A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability

The human genome encodes thousands of long noncoding RNA (lncRNA) genes; the function of majority of them is poorly understood. Aberrant expression of a significant number of lncRNAs is observed in various diseases, including cancer. To gain insights into the role of lncRNAs in breast cancer progression, we performed genome-wide transcriptome analyses in an isogenic, triple negative breast cancer (TNBC/basal-like) progression cell lines using a 3D cell culture model. We identified significantly altered expression of 1853 lncRNAs, including ~500 natural antisense transcript (NATs) lncRNAs. A significant number of breast cancer-deregulated NATs displayed co-regulated expression with oncogenic and tumor suppressor protein-coding genes in cis. Further studies on one such NAT, PDCD4-AS1 lncRNA reveal that it positively regulates the expression and activity of the tumor suppressor PDCD4 in mammary epithelial cells. Both PDCD4-AS1 and PDCD4 show reduced expression in TNBC cell lines and in patients, and depletion of PDCD4-AS1 compromised the cellular levels and activity of PDCD4. Further, tumorigenic properties of PDCD4-AS1-depleted TNBC cells were rescued by exogenous expression of PDCD4, implying that PDCD4-AS1 acts upstream of PDCD4. Mechanistically, PDCD4-AS1 stabilizes PDCD4 RNA by forming RNA duplex and controls the interaction between PDCD4 RNA and RNA decay promoting factors such as HuR. Our studies demonstrate crucial roles played by NAT lncRNAs in regulating post-transcriptional gene expression of key oncogenic or tumor suppressor genes, thereby contributing to TNBC progression.

人类基因组编码数千个长链非编码RNA（long noncoding RNA，lncRNA）基因，其中绝大多数的功能尚未得到充分阐明。大量lncRNA的异常表达已在包括癌症在内的多种疾病中被检测到。为深入解析lncRNA在乳腺癌进展中的作用，我们利用三维细胞培养模型，对一组同基因的三阴性乳腺癌（triple negative breast cancer，TNBC）/基底样型进展细胞系开展了全基因组转录组分析。我们鉴定出1853个表达发生显著改变的lncRNA，其中包含约500个天然反义转录本（natural antisense transcript，NAT）型lncRNA。大量在乳腺癌中表达失调的NAT型lncRNA，可与致癌基因及抑癌蛋白编码基因在顺式位置呈现共表达特征。我们针对其中一类NAT——PDCD4-AS1 lncRNA展开了进一步研究，结果显示其可在乳腺上皮细胞中正向调控抑癌基因PDCD4的表达与活性。在TNBC细胞系及患者样本中，PDCD4-AS1与PDCD4的表达均出现下调；敲低PDCD4-AS1会降低细胞内PDCD4的表达水平与活性。进一步实验证实，通过外源过表达PDCD4可挽救PDCD4-AS1敲低的TNBC细胞的致瘤特性，这表明PDCD4-AS1作用于PDCD4的上游调控通路。从分子机制层面来看，PDCD4-AS1可通过形成RNA双链结构稳定PDCD4 RNA，并调控PDCD4 RNA与RNA降解促进因子（如HuR）之间的相互作用。本研究证实，NAT型lncRNA在调控关键致癌基因或抑癌基因的转录后基因表达中发挥关键作用，进而参与TNBC的进展过程。