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.