Abstract P1-05-25: Patterns of translational dysregulation in models of estrogen receptor(+) and (-) breast cancer
Authors: Vaklavas C , Myers RM , Grizzle WE , Blume SW 
Published: March 2017

Abstract
Although our understanding of transcriptional dysregulation in cancer has expanded dramatically over the recent years, comparatively little is known about dysregulation in gene expression at the translational level. Yet, gene expression is extensively modulated at the level of translation. Leveraging the unbiased nature of next generation sequencing, we utilized the ribosome profiling strategy to characterize the translational profiles of a representative ER(+) (T47D) and ER(-) (SUM159) breast cancer cell line and compared them with the profiles of non-malignant human mammary epithelial cells (HMECs). The overarching hypothesis is that cancer cells differ from their non-malignant counterparts not only at the level of transcription but also at the level of translation and coordinate changes in transcription and translation lead to the phenotypic hallmarks of cancer.
The results show that the median translational efficiency was higher and more variable in malignant cells as compared to HMECs (HMECs 1.09; T47D 1.6; SUM159 1.29. Variance of the log2 transformed values, 2.37; 3.92; 4.16, respectively). When cells were deprived of serum for 24 hours, translation was uniformly upregulated but this upregulation was more pronounced in malignant cells. A larger number of genes were differentially expressed at the translational as compared to the transcriptional level between non-malignant and malignant cells. There was an imperfect correlation between RNA levels and translational efficiency. In addition, individual transcripts were translated with variable efficiency between malignant and non-malignant cells suggesting that the translation of the same RNA sequence is modulated in a context-dependent manner.
Although translation is globally upregulated in malignant cells, this upregulation is not uniform and the translational efficiency of multiple cancer-related mRNAs is not proportional to their abundance. For example, while the abundance of the CDK1 mRNA was not significantly different among the 3 cell lines, its translational efficiency was 1.5 and 2 times higher in the SUM159 and T47D cells, respectively. On the other hand, the mRNA of its cognate inhibitor CDKN1A was not only 4 times less abundant in the malignant cells but also half as efficiently translated as compared to HMECs.
Ribosome profiling has consistently revealed translation outside of canonical protein-coding regions. While in HMECs only 5.3% of unique ribosome protected fragments aligned to non-protein encoding transcripts, the respective fractions were 8% for T47D and 19.2% for SUM159 cells and were consistently higher in malignant cells across all conditions tested. We found that the translation of RNAs previously thought to be noncoding, especially lincRNAs, was pervasively upregulated and to similar levels in T47D and SUM159 cells as compared to HMECs.
Collectively, these results begin to unravel components of dysregulation in gene expression at the level of translation with important implications for the molecular pathophysiology of breast cancer and set the stage to advance such studies in primary human tumor samples.
Citation Format: Vaklavas C, Myers RM, Grizzle WE, Blume SW. Patterns of translational dysregulation in models of estrogen receptor(+) and (-) breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-25.