Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.
Endoscopy Center, Zhongshan Hospital and Endoscopy Research Institute, Fudan University, Shanghai, China.
Oncogene. 2019 May;38(21):4154-4168. doi: 10.1038/s41388-019-0714-9. Epub 2019 Jan 31.
Alternative polyadenylation (APA) has emerged as a prevalent feature associated with cancer development and progression. The advantage of APA to tumor progression is to induce oncogenes through 3'-UTR shortening, and to inactivate tumor suppressor genes via the re-routing of microRNA competition. We previously identified the Mammalian Cleavage Factor I-25 (CFIm25) (encoded by Nudt21 gene) as a master APA regulator whose expression levels directly impact the tumorigenicity of glioblastoma (GBM) in vitro and in vivo. Despite its importance, the role of Nudt21 in GBM development is not known and the genes subject to Nudt21 APA regulation that contribute to GBM progression have not been identified. Here, we find that Nudt21 is reduced in low grade glioma (LGG) and all four subtypes of high grade glioma (GBM). Reduced expression of Nudt21 associates with worse survival in TCGA LGG cohorts and two TCGA GBM cohorts. Moreover, although CFIm25 was initially identified as biochemically associated with both CFIm59 and CFIm68, we observed three CFIm distinct subcomplexes exist and CFIm59 protein level is dependent on Nudt21 expression in GBM cells, but CFIm68 is not, and that only CFIm59 predicts prognosis of GBM patients similar to Nudt21. Through the use of Poly(A)-Click-Seq to characterize APA, we define the mRNAs subject to 3'-UTR shortening upon Nudt21 depletion in GBM cells and observed enrichment in genes important in the Ras signaling pathway, including Pak1. Remarkably, we find that Pak1 expression is regulated by Nudt21 through its 3'-UTR APA, and the combination of Pak1 and Nudt21 expression generates an even stronger prognostic indicator of GBM survival versus either value used alone. Collectively, our data uncover Nudt21 and its downstream target Pak1 as a potential "combination biomarker" for predicting prognosis of GBM patients.
可变多聚腺苷酸化（APA）已成为与癌症发展和进展相关的普遍特征。APA 促进肿瘤进展的优势在于通过 3'UTR 缩短诱导癌基因，以及通过重新路由 microRNA 竞争使肿瘤抑制基因失活。我们之前确定哺乳动物切割因子 I-25（CFIm25）（由 Nudt21 基因编码）为主要 APA 调节剂，其表达水平直接影响体外和体内神经胶质瘤（GBM）的致瘤性。尽管其重要性，但 Nudt21 在 GBM 发育中的作用尚不清楚，也尚未确定受 Nudt21 APA 调节并有助于 GBM 进展的基因。在这里，我们发现 Nudt21 在低级别神经胶质瘤（LGG）和所有四种高级别神经胶质瘤（GBM）亚型中减少。Nudt21 表达降低与 TCGA LGG 队列和两个 TCGA GBM 队列中的生存预后不良相关。此外，虽然 CFIm25 最初被鉴定为与 CFIm59 和 CFIm68 具有生化关联，但我们观察到存在三个 CFIm 不同的亚复合物，并且在 GBM 细胞中 CFIm59 蛋白水平依赖于 Nudt21 的表达，但 CFIm68 不是，并且只有 CFIm59 与 Nudt21 相似地预测 GBM 患者的预后。通过使用 Poly(A)-Click-Seq 来描述 APA，我们定义了在 GBM 细胞中 Nudt21 耗竭后发生 3'UTR 缩短的 mRNAs，并观察到在 Ras 信号通路中重要基因的富集，包括 Pak1。值得注意的是，我们发现 Pak1 表达受 Nudt21 通过其 3'UTR APA 调节，Pak1 和 Nudt21 表达的组合比单独使用任何一个值生成更强的 GBM 生存预后指标。总的来说，我们的数据揭示了 Nudt21 和其下游靶标 Pak1 作为预测 GBM 患者预后的潜在“组合生物标志物”。
