Identification of potential targets of PPDPF in cholangiacarcinoma via transcriptome-wide RNA-seq

Tumor cells display profound changes in the branched-chain amino acid (BCAA) metabolism. However, how these changes are regulated and aids the development of tumor is not fully understood. Here, we have identified PPDPF as an amino acid-regulated protein after the extensive screening using Stable Isotope Labeling by Amino acids in Cell culture (SILAC). PPDPF is up-regulated in cholangiocarcinoma tissues and correlated with clinical features. PPDPF enhanced the tumorigenicity of cholangiocarcinoma cells by activating mTORC1 signaling pathway. The metabolic flux analysis revealed that PPDPF inhibits the catabolism of Leucine by preventing the interaction between MCCA and MCCB, thus leading to the elevation of BCAA content and the activation of mTORC1 signaling. Moreover, upon the amino acid starvation, the ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2) and the OTU deubiquitinase 4 (OTUD4) cooperatively regulated the stability of PPDPF protein by modulating the ubiquitination of K48/62/99 in PPDPF protein. Additionally, IL10, secreted by the monocyte/macrophage, elevated the BCAA content in the cholangiocarcinoma cells, and stabilized PPDPF protein even in the amino acid starvation. Furthermore, knockout of PPDPF or restriction of leucine intake significantly inhibited the progression of tumor in a cholangiocarcinoma mouse model. Thus, our study discovered an unexpected role of PPDPF in the progression of cholangiocarcinoma by activating mTORC1signaling through inhibiting the catabolism of Leucine, and targeting PPDPF or lowing the dietary Leucine may have translational significance. Overall design: To elucidate the molecular mechanism by which PPDPF promotes cholangiocarcinoma progression, we overexpressed PPDPF in human biliary cells(HIBEpiC) and subsequently extracted RNA from the cells for RNA-seq.