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Guo J, Teymur A, Tang C, Saxena R, Wu T. Advancing Point-of-Care Diagnosis: Digitalizing Combinatorial Biomarker Signals for Lupus Nephritis. BIOSENSORS 2024; 14:147. [PMID: 38534254 DOI: 10.3390/bios14030147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
To improve the efficiency and patient coverage of the current healthcare system, user-friendly novel homecare devices are urgently needed. In this work, we developed a smartphone-based analyzing and reporting system (SBARS) for biomarker detection in lupus nephritis (LN). This system offers a cost-effective alternative to traditional, expensive large equipment in signal detection and quantification. This innovative approach involves using a portable and affordable microscopic reader to capture biomarker signals. Through smartphone-based image processing techniques, the intensity of each biomarker signal is analyzed. This system exhibited comparable performance to a commercial Genepix scanner in the detection of two potential novel biomarkers of LN, VISG4 and TNFRSF1b. Importantly, this smartphone-based analyzing and reporting system allows for discriminating LN patients with active renal disease from healthy controls with the area-under-the-curve (AUC) value = 0.9 for TNFRSF1b and 1.0 for VSIG4, respectively, indicating high predictive accuracy.
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Affiliation(s)
- Jiechang Guo
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
- Department of Computer Science, University of Houston, Houston, TX 77024, USA
| | - Aygun Teymur
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
| | - Chenling Tang
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
| | - Ramesh Saxena
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX 77024, USA
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2
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Oraki Kohshour M, Kannaiyan NR, Falk AJ, Papiol S, Heilbronner U, Budde M, Kalman JL, Schulte EC, Rietschel M, Witt S, Forstner AJ, Heilmann-Heimbach S, Nöthen MM, Spitzer C, Malchow B, Müller T, Wiltfang J, Falkai P, Schmitt A, Rossner MJ, Nilsson P, Schulze TG. Comparative serum proteomic analysis of a selected protein panel in individuals with schizophrenia and bipolar disorder and the impact of genetic risk burden on serum proteomic profiles. Transl Psychiatry 2022; 12:471. [PMID: 36351892 PMCID: PMC9646817 DOI: 10.1038/s41398-022-02228-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
The diagnostic criteria for schizophrenia (SCZ) and bipolar disorder (BD) are based on clinical assessments of symptoms. In this pilot study, we applied high-throughput antibody-based protein profiling to serum samples of healthy controls and individuals with SCZ and BD with the aim of identifying differentially expressed proteins in these disorders. Moreover, we explored the influence of polygenic burden for SCZ and BD on the serum levels of these proteins. Serum samples from 113 individuals with SCZ and 125 with BD from the PsyCourse Study and from 44 healthy controls were analyzed by using a set of 155 antibodies in an antibody-based assay targeting a selected panel of 95 proteins. For the cases, genotyping and imputation were conducted for DNA samples and SCZ and BD polygenic risk scores (PRS) were calculated. Univariate linear and logistic models were used for association analyses. The comparison between SCZ and BD revealed two serum proteins that were significantly elevated in BD after multiple testing adjustment: "complement C9" and "Interleukin 1 Receptor Accessory Protein". Moreover, the first principal component of variance in the proteomics dataset differed significantly between SCZ and BD. After multiple testing correction, SCZ-PRS, BD-PRS, and SCZ-vs-BD-PRS were not significantly associated with the levels of the individual proteins or the values of the proteome principal components indicating no detectable genetic effects. Overall, our findings contribute to the evidence suggesting that the analysis of circulating proteins could lead to the identification of distinctive biomarkers for SCZ and BD. Our investigation warrants replication in large-scale studies to confirm these findings.
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Affiliation(s)
- Mojtaba Oraki Kohshour
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany ,grid.411230.50000 0000 9296 6873Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nirmal R. Kannaiyan
- grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - August Jernbom Falk
- grid.5037.10000000121581746Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Sergi Papiol
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany ,grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Urs Heilbronner
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Monika Budde
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Janos L. Kalman
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany ,grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany ,grid.419548.50000 0000 9497 5095International Max Planck Research School for Translational Psychiatry (IMPRS-TP), Max Planck Institute of Psychiatry, Munich, Germany
| | - Eva C. Schulte
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany ,grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Marcella Rietschel
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie Witt
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas J. Forstner
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Stefanie Heilmann-Heimbach
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M. Nöthen
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carsten Spitzer
- grid.413108.f0000 0000 9737 0454Department of Psychosomatic Medicine and Psychotherapy, University Medical Center Rostock, Rostock, Germany
| | - Berend Malchow
- grid.411984.10000 0001 0482 5331Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Thorsten Müller
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Jens Wiltfang
- grid.411984.10000 0001 0482 5331Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany ,grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany ,grid.7311.40000000123236065iBiMED, Medical Sciences Department, University of Aveiro, Aveiro, Portugal
| | - Peter Falkai
- grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Andrea Schmitt
- grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany ,grid.11899.380000 0004 1937 0722Laboratory of Neuroscience (LIM27), Institute of Psychiatry, University of Sao Paulo, São Paulo, SP Brazil
| | - Moritz J. Rossner
- grid.5252.00000 0004 1936 973XDepartment of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Peter Nilsson
- grid.5037.10000000121581746Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Thomas G. Schulze
- grid.5252.00000 0004 1936 973XInstitute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany ,grid.411023.50000 0000 9159 4457Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY USA ,grid.21107.350000 0001 2171 9311Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA
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Genetics meets proteomics: perspectives for large population-based studies. Nat Rev Genet 2020; 22:19-37. [PMID: 32860016 DOI: 10.1038/s41576-020-0268-2] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2020] [Indexed: 12/22/2022]
Abstract
Proteomic analysis of cells, tissues and body fluids has generated valuable insights into the complex processes influencing human biology. Proteins represent intermediate phenotypes for disease and provide insight into how genetic and non-genetic risk factors are mechanistically linked to clinical outcomes. Associations between protein levels and DNA sequence variants that colocalize with risk alleles for common diseases can expose disease-associated pathways, revealing novel drug targets and translational biomarkers. However, genome-wide, population-scale analyses of proteomic data are only now emerging. Here, we review current findings from studies of the plasma proteome and discuss their potential for advancing biomedical translation through the interpretation of genome-wide association analyses. We highlight the challenges faced by currently available technologies and provide perspectives relevant to their future application in large-scale biobank studies.
