Aberrant insulin-like growth factor I receptor (IGF1R) signaling pathway serves as a well-established target for cancer drug therapy. The intragenic antisense long noncoding RNA (lncRNA) IRAIN, a putative tumor suppressor, is downregulated in breast cancer cells, while IGF1R is overexpressed, leading to an abnormal IGF1R/IRAIN ratio that promotes tumor growth. To precisely target this pathway, we developed an “antisense lncRNA-mediated intragenic cis competition” (ALIC) approach to therapeutically correct the elevated IGF1R/IRAIN bias in breast cancer cells. We used CRISPR-Cas9 gene editing to target the weak promoter of IRAIN antisense lncRNA and showed that in targeted clones, intragenic activation of the antisense lncRNA potently competed in cis with the promoter of the IGF1R sense mRNA. Notably, the normalization of IGF1R/IRAIN transcription inhibited the IGF1R signaling pathway in breast cancer cells, decreasing cell proliferation, tumor sphere formation, migration, and invasion. Using “nuclear RNA reverse transcription-associated trap” sequencing, we uncovered an IRAIN lncRNA-specific interactome containing gene targets involved in cell metastasis, signaling pathways, and cell immortalization. These data suggest that aberrantly upregulated IGF1R in breast cancer cells can be precisely targeted by cis transcription competition, thus providing a useful strategy to target disease genes in the development of novel precision medicine therapies.

异常的胰岛素样生长因子I受体（IGF1R）信号转导通路已成为癌症药物治疗的既定目标。内源性反义长非编码RNA（lncRNA）IRAIN（一种假定的肿瘤抑制因子）在乳腺癌细胞中被下调，而IGF1R则过表达，导致异常的IGF1R / IRAIN比值促进肿瘤生长。为了精确地靶向该途径，我们开发了一种“反义lncRNA介导的基因内顺式竞争”（ALIC ）方法，以治疗性纠正乳腺癌细胞中升高的IGF1R / IRAIN偏倚。我们使用了CRISPR-Cas9基因编辑来靶向弱启动子IRAIN反义lncRNA并显示在靶向克隆中，反义lncRNA的基因内激活有效地与IGF1R有义mRNA的启动子竞争顺式竞争。值得注意的是，IGF1R / IRAIN转录的正常化抑制了乳腺癌细胞中的IGF1R信号传导途径，从而降低了细胞增殖，肿瘤球的形成，迁移和侵袭。使用“核RNA逆转录相关陷阱”测序，我们发现了一个IRAIN lncRNA特异性相互作用组，该相互作用组包含与细胞转移，信号通路和细胞永生化有关的基因靶标。这些数据表明IGF1R异常上调顺式转录竞争可以精确地靶向乳腺癌细胞中的“靶点” ，从而在新型精密药物疗法的开发中提供了一种靶向疾病基因的有用策略。