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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] [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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2
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Kousted TM, Kalliokoski O, Christensen SK, Winther JR, Hau J. Exploring the antigenic response to multiplexed immunizations in a chicken model of antibody production. Heliyon 2017; 3:e00267. [PMID: 28367512 PMCID: PMC5362046 DOI: 10.1016/j.heliyon.2017.e00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/22/2017] [Accepted: 03/09/2017] [Indexed: 11/28/2022] Open
Abstract
Hens have a tremendous capacity for producing polyclonal antibodies that can subsequently be isolated in high concentrations from their eggs. An approach for further maximizing their potential is to produce multiple antisera in the same individual through multiplexed (multiple simultaneous) immunizations. An unknown with this approach is how many immunogens a single bird is capable of mounting a sizeable antigenic response toward. At what point does it become counter-productive to add more immunogens to the same immunization regimen? In the present study we were able to demonstrate that the competing effects of co-administering multiple immunogens effectively limit the antibody specificities that can be raised in a single individual to a fairly low number. Two potent model immunogens, KLH and CRM197, were administered together with competing antigens in various concentrations and complexities. With an upper limit of 1 mg protein material recommended for chicken immunizations, we found that the maximum number of immunogens that can be reliably used is most likely in the low double digits. The limiting factor for a response to an immunogen could not be related to the number of splenic plasma cells producing antibodies against it. When administering KLH alone, up to 70% of the IgY-producing splenic plasma cells were occupied with producing anti-KLH antibodies; but when simultaneously being exposed to a plethora of other antigens, a response of a comparable magnitude could be mounted with a splenic plasma cell involvement of less than 5%. Two breeds of egg-layers were compared with respect to antibody production in an initial experiment, but differences in antibody productivity were negligible. Although our findings support the use of multiplexed immunizations in the hen, we find that the number of immunogens cannot be stretched much higher than the handful that has been used in mammalian models to date.
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Affiliation(s)
- Tina M. Kousted
- Department of Experimental Medicine, University of Copenhagen, Denmark
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark
| | - Otto Kalliokoski
- Department of Experimental Medicine, University of Copenhagen, Denmark
- Corresponding author at: Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
| | | | - Jakob R. Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Denmark
| | - Jann Hau
- Department of Experimental Medicine, University of Copenhagen, Denmark
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3
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Hoheisel JD, Alhamdani MSS, Schröder C. Affinity-based microarrays for proteomic analysis of cancer tissues. Proteomics Clin Appl 2014; 7:8-15. [PMID: 23341233 DOI: 10.1002/prca.201200114] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 11/09/2012] [Accepted: 11/14/2012] [Indexed: 01/21/2023]
Abstract
Based on about a decade of technical developments in analysing the human proteome with antibody microarrays and experience in performing such analyses, now there are the means at hand for detailed and simultaneously global investigations of this kind. Many technical aspects have been dealt with of both the microarray format itself - such as overcoming kinetic and mass transport limitations and thus achieving accurate measurements - and ancillary processes - such as extraction procedures that provide good protein solubilisation, produce reproducible yields and preserve the native protein conformation as much as possible. The overall analysis process is robust and reproducible, highly sensitive down to the level of single-molecule detection and permits an analysis of several parameters on many molecules at a time. While the study of body liquids is widely applied, analyses of tissue proteomes are still scarce. However, conditions do exist to perform the latter at a quality level that meets the standards for clinical applications. This review highlights methodological aspects relevant for a biomedically useful analysis of cellular samples and discusses the potential of such studies, in particular, in view of personalised medicine approaches.
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Affiliation(s)
- Jörg D Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany.
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4
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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5
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Ray P, Sullenger BA, White RR. Further characterization of the target of a potential aptamer biomarker for pancreatic cancer: cyclophilin B and its posttranslational modifications. Nucleic Acid Ther 2013; 23:435-42. [PMID: 24152208 DOI: 10.1089/nat.2013.0439] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Posttranslational modifications on proteins can serve as useful biomarkers for disease. However, their discovery and detection in biological fluids is challenging. Aptamers are oligonucleotide ligands that demonstrate high affinity toward their target proteins and can discriminate closely related proteins with superb specificity. Previously, we generated a cyclophilin B aptamer (M9-5) that could discriminate sera from pancreatic cancer patients and healthy volunteers with high specificity and sensitivity. In our present work we further characterize the aptamer and the target protein, cyclophilin B, and demonstrate that the aptamer could discriminate between cyclophilin B expressed in human cells versus bacteria. Using mass-spectrometric analysis, we discovered post-translational modifications on cyclophilin B that might be responsible for the M9-5 selectivity. The ability to distinguish between forms of the same protein with differing post-translational modifications is an important advantage of aptamers as tools for identification and detection of biomarkers.
