Environmental Toxicology Graduate Program, Riverside, California, USA.
Department of Chemistry, University of California, Riverside, California, USA.
Proteomics. 2023 Feb;23(3-4):e2200059. doi: 10.1002/pmic.202200059. Epub 2022 Apr 26.
RNA contains more than 170 types of chemical modifications, and these modified nucleosides are recognized, installed and removed by their reader, writer, and eraser (RWE) proteins, respectively. Here, we employed a parallel-reaction monitoring (PRM)-based targeted proteomic method, in conjunction with stable isotope labeling by amino acids in cell culture (SILAC), to examine comprehensively the differential expression of epitranscriptomic RWE proteins in a matched pair of primary/metastatic colorectal cancer (CRC) cells, namely SW480/SW620. We were able to quantify 113 nonredundant epitranscriptomic RWE proteins; among them, 48 and 5 were up- and down-regulated by >1.5-fold in SW620 over SW480 cells, respectively. Some of those proteins with marked up-regulation in metastatic CRC cells, including NAT10, hnRNPC, and DKC1, were documented to assume important roles in the metastasis of CRC and other types of cancer. Interrogation of the Clinical Proteomic Tumor Analysis Consortium data revealed the involvement of DUS1L in the initiation and metastatic transformation of CRC. It can be envisaged that the PRM method can be utilized, in the future, to identify epitranscriptomic RWE proteins involved in the metastatic transformations of other types of cancer.
RNA 含有 170 多种类型的化学修饰，这些修饰核苷分别被其读者、写入器和橡皮擦（RWE）蛋白识别、安装和去除。在这里，我们采用了一种平行反应监测 (PRM) 为基础的靶向蛋白质组学方法，结合稳定同位素标记的细胞培养氨基酸 (SILAC)，全面检查了配对的原发性/转移性结直肠癌 (CRC) 细胞即 SW480/SW620 中差异表达的转录后 RNA 修饰 RWE 蛋白。我们能够定量 113 个非冗余的转录后 RNA 修饰 RWE 蛋白；其中，在 SW620 细胞中，有 48 个和 5 个蛋白分别上调了>1.5 倍。在转移性 CRC 细胞中上调明显的一些蛋白，包括 NAT10、hnRNPC 和 DKC1，被证明在 CRC 和其他类型癌症的转移中起重要作用。对临床蛋白质组肿瘤分析联盟数据的查询表明，DUS1L 参与了 CRC 的起始和转移转化。可以预见，PRM 方法未来可用于鉴定参与其他类型癌症转移转化的转录后 RNA 修饰 RWE 蛋白。
