Rajasekaran Swetha, Nagarajha Selvan Lakshmi Dhevi, Dotts Kathleen, Kumar Ranjith, Rishi Pukhraj, Khetan Vikas, Bisht Madhoolika, Sivaraman Karthikeyan, Krishnakumar Subrmanian, Sahoo Debashis, Campbell Moray J, Elchuri Sailaja V, Miles Wayne O
Department of Molecular Genetics, The Ohio State University, Columbus, OH, United States.
The Ohio State University Comprehensive Cancer Center, Columbus, OH,, United States.
Front Oncol. 2019 Apr 16;9:221. doi: 10.3389/fonc.2019.00221. eCollection 2019.
Retinoblastoma is a rare pediatric tumor of the retina, caused by the homozygous loss of the Retinoblastoma 1 (RB1) tumor suppressor gene. Previous microarray studies have identified changes in the expression profiles of coding genes; however, our understanding of how non-coding genes change in this tumor is absent. This is an important area of research, as in many adult malignancies, non-coding genes including LNC-RNAs are used as biomarkers to predict outcome and/or relapse. To establish a complete and in-depth RNA profile, of both coding and non-coding genes, in Retinoblastoma tumors, we conducted RNA-seq from a cohort of tumors and normal retina controls. This analysis identified widespread transcriptional changes in the levels of both coding and non-coding genes. Unexpectedly, we also found rare RNA fusion products resulting from genomic alterations, specific to Retinoblastoma tumor samples. We then determined whether these gene expression changes, of both coding and non-coding genes, were also found in a completely independent Retinoblastoma cohort. Using our dataset, we then profiled the potential effects of deregulated LNC-RNAs on the expression of neighboring genes, the entire genome, and on mRNAs that contain a putative area of homology. This analysis showed that most deregulated LNC-RNAs do not act locally to change the transcriptional environment, but potentially function to modulate genes at distant sites. From this analysis, we selected a strongly down-regulated LNC-RNA in Retinoblastoma, DRAIC, and found that restoring DRAIC RNA levels significantly slowed the growth of the Y79 Retinoblastoma cell line. Collectively, our work has generated the first non-coding RNA profile of Retinoblastoma tumors and has found that these tumors show widespread transcriptional deregulation.
视网膜母细胞瘤是一种罕见的儿童视网膜肿瘤，由视网膜母细胞瘤1（RB1）肿瘤抑制基因的纯合缺失引起。先前的微阵列研究已经确定了编码基因表达谱的变化；然而，我们对该肿瘤中非编码基因如何变化尚不清楚。这是一个重要的研究领域，因为在许多成人恶性肿瘤中，包括长链非编码RNA（Lnc-RNAs）在内的非编码基因被用作预测预后和/或复发的生物标志物。为了建立视网膜母细胞瘤肿瘤中编码基因和非编码基因完整且深入的RNA图谱，我们对一组肿瘤和正常视网膜对照进行了RNA测序。该分析确定了编码基因和非编码基因水平上广泛的转录变化。出乎意料的是，我们还发现了由基因组改变产生的罕见RNA融合产物，这些产物特定于视网膜母细胞瘤肿瘤样本。然后，我们确定在一个完全独立的视网膜母细胞瘤队列中是否也发现了这些编码基因和非编码基因的表达变化。利用我们的数据集，我们随后分析了失调的Lnc-RNAs对邻近基因、整个基因组以及包含假定同源区域的mRNA表达的潜在影响。该分析表明，大多数失调的Lnc-RNAs并非在局部起作用来改变转录环境，而是可能在远处位点调节基因功能。通过该分析，我们在视网膜母细胞瘤中选择了一个强烈下调的Lnc-RNA，即DRAIC，并发现恢复DRAIC RNA水平可显著减缓Y79视网膜母细胞瘤细胞系的生长。总的来说，我们的工作生成了首个视网膜母细胞瘤肿瘤的非编码RNA图谱，并发现这些肿瘤表现出广泛的转录失调。