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Affiliation(s)
- Partha Ray
- Department of Surgery, Duke University School of Medicine , Durham, North Carolina
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6
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Microfluidic strategies applied to biomarker discovery and validation for multivariate diagnostics. Bioanalysis 2012; 3:2233-51. [PMID: 21985417 DOI: 10.4155/bio.11.224] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Complex diseases are caused by combinatorial genetic, environmental and lifestyle factors. The emergence of multibiomarker tests to define these diseases and to identify the early, presymptomatic stages offers several advantages to the conventional use of single marker tests. The development of multibiomarker protein-based tests remains constrained by technological and operational limitations in assaying hundreds to thousands of proteins in thousands of samples. In order to develop a multibiomarker test that stratifies risk for Type 2 diabetes, we took a candidate-driven immunoassay approach utilizing a microfluidics platform to analyze 89 candidate proteins in thousands of samples, which allowed us to move from discovery to a commercial test in 2 years. Future multibiomarker test development will be enhanced by advancements in the number of proteins that can be analyzed, analytical sensitivity and throughput, and sample volume requirements, all of which depend on the further advancement of microfluidics, detection technologies and affinity-based reagents.
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7
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Liu R, Jiang B, Yu H, Chaput JC. Generating DNA synbodies from previously discovered peptides. Chembiochem 2011; 12:1813-7. [PMID: 21692159 PMCID: PMC3390916 DOI: 10.1002/cbic.201100284] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Indexed: 12/31/2022]
Affiliation(s)
- Rui Liu
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
| | - Bing Jiang
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
| | - Hanyang Yu
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
| | - John C. Chaput
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5301, Fax: (+1) (480) 727-6947
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9
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Mustafa SA, Hoheisel JD, Alhamdani MSS. Secretome profiling with antibody microarrays. MOLECULAR BIOSYSTEMS 2011; 7:1795-801. [DOI: 10.1039/c1mb05071k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Schwenk JM, Igel U, Neiman M, Langen H, Becker C, Bjartell A, Ponten F, Wiklund F, Grönberg H, Nilsson P, Uhlen M. Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays. Mol Cell Proteomics 2010; 9:2497-507. [PMID: 20682762 DOI: 10.1074/mcp.m110.001560] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal altered protein profiles upon epitope retrieval at elevated temperatures with limits of detection improving into lower ng/ml ranges. In a study based on prostate cancer patients, several proteins with differential profiles were discovered and subsequently validated in an independent cohort. For one of the potential biomarkers, the human carnosine dipeptidase 1 protein (CNDP1), the differences were determined to be related to the glycosylation status of the targeted protein. The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format.
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Affiliation(s)
- Jochen M Schwenk
- Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, Sweden.
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11
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Wang D, Hincapie M, Guergova-Kuras M, Kadas J, Takacs L, Karger BL. Antigen identification and characterization of lung cancer specific monoclonal antibodies produced by mAb proteomics. J Proteome Res 2010; 9:1834-42. [PMID: 20146545 DOI: 10.1021/pr900997z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A mass spectrometric (MS)-based strategy for antigen (Ag) identification and characterization of globally produced monoclonal antibodies (mAbs) is described. Mice were immunized with a mixture of native glycoproteins, isolated from the pooled plasma of patients with nonsmall cell lung cancer (NSCLC), to generate a library of IgG-secreting hybridomas. Prior to immunization, the pooled NSCLC plasma was subjected to 3-sequential steps of affinity fractionation, including high abundant plasma protein depletion, glycoprotein enrichment, and polyclonal antibody affinity chromatography normalization. In this paper, to demonstrate the high quality of the globally produced mAbs, we selected 3 mAbs of high differentiating power against a matched, pooled normal plasma sample. After production of large quantities of the mAbs from ascites fluids, Ag identification was achieved by immunoaffinity purification, SDS-PAGE, Western blotting, and MS analysis of in-gel digest products. One antigen was found to be complement factor H, and the other two were mapped to different subunits of haptoglobin (Hpt). The 2 Hpt mAbs were characterized in detail to assess the quality of the mAbs produced by the global strategy. The affinity of one of the mAbs to the Hpt native tetramer form was found to have a K(D) of roughly 10(-9) M and to be 2 orders of magnitude lower than the reduced form, demonstrating the power of the mAb proteomics technology in generating mAbs to the natural form of the proteins in blood. The binding of this mAb to the beta-chain of haptoglobin was also dependent on glycosylation on this chain. The characterization of mAbs in this work reveals that the global mAb proteomics process can generate high-quality lung cancer specific mAbs capable of recognizing proteins in their native state.
