Cancer stem-like cell is a key barrier for therapeutic resistance and metastasis in various cancers, including breast cancer, yet the underlying mechanisms are still elusive. Through a genome-wide lncRNA expression profiling, we identified that LINC00115 is robustly upregulated in chemoresistant breast cancer stem-like cells (BCSCs). LncRNA microarray assay was performed to document abundance changes of lncRNAs in paclitaxel (PTX)-resistant MDA-MB-231 BCSC (ALDH+) and non-BCSC (ALDH−). RNA pull-down and RNA immunoprecipitation (RIP) assays were performed to determine the binding proteins of LINC00115. The clinical significance of the LINC00115 pathway was examined in TNBC metastatic lymph node tissues. The biological function of LINC00115 was investigated through gain- and loss-of-function studies. The molecular mechanism was explored through RNA sequencing, mass spectrometry, and the CRISPR/Cas9-knockout system. The therapeutic potential of LINC00115 was examined through xenograft animal models. LINC00115 functions as a scaffold lncRNA to link SETDB1 and PLK3, leading to enhanced SETDB1 methylation of PLK3 at both K106 and K200 in drug-resistant BCSC. PLK3 methylation decreases PLK3 phosphorylation of HIF1α and thereby increases HIF1α stability. HIF1α, in turn, upregulates ALKBH5 to reduce m6A modification of LINC00115, resulting in attenuated degradation of YTHDF2-dependent m6A-modified RNA and enhanced LINC00115 stability. Thus, this positive feedback loop provokes BCSC phenotypes and enhances chemoresistance and metastasis in triple-negative breast cancer. SETDB1 inhibitor TTD-IN with LINC00115 ASO sensitizes PTX-resistant cell response to chemotherapy in a xenograft animal model. Correlative expression of LINC00115, methylation PLK3, SETDB1, and HIF1α are prognostic for clinical triple-negative breast cancers. Our findings uncover LINC00115 as a critical regulator of BCSC and highlight targeting LINC00115 and SETDB1 as a potential therapeutic strategy for chemotherapeutic resistant breast cancer.

中文翻译：

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LINC00115通过SETDB1/PLK3/HIF1α信号传导促进化疗耐药乳腺癌干细胞样细胞的干性和转移

癌症干细胞样细胞是包括乳腺癌在内的各种癌症治疗耐药和转移的关键障碍，但其潜在机制仍不清楚。通过全基因组 lncRNA 表达谱分析，我们发现 LINC00115 在化疗耐药性乳腺癌干细胞样细胞 (BCSC) 中显着上调。进行 LncRNA 微阵列测定以记录紫杉醇 (PTX) 抗性 MDA-MB-231 BCSC (ALDH+) 和非 BCSC (ALDH−) 中 lncRNA 的丰度变化。进行 RNA Pull-down 和 RNA 免疫沉淀 (RIP) 测定以确定 LINC00115 的结合蛋白。在 TNBC 转移淋巴结组织中检查了 LINC00115 通路的临床意义。通过功能获得和功能丧失研究来研究 LINC00115 的生物学功能。通过RNA测序、质谱和CRISPR/Cas9敲除系统探索了分子机制。通过异种移植动物模型检查了 LINC00115 的治疗潜力。 LINC00115 作为支架 lncRNA 连接 SETDB1 和 PLK3，导致耐药 BCSC 中 PLK3 K106 和 K200 处的 SETDB1 甲基化增强。 PLK3 甲基化会降低 HIF1α 的 PLK3 磷酸化，从而增加 HIF1α 的稳定性。反过来，HIF1α 上调 ALKBH5 以减少 LINC00115 的 m6A 修饰，从而减弱 YTHDF2 依赖性 m6A 修饰 RNA 的降解并增强 LINC00115 的稳定性。因此，这种正反馈回路会引发 BCSC 表型并增强三阴性乳腺癌的化疗耐药性和转移。 SETDB1 抑制剂 TTD-IN 与 LINC00115 ASO 在异种移植动物模型中使 PTX 耐药细胞对化疗的反应敏感。 LINC00115、甲基化 PLK3、SETDB1 和 HIF1α 的相关表达可预测临床三阴性乳腺癌。我们的研究结果发现 LINC00115 是 BCSC 的关键调节因子，并强调以 LINC00115 和 SETDB1 为靶点作为化疗耐药乳腺癌的潜在治疗策略。