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Häussler RS, Bendes A, Iglesias M, Sanchez-Rivera L, Dodig-Crnković T, Byström S, Fredolini C, Birgersson E, Dale M, Edfors F, Fagerberg L, Rockberg J, Tegel H, Uhlén M, Qundos U, Schwenk JM. Systematic Development of Sandwich Immunoassays for the Plasma Secretome. Proteomics 2019; 19:e1900008. [PMID: 31278833 DOI: 10.1002/pmic.201900008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/17/2019] [Indexed: 12/15/2022]
Abstract
The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, ≈1800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.
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Affiliation(s)
- Ragna S Häussler
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Annika Bendes
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - MariaJesus Iglesias
- Division of Cellular and Clinical Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
- K.G. Jebsen - Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, 9010, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, 9010, Tromsø, Norway
| | - Laura Sanchez-Rivera
- Division of Cellular and Clinical Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Tea Dodig-Crnković
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Sanna Byström
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Claudia Fredolini
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Elin Birgersson
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Matilda Dale
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Fredrik Edfors
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Linn Fagerberg
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Johan Rockberg
- Division of Protein Technology, Department of Protein Science, KTH - Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Hanna Tegel
- Division of Protein Technology, Department of Protein Science, KTH - Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Mathias Uhlén
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | | | - Jochen M Schwenk
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
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Fredolini C, Byström S, Sanchez-Rivera L, Ioannou M, Tamburro D, Pontén F, Branca RM, Nilsson P, Lehtiö J, Schwenk JM. Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles. Sci Rep 2019; 9:8324. [PMID: 31171813 PMCID: PMC6554399 DOI: 10.1038/s41598-019-43552-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 04/27/2019] [Indexed: 11/16/2022] Open
Abstract
There is a strong need for procedures that enable context and application dependent validation of antibodies. Here, we applied a magnetic bead assisted workflow and immunoprecipitation mass spectrometry (IP-MS/MS) to assess antibody selectivity for the detection of proteins in human plasma. A resource was built on 414 IP experiments using 157 antibodies (targeting 120 unique proteins) in assays with heat-treated or untreated EDTA plasma. For each protein we determined their antibody related degrees of enrichment using z-scores and their frequencies of identification across all IP assays. Out of 1,313 unique endogenous proteins, 426 proteins (33%) were detected in >20% of IPs, and these background components were mainly comprised of proteins from the complement system. For 45% (70/157) of the tested antibodies, the expected target proteins were enriched (z-score ≥ 3). Among these 70 antibodies, 59 (84%) co-enriched other proteins beside the intended target and mainly due to sequence homology or protein abundance. We also detected protein interactions in plasma, and for IGFBP2 confirmed these using several antibodies and sandwich immunoassays. The protein enrichment data with plasma provide a very useful and yet lacking resource for the assessment of antibody selectivity. Our insights will contribute to a more informed use of affinity reagents for plasma proteomics assays.
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Affiliation(s)
- Claudia Fredolini
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Sanna Byström
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Laura Sanchez-Rivera
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Marina Ioannou
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Davide Tamburro
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Rui M Branca
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Janne Lehtiö
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Jochen M Schwenk
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden.
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Zheng K, Chen C, Chen X, Xu M, Chen L, Hu Y, Bai Y, Liu B, Yan C, Wang H, Li J. Graphically encoded suspension array for multiplex immunoassay and quantification of autoimmune biomarkers in patient sera. Biosens Bioelectron 2019; 132:47-54. [DOI: 10.1016/j.bios.2019.02.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 02/06/2023]
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Månberg A, Bradley F, Qundos U, Guthrie BL, Birse K, Noël-Romas L, Lindskog C, Bosire R, Kiarie J, Farquhar C, Burgener AD, Nilsson P, Broliden K. A High-throughput Bead-based Affinity Assay Enables Analysis of Genital Protein Signatures in Women At Risk of HIV Infection. Mol Cell Proteomics 2019; 18:461-476. [PMID: 30504243 PMCID: PMC6398207 DOI: 10.1074/mcp.ra118.000757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 11/29/2018] [Indexed: 01/28/2023] Open
Abstract
Women at high risk of HIV infection, including sex workers and those with active genital inflammation, have molecular signatures of immune activation and epithelial barrier remodeling in samples of their genital mucosa. These alterations in the local immunological milieu are likely to impact HIV susceptibility. We here analyze host genital protein signatures in HIV uninfected women, with high frequency of condom use, living in HIV-serodiscordant relationships. Cervicovaginal secretions from women living in HIV-serodiscordant relationships (n = 62) were collected at three time points over 12 months. Women living in HIV-negative seroconcordant relationships (controls, n = 25) were sampled at one time point. All study subjects were examined for demographic parameters associated with susceptibility to HIV infection. The cervicovaginal samples were analyzed using a high-throughput bead-based affinity assay. Proteins involved in epithelial barrier function and inflammation were increased in HIV-serodiscordant women. By combining several methods of analysis, a total of five proteins (CAPG, KLK10, SPRR3, elafin/PI3, CSTB) were consistently associated with this study group. Proteins analyzed using the affinity set-up were further validated by label-free tandem mass spectrometry in a partially overlapping cohort with concordant results. Women living in HIV-serodiscordant relationships thus had elevated levels of proteins involved in epithelial barrier function and inflammation despite low prevalence of sexually transmitted infections and a high frequency of safe sex practices. The identified proteins are important markers to follow during assessment of mucosal HIV susceptibility factors and a high-throughput bead-based affinity set-up could be a suitable method for such evaluation.