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Affiliation(s)
- Dongdong Wang
- Barnett Institute, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusettes, USA
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12
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Diehnelt CW, Shah M, Gupta N, Belcher PE, Greving MP, Stafford P, Johnston SA. Discovery of high-affinity protein binding ligands--backwards. PLoS One 2010; 5:e10728. [PMID: 20502719 PMCID: PMC2873402 DOI: 10.1371/journal.pone.0010728] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 04/13/2010] [Indexed: 12/31/2022] Open
Abstract
Background There is a pressing need for high-affinity protein binding ligands for all proteins in the human and other proteomes. Numerous groups are working to develop protein binding ligands but most approaches develop ligands using the same strategy in which a large library of structured ligands is screened against a protein target to identify a high-affinity ligand for the target. While this methodology generates high-affinity ligands for the target, it is generally an iterative process that can be difficult to adapt for the generation of ligands for large numbers of proteins. Methodology/Principal Findings We have developed a class of peptide-based protein ligands, called synbodies, which allow this process to be run backwards – i.e. make a synbody and then screen it against a library of proteins to discover the target. By screening a synbody against an array of 8,000 human proteins, we can identify which protein in the library binds the synbody with high affinity. We used this method to develop a high-affinity synbody that specifically binds AKT1 with a Kd<5 nM. It was found that the peptides that compose the synbody bind AKT1 with low micromolar affinity, implying that the affinity and specificity is a product of the bivalent interaction of the synbody with AKT1. We developed a synbody for another protein, ABL1 using the same method. Conclusions/Significance This method delivered a high-affinity ligand for a target protein in a single discovery step. This is in contrast to other techniques that require subsequent rounds of mutational improvement to yield nanomolar ligands. As this technique is easily scalable, we believe that it could be possible to develop ligands to all the proteins in any proteome using this approach.
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Affiliation(s)
- Chris W. Diehnelt
- Center for Innovations in Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Miti Shah
- Center for Innovations in Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nidhi Gupta
- Center for Innovations in Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Paul E. Belcher
- Center for Innovations in Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Matthew P. Greving
- Center for BioOptical Nanotechnology, The Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Phillip Stafford
- Center for Innovations in Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Stephen Albert Johnston
- Center for Innovations in Medicine, Arizona State University, Tempe, Arizona, United States of America
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- * E-mail:
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13
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Exploring epitopes of antibodies toward the human tryptophanyl-tRNA synthetase. N Biotechnol 2010; 27:129-37. [DOI: 10.1016/j.nbt.2009.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/29/2009] [Accepted: 11/01/2009] [Indexed: 11/20/2022]
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14
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15
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Williams BAR, Diehnelt CW, Belcher P, Greving M, Woodbury NW, Johnston SA, Chaput JC. Creating protein affinity reagents by combining peptide ligands on synthetic DNA scaffolds. J Am Chem Soc 2009; 131:17233-41. [PMID: 19894711 PMCID: PMC2796340 DOI: 10.1021/ja9051735] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A full understanding of the proteome will require ligands to all of the proteins encoded by genomes. While antibodies represent the principle affinity reagents used to bind proteins, their limitations have created a need for new ligands to large numbers of proteins. Here we propose a general concept to obtain protein affinity reagents that avoids animal immunization and iterative selection steps. Central to this process is the idea that small peptide libraries contain sequences that will bind to independent regions on a protein surface and that these ligands can be combined on synthetic scaffolds to create high affinity bivalent reagents. To demonstrate the feasibility of this approach, an array of 4000 unique 12-mer peptides was screened to identify sequences that bind to nonoverlapping sites on the yeast regulatory protein Gal80. Individual peptide ligands were screened at different distances using a novel DNA linking strategy to identify the optimal peptide pair and peptide pair separation distance required to transform two weaker ligands into a single high affinity protein capture reagent. A synthetic antibody or synbody was created with 5 nM affinity to Gal80 that functions in conventional ELISA and pull-down assays. We validated our synthetic antibody approach by creating a second synbody to human transferrin. In both cases, we observed an increase in binding affinity of approximately 1000-fold (DeltaDeltaG = approximately 4.1 kcal/mol) between the individual peptides and final bivalent synbody construct.
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Affiliation(s)
- Berea A. R. Williams
- Center for BioOptical Nanotechnology, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5201
| | - Chris W. Diehnelt
- Center for Innovations in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
| | - Paul Belcher
- Center for Innovations in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
| | - Matthew Greving
- Center for BioOptical Nanotechnology, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5201
| | - Neal W. Woodbury
- Center for BioOptical Nanotechnology, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5201
| | - Stephen A. Johnston
- Center for Innovations in Medicine, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287-5201
| | - John C. Chaput
- Center for BioOptical Nanotechnology, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5201
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Stadler C, Skogs M, Brismar H, Uhlén M, Lundberg E. A single fixation protocol for proteome-wide immunofluorescence localization studies. J Proteomics 2009; 73:1067-78. [PMID: 19896565 DOI: 10.1016/j.jprot.2009.10.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 10/16/2009] [Accepted: 10/29/2009] [Indexed: 11/29/2022]
Abstract
Immunofluorescence microscopy is a valuable tool for analyzing protein expression and localization at a subcellular level thus providing information regarding protein function, interaction partners and its role in cellular processes. When performing sample fixation, parameters such as difference in accessibility of proteins present in various cellular compartments as well as the chemical composition of the protein to be studied, needs to be taken into account. However, in systematic and proteome-wide efforts, a need exists for standard fixation protocol(s) that works well for the majority of all proteins independent of subcellular localization. Here, we report on a study with the goal to find a standardized protocol based on the analysis of 18 human proteins localized in 11 different organelles and subcellular structures. Six fixation protocols were tested based on either dehydration by alcohols (methanol, ethanol or iso-propanol) or cross-linking by paraformaldehyde followed by detergent permeabilization (Triton X-100 or saponin) in three human cell lines. Our results show that cross-linking is essential for proteome-wide localization studies and that cross-linking using paraformaldehyde followed by Triton X-100 permeabilization successfully can be used as a single fixation protocol for systematic studies.
