dataset posted on 2023-03-31, 04:28 authored by Xinyao Qiu, Shuai Yang, Shan Wang, Jianmin Wu, Bo Zheng, Kaiting Wang, Siyun Shen, Seogsong Jeong, Zhixuan Li, Yanjing Zhu, Tong Wu, Xuan Wu, Rui Wu, Weiwei Liu, Hong-Yang Wang, Lei Chen
Supplementary Table S5. RNA-seq: Significant DEGs (differentially expressed genes) with log|foldchange| > 1 and p-value <0.05. Supplementary Table S6. m6A-seq: RBE- shALKBH5 peaks related genes. Supplementary Table S7. m6A-seq: RBE- shCtrl peaks related genes. Supplementary Table S8. m6A-seq: RBE-shALKBH5 unique peaks related genes. Supplementary Table S9. m6A-seq: RBE-shCtrl unique peaks related genes. Supplementary Table S10. m6A-seq: common differential peaks related genes Supplementary Table S11. RNA-seq: log2normalized_count.
National Research Program of China
National Natural Science Foundation of China
National Natural Science Foundation of Shanghai
Youth Foundation of Fudan University Shanghai Cancer Center
ARTICLE ABSTRACTN6-methyladenosine (m6A) has been reported as an important mechanism of posttranscriptional regulation. Programmed death-ligand 1 (PD-L1) is a primary immune inhibitory molecule expressed on tumor cells that promotes immune evasion. Here we report ALKBH5 as an important m6A demethylase that orchestrates PD-L1 expression in intrahepatic cholangiocarcinoma (ICC). Regulation of PD-L1 expression by ALKBH5 was confirmed in human ICC cell lines. Sequencing of the m6A methylome identified PD-L1 mRNA as a direct target of m6A modification whose levels were regulated by ALKBH5. Furthermore, ALKBH5 and PD-L1 mRNA were shown to interact. ALKBH5 deficiency enriched m6A modification in the 3′UTR region of PD-L1 mRNA, thereby promoting its degradation in a YTHDF2-dependent manner. In vitro and in vivo, tumor-intrinsic ALKBH5 inhibited the expansion and cytotoxicity of T cells by sustaining tumor cell PD-L1 expression. The ALKBH5-PD-L1–regulating axis was further confirmed in human ICC specimens. Single-cell mass cytometry analysis unveiled a complex role of ALKBH5 in the tumor immune microenvironment by promoting the expression of PD-L1 on monocytes/macrophages and decreasing the infiltration of myeloid-derived suppressor-like cells. Analysis of specimens from patients receiving anti-PD1 immunotherapy suggested that tumors with strong nuclear expression patterns of ALKBH5 are more sensitive to anti-PD1 immunotherapy. Collectively, these results describe a new regulatory mechanism of PD-L1 by mRNA epigenetic modification by ALKBH5 and the potential role of ALKBH5 in immunotherapy response, which might provide insights for cancer immunotherapies.
This study identifies PD-L1 mRNA as a target of ALKBH5 and reveals a role for ALKBH5 in regulating the tumor immune microenvironment and immunotherapy efficacy.