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Affiliation(s)
- Anna Månberg
- From the ‡Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Frideborg Bradley
- §Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden;
| | - Ulrika Qundos
- From the ‡Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Brandon L Guthrie
- ¶Department of Global Health and Department of Epidemiology Health, University of Washington, Seattle, Washington
| | - Kenzie Birse
- ‖Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- **National HIV and Retrovirology Labs, JC Wilt Infectious Disease Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Laura Noël-Romas
- ‖Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- **National HIV and Retrovirology Labs, JC Wilt Infectious Disease Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Cecilia Lindskog
- ‡‡SciLifeLab, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rose Bosire
- §§Kenya Medical Research Institute, Nairobi, Kenya
| | - James Kiarie
- ¶¶Department of Obstetrics and Gynecology, University of Nairobi, Nairobi, Kenya
| | - Carey Farquhar
- ‖‖Department of Medicine, Global Health, and Epidemiology, University of Washington, Seattle, Washington
| | - Adam D Burgener
- §Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- ‖Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- **National HIV and Retrovirology Labs, JC Wilt Infectious Disease Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Peter Nilsson
- From the ‡Affinity Proteomics, SciLifeLab, Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Kristina Broliden
- §Department of Medicine Solna, Unit of Infectious Diseases, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
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Mu H, Sun J, Li L, Yin J, Hu N, Zhao W, Ding D, Yi L. Ionizing radiation exposure: hazards, prevention, and biomarker screening. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:15294-15306. [PMID: 29705904 DOI: 10.1007/s11356-018-2097-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Radiation is a form of energy derived from a source that is propagated through material in space. It consists of ionizing radiation or nonionizing radiation. Ionizing radiation is a feature of the environment and an important tool in medical treatment, but it can cause serious damage to organisms. A number of protective measures and standards of protection have been proposed to protect against radiation. There is also a need for biomarkers to rapidly assess individual doses of radiation, which can not only estimate the dose of radiation but also determine its effects on health. Proteomics, genomics, metabolomics, and lipidomics have been widely used in the search for such biomarkers. These topics are discussed in depth in this review.
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Affiliation(s)
- Hongxiang Mu
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Jing Sun
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Linwei Li
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Jie Yin
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Nan Hu
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Weichao Zhao
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Dexin Ding
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China
| | - Lan Yi
- Institute of Cytology and Genetics, College of pharmaceutical and biological science, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China.
- Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang, 421001, Hunan Province, People's Republic of China.
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Makris K, Haliassos A, Chondrogianni M, Tsivgoulis G. Blood biomarkers in ischemic stroke: potential role and challenges in clinical practice and research. Crit Rev Clin Lab Sci 2018; 55:294-328. [DOI: 10.1080/10408363.2018.1461190] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Konstantinos Makris
- Clinical Biochemistry Department, KAT General Hospital, Kifissia, Athens, Greece
| | | | - Maria Chondrogianni
- Second Department of Neurology, Attikon Hospital, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Georgios Tsivgoulis
- Second Department of Neurology, Attikon Hospital, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
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Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. J Proteome Res 2017; 16:4299-4310. [PMID: 28938075 PMCID: PMC5864247 DOI: 10.1021/acs.jproteome.7b00467] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields ∼43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely mapping peptides of nine amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target ∼2000 proteins. Finally, we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.
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Affiliation(s)
- Jochen M. Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2218, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie University, NSW, 2109. Australia
| | - Christopher M. Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
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11
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Sievers S, Cretich M, Gagni P, Ahrens B, Grishina G, Sampson HA, Niggemann B, Chiari M, Beyer K. Performance of a polymer coated silicon microarray for simultaneous detection of food allergen-specific IgE and IgG4. Clin Exp Allergy 2017; 47:1057-1068. [DOI: 10.1111/cea.12929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/13/2017] [Accepted: 03/20/2017] [Indexed: 01/26/2023]
Affiliation(s)
- S. Sievers
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
- Department of Biology, Chemistry and Pharmacy; Free University; Berlin Germany
| | - M. Cretich
- Istituto di Chimica del Riconoscimento Molecolare (ICRM); Consiglio Nazionale delle Ricerche; Milano Italy
| | - P. Gagni
- Istituto di Chimica del Riconoscimento Molecolare (ICRM); Consiglio Nazionale delle Ricerche; Milano Italy
| | - B. Ahrens
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
| | - G. Grishina
- Icahn School of Medicine at Mount Sinai; New York NY USA
| | - H. A. Sampson
- Icahn School of Medicine at Mount Sinai; New York NY USA
| | - B. Niggemann
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
| | - M. Chiari
- Istituto di Chimica del Riconoscimento Molecolare (ICRM); Consiglio Nazionale delle Ricerche; Milano Italy
| | - K. Beyer
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
- Icahn School of Medicine at Mount Sinai; New York NY USA
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12
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Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence. Transl Oncol 2017; 10:385-395. [PMID: 28433799 PMCID: PMC5403766 DOI: 10.1016/j.tranon.2017.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/02/2017] [Accepted: 03/06/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Blood-based proteomic profiling may aid and expand our understanding of diseases and their different phenotypes. The aim of the presented study was to profile serum samples from patients with malignant melanoma using affinity proteomic assays to describe proteins in the blood stream that are associated to stage or recurrence of melanoma. MATERIAL AND METHODS Multiplexed protein analysis was conducted using antibody suspension bead arrays. A total of 232 antibodies against 132 proteins were selected from (i) a screening with 4595 antibodies and 32 serum samples from melanoma patients and controls, (ii) antibodies used for immunohistochemistry, (iii) protein targets previously related with melanoma. The analysis was performed with 149 serum samples from patients with malignant melanoma. Antibody selectivity was then assessed by Western blot, immunocapture mass spectrometry, and epitope mapping. Lastly, indicative antibodies were applied for IHC analysis of melanoma tissues. RESULTS Serum levels of regucalcin (RGN) and syntaxin 7 (STX7) were found to be lower in patients with both recurring tumors and a high Breslow's thickness (T-stage 3/4) compared to low thickness (T-stage 1/2) without disease recurrence. Serum levels of methylenetetrahydrofolate dehydrogenase 1-like (MTHFD1L) were instead elevated in sera of T3/4 patients with recurrence. The analysis of tissue sections with S100A6 and MTHFD1L showed positive staining in a majority of patients with melanoma, and S100A6 was significantly associated to T-stage. CONCLUSIONS Our findings provide a starting point to further study RGN, STX7, MTHFD1L and S100A6 in serum to elucidate their involvement in melanoma progression and to assess a possible contribution to support clinical indications.
