Genome Wide Proteomics of Inflammatory Breast Cancer

Researchers led by Dr. William S. Hancock at the Barnett Institute and the Department of Chemistry and Chemical Biology, Northeastern University (Boston, MA) report on genome-wide proteomics of specific oncogenes and oncogenic pathways in inflammatory breast cancer.¹ They describe protein expression profiles in primary inflammatory breast cancer tumors using three established breast cancer cell lines—SKBR3, SUM149 and SUM190.

The cell lines SUM149 and SUM190 are estrogen receptor and progesterone receptor. The SKBR3 cell line is known to express high levels of v-erb-b2 erythroblastic (ERBB2) leukemia viral oncogene homolog 2, and is also estrogen receptor and progesterone receptor. These cell lines show different oncogene expression levels in ERBB2 and epidermal growth factor receptor (EGFR) signaling pathways. The American Society of Clinical Oncology recommends determination of ERBB2 status as a marker for diagnosis and evaluation in primary invasive breast cancer.²

The trypsin-digested peptides of the SKBR3, SUM149 and SUM190 cells were subjected to liquid chromatography–mass spectrometry (LC–MS) analysis using a linear ion trap coupled to a Fourier Transform Mass Spectrometer (LTQ-FTMS, Thermo Scientific). Peptide sequences were identified, using Thermo Scientific Proteome Discoverer 1.3, from a human database SP.human.56.5 with full trypsin specificity. The researchers used RNA-Seq data to identify the oncogenes with significant expression levels in these cell lines. They then queried the corresponding proteomic data sets for proteins with significant interaction values with these oncogenes.

Comparison of proteomic observations among cell lines indicates five RAS-related proteins with two-fold higher relative abundance in SUM190 and SKBR3, as compared to SUM149. RAS-associated proteins are usually activated in tumors in which ERBB2 is overexpressed. Cathepsin D, a marker of breast cancer, was elevated six-fold and ten-fold in SUM190 and SKBR3, compared to SUM149.

The results show the top three oncogenes with the greatest number of interactions with observed proteins; these include MYC, GRB2 and EGFR, with 268, 235 and 143 interactions, respectively, for SUM149.

Based on the integration of transcriptomic, proteomic and interaction data, the investigators identified cancer-relevant pathways. The four pathways identified in addition to ERBB2 signaling are EGFR, integrin, MYC signaling and PI3K signaling. They comprise many of the oncogene-interacting proteins. Proteins correlated with higher levels of EGFR or ERBB2 transcript are:

EGFR signaling: caveolin 1 (CAV1), plectin (PLEC) (EGFR); growth factor receptor-bound protein 7 (GRB7), CRK-like protein (CRKL) and Catenin delta-1 (CTNND1) (ERBB2)

Integrin signaling: filamin A (FLNA) and actinin alpha1 (ACTN1) (EGFR)

MYC signaling: branched chain amino-acid transaminase 1 (BCAT1), carbamoyl-phosphate synthetase (CAD), nucleolin (NCL), transferrin receptor (TFRC), metadherin (MTDH) (ERBB2)

p53 signaling: S100-A2 protein (S100A2), caveolin 1 (CAV1), Serpin B5 (SERPINB5), stratifin (SFN), PYD and CARD domain containing (PYCARD), and EPH receptor A2 (EPHA2) (EGFR)

Researchers hope to investigate the proteins identified in this study as potential markers of ERBB2 and EGFR signaling. Exploring the role of the marker proteins in the activation of the oncogenes MYC and GRB2 in inflammatory breast cancer should be of diagnostic and therapeutic value.

References

1. Zhang, E.Y., et al. (2013, May 22) “Genome Wide Proteomics of ERBB2 and EGFR and Other Oncogenic Pathways in Inflammatory Breast Cancer,” Journal of Proteome Research, doi: 10.1021/pr4001527.

2. Harris, L., et al. (2007) “American Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancer,” Journal of Clinical Oncology, 25(33) (pp. 5287–312), doi: 10.1200/JCO.2007.14.2364.