Beaver Laura M, Kuintzle Rachael, Buchanan Alex, Wiley Michelle W, Glasser Sarah T, Wong Carmen P, Johnson Gavin S, Chang Jeff H, Löhr Christiane V, Williams David E, Dashwood Roderick H, Hendrix David A, Ho Emily
Biological and Population Health Sciences, Oregon State University, 103 Milam Hall, Corvallis, OR 97331; Linus Pauling Institute, Oregon State University, 307 Linus Pauling Science Center, Corvallis, OR 97331.
Department of Biochemistry and Biophysics, Oregon State University, 2011 Agriculture and Life Sciences Building, Corvallis, OR 97331.
J Nutr Biochem. 2017 Apr;42:72-83. doi: 10.1016/j.jnutbio.2017.01.001. Epub 2017 Jan 12.
Long noncoding RNAs (lncRNAs) have emerged as important in cancer development and progression. The impact of diet on lncRNA expression is largely unknown. Sulforaphane (SFN), obtained from vegetables like broccoli, can prevent and suppress cancer formation. Here we tested the hypothesis that SFN attenuates the expression of cancer-associated lncRNAs. We analyzed whole-genome RNA-sequencing data of normal human prostate epithelial cells and prostate cancer cells treated with 15 μM SFN or dimethylsulfoxide. SFN significantly altered expression of ~100 lncRNAs in each cell type and normalized the expression of some lncRNAs that were differentially expressed in cancer cells. SFN-mediated alterations in lncRNA expression correlated with genes that regulate cell cycle, signal transduction and metabolism. LINC01116 was functionally investigated because it was overexpressed in several cancers, and was transcriptionally repressed after SFN treatment. Knockdown of LINC01116 with siRNA decreased proliferation of prostate cancer cells and significantly up-regulated several genes including GAPDH (regulates glycolysis), MAP1LC3B2 (autophagy) and H2AFY (chromatin structure). A four-fold decrease in the ability of the cancer cells to form colonies was found when the LINC01116 gene was disrupted through a CRISPR/CAS9 method, further supporting an oncogenic function for LINC01116 in PC-3 cells. We identified a novel isoform of LINC01116 and bioinformatically investigated the possibility that LINC01116 could interact with target genes via ssRNA:dsDNA triplexes. Our data reveal that chemicals from the diet can influence the expression of functionally important lncRNAs, and suggest a novel mechanism by which SFN may prevent and suppress prostate cancer.
长链非编码RNA（lncRNAs）已成为癌症发生和发展过程中的重要因素。饮食对lncRNA表达的影响在很大程度上尚不清楚。萝卜硫素（SFN）可从西兰花等蔬菜中获取，它能够预防和抑制癌症形成。在此，我们检验了SFN可减弱癌症相关lncRNAs表达这一假说。我们分析了用15μM SFN或二甲基亚砜处理的正常人前列腺上皮细胞和前列腺癌细胞的全基因组RNA测序数据。SFN显著改变了每种细胞类型中约100种lncRNAs的表达，并使癌细胞中差异表达的一些lncRNAs的表达正常化。SFN介导的lncRNA表达改变与调节细胞周期、信号转导和代谢的基因相关。对LINC01116进行了功能研究，因为它在多种癌症中过表达，且在SFN处理后转录受到抑制。用小干扰RNA（siRNA）敲低LINC01116可降低前列腺癌细胞的增殖，并显著上调包括甘油醛-3-磷酸脱氢酶（调节糖酵解）、微管相关蛋白1轻链3β2（自噬）和核小体核心组蛋白H2A（染色质结构）在内的多个基因。当通过CRISPR/CAS9方法破坏LINC01116基因时，发现癌细胞形成集落的能力下降了四倍，这进一步支持了LINC01116在PC-3细胞中的致癌功能。我们鉴定出LINC01116的一种新型异构体，并通过生物信息学方法研究了LINC01116通过单链RNA：双链DNA三链体与靶基因相互作用的可能性。我们的数据表明，饮食中的化学物质可影响功能重要的lncRNAs的表达，并提示了SFN预防和抑制前列腺癌的一种新机制。