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13
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Discovery of circulating proteins associated to knee radiographic osteoarthritis. Sci Rep 2017; 7:137. [PMID: 28273936 PMCID: PMC5427840 DOI: 10.1038/s41598-017-00195-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/14/2017] [Indexed: 11/10/2022] Open
Abstract
Currently there are no sufficiently sensitive biomarkers able to reflect changes in joint remodelling during osteoarthritis (OA). In this work, we took an affinity proteomic approach to profile serum samples for proteins that could serve as indicators for the diagnosis of radiographic knee OA. Antibody suspension bead arrays were applied to analyze serum samples from patients with OA (n = 273), control subjects (n = 76) and patients with rheumatoid arthritis (RA, n = 244). For verification, a focused bead array was built and applied to an independent set of serum samples from patients with OA (n = 188), control individuals (n = 83) and RA (n = 168) patients. A linear regression analysis adjusting for sex, age and body mass index (BMI) revealed that three proteins were significantly elevated (P < 0.05) in serum from OA patients compared to controls: C3, ITIH1 and S100A6. A panel consisting of these three proteins had an area under the curve of 0.82 for the classification of OA and control samples. Moreover, C3 and ITIH1 levels were also found to be significantly elevated (P < 0.05) in OA patients compared to RA patients. Upon validation in additional study sets, the alterations of these three candidate serum biomarker proteins could support the diagnosis of radiographic knee OA.
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14
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Hellström C, Dodig-Crnković T, Hong MG, Schwenk JM, Nilsson P, Sjöberg R. High-Density Serum/Plasma Reverse Phase Protein Arrays. Methods Mol Biol 2017; 1619:229-238. [PMID: 28674890 DOI: 10.1007/978-1-4939-7057-5_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay.
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Affiliation(s)
- Cecilia Hellström
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden.
| | - Ronald Sjöberg
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
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15
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Evaluation of Solid Supports for Slide- and Well-Based Recombinant Antibody Microarrays. MICROARRAYS 2016; 5:microarrays5020016. [PMID: 27600082 PMCID: PMC5003492 DOI: 10.3390/microarrays5020016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 11/17/2022]
Abstract
Antibody microarrays have emerged as an important tool within proteomics, enabling multiplexed protein expression profiling in both health and disease. The design and performance of antibody microarrays and how they are processed are dependent on several factors, of which the interplay between the antibodies and the solid surfaces plays a central role. In this study, we have taken on the first comprehensive view and evaluated the overall impact of solid surfaces on the recombinant antibody microarray design. The results clearly demonstrated the importance of the surface-antibody interaction and showed the effect of the solid supports on the printing process, the array format of planar arrays (slide- and well-based), the assay performance (spot features, reproducibility, specificity and sensitivity) and assay processing (degree of automation). In the end, two high-end recombinant antibody microarray technology platforms were designed, based on slide-based (black polymer) and well-based (clear polymer) arrays, paving the way for future large-scale protein expression profiling efforts.
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16
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Abstract
Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.
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17
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Abstract
Noninvasive molecular biomarkers are becoming attractive tools to monitor disease progression, aid drug development programs and use as surrogate outcome measures in clinical trials. Cutting edge proteomic methods to assay biomarkers in body fluids have been developed in the past few years, but transitioning them to clinical practice has been slow and depends on the qualification of both the method and the biomarker.
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Affiliation(s)
- Yetrib Hathout
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA
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18
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Ayoglu B, Birgersson E, Mezger A, Nilsson M, Uhlén M, Nilsson P, Schwenk JM. Multiplexed protein profiling by sequential affinity capture. Proteomics 2016; 16:1251-6. [PMID: 26935855 PMCID: PMC5071697 DOI: 10.1002/pmic.201500398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/18/2016] [Accepted: 02/29/2016] [Indexed: 01/07/2023]
Abstract
Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off‐target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi‐automated sequential capture assay. This novel bead‐based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read‐out by a secondary capture bead array. We demonstrate in a proof‐of‐concept setting that target detection via two sequential affinity interactions reduced off‐target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA‐based signal amplification, and demonstrate the applicability of the dual capture bead‐based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond.
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Affiliation(s)
- Burcu Ayoglu
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Elin Birgersson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anja Mezger
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, Solna, Sweden
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, SciLifeLab, Stockholm University, Solna, Sweden
| | - Mathias Uhlén
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
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19
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Fredolini C, Byström S, Pin E, Edfors F, Tamburro D, Iglesias MJ, Häggmark A, Hong MG, Uhlen M, Nilsson P, Schwenk JM. Immunocapture strategies in translational proteomics. Expert Rev Proteomics 2015; 13:83-98. [PMID: 26558424 PMCID: PMC4732419 DOI: 10.1586/14789450.2016.1111141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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Affiliation(s)
- Claudia Fredolini
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Elisa Pin
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Fredrik Edfors
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Davide Tamburro
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, SciLifeLab, Karolinska Institutet, Solna, Sweden
| | - Maria Jesus Iglesias
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlen
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
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20
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Boström T, Takanen JO, Hober S. Antibodies as means for selective mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1021:3-13. [PMID: 26565067 DOI: 10.1016/j.jchromb.2015.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 01/21/2023]
Abstract
For protein analysis of biological samples, two major strategies are used today; mass spectrometry (MS) and antibody-based methods. Each strategy offers advantages and drawbacks. However, combining the two using an immunoenrichment step with MS analysis brings together the benefits of each method resulting in increased sensitivity, faster analysis and possibility of higher degrees of multiplexing. The immunoenrichment can be performed either on protein or peptide level and quantification standards can be added in order to enable determination of the absolute protein concentration in the sample. The combination of immunoenrichment and MS holds great promise for the future in both proteomics and clinical diagnostics. This review describes different setups of immunoenrichment coupled to mass spectrometry and how these can be utilized in various applications.
