N1-methyladenosine methylations in tRNA drive liver tumorigenesis by PPARd-mediated cholesterol synthesis

Increased protein translation plays a critical role in cancer development and treatment1,2. However, the molecular mechanism that is involved in this process remains poorly understood. N1-methyladenosine (m1A) methylation in RNA accounts for regulating mRNA translation in a post-transcriptional manner3,4. Here we show that m1A methylation levels are remarkably elevated in hepatocellular carcinoma (HCC) patient tumor tissues, especially in patients with microscopic vascular invasion (MVI). Moreover, m1A methylation signals are increased in liver cancer stem cells (CSCs) and are negatively correlated with HCC patient survival. Consistently, TRMT6 and TRMT61A, forming m1A methyltransferase complex, are highly expressed in advanced HCC tumors and are negatively correlated with HCC survival. TRMT6/TRMT61A-mediated m1A methylations are required for self-renewal of liver CSCs and tumorigenesis. Mechanistically, TRMT6/TRMT61A-dependent m1A in tRNA boost PPARd expression, which triggers cholesterol synthesis to activate Hedgehog signaling, driving self-renewal of liver CSCs and tumorigenesis. For potential therapeutic benefit, we further identify a specific inhibitor against TRMT6/TRMT61A complex that exerts effective therapeutic effect on liver cancer with high m1A methylations. Our findings provide novel insights into the function and molecular mechanism of m1A modifications underlying liver tumorigenesis and drug target, which will serve as a new biomarker for HCC and pave a new way to develop more effective therapeutic strategies for HCC patients. Overall design: We find that the overall m1A methylation signal as well as the relevant m1A-methyltransferase TRMT6/61A are of abberrently high level in HCC tumor samples. By performing m1A sequencing for small RNA populations, we discovered several tRNAs with elevated m1A58 methylation stoicheometry. Then we evaluate the influenences on gene expression via Ribo-seq, and proved that TRMT6/TRMT61A-dependent m1A in tRNA boost expression of some metabolic pathway genes, which trigger cholesterol synthesis to activate Hedgehog signaling, driving self-renewal of liver CSCs and tumorigenesis.