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Affiliation(s)
- Charlotte Stadler
- School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden
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17
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Williams BAR, Lin L, Lindsay SM, Chaput JC. Evolution of a histone H4-K16 acetyl-specific DNA aptamer. J Am Chem Soc 2009; 131:6330-1. [PMID: 19385619 PMCID: PMC2715991 DOI: 10.1021/ja900916p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the in vitro selection of DNA aptamers that bind to histone H4 proteins acetylated at lysine 16. The best aptamer identified in this selection binds to the target protein with a K(d) of 21 nM and discriminates against both the nonacetylated protein and histone H4 proteins acetylated at lysine 8. Comparative binding assays performed with a chip-quality antibody reveal that this aptamer binds to the acetylated histone target with similar affinity to a commercial antibody but shows significantly greater specificity (15-fold versus 2400-fold) for the target molecule. This result demonstrates that aptamers that are both modification and location specific can be generated to bind specific protein post-translational modifications.
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Affiliation(s)
- Berea A. R. Williams
- Center for BioOptical Nanotechnology, Arizona State University, Tempe, Arizona 85287-5201
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5201
| | - Liyun Lin
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
- Department of Physics, Arizona State University, Tempe, Arizona 85287-5201
| | - Stuart M. Lindsay
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287-5201
- Department of Physics, Arizona State University, Tempe, Arizona 85287-5201
| | - John C. Chaput
- Center for BioOptical Nanotechnology, Arizona State University, Tempe, Arizona 85287-5201
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-5201
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18
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Mulder J, Björling E, Jonasson K, Wernérus H, Hober S, Hökfelt T, Uhlén M. Tissue profiling of the mammalian central nervous system using human antibody-based proteomics. Mol Cell Proteomics 2009; 8:1612-22. [PMID: 19351664 DOI: 10.1074/mcp.m800539-mcp200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A need exists for mapping the protein profiles in the human brain both during normal and disease conditions. Here we studied 800 antibodies generated toward human proteins as part of a Human Protein Atlas program and investigated their suitability for detailed analysis of various levels of a rat brain using immuno-based methods. In this way, the parallel, rather limited analysis of the human brain, restricted to four brain areas (cerebellum, cerebral cortex, hippocampus, and lateral subventricular zone), could be extended in the rat model to 25 selected areas of the brain. Approximately 100 antibodies (12%) revealed a distinct staining pattern and passed validation of specificity using Western blot analysis. These antibodies were applied to coronal sections of the rat brain at 0.7-mm intervals covering the entire brain. We have now produced detailed protein distribution profiles for these antibodies and acquired over 640 images that form the basis of a publicly available portal of an antibody-based Rodent Brain Protein Atlas database (www.proteinatlas.org/rodentbrain). Because of the systematic selection of target genes, the majority of antibodies included in this database are generated against proteins that have not been studied in the brain before. Furthermore optimized tissue processing and colchicine treatment allow a high quality, more extended annotation and detailed analysis of subcellular distributions and protein dynamics.
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Affiliation(s)
- Jan Mulder
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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Uhlén M, Hober S. Generation and validation of affinity reagents on a proteome-wide level. J Mol Recognit 2009; 22:57-64. [PMID: 18546091 DOI: 10.1002/jmr.891] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
There is a need for protein-specific affinity reagents to explore the gene products encoded by the genome. Recently, systematic efforts to generate validated affinity reagents on a whole human proteome level have been initiated. There are several issues for such efforts, including choice of antigen, type of affinity reagent, and the subsequent validation of the generated protein-specific binders. The advantages and disadvantages with the different approaches are discussed and the problems related to quality assessment of antibodies to be used in multi-platform applications are addressed. This review also describes the efforts to create a virtual resource of validated antibodies using a community-based portal and summarizes the status and visions for the publicly available human protein atlas (http://www.proteinatlas.org) showing the human protein profiles in a large number of normal and cancer tissues as well as a large set of human cell lines.