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Affiliation(s)
- Tove Boström
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Jenny Ottosson Takanen
- School of Biotechnology, Division of Proteomics and Nanobiotechnology, KTH-Royal Institute ofTechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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21
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Qundos U, Drobin K, Mattsson C, Hong MG, Sjöberg R, Forsström B, Solomon D, Uhlén M, Nilsson P, Michaëlsson K, Schwenk JM. Affinity proteomics discovers decreased levels of AMFR in plasma from Osteoporosis patients. Proteomics Clin Appl 2015; 10:681-90. [PMID: 25689831 PMCID: PMC5029581 DOI: 10.1002/prca.201400167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/22/2014] [Accepted: 02/11/2015] [Indexed: 12/27/2022]
Abstract
PURPOSE Affinity proteomic approaches by antibody bead arrays enable multiplexed analysis of proteins in body fluids. In the presented study, we investigated blood plasma within osteoporosis to discovery differential protein profiles and to propose novel biomarkers candidates for subsequent studies. EXPERIMENTAL DESIGN Starting with 4608 antibodies and plasma samples from 22 women for an untargeted screening, a set of 72 proteins were suggested for further analysis. Complementing these with targets from literature and other studies, a targeted bead array of 180 antibodies was built to profile for 92 proteins in plasma samples of 180 women from two independent population-based studies. RESULTS Differential profiles between osteoporosis patients and matched controls were discovered for 12 proteins in at least one of the two study sets. Among these targets, the levels of autocrine motility factor receptor (AMFR) were concordantly lower in plasma of female osteoporosis patients. Subsequently, verification of anti-AMFR antibody selectivity was conducted using high-density peptide and protein arrays, and Western blotting. CONCLUSIONS AND CLINICAL RELEVANCE Further validation in additional study sets will be needed to determine the clinical value of the observed decrease in AMFR plasma levels in osteoporosis patients, but AMFR may aid our understanding of disease mechanisms and could support existing tools for diagnosis and monitoring of patient mobility within osteoporosis.
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Affiliation(s)
- Ulrika Qundos
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Kimi Drobin
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Cecilia Mattsson
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Ronald Sjöberg
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Björn Forsström
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - David Solomon
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlén
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
| | - Karl Michaëlsson
- Department of Surgical Sciences, Section of Orthopedics, Uppsala University, Uppsala, Sweden.,Uppsala Clinical Research Centre, Uppsala University, Uppsala, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, KTH-Royal Institute of Technology, Solna, Sweden
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22
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Byström S, Ayoglu B, Häggmark A, Mitsios N, Hong MG, Drobin K, Forsström B, Fredolini C, Khademi M, Amor S, Uhlén M, Olsson T, Mulder J, Nilsson P, Schwenk JM. Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis. J Proteome Res 2014; 13:4607-19. [PMID: 25231264 DOI: 10.1021/pr500609e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.
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Affiliation(s)
- Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology , Stockholm 171 21, Sweden
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23
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Boström T, Johansson HJ, Lehtiö J, Uhlén M, Hober S. Investigating the Applicability of Antibodies Generated within the Human Protein Atlas as Capture Agents in Immunoenrichment Coupled to Mass Spectrometry. J Proteome Res 2014; 13:4424-35. [DOI: 10.1021/pr500691a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Tove Boström
- Department
of Protein Technology, KTH—Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Henrik J. Johansson
- Science
for Life Laboratory, Cancer Proteomics Mass Spectrometry, Department
of Oncology−Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden
| | - Janne Lehtiö
- Science
for Life Laboratory, Cancer Proteomics Mass Spectrometry, Department
of Oncology−Pathology, Karolinska Institute, SE-171 21 Stockholm, Sweden
| | - Mathias Uhlén
- Science
for Life Laboratory, Department of Proteomics, KTH—Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Sophia Hober
- Department
of Protein Technology, KTH—Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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24
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Pernemalm M, Lehtiö J. Mass spectrometry-based plasma proteomics: state of the art and future outlook. Expert Rev Proteomics 2014; 11:431-48. [PMID: 24661227 DOI: 10.1586/14789450.2014.901157] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mass spectrometry-based plasma proteomics is a field where intense research has been performed during the last decade. Being closely linked to biomarker discovery, the field has received a fair amount of criticism, mostly due to the low number of novel biomarkers reaching the clinic. However, plasma proteomics is under gradual development with improvements on fractionation methods, mass spectrometry instrumentation and analytical approaches. These recent developments have contributed to the revival of plasma proteomics. The goal of this review is to summarize these advances, focusing in particular on fractionation methods, both for targeted and global mass spectrometry-based plasma analysis.
