title: Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.
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.
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.
authors.forename: Julia Fangfei
authors.initials: JF
authors.lastname: Yan
authors.affiliation: Yonsei University College of Medicine, Yonsei University , 50-1 Yonsei-Ro, Seodaemun-gu, Seoul 120-752, Korea.
authors.forename: Hoguen
authors.initials: H
authors.lastname: Kim
authors.affiliation: Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea.
authors.forename: Seul-Ki
authors.initials: SK
authors.lastname: Jeong
authors.affiliation: Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea.
authors.forename: Hyoung-Joo
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia.
authors.forename: Manveen K
authors.initials: MK
authors.lastname: Sethi
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia.
authors.forename: Ling Y
authors.initials: LY
authors.lastname: Lee
authors.affiliation: Department of Biochemistry and Medical Genetics, Faculty of Health Sciences, University of Manitoba , 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada.
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Beavis
authors.affiliation: Department of Genetics, Stanford University , Stanford, California 94305, United States.
authors.forename: Hogune
authors.initials: H
authors.lastname: Im
authors.affiliation: Department of Genetics, Stanford University , Stanford, California 94305, United States.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Snyder
authors.affiliation: Department of Computer Science and Engineering, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Matan
authors.initials: M
authors.lastname: Hofree
authors.affiliation: Program in Bioinformatics, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States.
authors.forename: Trey
authors.initials: T
authors.lastname: Ideker
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.
authors.forename: Shiaw-Lin
authors.initials: SL
authors.lastname: Wu
authors.affiliation: Yonsei University College of Medicine, Yonsei University , 50-1 Yonsei-Ro, Seodaemun-gu, Seoul 120-752, Korea.|Yonsei Proteome Research Center, Yonsei University , 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea.
authors.forename: Young-Ki
authors.initials: YK
authors.lastname: Paik
authors.affiliation: Department of Biomedical Sciences, Macquarie University , Sydney, New South Wales 2109, Australia.
authors.forename: Susan
authors.initials: S
authors.lastname: Fanayan
authors.affiliation: Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.
authors.forename: William S
authors.initials: WS
authors.lastname: Hancock
mesh_terms: D016022:Case-Control Studies; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000378:metabolism*; D013274:Stomach Neoplasms / Q000235:genetics* / Q000378:metabolism*
chemical_list: D018719:Erb-b2 Receptor Tyrosine Kinases; C508053:ERBB2 protein, human
keywords: Chromosome-centric Human Proteome Project; EGFR; ERBB2; GRB2; RNA-Seq; gastric cancer patient tissues