Abstract 2885: Differential expression of long non-coding RNAs in ovarian cancer-associated fibroblasts versus normal ovarian fibroblasts

Abstract

Abstract Ovarian cancer is the most lethal gynecological malignancy in women. Expression profiling of the high-grade serous subtype has revealed that patients exhibiting a “stromal expression signature” demonstrate the poorest prognosis1. However, genetic aberrations in ovarian cancer-associated fibroblasts (CAFs) are extremely rare2, raising the possibility that alternative mechanisms that regulate gene expression, such as long non-coding RNAs (lncRNAs), are present in CAFs. LncRNAs are polyadenylated RNA transcripts that do not encode for protein, but have been shown to correlate with cancer progression and outcome. Therefore, our aim was to investigate the presence of differentially expressed lncRNAs in ovarian CAFs versus normal ovarian fibroblasts. CAFs were laser-capture microdissected from 51 advanced-stage high-grade serous ovarian cancers and 10 normal ovaries removed from women for non-cancer reasons. RNA was extracted from the microdissected samples and expression analyzed using Affymetrix U133 Plus 2.0 Arrays. Probes previously identified as lncRNAs were used in this analysis3. Samples were normalized and background corrected using the robust multi-arrray average (RMA) method and expression values were log2 transformed. Differentially expressed probes between cancer versus normal samples were calculated using linear models for microarray data (limma) package from Bioconductor and a moderated t-statistic used to assess significance. Based on a significance cutoff of fold-change > 2 and a p-value < 0.05, 54 lncRNAs were identified as differentially expressed in cancer versus normal fibroblasts. These included lncRNAs previously implicated in ovarian cancer such as XIST and H19, the p53-regulated lncRNA TUG1, as well as several lncRNAs that are known to play a role in other cancer types such as NEAT1, GAS5 and CASC2. In addition, 16 lncRNAs were differentially expressed between patients with short (<15 months) versus patients with long (>15 months) overall survival. These included MALAT1, MEG3, TUG1, XIST and CRNDE. In summary, we have identified lncRNAs that are differentially expressed in ovarian CAFs compared to normal ovarian fibroblasts, as well as lncRNAs that are differentially expressed based on survival. Given that CAFs are known to promote tumor progression and metastasis, these lncRNAs present suitable candidates for their role in the tumor-promoting function of CAFs.