| 1. |
- Uhlén, Mathias, et al.
(author)
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A human protein atlas for normal and cancer tissues based on antibody proteomics
- 2005
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In: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:12, s. 1920-1932
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Journal article (peer-reviewed)abstract
- 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.
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| 2. |
- Berglund, Lisa, et al.
(author)
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Generation of validated antibodies towards the human proteome
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Journal article (other academic/artistic)abstract
- Here we show the results from a large effort to generate antibodies towards the human proteome. A high-throughput strategy was developed based on cloning and expression of antigens as recombitant protein epitope signature tags (PrESTs) Affinity purified polyclonal antibodies were generated, followed by validation by protein microarrays, Western blotting and microarray-based immunohistochemistry. PrESTs were selected based on sequence uniqueness relative the proteome and a bioinformatics analysis showed that unique antigens can be found for at least 85% of the proteome using this general strategy. The success rate from antigen selection to validated antibodies was 31%, and from protein to antibody 55%. Interestingly, membrane-bound and soluble proteins performed equally and PrEST lengths between 75 and 125 amino acids were found to give the highest yield of validated antibodies. Multiple antigens were selected for many genes and the results suggest that specific antibodies can be systematically generated to most human proteibs.
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| 3. |
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| 4. |
- Bjorklund, Marcus Gry, et al.
(author)
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Microarray analysis using disiloxyl 70mer oligonucleotides
- 2008
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 36:4, s. 1334-1342
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Journal article (peer-reviewed)abstract
- DNA microarray technology has evolved dramatically in recent years, and is now a common tool in researchers portfolios. The scope of the technique has expanded from small-scale studies to extensive studies such as classification of disease states. Technical knowledge regarding solid phase microarrays has also increased, and the results acquired today are more reliable than those obtained just a few years ago. Nevertheless, there are various aspects of microarray analysis that could be improved. In this article we show that the proportions of full-length probes used significantly affects the results of global analyses of transcriptomes. In particular, measurements of transcripts in low abundance are more sensitive to truncated probes, which generally increase the degree of cross hybridization and loss of specific signals. In order to improve microarray analysis, we here introduce a disiloxyl purification step, which ensures that all the probes on the microarray are at full length. We demonstrate that when the features on microarrays consist of full-length probes the signal intensity is significantly increased. The overall increase in intensity enables the hybridization stringency to be increased, and thus enhance the robustness of the results.
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| 5. |
- Fagerberg, Linn, et al.
(author)
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Large-Scale Protein Profiling in Human Cell Lines Using Antibody-Based Proteomics
- 2011
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In: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 10:9, s. 4066-4075
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Journal article (peer-reviewed)abstract
- Human cancer cell lines grown in vitro are frequently used to decipher basic cell biological phenomena and to also specifically study different forms of cancer. Here we present the first large-scale study of protein expression patterns in cell lines using an antibody-based proteomics approach. We analyzed the expression pattern of 5436 proteins in 45 different cell lines using hierarchical clustering, principal component analysis, and two-group comparisons for the identification of differentially expressed proteins. Our results show that immunohistochemically determined protein profiles can categorize cell lines into groups that overall reflect the tumor tissue of origin and that hematological cell lines appear to retain their protein profiles to a higher degree than cell lines established from solid tumors. The two-group comparisons reveal well-characterized proteins as well as previously unstudied proteins that could be of potential interest for further investigations. Moreover, multiple myeloma cells and cells of myeloid origin were found to share a protein profile, relative to the protein profile of lymphoid leukemia and lymphoma cells, possibly reflecting their common dependency of bone marrow microenvironment. This work also provides an extensive list of antibodies, for which high-resolution images as well as validation data are available on the Human Protein Atlas (www.proteinatlas.org), that are of potential use in cell line studies.
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| 6. |
- Fagerberg, Linn, et al.
