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Open Access Open Badges Research

Protein-based identification of quantitative trait loci associated with malignant transformation in two HER2+ cellular models of breast cancer

Yogesh M Kulkarni1 and David J Klinke12*

Author Affiliations

1 Department of Chemical Engineering, College of Engineering and Mineral Resources, West Virginia University, Morgantown, WV 26506, USA

2 Department of Microbiology, Immunology and Cell Biology and Mary Babb Randolph Cancer Center, School of Medicine, West Virginia University, Morgantown, WV 26506, USA

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Proteome Science 2012, 10:11  doi:10.1186/1477-5956-10-11

Published: 22 February 2012



A contemporary view of the cancer genome reveals extensive rearrangement compared to normal cells. Yet how these genetic alterations translate into specific proteomic changes that underpin acquiring the hallmarks of cancer remains unresolved. The objectives of this study were to quantify alterations in protein expression in two HER2+ cellular models of breast cancer and to infer differentially regulated signaling pathways in these models associated with the hallmarks of cancer.


A proteomic workflow was used to identify proteins in two HER2 positive tumorigenic cell lines (BT474 and SKBR3) that were differentially expressed relative to a normal human mammary epithelial cell line (184A1). A total of 64 (BT474-184A1) and 69 (SKBR3-184A1) proteins were uniquely identified that were differentially expressed by at least 1.5-fold. Pathway inference tools were used to interpret these proteins in terms of functionally enriched pathways in the tumor cell lines. We observed "protein ubiquitination" and "apoptosis signaling" pathways were both enriched in the two breast cancer models while "IGF signaling" and "cell motility" pathways were enriched in BT474 and "amino acid metabolism" were enriched in the SKBR3 cell line.


While "protein ubiquitination" and "apoptosis signaling" pathways were common to both the cell lines, the observed patterns of protein expression suggest that the evasion of apoptosis in each tumorigenic cell line occurs via different mechanisms. Evidently, apoptosis is regulated in BT474 via down regulation of Bid and in SKBR3 via up regulation of Calpain-11 as compared to 184A1.

MALDI-TOF MS; Proteomics; Breast cancer; Malignant transformation; Two dimensional gel electrophoresis; Ingenuity pathway analysis