Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China.
Prostate. 2024 Jul;84(10):967-976. doi: 10.1002/pros.24714. Epub 2024 Apr 17.
Ribosome biogenesis is excessively activated in tumor cells, yet it is little known whether oncogenic transcription factors (TFs) are involved in the ribosomal RNA (rRNA) transactivation.
Nucleolar proteomics data and large-scale immunofluorescence were re-analyzed to jointly identify the proteins localized at nucleolus. RNA-Seq data of five prostate cancer (PCa) cohorts were combined and integrated with multi-dimensional data to define the upregulated nucleolar TFs in PCa tissues. Then, ChIP-Seq data of PCa cell lines and two PCa clinical cohorts were re-analyzed to reveal the TF binding patterns at ribosomal DNA (rDNA) repeats. The TF binding at rDNA was validated by ChIP-qPCR. The effect of the TF on rRNA transcription was determined by rDNA luciferase reporter, nascent RNA synthesis, and global protein translation assays.
In this study, we reveal the role of oncogenic TF FOXA1 in regulating rRNA transcription within nucleolar organization regions. By analyzing human TFs in prostate cancer clinical datasets and nucleolar proteomics data, we identified that FOXA1 is partially localized in the nucleolus and correlated with global protein translation. Our extensive FOXA1 ChIP-Seq analysis provides robust evidence of FOXA1 binding across rDNA repeats in prostate cancer cell lines, primary tumors, and castration-resistant variants. Notably, FOXA1 occupancy at rDNA repeats correlates with histone modifications associated with active transcription, namely H3K27ac and H3K4me3. Reducing FOXA1 expression results in decreased transactivation at rDNA, subsequently diminishing global protein synthesis.
Our results suggest FOXA1 regulates aberrant ribosome biogenesis downstream of oncogenic signaling in prostate cancer.
核糖体生物发生在肿瘤细胞中过度激活，但目前尚不清楚致癌转录因子（TFs）是否参与 rRNA（核糖体 RNA）的反式激活。
重新分析核仁蛋白质组学数据和大规模免疫荧光，以共同鉴定定位于核仁的蛋白质。对五个前列腺癌（PCa）队列的 RNA-Seq 数据进行了合并和多维数据分析，以确定 PCa 组织中上调的核仁 TF。然后，重新分析了 PCa 细胞系和两个 PCa 临床队列的 ChIP-Seq 数据，以揭示 TF 在核糖体 DNA（rDNA）重复序列上的结合模式。通过 ChIP-qPCR 验证了 TF 在 rDNA 上的结合。通过 rDNA 荧光素酶报告基因、新生 RNA 合成和全蛋白翻译测定实验确定了 TF 对 rRNA 转录的影响。
在这项研究中，我们揭示了致癌 TF FOXA1 在调节核仁组织区域内 rRNA 转录中的作用。通过分析前列腺癌临床数据集和核仁蛋白质组学数据中的人类 TF，我们发现 FOXA1 部分定位于核仁中，与全蛋白翻译相关。我们广泛的 FOXA1 ChIP-Seq 分析为 FOXA1 在前列腺癌细胞系、原发肿瘤和去势抵抗变体中的 rDNA 重复序列上的结合提供了有力的证据。值得注意的是，FOXA1 在 rDNA 重复序列上的占据与与活跃转录相关的组蛋白修饰（即 H3K27ac 和 H3K4me3）相关。降低 FOXA1 的表达导致 rDNA 的反式激活减少，从而减少全蛋白合成。
我们的研究结果表明，FOXA1 调节了前列腺癌中致癌信号下游的异常核糖体生物发生。
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