Long Non-Coding RNA Expression Levels Correlate with Proliferation Index in Breast Carcinoma.
Karen M Chisholm, Rui Li, Yue Wan, Howard Y Chang, Robert B West. Stanford University School of Medicine, CA
Background: Long intervening non-coding RNAs (lincRNAs) are RNAs that do not code for proteins but can interact with proteins, and some are thought to influence chromatin remodeling. Experimental evidence suggests that in cancer, they can influence Polycomb repressive complexes to retarget to an occupancy pattern resembling that of the embryonic state. In a recent paper by Gupta et al., 2010, the expression level of lincRNA in the HOX locus, including HOTAIR, is a predictor of breast cancer metastasis. The current project is undertaken to determine if lincRNAs can be measured in formalin-fixed paraffin-embedded tissue, and to see if HOX locus lincRNAs correlate with clinicopathologic features.
Design: The expression levels of HOTAIR and two other HOX locus lincRNAs (ncHoxA1 and ncHoxD4), which were identified in the Gupta et al., 2010 paper to cluster with metastatic breast carcinomas, are observed in breast carcinoma. Probes of 400 to 500 nucleotides were created based upon unique non-conserved sequences. These probes were hybridized to tissue microarrays containing 283 primary breast carcinomas and control specimens from formalin-fixed paraffin embedded tissues. The stains were then scored by eye on a two- or three-tiered scoring system, and were correlated with known clinicopathologic features of the breast carcinomas including metastasis, hormone status (ER, PR, and HER2/neu), and Ki67.
Results: Increased HOTAIR expression correlated with an increased proliferation rate (p = 0.042), while increased ncHoxA1 expression demonstrated a trend with increased proliferation rate. In addition, ncHoxA1 and ncHoxD4 lincRNAs had correlating expression levels (p = <0.0001). When these latter two lincRNAs had correlating expression levels, the proliferation rate was more often increased (p = 0.043), especially when they both had increased expression (p = 0.052).
Conclusions: This is the first study to show that RNA in situ hybridization of formalin fixed paraffin-embedded clinical material can be used to quantify levels of long non-coding RNAs. This approach offers a method to make observations on lincRNAs that may influence the cancer epigenome in a tissue-based technique. The current study provides evidence that these HOX locus lincRNAs correlate with proliferation index in carcinoma; this finding could be due to their influence on chromatin remodeling.
Monday, February 28, 2011 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 23, Monday Morning