Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues

Julia Fangfei Yan, Hoguen Kim, Seul Ki Jeong, Hyoung Joo Lee, Manveen K. Sethi, Ling Y. Lee, Ronald C. Beavis, Hogune Im, Michael P. Snyder, Matan Hofree, Trey Ideker, Shiaw Lin Wu, Young-Ki Paik, Susan Fanayan, William S. Hancock

Research output: Contribution to journalArticle

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Abstract

V-erb-b2 erythroblastic leukemia viral oncogene homologue 2, known as ERBB2, is an important oncogene in the development of certain cancers. It can form a heterodimer with other epidermal growth factor receptor family members and activate kinase-mediated downstream signaling pathways. ERBB2 gene is located on chromosome 17 and is amplified in a subset of cancers, such as breast, gastric, and colon cancer. Of particular interest to the Chromosome-Centric Human Proteome Project (C-HPP) initiative is the amplification mechanism that typically results in overexpression of a set of genes adjacent to ERBB2, which provides evidence of a linkage between gene location and expression. In this report we studied patient samples from ERBB2-positive together with adjacent control nontumor tissues. In addition, non-ERBB2-expressing patient samples were selected as comparison to study the effect of expression of this oncogene. We detected 196 proteins in ERBB2-positive patient tumor samples that had minimal overlap (29 proteins) with the non-ERBB2 tumor samples. Interaction and pathway analysis identified extracellular signal regulated kinase (ERK) cascade and actin polymerization and actinmyosin assembly contraction as pathways of importance in ERBB2+ and ERBB2- gastric cancer samples, respectively. The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB.

Original languageEnglish
Pages (from-to)4995-5006
Number of pages12
JournalJournal of Proteome Research
Volume14
Issue number12
DOIs
Publication statusPublished - 2015 Dec 4

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Proteomics
Stomach Neoplasms
Genes
Oncogenes
Tissue
Chromosomes
Tumors
Neoplasms
Extracellular Signal-Regulated MAP Kinases
Proteome
Epidermal Growth Factor Receptor
Chromosomes, Human, Pair 17
Amplification
Actins
Information Storage and Retrieval
Human Chromosomes
Proteins
Phosphotransferases
Polymerization
Colonic Neoplasms

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

Yan, J. F., Kim, H., Jeong, S. K., Lee, H. J., Sethi, M. K., Lee, L. Y., ... Hancock, W. S. (2015). Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. Journal of Proteome Research, 14(12), 4995-5006. https://doi.org/10.1021/acs.jproteome.5b00827
Yan, Julia Fangfei ; Kim, Hoguen ; Jeong, Seul Ki ; Lee, Hyoung Joo ; Sethi, Manveen K. ; Lee, Ling Y. ; Beavis, Ronald C. ; Im, Hogune ; Snyder, Michael P. ; Hofree, Matan ; Ideker, Trey ; Wu, Shiaw Lin ; Paik, Young-Ki ; Fanayan, Susan ; Hancock, William S. / Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. In: Journal of Proteome Research. 2015 ; Vol. 14, No. 12. pp. 4995-5006.
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Yan, JF, Kim, H, Jeong, SK, Lee, HJ, Sethi, MK, Lee, LY, Beavis, RC, Im, H, Snyder, MP, Hofree, M, Ideker, T, Wu, SL, Paik, Y-K, Fanayan, S & Hancock, WS 2015, 'Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues', Journal of Proteome Research, vol. 14, no. 12, pp. 4995-5006. https://doi.org/10.1021/acs.jproteome.5b00827

Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. / Yan, Julia Fangfei; Kim, Hoguen; Jeong, Seul Ki; Lee, Hyoung Joo; Sethi, Manveen K.; Lee, Ling Y.; Beavis, Ronald C.; Im, Hogune; Snyder, Michael P.; Hofree, Matan; Ideker, Trey; Wu, Shiaw Lin; Paik, Young-Ki; Fanayan, Susan; Hancock, William S.

In: Journal of Proteome Research, Vol. 14, No. 12, 04.12.2015, p. 4995-5006.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues

AU - Yan, Julia Fangfei

AU - Kim, Hoguen

AU - Jeong, Seul Ki

AU - Lee, Hyoung Joo

AU - Sethi, Manveen K.

AU - Lee, Ling Y.

AU - Beavis, Ronald C.

AU - Im, Hogune

AU - Snyder, Michael P.

AU - Hofree, Matan

AU - Ideker, Trey

AU - Wu, Shiaw Lin

AU - Paik, Young-Ki

AU - Fanayan, Susan

AU - Hancock, William S.

PY - 2015/12/4

Y1 - 2015/12/4

N2 - V-erb-b2 erythroblastic leukemia viral oncogene homologue 2, known as ERBB2, is an important oncogene in the development of certain cancers. It can form a heterodimer with other epidermal growth factor receptor family members and activate kinase-mediated downstream signaling pathways. ERBB2 gene is located on chromosome 17 and is amplified in a subset of cancers, such as breast, gastric, and colon cancer. Of particular interest to the Chromosome-Centric Human Proteome Project (C-HPP) initiative is the amplification mechanism that typically results in overexpression of a set of genes adjacent to ERBB2, which provides evidence of a linkage between gene location and expression. In this report we studied patient samples from ERBB2-positive together with adjacent control nontumor tissues. In addition, non-ERBB2-expressing patient samples were selected as comparison to study the effect of expression of this oncogene. We detected 196 proteins in ERBB2-positive patient tumor samples that had minimal overlap (29 proteins) with the non-ERBB2 tumor samples. Interaction and pathway analysis identified extracellular signal regulated kinase (ERK) cascade and actin polymerization and actinmyosin assembly contraction as pathways of importance in ERBB2+ and ERBB2- gastric cancer samples, respectively. The raw data files are deposited at ProteomeXchange (identifier: PXD002674) as well as GPMDB.

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