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Affiliation(s)
- Mathias Uhlén
- Department of Proteomics, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Stockholm, Sweden.
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20
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Libraries against libraries for combinatorial selection of replicating antigen-antibody pairs. Proc Natl Acad Sci U S A 2009; 106:1380-5. [PMID: 19139405 DOI: 10.1073/pnas.0812291106] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Antibodies are among the most highly selective tight-binding ligands for proteins. Because the human genome project has deciphered the proteome, there is an opportunity to use combinatorial antibody libraries to select high-affinity antibodies to every protein encoded by the genome. However, this is a large task because the selection formats used today for combinatorial antibody libraries are geared toward generating antibodies to one antigen at a time. Here, we describe a method that accelerates the identification of antibodies to a multitude of antigens simultaneously by matching combinatorial antibody libraries against eukaryotic antigen libraries so that replication-competent cognate antigen-antibody pairs can be directly selected. Phage and yeast display systems are used because they each link genotype to phenotype and can be replicated individually. When combined with cell sorting, the two libraries can be selected against each other for recovery of cognate antigen-antibody clones in a single experiment.
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Abstract
Tissue-based diagnostics and research is incessantly evolving with the development of new molecular tools. It has long been realized that immunohistochemistry can add an important new level of information on top of morphology and that protein expression patterns in a cancer may yield crucial diagnostic and prognostic information. We have generated an immunohistochemistry-based map of protein expression profiles in normal tissues, cancer and cell lines. For each antibody, altogether 708 spots of tissues and cells are analysed and the resulting images and data are presented as freely available in the Human Protein Atlas (www.proteinatlas.org). The new version 4 of the atlas, including more than 5 million images of immunohistochemically stained tissues and cells, is based on 6122 antibodies, representing 5011 human proteins encoded by approximately 25% of the human genome. The gene-centric database includes a putative classification of proteins in various protein classes, both functional classes, such as kinases or transcription factors and project-related classes, such as candidate genes for cancer or cardiovascular diseases. For each of the internally generated antibodies, the exact antigen sequence is presented, together with a visualization of application-specific validation data, including a protein array assay, western blot analysis, immunohistochemistry and, in most cases, immunofluorescent-based confocal microscopy. The updated version also includes new search algorithms to allow complex queries regarding expression profiles, protein classes and chromosome location. Thus, the presented Human Protein Atlas provides a resource for pathology-based biomedical research, including protein science and biomarker discovery.
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Affiliation(s)
- F Pontén
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
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22
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Berglund L, Björling E, Oksvold P, Fagerberg L, Asplund A, Szigyarto CAK, Persson A, Ottosson J, Wernérus H, Nilsson P, Lundberg E, Sivertsson A, Navani S, Wester K, Kampf C, Hober S, Pontén F, Uhlén M. A genecentric Human Protein Atlas for expression profiles based on antibodies. Mol Cell Proteomics 2008; 7:2019-27. [PMID: 18669619 DOI: 10.1074/mcp.r800013-mcp200] [Citation(s) in RCA: 488] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An attractive path forward in proteomics is to experimentally annotate the human protein complement of the genome in a genecentric manner. Using antibodies, it might be possible to design protein-specific probes for a representative protein from every protein-coding gene and to subsequently use the antibodies for systematical analysis of cellular distribution and subcellular localization of proteins in normal and disease tissues. A new version (4.0) of the Human Protein Atlas has been developed in a genecentric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide, and protein domains and new plots showing the uniqueness (sequence similarity) of every fraction of each protein toward all other human proteins. The new version is based on tissue profiles generated from 6120 antibodies with more than five million immunohistochemistry-based images covering 5067 human genes, corresponding to approximately 25% of the human genome. Version 4.0 includes a putative list of members in various protein classes, both functional classes, such as kinases, transcription factors, G-protein-coupled receptors, etc., and project-related classes, such as candidate genes for cancer or cardiovascular diseases. The exact antigen sequence for the internally generated antibodies has also been released together with a visualization of the application-specific validation performed for each antibody, including a protein array assay, Western blot analysis, immunohistochemistry, and, for a large fraction, immunofluorescence-based confocal microscopy. New search functionalities have been added to allow complex queries regarding protein expression profiles, protein classes, and chromosome location. The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery.
