Fig. 1

Hyper-upregulation of m⁶A-mRNAs and downregulation of YTHDF2 in human HCC. (a) m⁶A levels in paired tumor and paratumor mRNA, as assessed using LC-MS/MS. n = 37 patients. (b) Percentages of altered m⁶A-mRNAs (classified as hypo-up, hypo-down, hyper-up and hyper-down) in tumor compared to paratumor, as determined by MeRIP-Seq. n = 8 patients. (c) Gene-set enrichment analysis of hypoxia-signature gene expression in paired tumor versus paratumor mRNA, as determined by RNA-seq. n = 8 patients. NES, normalized enrichment score. (d) m⁶A levels in mRNAs of human HCC cell lines grown for 0, 6, 12 or 24 h under hypoxia, as assessed using LC-MS/MS. n = 2 independent experiments. (e) Changes in m⁶A peaks of SMMC7721 cells upon 24 h of hypoxia (Hx) versus normoxia (Nx), as detected using MeRIP-Seq. Peaks gaining (violet) or losing (light blue) m⁶A are highlighted at P < 0.05 and 5% FDR adjustment. (f) Fraction of m⁶A peaks in diverse transcript segments, under either hypoxic or normoxic condition. (g) Expression changes of mRNAs in hypermethylated peaks. (h) Immunoblot of YTHDF2 in paired tumor (T) and paratumor (P) tissues. n = 7 patients. (i) YTHDF2 mRNA levels in paired tumor and paratumor tissues, as assessed by RT-qPCR. n = 51 patients. (j) Scatter plots showing the correlation between m⁶A level and YTHDF2 expression. The linear best fit line, Pearson correlation coefficient (r) and P-value (P) are shown. n = 37 patients. (k) Kaplan-Meier analyses of the correlation between YTHDF2 expression level and overall survival (left) or recurrence-free survival (right) in HCC patients. n = 200 patients in total. Error bars indicate means ± SEM *P < 0.05, **P < 0.01, ***P < 0.001, **** P < 0.0001. P-values were determined by two tailed t-test