(author)
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The Global Protein Expression Pattern in Human Cell Lines
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Other publication (other academic/artistic)abstract
- Human cancer cell lines grown in vitro are frequently used to decipher basic cell biological phenomena but also to specifically study different forms of cancer. Here we present the first large-scale study of protein expression patterns in cell lines using an antibody-based proteomics approach. We analyzed the expression pattern of 5436 proteins in 45 different cell lines using hierarchical clustering, principal component analysis and two-group comparisons for the identification of differentially expressed proteins. The results show that protein profiles of cell lines, as determined using immunohistochemistry, allow for a hierarchical clustering that overall reflects tumor tissues of origin. Hematological cell lines appear to retain their protein profiles to a higher degree than cell lines established from solid tumors, resulting in a clustering that well reflects progenitor cell types. The discrepancy may reflect different levels of in vitro induced alterations in adherent and suspension grown cell lines, respectively. In addition, multiple myeloma cells and cells of myeloid origin were found to share a protein profile, relative the protein profile of lymphoid leukemia and lymphoma cells, possibly reflecting their common dependency of bone marrow microenvironment.
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| 7. |
- Gry, Marcus, et al.
(author)
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Correlations between RNA and protein expression profiles in 23 human cell lines
- 2009
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 10
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Journal article (peer-reviewed)abstract
- Background: The Central Dogma of biology holds, in famously simplified terms, that DNA makes RNA makes proteins, but there is considerable uncertainty regarding the general, genome-wide correlation between levels of RNA and corresponding proteins. Therefore, to assess degrees of this correlation we compared the RNA profiles (determined using both cDNA- and oligo-based microarrays) and protein profiles (determined immunohistochemically in tissue microarrays) of 1066 gene products in 23 human cell lines. Results: A high mean correlation coefficient (0.52) was obtained from the pairwise comparison of RNA levels determined by the two platforms. Significant correlations, with correlation coefficients exceeding 0.445, between protein and RNA levels were also obtained for a third of the specific gene products. However, the correlation coefficients between levels of RNA and protein products of specific genes varied widely, and the mean correlations between the protein and corresponding RNA levels determined using the cDNA- and oligo-based microarrays were 0.25 and 0.20, respectively. Conclusion: Significant correlations were found in one third of the examined RNA species and corresponding proteins. These results suggest that RNA profiling might provide indirect support to antibodies’ specificity, since whenever a evident correlation between the RNA and protein profiles exists, this can sustain that the antibodies used in the immunoassay recognized their cognate antigens.
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| 8. |
- Gry, Marcus, 1975-
(author)
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Global expression analysis of human cells and tissues using antibodies
- 2008
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Doctoral thesis (other academic/artistic)abstract
- To construct a complete map of the human proteome landscape is a vital part of the total understanding of the human body. Such a map could enrich the mankind to the extent that many severe diseases could be fully understood and hence could be treated with appropriate methods. In this study, immunohistochemical (IHC) data from ~6000 proteins, 65 cell types in 48 tissues and 47 cell lines has been used to investigate the human proteome regarding protein expression and localization. In order to analyze such a large data set, different statistical methods and algorithms has been applied and by using these tools, interesting features regarding the proteome was found. By using all available IHC data from 65 cell types in 48 tissues, it was found that the amount of tissue specific protein expression was surprisingly small, and the general impression from the analysis is that almost all proteins are present at all times in the cellular environment. Rather than tissue specific protein expression, the localization and minor concentration fluctuations of the proteins in the cell is responsible for molecular interaction and tissue specific cellular behavior. However, if a quarter of all proteins are used to distinguish different tissues types, there are a proportion of proteins that have certain expression profiles, which defines clusters of tissues of the same kind and embryonic origin. The estimation of expression levels using IHC is a labor-intensive method, which suffers from large variation between manual annotators. An automated image software tool was developed to circumvent this problem. The automated image software was shown to be more robust then manual annotators, and the quantification of expressed protein levels of the stained imaged was in the same range as the manual annotations. A more thorough investigation of the stained image estimations made by the automated software revield a significant correlation between the estimated protein expression and the cell size parameters provided by the automated software. To make it feasible to compare protein expression levels across different cell lines, without the cell line size bias, a normalization procedure was implemented and evaluated. It was found that when the normalization procedure was applied to the protein expression data, the correlation between protein expression values and cell size was minimized, and hence comparisons between cell lines regarding protein expression is possible. In addition, using the normalized protein expression data, an analysis to investigate the degree of correlation between mRNA levels and proteins for 1065 gene products was performed. By using two individual microarray data sets for estimation of RNA levels, and normalized protein data measured by the automated software as estimation of the protein levels, a mean correlation of ~0.3 for was found. This result indicates that a significant proportion of the manufactured antibodies, when used in IHC setup, are indeed an accurate measurement of protein expression levels. By using antibodies directed towards human proteins, plasma samples were investigated regarding metabolic dysfunctions. Since plasma is a complex sample, an optimization regarding protocol for quantification of expressed proteins was made. By using certain characteristics within the dataset, and by using a suspension bead microarray, the protocol could be evaluated. Expected characteristics within the dataset were found in the subsequent analysis, which showed that the protocol was functional. Using the same experimental outline will facilitate future applications, e.g. biomarker discovery.
