Prioritization of cancer marker candidates based on the immunohistochemistry staining images deposited in the Human Protein Atlas

Su Chien Chiang, Chia Li Han, Kun Hsing Yu, Yu Ju Chen, Kun Pin Wu

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Cancer marker discovery is an emerging topic in high-throughput quantitative proteomics. However, the omics technology usually generates a long list of marker candidates that requires a labor-intensive filtering process in order to screen for potentially useful markers. Specifically, various parameters, such as the level of overexpression of the marker in the cancer type of interest, which is related to sensitivity, and the specificity of the marker among cancer groups, are the most critical considerations. Protein expression profiling on the basis of immunohistochemistry (IHC) staining images is a technique commonly used during such filtering procedures. To systematically investigate the protein expression in different cancer versus normal tissues and cell types, the Human Protein Atlas is a most comprehensive resource because it includes millions of high-resolution IHC images with expert-curated annotations. To facilitate the filtering of potential biomarker candidates from large-scale omics datasets, in this study we have proposed a scoring approach for quantifying IHC annotation of paired cancerous/normal tissues and cancerous/normal cell types. We have comprehensively calculated the scores of all the 17219 tested antibodies deposited in the Human Protein Atlas based on their accumulated IHC images and obtained 457110 scores covering 20 different types of cancers. Statistical tests demonstrate the ability of the proposed scoring approach to prioritize cancer-specific proteins. Top 100 potential marker candidates were prioritized for the 20 cancer types with statistical significance. In addition, a model study was carried out of 1482 membrane proteins identified from a quantitative comparison of paired cancerous and adjacent normal tissues from patients with colorectal cancer (CRC). The proposed scoring approach demonstrated successful prioritization and identified four CRC markers, including two of the most widely used, namely CEACAM5 and CEACAM6. These results demonstrate the potential of this scoring approach in terms of cancer marker discovery and development. All the calculated scores are available at http://bal.ym.edu.tw/hpa/.

Original languageEnglish
Article numbere81079
JournalPLoS One
Volume8
Issue number11
DOIs
Publication statusPublished - Nov 26 2013
Externally publishedYes

Fingerprint

prioritization
Atlases
immunohistochemistry
Immunohistochemistry
Staining and Labeling
neoplasms
Neoplasms
Tissue
Proteins
proteins
colorectal neoplasms
Statistical tests
Biomarkers
Colorectal Neoplasms
protein synthesis
Membrane Proteins
Matched-Pair Analysis
Throughput
staining
Personnel

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Prioritization of cancer marker candidates based on the immunohistochemistry staining images deposited in the Human Protein Atlas. / Chiang, Su Chien; Han, Chia Li; Yu, Kun Hsing; Chen, Yu Ju; Wu, Kun Pin.

In: PLoS One, Vol. 8, No. 11, e81079, 26.11.2013.

Research output: Contribution to journalArticle

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