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Affiliation(s)
- Maria Pernemalm
- Karolinska Institutet, Science for Life Laboratory, Tomtebodavägen 23, 171 65, Solna, Sweden
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25
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Qundos U, Johannesson H, Fredolini C, O’Hurley G, Branca R, Uhlén M, Wiklund F, Bjartell A, Nilsson P, Schwenk JM. Analysis of plasma from prostate cancer patients links decreased carnosine dipeptidase 1 levels to lymph node metastasis. TRANSLATIONAL PROTEOMICS 2014. [DOI: 10.1016/j.trprot.2013.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Drobin K, Nilsson P, Schwenk JM. Highly multiplexed antibody suspension bead arrays for plasma protein profiling. Methods Mol Biol 2014; 1023:137-45. [PMID: 23765623 DOI: 10.1007/978-1-4614-7209-4_8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Alongside the increasing availability of affinity reagents, antibody microarrays have become a powerful tool to screen for target proteins in complex samples. Applying directly labeled samples onto arrays instead of using sandwich assays offers an approach to facilitate a systematic, high-throughput, and flexible exploration of protein profiles in body fluids such as serum or plasma. As an alternative to planar arrays, a system based on color-coded beads for the creation of antibody arrays in suspension has become available to offer a microtiter plate-based option for screening larger number of samples with variable sets of capture reagents. A procedure was established for analyzing biotinylated samples without the necessity to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher pg/ml levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 samples for up to 384 proteins per assay.
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Affiliation(s)
- Kimi Drobin
- Science for Life Laboratory Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
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27
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The application of high-throughput analyses to cancer diagnosis and prognosis. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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28
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Häggmark A, Byström S, Ayoglu B, Qundos U, Uhlén M, Khademi M, Olsson T, Schwenk JM, Nilsson P. Antibody-based profiling of cerebrospinal fluid within multiple sclerosis. Proteomics 2013; 13:2256-67. [PMID: 23696371 DOI: 10.1002/pmic.201200580] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/19/2013] [Accepted: 04/09/2013] [Indexed: 12/11/2022]
Abstract
Antibody suspension bead arrays have proven to enable multiplexed and high-throughput protein profiling in unfractionated plasma and serum samples through a direct labeling approach. We here describe the development and application of an assay for protein profiling of cerebrospinal fluid (CSF). While setting up the assay, systematic intensity differences between sample groups were observed that reflected inherent sample specific total protein amounts. Supplementing the labeling reaction with BSA and IgG diminished these differences without impairing the apparent sensitivity of the assay. We also assessed the effects of heat treatment on the analysis of CSF proteins and applied the assay to profile 43 selected proteins by 101 antibodies in 339 CSF samples from a multiple sclerosis (MS) cohort. Two proteins, GAP43 and SERPINA3 were found to have a discriminating potential with altered intensity levels between sample groups. GAP43 was detected at significantly lower levels in secondary progressive MS compared to early stages of MS and the control group of other neurological diseases. SERPINA3 instead was detected at higher levels in all MS patients compared to controls. The developed assay procedure now offers new possibilities for broad-scale protein profiling of CSF within neurological disorders.
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Affiliation(s)
- Anna Häggmark
- SciLifeLab Stockholm, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
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Ayoglu B, Häggmark A, Khademi M, Olsson T, Uhlén M, Schwenk JM, Nilsson P. Autoantibody profiling in multiple sclerosis using arrays of human protein fragments. Mol Cell Proteomics 2013; 12:2657-72. [PMID: 23732997 PMCID: PMC3769337 DOI: 10.1074/mcp.m112.026757] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing ∼38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.
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Affiliation(s)
- Burcu Ayoglu
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
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30
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Qundos U, Hong MG, Tybring G, Divers M, Odeberg J, Uhlen M, Nilsson P, Schwenk JM. Profiling post-centrifugation delay of serum and plasma with antibody bead arrays. J Proteomics 2013; 95:46-54. [PMID: 23631827 DOI: 10.1016/j.jprot.2013.04.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 03/22/2013] [Accepted: 04/09/2013] [Indexed: 12/22/2022]
Abstract
UNLABELLED Several biobanking initiatives have emerged to create extensive collections of specimen for biomedical studies and various analytical platforms. An affinity proteomic analysis with antibody suspension bead arrays was conducted to investigate the influence of the pre-analytical time and temperature conditions on blood derived samples. Serum and EDTA plasma prepared from 16 individuals was centrifuged and aliquots were kept either at 4°C or in ambient temperature for 1h and up to 36h prior to first storage. Multiplexed protein profiles of post-centrifugation delay were generated in 384 biotinylated samples using 373 antibodies that targeted 343 unique proteins. Very few profiles were observed as significantly altered by the studied temperature and time intervals. Single binder and sandwich assays revealed decreasing levels of caldesmon 1 (CALD1) related to EDTA standard tubes and prolonged post-centrifugation delay of 36h. Indications from changes in CALD1 levels require further confirmation in independent material, but the current data suggests that samples should preferentially be frozen during the day of collection when to be profiled with antibody arrays selected for this study. BIOLOGICAL SIGNIFICANCE Affinity-based profiling of serum and plasma by microarray assays can provide unique opportunities for the discovery of biomarkers. It is though often not known how differences in sample handling after collection influence the downstream analysis. By profiling three types of blood preparations for alterations in protein profiles with respect to time and temperature post centrifugation, we addressed an important component in the analysis and of such specimen. We believe that this analysis adds valuable information to be considered when biobanking blood derived samples. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.