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| 9. |
- Gry, Marcus, et al.
(author)
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Tissue-specific protein expression in human cells, tissues and organs
- 2010
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In: Journal of Proteomics and Bioinformatics. - : OMICS Publishing Group. - 0974-276X. ; 3:10, s. 286-293
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Journal article (peer-reviewed)abstract
- An important part of understanding human biology is the study of tissue-specific expression both at the gene and protein level. In this study, the analysis of tissue specific protein expression was performed based on tissue micro array data available on the public Human Protein Atlas database (www.proteinatlas.org). An analysis of human proteins, corresponding to approximately one third of the protein-encoding genes, was carried out in 65 human tissues and cell types. The spatial distribution and relative abundance of 6,678 human proteins, were analyzed in different cell populations from various organs and tissues in the human body using unsupervised methods, such as hierarchical clustering and principal component analysis, as well as with supervised methods (Breiman, 2001). Well-known markers, such as neuromodulin for the central nervous system, keratin 20 for gastrointestinal tract and CD45 for hematopoietic cells, were identified as tissue-specific. Proteins expressed in a tissue-specific manner were identified for cells in all of the investigated tissues, including the central nervous system, hematopoietic system, squamous epithelium, mesenchymal cells and cells from the gastrointestinal tract. Several proteins not yet associated with tissue-specificity were identified, providing starting points for further studies to explore tissue-specific functions. This includes proteins with no known function, such as ZNF509 expressed in CNS and C1orf201 expressed in the gastro-intestinal tract. In general, the majority of the gene products are expressed in a ubiquitous manner and few proteins are detected exclusively in cells from a particular tissue class, as exemplified by less than 1% of the analyzed proteins found only in the brain.
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| 10. |
- Klevebring, Daniel, 1981-, et al.
(author)
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Automation of cDNA Synthesis and Labelling Improves Reproducibility
- 2009
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In: Journal of Biomedicine and Biotechnology. - : Hindawi Limited. - 1110-7243 .- 1110-7251. ; 2009, s. 396808-
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Journal article (peer-reviewed)abstract
- Background. Several technologies, such as in-depth sequencing and microarrays, enable large-scale interrogation of genomes and transcriptomes. In this study, we asses reproducibility and throughput by moving all laboratory procedures to a robotic workstation, capable of handling superparamagnetic beads. Here, we describe a fully automated procedure for cDNA synthesis and labelling for microarrays, where the purification steps prior to and after labelling are based on precipitation of DNA on carboxylic acid-coated paramagnetic beads. Results. The fully automated procedure allows for samples arrayed on a microtiter plate to be processed in parallel without manual intervention and ensuring high reproducibility. We compare our results to a manual sample preparation procedure and, in addition, use a comprehensive reference dataset to show that the protocol described performs better than similar manual procedures. Conclusions. We demonstrate, in an automated gene expression microarray experiment, a reduced variance between replicates, resulting in an increase in the statistical power to detect differentially expressed genes, thus allowing smaller differences between samples to be identified. This protocol can with minor modifications be used to create cDNA libraries for other applications such as in-depth analysis using next-generation sequencing technologies.
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