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Databases for antibody-based proteomics
KTH, School of Biotechnology (BIO). (Proteomics)
2008 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Humans are believed to have ~20,500 protein-coding genes andmuch effort has over the last years been put into the characterizationand localization of the encoded proteins in order to understand theirfunctions. One such effort is the Human Proteome Resource (HPR)project, started in Sweden 2003 with the aim to generate specificantibodies to each human protein and to use those antibodies toanalyze the human proteome by screening human tissues and cells.The work reported in this thesis deals with structuring of data fromantibody-based proteomics assays, with focus on the importance ofaggregating and presenting data in a way that is easy to apprehend.The goals were to model and build databases for collecting, searchingand analyzing data coming out of the large-scale HPR project and tomake all collected data publicly available. A public website, theHuman Protein Atlas, was developed giving all end-users in thescientific community access to the HPR database with proteinexpression data. In 2008, the Human Protein Atlas was released in its4th version containing more than 6000 antibodies, covering more than25% of the human proteins. All the collected protein expression datais searchable on the public website. End-users can query for proteinsthat show high expression in one tissue and no expression in anotherand possibly find tissue specific biomarkers. Queries can also beconstructed to find proteins with different expression levels in normalvs. cancer tissues. The proteins found by such a query could identifypotential biomarkers for cancer that could be used as diagnosticmarkers and maybe even be involved in cancer therapy in the future.Validation of antibodies is important in order to get reliable resultsfrom different assays. It has been noted that some antibodies arereliable in certain assays but not in others and therefore anotherpublicly available database, the Antibodypedia, has been createdwhere any antibody producer can submit their binders together withthe validation data in order for end users to purchase the bestantibody for their protein target and their intended assay.

Place, publisher, year, edition, pages
Stockholm: KTH , 2008. , 68 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2008:24
Keyword [en]
proteomics, antibodies, database, biomarker, website
National Category
Industrial Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-9658ISBN: 978-91-7415-161-9 (print)OAI: oai:DiVA.org:kth-9658DiVA: diva2:126848
Public defence
2008-12-19, FD5, AlbaNova, Roslagstullsbacken 21, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20100708Available from: 2008-12-05 Created: 2008-11-24 Last updated: 2010-07-08Bibliographically approved
List of papers
1. A human protein atlas for normal and cancer tissues based on antibody proteomics
Open this publication in new window or tab >>A human protein atlas for normal and cancer tissues based on antibody proteomics
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2005 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 4, no 12, 1920-1932 p.Article in journal (Refereed) Published
Abstract [en]

Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.

Keyword
MESSENGER-RNA, FACTOR TFIIH, IN-VITRO, EXPRESSION, FAMILY, MICROARRAYS, SUBUNIT, DISPLAY, GENES, CRIM1
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-14023 (URN)10.1074/mcp.M500279-MCP200 (DOI)000233774200008 ()2-s2.0-29244477844 (Scopus ID)
Note

QC 20100708

Available from: 2010-07-08 Created: 2010-07-08 Last updated: 2017-12-12Bibliographically approved
2. A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues
Open this publication in new window or tab >>A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues
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2008 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, Vol. 7, no 5, 825-844 p.Article in journal (Refereed) Published
Abstract [en]

Here we report the development of a publicly available Web-based analysis tool for exploring proteins expressed in a tissue- or cancer-specific manner. The search queries are based on the human tissue profiles in normal and cancer cells in the Human Protein Atlas portal and rely on the individual annotation performed by pathologists of images representing immunohistochemically stained tissue sections. Approximately 1.8 million images representing more than 3000 antibodies directed toward human proteins were used in the study. The search tool allows for the systematic exploration of the protein atlas to discover potential protein biomarkers. Such biomarkers include tissue-specific markers, cell type-specific markers, tumor type-specific markers, markers of malignancy, and prognostic or predictive markers of cancers. Here we show examples of database queries to generate sets of candidate biomarker proteins for several of these different categories. Expression profiles of candidate proteins can then subsequently be validated by examination of the underlying high resolution images. The present study shows examples of search strategies revealing several potential protein biomarkers, including proteins specifically expressed in normal cells and in cancer cells from specified tumor types. The lists of candidate proteins can be used as a starting point for further validation in larger patient cohorts using both immunological approaches and technologies utilizing more classical proteomics tools.

Keyword
ANTIBODY-BASED PROTEOMICS; HUMAN BREAST-CANCER; PROSTATE-CANCER; GENE-EXPRESSION; IMMUNOHISTOCHEMICAL MARKERS; CELL MICROARRAYS; METASTASIS; RESOURCE; ANTIGEN; GROWTH
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-9744 (URN)10.1074/mcp.M700411-MCP200 (DOI)000255830200001 ()2-s2.0-43849094501 (Scopus ID)
Note
QC 20100708Available from: 2008-12-05 Created: 2008-12-05 Last updated: 2011-09-02Bibliographically approved
3. A genecentric human protein atlas for expression profiles based on antibodies
Open this publication in new window or tab >>A genecentric human protein atlas for expression profiles based on antibodies
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2008 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, Vol. 7, no 10, 2019-2027 p.Article in journal (Refereed) Published
Abstract [en]

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 similar to 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.

Keyword
CANCER TISSUES; PROTEOMICS; RESOURCE; DATABASE; MICROARRAYS; GENERATION; LIBRARIES; PEPTIDES; GENOME
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-9745 (URN)10.1074/mcp.R800013-MCP200 (DOI)000260424700018 ()
Note
QC 20100708Available from: 2008-12-05 Created: 2008-12-05 Last updated: 2010-07-08Bibliographically approved
4. Antibodypedia: a portal for sharing antibody and antigen validation data
Open this publication in new window or tab >>Antibodypedia: a portal for sharing antibody and antigen validation data
2008 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, Vol. 7, no 10, 2028-2037 p.Article in journal (Refereed) Published
Abstract [en]

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.

Keyword
B-CELL EPITOPES; HUMAN PROTEOME; CANCER TISSUES; RESOURCE; ATLAS; GENERATION; PREDICTION; PEPTIDES; PROTEINS; ENSEMBL
National Category
Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-9746 (URN)10.1074/mcp.M800264-MCP200 (DOI)000260424700019 ()2-s2.0-53249092612 (Scopus ID)
Note
QC 20100708Available from: 2008-12-05 Created: 2008-12-05 Last updated: 2011-09-05Bibliographically approved

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