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Affiliation(s)
- Lisa Berglund
- Department of Proteomics, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
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23
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Rockberg J, Löfblom J, Hjelm B, Uhlén M, Ståhl S. Epitope mapping of antibodies using bacterial surface display. Nat Methods 2008; 5:1039-45. [PMID: 19029907 DOI: 10.1038/nmeth.1272] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 10/23/2008] [Indexed: 12/20/2022]
Abstract
We describe a method for mapping the epitopes recognized by antibodies, based on bacterial surface expression of antigen protein fragments followed by antibody-based flow-cytometric sorting. We analyzed the binding sites of both monoclonal and polyclonal antibodies directed to three human protein targets: (i) the human epidermal growth factor receptor 2 (HER2), (ii) ephrin-B3 and (iii) the transcription factor SATB2. All monoclonal antibodies bound a single epitope, whereas the polyclonal antibodies showed, in each case, a binding pattern with one to five separate epitopes. A comparison of polyclonal and monoclonal antibodies raised to the same antigen showed overlapping binding epitopes. We also demonstrated that bacterial cells with displayed protein fragments can be used as affinity ligands to generate epitope-specific antibodies. Our approach shows a path forward for systematic validation of antibodies for epitope specificity and cross-reactivity on a whole-proteome level.
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Affiliation(s)
- Johan Rockberg
- Department of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, SE-106 91 Stockholm, Sweden
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24
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Lundberg E, Gry M, Oksvold P, Kononen J, Andersson-Svahn H, Pontén F, Uhlén M, Asplund A. The correlation between cellular size and protein expression levels — Normalization for global protein profiling. J Proteomics 2008; 71:448-60. [DOI: 10.1016/j.jprot.2008.06.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/28/2008] [Accepted: 06/23/2008] [Indexed: 11/29/2022]
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Paulovich AG, Whiteaker JR, Hoofnagle AN, Wang P. The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline. Proteomics Clin Appl 2008; 2:1386-1402. [PMID: 20976028 DOI: 10.1002/prca.200780174] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The application of "omics" technologies to biological samples generates hundreds to thousands of biomarker candidates; however, a discouragingly small number make it through the pipeline to clinical use. This is in large part due to the incredible mismatch between the large numbers of biomarker candidates and the paucity of reliable assays and methods for validation studies. We desperately need a pipeline that relieves this bottleneck between biomarker discovery and validation. This paper reviews the requirements for technologies to adequately credential biomarker candidates for costly clinical validation and proposes methods and systems to verify biomarker candidates. Models involving pooling of clinical samples, where appropriate, are discussed. We conclude that current proteomic technologies are on the cusp of significantly affecting translation of molecular diagnostics into the clinic.
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26
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Hortin GL, Sviridov D, Anderson NL. High-abundance polypeptides of the human plasma proteome comprising the top 4 logs of polypeptide abundance. Clin Chem 2008; 54:1608-16. [PMID: 18687737 DOI: 10.1373/clinchem.2008.108175] [Citation(s) in RCA: 214] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Plasma contains thousands of proteins, but a small number of these proteins comprise the majority of protein molecules and mass. CONTENT We surveyed proteomic studies to identify candidates for high-abundance polypeptide chains. We searched the literature for information on the plasma concentrations of the most abundant components in healthy adults and for the molecular mass of the mature polypeptide chains in plasma. Because proteomic studies usually dissociate proteins into polypeptide chains or detect short peptide segments of proteins, we summarized data on individual peptide chains for proteins containing multiple subunits or polypeptides. We collected data on about 150 of the most abundant polypeptides in plasma. The abundant polypeptides span approximately the top 4 logs of concentration in plasma, from 650 to 0.06 micromol/L on a molar basis or from about 50,000 to 1 mg/L mass abundance. CONCLUSIONS Data on the concentrations of the high-abundance peptide chains in plasma assist in understanding the composition of plasma and potential approaches for clinical laboratory or proteomic analysis of plasma proteins. Development of more extensive databases regarding the plasma concentrations of proteins in health and diseases would promote diagnostic and proteomic advances.
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Affiliation(s)
- Glen L Hortin
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892-1508, USA.
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27
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Björling E, Uhlén M. Antibodypedia, a portal for sharing antibody and antigen validation data. Mol Cell Proteomics 2008; 7:2028-37. [PMID: 18667413 DOI: 10.1074/mcp.m800264-mcp200] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibodies are useful tools to characterize the components of the human proteome and to validate potential protein biomarkers discovered through various clinical proteomics efforts. The lack of validation results across various applications for most antibodies often makes it necessary to perform cumbersome investigations to ensure specificity of a particular antibody in a certain application. A need therefore exists for a standardized system for sharing validation data about publicly available antibodies and to allow antibody providers as well as users to contribute and edit experimental evidence data, including data also on the antigen. Here we describe a new publicly available portal called Antibodypedia, which has been developed to allow sharing of information regarding validation of antibodies in which providers can submit their own validation results and reliability scores. We report standardized validation criteria and submission rules for applications such as Western blots, protein arrays, immunohistochemistry, and immunofluorescence. The contributor is expected to provide experimental evidence and a validation score for each antibody, and the users can subsequently provide feedback and comments on the use of the antibody. The database thus provides a virtual resource of publicly available antibodies toward human proteins with accompanying experimental evidence supporting an individual validation score for each antibody in an application-specific manner.