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Affiliation(s)
- Ulrika Qundos
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, SE-171 21 Solna, Sweden
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31
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Sandström A, Andersson R, Segersvärd R, Löhr M, Borrebaeck CAK, Wingren C. Serum proteome profiling of pancreatitis using recombinant antibody microarrays reveals disease-associated biomarker signatures. Proteomics Clin Appl 2013; 6:486-96. [PMID: 22930578 DOI: 10.1002/prca.201200051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE Pancreatitis is an inflammatory state of the pancreas, for which high-performing serological biomarkers are lacking. The aim of the present study was to evaluate the use of affinity proteomics for identifying potential markers of disease and stratifying pancreatitis subtypes. EXPERIMENTAL DESIGN High-content, recombinant antibody microarrays were applied for serum protein expression profiling of 113 serum samples from patients with chronic, acute, and autoimmune pancreatitis, as well as healthy controls. The sample groups were compared using supervised classification based on support vector machine analysis. RESULTS This discovery study showed that pancreatitis subtypes could be discriminated with high accuracy. Using unfiltered data, the individual subtypes, as well as the combined pancreatitis cohort, were distinguished from healthy controls with high AUC values (0.96-1.00). Moreover, characteristic protein patterns and AUC values in the range of 0.69-0.95 were observed for the individual pancreatitis entities when compared to each other, and to all other samples combined. CONCLUSIONS AND CLINICAL RELEVANCE This study demonstrated the potential of the antibody microarray approach for stratification of pancreatitis. Distinct candidate multiplex serum biomarker signatures for chronic, acute, and autoimmune pancreatitis were defined, which could enhance our fundamental knowledge of the underlying molecular mechanisms, and potentially lead to improved diagnosis.
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Affiliation(s)
- Anna Sandström
- Department of Immunotechnology, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden
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Olsson N, James P, Borrebaeck CAK, Wingren C. Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry. Mol Cell Proteomics 2012; 11:342-54. [PMID: 22543061 PMCID: PMC3412966 DOI: 10.1074/mcp.m111.016238] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The development of high-performance technology platforms for generating detailed protein expression profiles, or protein atlases, is essential. Recently, we presented a novel platform that we termed global proteome survey, where we combined the best features of affinity proteomics and mass spectrometry, to probe any proteome in a species independent manner while still using a limited set of antibodies. We used so called context-independent-motif-specific antibodies, directed against short amino acid motifs. This enabled enrichment of motif-containing peptides from a digested proteome, which then were detected and identified by mass spectrometry. In this study, we have demonstrated the quantitative capability, reproducibility, sensitivity, and coverage of the global proteome survey technology by targeting stable isotope labeling with amino acids in cell culture-labeled yeast cultures cultivated in glucose or ethanol. The data showed that a wide range of motif-containing peptides (proteins) could be detected, identified, and quantified in a highly reproducible manner. On average, each of six different motif-specific antibodies was found to target about 75 different motif-containing proteins. Furthermore, peptides originating from proteins spanning in abundance from over a million down to less than 50 copies per cell, could be targeted. It is worth noting that a significant set of peptides previously not reported in the PeptideAtlas database was among the profiled targets. The quantitative data corroborated well with the corresponding data generated after conventional strong cation exchange fractionation of the same samples. Finally, several differentially expressed proteins, with both known and unknown functions, many relevant for the central carbon metabolism, could be detected in the glucose- versus ethanol-cultivated yeast. Taken together, the study demonstrated the potential of our immunoaffinity-based mass spectrometry platform for reproducible quantitative proteomics targeting classes of motif-containing peptides.
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Affiliation(s)
- Niclas Olsson
- Department of Immunotechnology, Lund University, Lund, Sweden
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Schwenk JM, Poetz O, Zeillinger R, Joos TO. A Miniaturized Ligand Binding Assay for EGFR. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:247059. [PMID: 22577549 PMCID: PMC3332193 DOI: 10.1155/2012/247059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 01/17/2012] [Accepted: 01/18/2012] [Indexed: 12/04/2022]
Abstract
In order to study receptor abundance and its function in solutions or in homogenates from clinical specimen, methods such as sandwich or radioimmunoassays are most commonly employed. For the determination of epidermal growth factor receptor (EGFR), we describe the development of a miniaturized bead-based ligand binding assay using its ligand EGF as immobilized capture reagent. This assay was used to analyze lysates from cell lines, and the ligand-bound EGFR was detected using an EGFR-specific antibody combined with a fluorescence-based reporter system. In a proof-of concept study with lysates from breast biopsies, the assay allowed to classify breast cancer samples in accordance to clinically the relevant EGFR cut-off level. The study suggests that such a ligand binding receptor assay could become an integral part of protein profiling procedures to provide additional information about receptor functionality in addition to its abundance.
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Affiliation(s)
- Jochen M. Schwenk
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstraße 55, 72770 Reutlingen, Germany
- Science for Life Laboratory Stockholm, School of Biotechnology, KTH Royal Institute of Technology, P.O. Box 1031, 171 21 Solna, Sweden
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstraße 55, 72770 Reutlingen, Germany
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynecology, Medical University of Vienna, Währinger Gürtel 18-20, 5Q, 1090 Vienna, Austria
| | - Thomas O. Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstraße 55, 72770 Reutlingen, Germany
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Gantelius J, Bass T, Sjöberg R, Nilsson P, Andersson-Svahn H. A lateral flow protein microarray for rapid and sensitive antibody assays. Int J Mol Sci 2011; 12:7748-59. [PMID: 22174629 PMCID: PMC3233435 DOI: 10.3390/ijms12117748] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 10/31/2011] [Accepted: 11/03/2011] [Indexed: 01/28/2023] Open
Abstract
Protein microarrays are useful tools for highly multiplexed determination of presence or levels of clinically relevant biomarkers in human tissues and biofluids. However, such tools have thus far been restricted to laboratory environments. Here, we present a novel 384-plexed easy to use lateral flow protein microarray device capable of sensitive (<30 ng/mL) determination of antigen-specific antibodies in ten minutes of total assay time. Results were developed with gold nanobeads and could be recorded by a cell-phone camera or table top scanner. Excellent accuracy with an area under curve (AUC of 98% was achieved in comparison with an established glass microarray assay for 26 antigen-specific antibodies. We propose that the presented framework could find use in convenient and cost-efficient quality control of antibody production, as well as in providing a platform for multiplexed affinity-based assays in low-resource or mobile settings.
