Abstract B24: The diagnostic power of direct mRNA profiling in breast cancer core biopsy
Authors: Indira Prabakaran, Paul J. Zhang, Marina Guvakova
Journal: Cancer Research (2016)

Abstract Background: Worldwide, biopsy is the gold standard for pathological assessment of cancer. Routinely, immunohistochemistry (IHC) can be performed to evaluate various tumor markers on serial sections of formalin-fixed paraffin-embedded (FFPE) tissue. Comprehensive molecular analysis of biopsy is limited by the microscopic size of samples and the scarcity of quantitative tools for FFPE tissue examination. Development of the new tools for molecular analysis of biopsy is needed to stratify, as early as possible, a patient’s individual risk for tumor aggressiveness and sensitivity to therapy to avoid potential over- and under treatment. Objective: To assess the feasibility of direct mRNA expression profiling of all three classic clinical markers of cancer progression - estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) in routinely collected FFPE core needle biopsy (CNB) of the breast. Methods: We obtained tissue from the Department of Pathology and Laboratory Medicine at the University of Pennsylvania, the University of Pennsylvania Tumor Tissue and Biospecimen Bank and the Cooperative Human Tissue Network. Steroid hormone receptor and HER2 status, determined by FDA-approved methods, was obtained from the surgical pathology reports. For direct (i.e. without amplification) mRNA profiling, we ran the Panomics/Affymetrix QuantiGene Plex 2.0 assay on Luminex according to manufacturer’s protocol. After the removal of low-abundance housekeeping genes expressing samples, the relative activity of target genes, ERS1, PGR, ERBB2 encoding ER alpha, PR and HER2 was detected. mRNA profiling was completed in 107 breast samples: 6 clinically normal (N) cases from reduction mammoplasty, 17 ductal carcinoma in situ ( DCIS) on CNB , 42 invasive ductal carcinoma (IDC) and 42 non-malignant matched tissue from surgical excisions. Groups were compared using one-way analysis of variance (ANOVA). Results: A pair-wise comparison among tissue groups revealed 3-fold higher expression levels of ERS1 in ER+ DCIS on CNB (P=. 055), and statistically significantly higher expression levels of ERS1 in the ER+/PR+ (P= .021) and ER+/PR- (P= .004) subgroups of IDC than in the N group. Remarkably, compared with N tissue, ERS1 levels were already decreased in non-malignant tissue adjacent to ER-/PR-/HER2- subgroup of IDC and were further significantly decreased in ER-/PR-/HER2- IDC itself (P= .023). Compared to the N group, significant decreases in PGR levels were found only in ER-/PR-/HER2- subgroup of IDC (P= .003), whereas significant increases in ERBB2 levels were found in both HER2+ DCIS on CNB (P= . 037) and HER2+IDC in excisions (P= .005). Conclusions: Our study, for the first time, proved the feasibility of using FFPE CNB as an RNA source for direct mRNA expression profiling. These findings support the notion that IHC evaluation of ER, PR, and HER2 status in the CNB DCIS may be complemented by concurrent detection of ESR1/PGR/ERBB2 mRNA levels. Citation Format: Indira Prabakaran, Paul J. Zhang, Marina Guvakova. The diagnostic power of direct mRNA profiling in breast cancer core biopsy. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B24.