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Affiliation(s)
- Erik Björling
- School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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28
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Fang X, Zhang WW. Affinity separation and enrichment methods in proteomic analysis. J Proteomics 2008; 71:284-303. [PMID: 18619565 DOI: 10.1016/j.jprot.2008.06.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/24/2008] [Accepted: 06/24/2008] [Indexed: 12/24/2022]
Abstract
Protein separation or enrichment is one of the rate-limiting steps in proteomic studies. Specific capture and removal of highly-abundant proteins (HAP) with large sample-handling capacities are in great demand for enabling detection and analysis of low-abundant proteins (LAP). How to grasp and enrich these specific proteins or LAP in complex protein mixtures is also an outstanding challenge for biomarker discovery and validation. In response to these needs, various approaches for removal of HAP or capture of LAP in biological fluids, particularly in plasma or serum, have been developed. Among them, immunoaffinity subtraction methods based upon polyclonal IgY or IgG antibodies have shown to possess unique advantages for proteomic analysis of plasma, serum and other biological samples. In addition, other affinity methods that use recombinant proteins, lectins, peptides, or chemical ligands have also been developed and applied to LAP capture or enrichment. This review discusses in detail the need to put technologies and methods in affinity subtraction or enrichment into a context of proteomic and systems biology as "Separomics" and provides a prospective of affinity-mediated proteomics. Specific products, along with their features, advantages, and disadvantages will also be discussed.
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29
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Mathivanan S, Pandey A. Human Proteinpedia as a resource for clinical proteomics. Mol Cell Proteomics 2008; 7:2038-47. [PMID: 18573810 DOI: 10.1074/mcp.r800008-mcp200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clinical proteomics is an emerging field that deals with the use of proteomic technologies for medical applications. With a major objective of identifying proteins involved in pathological processes and as potential biomarkers, this field is already gaining momentum. Consequently, clinical proteomics data are being generated at a rapid pace, although mechanisms of sharing such data with the biomedical community lag far behind. Most of these data are either provided as supplementary information through journal web sites or directly made available by the authors through their own web resources. Integration of these data within a single resource that displays information in the context of individual proteins is likely to enhance the use of proteomic data in biomedical research. Human Proteinpedia is one such portal that unifies human proteomic data under a single banner. The goal of this resource is to ultimately capture and integrate all proteomic data obtained from individual studies on normal and diseased tissues. We anticipate that harnessing of these data will help prioritize experiments related to protein targets and also permit meta-analysis to uncover molecular signatures of disease. Finally, we encourage all biomedical investigators to maximize dissemination of their valuable proteomic data to rest of the community by active participation in existing repositories such as Human Proteinpedia.
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Affiliation(s)
- Suresh Mathivanan
- Institute of Bioinformatics, International Tech Park, Bangalore 560 066, India
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31
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Abstract
The use of affinity-based tools has become invaluable as a platform for basic research and in the development of drugs and diagnostics. Applications include affinity chromatography and affinity tag fusions for efficient purification of proteins as well as methods to probe the protein network interactions on a whole-proteome level. A variety of selection systems has been described for in vitro evolution of affinity reagents using combinatorial libraries, which make it possible to create high-affinity reagents to virtually all biomolecules, as exemplified by generation of therapeutic antibodies and new protein scaffold binders. The strategies for high-throughput generation of affinity reagents have also opened up the possibility of generating specific protein probes on a whole-proteome level. Recently, such affinity proteomics have allowed the detailed analysis of human protein expression in a comprehensive manner both in normal and disease tissue using tissue microarrays and confocal microscopy.
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Affiliation(s)
- Mathias Uhlén
- School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden.
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32
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Strawbridge RJ, Nistér M, Brismar K, Grönberg H, Li C. MUC1 as a Putative Prognostic Marker for Prostate Cancer. Biomark Insights 2008; 3:303-315. [PMID: 19578514 PMCID: PMC2688377 DOI: 10.4137/bmi.s666] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
MUC1 is expressed on the apical surface of glandular epithelium. With functions including protection, adhesion and signaling, MUC1 has been implicated in prostate cancer. There are many splice variants, the best characterized of which are MUC1/1 and MUC1/2 which are determined by a SNP (rs4072037, 3506G>A).Blood DNA from the general population, BPH, sporadic and hereditary prostate cancer subjects were genotyped for the rs4072037 SNP. G allele frequencies were significantly reduced in hereditary prostate cancer (15%) compared to population, BPH or sporadic prostate cancer samples (27%, 39% and 26% respectively). In addition, the G allele was lost from 3 of 8 heterozygous sporadic prostate tumor samples compared to matched blood DNA. Bioinformatics analysis of MUC1 protein sequences provides insight into differences between the variants which may be functionally relevant. The literature indicates discrepancies between immuno-histochemical studies, possibly due to the variety of MUC1 epitopes targeting diverse regions of the molecule. The contradictory findings in cell lines highlight the problem associated with inadequate experimental systems.This is the first report of genetic differences in MUC1 between blood and prostatic cancer tissue. This finding is important as proof of principle, given that many association studies focus on blood DNA rather than on the tumor DNA. As yet, potential functional differences between splice variants has been paid little attention. Antibodies which discriminate between the variants and standardization of methods would help to clarify whether there is a role for MUC1 as a prognostic marker.