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Affiliation(s)
- Jesper Gantelius
- Division of Nanobiotechnology, School of Biotechnology, KTH-Royal Institute of Technology, Albanova University Center, 106 91 Stockholm, Sweden;
| | - Tarek Bass
- Division of Molecular Biotechnology, School of Biotechnology, KTH-Royal Institute of Technology, Albanova University Center, 106 91 Stockholm, Sweden;
| | - Ronald Sjöberg
- Division of Proteomics, School of Biotechnology, KTH-Royal Institute of Technology, SciLifeLab, 171 21 Solna, Sweden; (R.S.); (P.N.)
| | - Peter Nilsson
- Division of Proteomics, School of Biotechnology, KTH-Royal Institute of Technology, SciLifeLab, 171 21 Solna, Sweden; (R.S.); (P.N.)
| | - Helene Andersson-Svahn
- Division of Nanobiotechnology, School of Biotechnology, KTH-Royal Institute of Technology, Albanova University Center, 106 91 Stockholm, Sweden;
- Author to whom correspondence should be addressed; ; Tel.: +46-8-5537-8322
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Pontén F, Schwenk JM, Asplund A, Edqvist PHD. The Human Protein Atlas as a proteomic resource for biomarker discovery. J Intern Med 2011; 270:428-46. [PMID: 21752111 DOI: 10.1111/j.1365-2796.2011.02427.x] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The analysis of tissue-specific expression at both the gene and protein levels is vital for understanding human biology and disease. Antibody-based proteomics provides a strategy for the systematic generation of antibodies against all human proteins to combine with protein profiling in tissues and cells using tissue microarrays, immunohistochemistry and immunofluorescence. The Human Protein Atlas project was launched in 2003 with the aim of creating a map of protein expression patterns in normal cells, tissues and cancer. At present, 11,200 unique proteins corresponding to over 50% of all human protein-encoding genes have been analysed. All protein expression data, including underlying high-resolution images, are published on the free and publically available Human Protein Atlas portal (http://www.proteinatlas.org). This database provides an important source of information for numerous biomedical research projects, including biomarker discovery efforts. Moreover, the global analysis of how our genome is expressed at the protein level has provided basic knowledge on the ubiquitous expression of a large proportion of our proteins and revealed the paucity of cell- and tissue-type-specific proteins.
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Affiliation(s)
- F Pontén
- Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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Häggmark A, Neiman M, Drobin K, Zwahlen M, Uhlén M, Nilsson P, Schwenk JM. Classification of protein profiles from antibody microarrays using heat and detergent treatment. N Biotechnol 2011; 29:564-70. [PMID: 22023822 DOI: 10.1016/j.nbt.2011.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/09/2011] [Accepted: 10/09/2011] [Indexed: 01/16/2023]
Abstract
Antibody microarrays offer new opportunities for exploring the proteome and to identify biomarker candidates in human serum and plasma. Here, we have investigated the effect of heat and detergents on an antibody-based suspension bead array (SBA) assay using polyclonal antibodies and biotinylated plasma samples. With protein profiles from more than 2300 antibodies generated in 384-plex antibody SBAs, three major classes of heat and detergent susceptibility could be described. The results show that washing of the beads with SDS (rather than Tween) after target binding lowered intensity levels of basically all profiles and that about 50% of the profiles appeared to be lowered to a similar extent by heating of the sample. About 33% of the profiles appeared to be insensitive to heat treatment while another 17% showed a positive influence of heat to yield elevated profiles. The results suggest that the classification of antibodies is driven by the molecular properties of the antibody-antigen interaction and can generally not be predicted based on protein class or Western blot data. The experimental scheme presented here can be used to systematically categorize antibodies and thereby combine antibodies with similar properties into targeted arrays for analysis of plasma and serum.
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Affiliation(s)
- Anna Häggmark
- Science for Life Laboratory Stockholm, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, SE-171 21 Solna, Sweden
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38
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Neiman M, Hedberg JJ, Dönnes PR, Schuppe-Koistinen I, Hanschke S, Schindler R, Uhlén M, Schwenk JM, Nilsson P. Plasma Profiling Reveals Human Fibulin-1 as Candidate Marker for Renal Impairment. J Proteome Res 2011; 10:4925-34. [DOI: 10.1021/pr200286c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Maja Neiman
- Science for Life Laboratory Stockholm, KTH - Royal Institute of Technology, Box 1031, SE-17121 Solna, Sweden
| | - Jesper J. Hedberg
- Department of Molecular Toxicology, Safety Assessment, AstraZeneca R&D Södertälje, SE-15185 Södertälje, Sweden
| | - Pierre R. Dönnes
- Department of Molecular Toxicology, Safety Assessment, AstraZeneca R&D Södertälje, SE-15185 Södertälje, Sweden
| | - Ina Schuppe-Koistinen
- Department of Molecular Toxicology, Safety Assessment, AstraZeneca R&D Södertälje, SE-15185 Södertälje, Sweden
| | - Stephan Hanschke
- Nephrology and Internal Intensive Care Medicine, Charité-Virchow Clinic, Augustenburger Platz 1, DE-13353 Berlin, Germany
| | - Ralf Schindler
- Nephrology and Internal Intensive Care Medicine, Charité-Virchow Clinic, Augustenburger Platz 1, DE-13353 Berlin, Germany
| | - Mathias Uhlén
- Science for Life Laboratory Stockholm, KTH - Royal Institute of Technology, Box 1031, SE-17121 Solna, Sweden
| | - Jochen M. Schwenk
- Science for Life Laboratory Stockholm, KTH - Royal Institute of Technology, Box 1031, SE-17121 Solna, Sweden
| | - Peter Nilsson
- Science for Life Laboratory Stockholm, KTH - Royal Institute of Technology, Box 1031, SE-17121 Solna, Sweden
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Data“-omics” and intensive care unit patient care*. Crit Care Med 2011; 39:1823-4. [DOI: 10.1097/ccm.0b013e31821caf44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Next-generation plasma profiling: affinity array potential. Bioanalysis 2011; 3:1543-6. [DOI: 10.4155/bio.11.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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