Cold-inducible RNA binding protein (CIRBP) is a stress-responsive protein that promotes cancer development and inflammation. Critical to most CIRBP functions is its capacity to bind and post-transcriptionally modulate mRNA. However, a transcriptome-wide analysis of CIRBP mRNA targets in cancer has not yet been performed. Here, we use an ex vivo breast cancer model to identify CIRBP targets and mechanisms. We find that CIRBP transcript levels correlate with breast cancer subtype and are an indicator of luminal A/B prognosis. Accordingly, over-expression of CIRBP in non-tumoral MCF-10A cells promotes cell growth and clonogenicity, while depletion of CIRBP from luminal A MCF-7 cells has opposite effects. We use RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq) to identify a set of 204 high confident CIRBP targets in MCF-7 cells. About 10% of these showed complementary changes after CIRBP manipulation in MCF-10 and MCF-7 cells, and were highly interconnected with known breast cancer genes. To test the potential of CIRBP-mediated regulation of these targets in breast cancer development, we focused on Cystatin C (CST3), one of the most highly interconnected genes and a protein that displays tumor suppressive capacities. CST3 depletion restored the effects of CIRBP depletion in MCF-7 cells, indicating that CIRBP functions, at least in part, by downregulating CST3 levels. Our data provide a resource of CIRBP targets in breast cancer, and identify CST3 as a novel downstream mediator of CIRBP function.

中文翻译：

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冷诱导 RNA 结合蛋白通过调节 Cystatin C 水平促进乳腺癌细胞恶性

冷诱导 RNA 结合蛋白 (CIRBP) 是一种应激反应蛋白，可促进癌症发展和炎症。大多数 CIRBP 功能的关键是其结合和转录后调节 mRNA 的能力。然而，尚未对癌症中的 CIRBP mRNA 靶标进行全转录组分析。在这里，我们使用离体乳腺癌模型来确定 CIRBP 靶点和机制。我们发现 CIRBP 转录水平与乳腺癌亚型相关，并且是管腔 A/B 预后的指标。因此，非肿瘤 MCF-10A 细胞中 CIRBP 的过度表达可促进细胞生长和克隆形成，而 luminal A MCF-7 细胞中 CIRBP 的消耗则具有相反的作用。我们使用 RNA 免疫沉淀和高通量测序 (RIP-Seq) 来鉴定 MCF-7 细胞中的一组 204 个高置信度 CIRBP 靶标。其中约 10% 在 MCF-10 和 MCF-7 细胞中进行 CIRBP 操作后显示出互补变化，并且与已知的乳腺癌基因高度相关。为了测试 CIRBP 介导的这些靶标在乳腺癌发展中的调节潜力，我们重点关注胱抑素 C (CST3)，它是相互关联性最高的基因之一，也是一种具有肿瘤抑制能力的蛋白质。CST3 消耗恢复了 MCF-7 细胞中 CIRBP 消耗的影响，表明 CIRBP 至少部分通过下调 CST3 水平发挥作用。我们的数据提供了乳腺癌中 CIRBP 靶标的资源，并将 CST3 确定为 CIRBP 功能的新型下游介质。