Paasch Thea P, Jarlstad Olesen Morten T, García-Rodríguez Juan L, Assmus Adrienne M, Fenton Robert A, Kjems Jørgen, Hager Henrik, Kristensen Lasse S
Department of Biomedicine, Aarhus University, Aarhus, Denmark.
Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark.
PLoS Genet. 2025 Jun 2;21(6):e1011726. doi: 10.1371/journal.pgen.1011726. eCollection 2025 Jun.
Circular RNAs (circRNAs) constitute a large class of non-coding RNAs with gene regulatory capabilities, mainly through microRNA binding, a mechanism that has been linked to cancer development. The circRNA ciRS-7 (also known as CDR1as) is an interesting candidate as it harbors over 60 binding sites for miR-7, which is known to have tumor-suppressing properties. Here, we investigated the spatial expression patterns and epigenetic regulation of ciRS-7 across nine different adenocarcinomas originating from the colon, pancreas, ovary, endometrium, breast, stomach, bile duct, lung, and prostate. The study included primary patient samples and 18 different cell lines. ciRS-7 expression was analyzed using Reverse Transcription-quantitative PCR (RT-qPCR), single molecule in situ hybridization, and Nanostring nCounter, while epigenetic modifications were examined through bisulfite sequencing, Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP), and chromatin immunoprecipitation. The functional relevance of epigenetic modifications was examined using DNA methyltransferase and histone deacetylase inhibitors. Across all adenocarcinomas, ciRS-7 was absent in the cancer cells in most of the primary tumor specimens, except for the breast tumors, while being expressed in the tumor microenvironment (TME). In line with this, ciRS-7 was not detected in most of the cell lines. Moreover, we demonstrated that DNA methylation and H3K9 acetylation, but not H3K27 methylation, are important epigenetic modifications that impact ciRS-7 expression. In conclusion, our data show that ciRS-7 is mainly expressed in the TME and is regulated through DNA methylation and histone acetylation across all major types of adenocarcinomas.
环状RNA（circRNAs）构成了一大类具有基因调控能力的非编码RNA，主要通过与微小RNA结合来实现，这种机制与癌症发展有关。环状RNA ciRS-7（也称为CDR1as）是一个有趣的候选对象，因为它含有超过60个miR-7的结合位点，而miR-7已知具有肿瘤抑制特性。在此，我们研究了ciRS-7在源自结肠、胰腺、卵巢、子宫内膜、乳腺、胃、胆管、肺和前列腺的九种不同腺癌中的空间表达模式和表观遗传调控。该研究包括原发性患者样本和18种不同的细胞系。使用逆转录定量PCR（RT-qPCR）、单分子原位杂交和纳米串nCounter分析ciRS-7的表达，同时通过亚硫酸氢盐测序、实时甲基化特异性PCR后的灵敏熔解分析（SMART-MSP）和染色质免疫沉淀检测表观遗传修饰。使用DNA甲基转移酶和组蛋白去乙酰化酶抑制剂检测表观遗传修饰的功能相关性。在所有腺癌中，除乳腺肿瘤外，大多数原发性肿瘤标本的癌细胞中不存在ciRS-7，而在肿瘤微环境（TME）中表达。与此一致的是，在大多数细胞系中未检测到ciRS-7。此外，我们证明DNA甲基化和H3K9乙酰化而非H3K27甲基化是影响ciRS-7表达的重要表观遗传修饰。总之，我们的数据表明ciRS-7主要在TME中表达，并在所有主要类型腺癌中通过DNA甲基化和组蛋白乙酰化进行调控。