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Abstract
In the post-genome era, there is a great need for protein-specific affinity reagents to explore the human proteome. Antibodies are suitable as reagents, but generation of antibodies with low cross-reactivity to other human proteins requires careful selection of antigens. Here we show the results from a proteome-wide effort to map linear epitopes based on uniqueness relative to the entire human proteome. The analysis was based on a sliding window sequence similarity search using short windows (8, 10, and 12 amino acid residues). A comparison of exact string matching (Hamming distance) and a heuristic method (BLAST) was performed, showing that the heuristic method combined with a grid strategy allows for whole proteome analysis with high accuracy and feasible run times. The analysis shows that it is possible to find unique antigens for a majority of the human proteins, with relatively strict rules involving low sequence identity of the possible linear epitopes. The implications for human antibody-based proteomics efforts are discussed.
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Affiliation(s)
- Lisa Berglund
- School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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34
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Grimsey NL, Goodfellow CE, Scotter EL, Dowie MJ, Glass M, Graham ES. Specific detection of CB1 receptors; cannabinoid CB1 receptor antibodies are not all created equal! J Neurosci Methods 2008; 171:78-86. [PMID: 18406468 DOI: 10.1016/j.jneumeth.2008.02.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 02/12/2008] [Accepted: 02/14/2008] [Indexed: 11/19/2022]
Abstract
The study of endogenous cannabinoid CB1 receptor proteins in neuronal tissues and cells relies on the availability of highly specific antibodies. We have tested the ability of a series of CB1 antibodies to detect endogenous receptors in brain as well as hemagglutinin (HA)-tagged receptors transfected into HEK-293 cells using a combination of immunological methods. An initial comparison of several CB1 antibodies in mouse brain revealed substantial differences in staining pattern to ligand binding by autoradiography. Antibodies were then tested immunocytochemically against HEK cells expressing HA-tagged rat and human CB1 receptors. None of the commercial antibodies tested were able to detect the receptor in this context. All antibodies were then screened by Western blotting using lysates from the HEK cells and rodent brain homogenates. Again, none of the commercially available antibodies detected proteins of the correct molecular weight in transfected cell lines or brain homogenates, although all recognized multiple proteins in brain tissues. We conclude that the commercially available antibodies we tested failed to detect CB1 receptors abundantly expressed in HEK cells or native receptors in brain slices or homogenates. As such, comprehensive validation of the specificity of these CB1 antibodies for a particular application is essential before use.
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Affiliation(s)
- Natasha L Grimsey
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Private Bag 92019, Auckland, New Zealand
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35
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Human protein atlas and the use of microarray technologies. Curr Opin Biotechnol 2008; 19:30-5. [DOI: 10.1016/j.copbio.2007.11.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 11/14/2007] [Accepted: 11/14/2007] [Indexed: 01/06/2023]
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36
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Zichi D, Eaton B, Singer B, Gold L. Proteomics and diagnostics: Let's Get Specific, again. Curr Opin Chem Biol 2008; 12:78-85. [DOI: 10.1016/j.cbpa.2008.01.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 01/15/2008] [Indexed: 12/21/2022]
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37
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Hassan S, Ferrario C, Mamo A, Basik M. Tissue microarrays: emerging standard for biomarker validation. Curr Opin Biotechnol 2007; 19:19-25. [PMID: 18053705 DOI: 10.1016/j.copbio.2007.10.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 10/14/2007] [Indexed: 12/11/2022]
Abstract
With the widespread use of DNA microarrays, hundreds of biomarkers are in need of validation in cohorts of well-annotated clinical samples. Tissue microarrays are emerging as the tool par excellence to rapidly perform DNA, RNA, and especially protein expression analyses on large numbers of clinical samples. Although still somewhat limited by the subjectivity of scoring methods and tissue sample representativeness, TMAs represent an increasingly validated means of understanding the clinical impact of diagnostic-related, prognostic-related, and therapy-related markers. Automated methods are being developed for TMA analysis and cell microarrays and frozen tissue TMAs have been better optimized. More and more biomarker studies are availing themselves of the high-throughput nature of TMAs, recognizing that they are becoming indispensable for rapid translation of laboratory data to the clinic.
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Affiliation(s)
- Saima Hassan
- Departments of Oncology and Surgery, Segal Cancer Center, 3755 Cote Ste Catherine Road, Montreal, Quebec, Canada H3T 1E2
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38
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