One 2014; 9:e116125. [PMID: 25551756 PMCID: PMC4281243 DOI: 10.1371/journal.pone.0116125] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/02/2014] [Indexed: 12/22/2022] Open
Abstract
To understand renal functions and disease, it is important to define the molecular constituents of the various compartments of the kidney. Here, we used comparative transcriptomic analysis of all major organs and tissues in the human body, in combination with kidney tissue micro array based immunohistochemistry, to generate a comprehensive description of the kidney-specific transcriptome and proteome. A special emphasis was placed on the identification of genes and proteins that were elevated in specific kidney subcompartments. Our analysis identified close to 400 genes that had elevated expression in the kidney, as compared to the other analysed tissues, and these were further subdivided, depending on expression levels, into tissue enriched, group enriched or tissue enhanced. Immunohistochemistry allowed us to identify proteins with distinct localisation to the glomeruli (n = 11), proximal tubules (n = 120), distal tubules (n = 9) or collecting ducts (n = 8). Among the identified kidney elevated transcripts, we found several proteins not previously characterised or identified as elevated in kidney. This description of the kidney specific transcriptome and proteome provides a resource for basic and clinical research to facilitate studies to understand kidney biology and disease.
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Affiliation(s)
- Masato Habuka
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan
| | - Linn Fagerberg
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Björn M. Hallström
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karolina Edlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Sivertsson
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Tadashi Yamamoto
- Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jacob Odeberg
- School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Medicine, Karolinska Institutet and Centre for Hematology, Karolinska University Hospital, Stockholm, Sweden
- * E-mail:
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19
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Stadler C, Fagerberg L, Sivertsson Å, Oksvold P, Zwahlen M, Hallström BM, Lundberg E, Uhlén M. RNA- and antibody-based profiling of the human proteome with focus on chromosome 19. J Proteome Res 2014; 13:2019-27. [PMID: 24579871 DOI: 10.1021/pr401156g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An important part of the Human Proteome Project is to characterize the protein complement of the genome with antibody-based profiling. Within the framework of this effort, a new version 12 of the Human Protein Atlas ( www.proteinatlas.org ) has been launched, including transcriptomics data for 27 tissues and 44 cell lines to complement the protein expression data from antibody-based profiling. Besides the extensive addition of transcriptomics data, the Human Protein Atlas now contains antibody-based protein profiles for 82% of the 20 329 putative protein-coding genes. The comprehensive data resulting from RNA-seq analysis and antibody-based profiling performed within the Human Protein Atlas as well as information from UniProt were used to generate evidence summary scores for each of the 20 329 genes, of which 94% now have experimental evidence at least at transcript level. The evidence scores for all individual genes are displayed with regards to both RNA- and antibody-based protein profiles, including chromosome-centric visualizations. An analysis of the human chromosome 19 shows that ∼43% of the genes are expressed at the transcript level in all 27 tissues analyzed, suggesting a "house-keeping" function, while 12% of the genes show a more tissue-specific pattern with enriched expression in one of the analyzed tissues only.
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Affiliation(s)
- Charlotte Stadler
- Science for Life Laboratory, KTH - Royal Institute of Technology , SE-171 21 Stockholm, Sweden
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20
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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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Sjöberg R, Sundberg M, Gundberg A, Sivertsson Å, Schwenk JM, Uhlén M, Nilsson P. Validation of affinity reagents using antigen microarrays. N Biotechnol 2012; 29:555-63. [DOI: 10.1016/j.nbt.2011.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 01/31/2023]
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Uhlén M, Oksvold P, Älgenäs C, Hamsten C, Fagerberg L, Klevebring D, Lundberg E, Odeberg J, Pontén F, Kondo T, Sivertsson Å. Antibody-based protein profiling of the human chromosome 21. Mol Cell Proteomics 2011; 11:M111.013458. [PMID: 22042635 PMCID: PMC3316724 DOI: 10.1074/mcp.m111.013458] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [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] [Indexed: 11/28/2022] Open
Abstract
The Human Proteome Project has been proposed to create a knowledge-based resource based on a systematical mapping of all human proteins, chromosome by chromosome, in a gene-centric manner. With this background, we here describe the systematic analysis of chromosome 21 using an antibody-based approach for protein profiling using both confocal microscopy and immunohistochemistry, complemented with transcript profiling using next generation sequencing data. We also describe a new approach for protein isoform analysis using a combination of antibody-based probing and isoelectric focusing. The analysis has identified several genes on chromosome 21 with no previous evidence on the protein level, and the isoform analysis indicates that a large fraction of human proteins have multiple isoforms. A chromosome-wide matrix is presented with status for all chromosome 21 genes regarding subcellular localization, tissue distribution, and molecular characterization of the corresponding proteins. The path to generate a chromosome-specific resource, including integrated data from complementary assay platforms, such as mass spectrometry and gene tagging analysis, is discussed.
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Affiliation(s)
- Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, SE-17121 Solna, Sweden.
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Berglund L, Björling E, Jonasson K, Rockberg J, Fagerberg L, Al-Khalili Szigyarto C, Sivertsson Å, Uhlén M. A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation. Proteomics 2008; 8:2832-9. [DOI: 10.1002/pmic.200800203] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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