Decoding the disease-associated proteins encoded in the human chromosome 4

Lien Chin Chen, Mei Ying Liu, Yung Chin Hsiao, Wai Kok Choong, Hsin Yi Wu, Wen Lian Hsu, Pao Chi Liao, Ting Yi Sung, Shih Feng Tsai, Jau Song Yu, Yu Ju Chen

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Abstract

Chromosome 4 is the fourth largest chromosome, containing approximately 191 megabases (∼6.4% of the human genome) with 757 protein-coding genes. A number of marker genes for many diseases have been found in this chromosome, including genetic diseases (e.g., hepatocellular carcinoma) and biomedical research (cardiac system, aging, metabolic disorders, immune system, cancer and stem cell) related genes (e.g., oncogenes, growth factors). As a pilot study for the chromosome 4-centric human proteome project (Chr 4-HPP), we present here a systematic analysis of the disease association, protein isoforms, coding single nucleotide polymorphisms of these 757 protein-coding genes and their experimental evidence at the protein level. We also describe how the findings from the chromosome 4 project might be used to drive the biomarker discovery and validation study in disease-oriented projects, using the examples of secretomic and membrane proteomic approaches in cancer research. By integrating with cancer cell secretomes and several other existing databases in the public domain, we identified 141 chromosome 4-encoded proteins as cancer cell-secretable/shedable proteins. Additionally, we also identified 54 chromosome 4-encoded proteins that have been classified as cancer-associated proteins with successful selected or multiple reaction monitoring (SRM/MRM) assays developed. From literature annotation and topology analysis, 271 proteins were recognized as membrane proteins while 27.9% of the 757 proteins do not have any experimental evidence at the protein-level. In summary, the analysis revealed that the chromosome 4 is a rich resource for cancer-associated proteins for biomarker verification projects and for drug target discovery projects.

Original languageEnglish
Pages (from-to)33-44
Number of pages12
JournalJournal of Proteome Research
Volume12
Issue number1
DOIs
Publication statusPublished - 2013 Jan 4

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All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

Chen, L. C., Liu, M. Y., Hsiao, Y. C., Choong, W. K., Wu, H. Y., Hsu, W. L., Liao, P. C., Sung, T. Y., Tsai, S. F., Yu, J. S., & Chen, Y. J. (2013). Decoding the disease-associated proteins encoded in the human chromosome 4. Journal of Proteome Research, 12(1), 33-44. https://doi.org/10.1021/pr300829r