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Biowire Fall 2010 — A Look into the Future of Gene Editing

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Mapping the Human Proteome using Prestige Antibodies® Powered by Atlas Antibodies

Prestige Antibodies and the Human Protein Atlas
Tissue specific protein expression
Global protein expression analysis using confocal microscopy
Summary

Prestige Antibodies and the Human Protein Atlas
For the first time ever, a comprehensive localization analysis has been performed on 8,000+ human proteins in a standardized setup manner1,2. The analysis has been performed in several levels using different methodologies. All results are presented on www.proteinatlas.org, a portal run by the "Human Protein Atlas" (HPA) project. The HPA project is an international 10-year research effort that aims to map the full human proteome and present the data on a public web portal to researchers all over the world. The Human Protein Atlas portal contains expression profiles for proteins corresponding to over 40% of the human proteome. Each year characterization data of ~2,500 new proteins are added. By the end of 2014, a first draft of the localization of the full human proteome will be available.

The HPA project involves over 100 researchers working full time on developing and characterizing HPA antibodies for protein expression and localization studies1,2. Late 2010, the project will have mapped 50% of all human proteins by the use of HPA antibodies. About 20 new HPA antibodies are generated each day, and successfully validated antibodies are made available to the research community under the brand name Prestige Antibodies.

The results presented on the HPA portal can be used to study and compare tissue distribution of proteins from immunohistochemistry (IHC) images in human normal, as well as diseased, tissues and cells. In addition, subcellular localization information from immunofluorescence (IF) analysis of 3,500+ proteins can be viewed and compared. For example, IHC images from over 8,000 proteins revealed a highly ubiquitous expression of most proteins with a minority of the proteins detected in a single cell type3. These cell- or tissue-specific proteins may be interesting starting points for further studies, facilitated by the publicly available annotation results and the underlying original images on the Human Protein Atlas.

By studying protein expression profiles of tissues and organs, the unique characteristics of the various cell types in the human body can be elucidated.

Protein expression profiles for 4,842 proteins in 48 human tissues and 45 human cell lines have recently been defined and investigated3. More than 2 million high resolution IHC images have manually been annotated by certified pathologists who have determined the relative level of expression for each specific protein.

A hierarchical clustering analysis was carried out based on the protein levels in 65 normal cell types. The analysis showed that cells cluster into groups that could be expected on the basis of traditional embryology, histology and anatomy, and most of the cells cluster into the six major groups shown in Figure 1.

Biowire Fall 2010 Mapping the Human Proteome Figure 1

Figure 1.
Global protein expression profiling in 65 normal human cell types using 5,934 antibodies corresponding to 4,842 proteins. The dendrogram was constructed by hierarchical clustering; the inset shows the original heatmap. Dendrogram bars are colored according to embryonic origin, ectoderm (blue), mesoderm (red) and endoderm (green). The cell types were classified into six categories according to the color code in the figure.

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Tissue specific protein expression
The results from an analysis of the fraction of cell types expressing each protein is shown in Figure 2A. The analysis indicated that a high fraction of the proteome is expressed in most cell types and tissues and very few proteins are expressed in a single cell type. Figure 2B shows the fraction of proteins that are expressed in a specific cell type. An average of 68% of all proteins expressed were present in any given cell type. Figure 2C shows an example of a previously non-characterized cell-type specific protein, angiomoitin-like protein 1 (AMOTL1). Immunohistochemical staining using anti-AMOTL1 (Prestige Antibody HPA001196) in placental tissue shows distinct expression in basal cytotrophoblasts and in the brush-border membrane overlying syncytiotrophoblasts.

Biowire Fall 2010 Mapping the Human Proteome Figure 2

Figure 2.
Tissue specific protein expression. Expression intensity is color-coded as follows: red=strong, orange=medium, yellow=weak. (A) The fraction (%) of cells in which a particular protein was expressed. Cell-type specific proteins are arranged to the left and "housekeeping proteins" to the right. (B) The fraction (%) of proteins expressed in a specific cell type. The bar at the bottom display the six major categories of cell types described in Figure 1 (black represents missing data). (C) Immunohistochemistry staining of angiomoitin-like protein 1 (anti-AMOTL1, HPA001196) in human placental tissue.

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Global protein expression analysis using confocal microscopy
Subcellular analysis on 466 proteins in three human cell lines has been performed using Prestige Antibodies and confocal microscopy4. Similarly as for the IHC analysis, the results showed a ubiquitous expression pattern of the proteins with more than 70% of the analyzed proteins detected in the three cell lines. Figure 3A, B, C show the distribution of localization in three major compartments for the three cell lines and a more detailed overview of the subcellular localizations. In Figure 3D, only antibodies specific to one organelle are included. Out of the 466 proteins investigated, about 200 showed a strict localization, 200 were present in multiple cellular compartments, and about 70 were considered unspecific (or negative).


Biowire Fall 2010 Mapping the Human Proteome Figure 3

Figure 3.
Localization distribution into broad compartments for U-2OS (A), U-251MG (B) and A-431 (C) cell lines. (D) More detailed subcellular distribution in U-2OS, U-251MG and A-431. (ER, endoplasmic reticulum; ECM, extracellular matrix).

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Summary

  • The analysis revealed a highly ubiquitous expression of the majority of the proteins with very few proteins detected in a single cell type.
  • These studies suggest that tissue and cell specificity is achieved by precise regulation of protein levels in space and time and not by whether proteins are expressed or not.
  • The Human Protein Atlas portal can be used for global protein expression analyses.
  • All Prestige Antibody annotation results and the underlying original images are available as a public resource in the Human Protein Atlas portal at www.proteinatlas.org.
  • The Human Protein Atlas portal has an advanced search function to allow complex queries, including combined searches based on protein classes, chromosomal location and/or tissue profiles.

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References

  1. A gene-centric human protein atlas for expression profiles based on antibodies. Berglund, L., et al., Molecular & Cellular Proteomic, 7, 2019-2027, (2008).
  2. A human protein atlas for normal and cancer tissues based on antibody proteomics. Uhlén, M., et. al., Molecular & Cellular Proteomic, 12, 1920-1932 (2005).
  3. A global view of protein expression in human cells, tissues, and organs. Pontén, F., et al., Molecular System Biology, 5, 337 (2009).
  4. Toward a confocal subcellular atlas of the human proteome. Barbe, L., et. al., Molecular & Cellular Proteomic, 3, 499-508 (2008).

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