Abstract 1828: RNA-seq reveals association of pCR and changes in lncRNA expression in pre-operative bevacizumab treatment of breast cancer.
Authors: Banerjee Nilanjana , Varadan Vinay , Kamalakaran Sitharthan , Janevski Angel , Miskimen Kristy , Williams Nicole , Abu-Khalaf Maysa , Sikov William , Harris Lyndsay N. , Dimitrova Nevenka 
Published: August 2014

Abstract
Background: Long non-coding RNAs (lncRNAs) are pervasively transcribed in the genome yet their role in human disease is not well understood. Recent studies show that expression of the lncRNA HOTAIR is increased in primary breast tumors and is a predictor of metastasis. However, to date, it is unclear how changes in lncRNA expression with treatment correlate with response. We performed an RNA-seq study to characterize changes in lncRNA expression following exposure to chemotherapy or biologic therapy and evaluate association to achievement of pathologic complete response (pCR) to neoadjuvant therapy.
Methods: We sequenced transcriptomes of core biopsy RNA from 50 pairs of breast tumors obtained from neoadjuvant clinical trials BrUOG 211A/211B. Patients were given a run-in dose of bevacizumab (B), nab-paclitaxel (N) or trastuzumab (T), followed by combination biologic/chemotherapy (HER2- with B/carboplatin/N; HER2+ with T/carboplatin/N). RNA was derived from biopsy pairs obtained pre/post 10 day exposure to run-in monotherapy. Paired-end sequencing was performed with 74bp read length, yielding genome-wide transcriptomic data. Transcriptomic abundance and differential expression were estimated assuming Poisson-distributed read-counts. Paired-end sequence data was aligned to a lncRNA database containing 14,572 unique lncRNAs. Changes in relative abundance of lncRNA transcripts were tested for association with pCR using the Wilcoxon rank-sum test.
Results: On average, in each patient 1500 lncRNAs were differentially expressed between pre and post samples (p&lt;0.05). Within each treatment arm 600-700 lncRNAs were differentially expressed across a majority of the patients (65%). There are many lncRNAs common among the three treatment arms (80% overlap). Genes from the transcribed loci are enriched in Kegg pathways such as primary immunodeficiency, cytosolic DNA sensing, B-cell receptor signaling and T-cell receptor signaling. For the B arm, where response data was available, we identified 38 lncRNAs for which change in level of expression correlated with pCR after multiple hypothesis correction, of which 25 were differentially expressed in the other treatment arms. Previously characterized lncRNAs in breast cancer, MEG3 and GAS5 were identified to be uniquely associated with response in the B arm.
Discussion: This is the first study to report that changes in lncRNA expression upon brief exposure to B are associated with achievement of pCR to subsequent neoadjuvant therapy. The overlapping changes in lncRNAs across different treatment arms suggest systematic lncRNA-mediated mechanisms at play. These preliminary observations need to be explored in a larger group of patients. Next generation sequencing technologies will likely allow further characterization of lncRNAs leading to improved methods of stratifying, subclassifying and managing breast cancers.
Citation Format: Nilanjana Banerjee, Vinay Varadan, Sitharthan Kamalakaran, Angel Janevski, Kristy Miskimen, Nicole Williams, Maysa Abu-Khalaf, William Sikov, Lyndsay N. Harris, Nevenka Dimitrova. RNA-seq reveals association of pCR and changes in lncRNA expression in pre-operative bevacizumab treatment of breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1828. doi:10.1158/1538-7445.AM2013-1828