Research Papers:

Transcriptome-wide identification of mRNAs and lincRNAs associated with trastuzumab-resistance in HER2-positive breast cancer

Callie R. Merry, Sarah McMahon, Megan E. Forrest, Cynthia F. Bartels, Alina Saiakhova, Courtney A. Bartel, Peter C. Scacheri, Cheryl L. Thompson, Mark W. Jackson, Lyndsay N. Harris and Ahmad M. Khalil _

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Oncotarget. 2016; 7:53230-53244. https://doi.org/10.18632/oncotarget.10637

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Callie R. Merry1,2, Sarah McMahon1, Megan E. Forrest1, Cynthia F. Bartels1, Alina Saiakhova1, Courtney A. Bartel3, Peter C. Scacheri1,3, Cheryl L. Thompson3,5, Mark W. Jackson3, Lyndsay N. Harris3,4, Ahmad M. Khalil1,2,3

1Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA

2Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA

3Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA

4Department of Medicine and Case Western Reserve University, Cleveland, OH 44106, USA

5Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106, USA

Correspondence to:

Ahmad M. Khalil, email: [email protected]

Keywords: breast cancer, HER2, drug resistance, trastuzumab-resistance, cancer therapy

Received: March 11, 2016     Accepted: July 09, 2016     Published: July 16, 2016


Approximately, 25–30% of early-stage breast tumors are classified at the molecular level as HER2-positive, which is an aggressive subtype of breast cancer. Amplification of the HER2 gene in these tumors results in a substantial increase in HER2 mRNA levels, and consequently, HER2 protein levels. HER2, a transmembrane receptor tyrosine kinase (RTK), is targeted therapeutically by a monoclonal antibody, trastuzumab (Tz), which has dramatically improved the prognosis of HER2-driven breast cancers. However, ~30% of patients develop resistance to trastuzumab and recur; and nearly all patients with advanced disease develop resistance over time and succumb to the disease. Mechanisms of trastuzumab resistance (TzR) are not well understood, although some studies suggest that growth factor signaling through other receptors may be responsible. However, these studies were based on cell culture models of the disease, and thus, it is not known which pathways are driving the resistance in vivo. Using an integrative transcriptomic approach of RNA isolated from trastuzumab-sensitive and trastuzumab-resistant HER2+ tumors, and isogenic cell culture models, we identified a small set of mRNAs and lincRNAs that are associated with trastuzumab-resistance (TzR). Functional analysis of a top candidate gene, S100P, demonstrated that inhibition of S100P results in reversing TzR. Mechanistically, S100P activates the RAS/MEK/MAPK pathway to compensate for HER2 inhibition by trastuzumab. Finally, we demonstrated that the upregulation of S100P appears to be driven by epigenomic changes at the enhancer level. Our current findings should pave the path toward new therapies for breast cancer patients.

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