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RNA modification-mediated mRNA translation regulation in liver cancer: mechanisms and clinical perspectives

Abstract

Malignant liver cancer is characterized by rapid tumour progression and a high mortality rate, whereas the molecular mechanisms underlying liver cancer initiation and progression are still poorly understood. The dynamic and reversible RNA modifications have crucial functions in gene expression regulation by modulating RNA processing and mRNA translation. Emerging evidence has revealed that alterations in RNA modifications facilitate the selective translation of oncogenic transcripts and promote the diverse tumorigenic processes of liver cancer. In this Review, we first highlight the current progress on the functions and mechanisms underlying RNA modifications in the regulation of mRNA translation and then summarize the exciting discoveries on aberrant RNA modification-mediated mRNA translation in the regulation of tumour initiation, metastasis, metabolism, tumour microenvironment, and drug and radiotherapy resistance in liver cancer. Finally, we discuss the diagnostic and therapeutic potentials of targeting RNA modifications and mRNA translation for the clinical management of liver cancer.

Key points

  • Epigenetic changes, including DNA methylation, histone modifications and RNA modifications, have critical roles in liver cancer initiation and progression.

  • The dynamic and reversible RNA modifications have crucial functions in the regulation of RNA processing and mRNA translation.

  • Aberrant modifications on mRNAs, tRNAs and ribosomal RNAs regulate the translation of oncogenic transcripts and promote diverse tumorigenic aspects of liver cancer.

  • Targeting aberrant RNA modification-mediated mRNA translation could be promising for the development of effective diagnostic and therapeutic strategies for liver cancer.

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Fig. 1: Role of RNA modifications in mRNA translation regulation.
Fig. 2: tRNA modification pathway and its functions in liver cancer.
Fig. 3: Modifications on the rRNAs can drive liver cancer development.

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References

  1. Llovet, J. M. et al. Hepatocellular carcinoma. Nat. Rev. Dis. Prim. 7, 6 (2021).

    Article  PubMed  Google Scholar 

  2. Rumgay, H. et al. Global burden of primary liver cancer in 2020 and predictions to 2040. J. Hepatol. 77, 1598–1606 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Villanueva, A. Hepatocellular carcinoma. N. Engl. J. Med. 380, 1450–1462 (2019).

    Article  CAS  PubMed  Google Scholar 

  4. Hama, N. et al. Epigenetic landscape influences the liver cancer genome architecture. Nat. Commun. 9, 1643 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  5. Boccaletto, P. et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 50, D231–D235 (2022).

    Article  CAS  PubMed  Google Scholar 

  6. Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Zhao, Z. et al. Epitranscriptomics in liver disease: basic concepts and therapeutic potential. J. Hepatol. 73, 664–679 (2020).

    Article  CAS  PubMed  Google Scholar 

  8. Nusinow, D. P. et al. Quantitative proteomics of the cancer cell line encyclopedia. Cell 180, 387–402.e16 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Bhat, M. et al. Targeting the translation machinery in cancer. Nat. Rev. Drug. Discov. 14, 261–278 (2015).

    Article  CAS  PubMed  Google Scholar 

  10. Frye, M., Harada, B. T., Behm, M. & He, C. RNA modifications modulate gene expression during development. Science 361, 1346–1349 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Suzuki, T. The expanding world of tRNA modifications and their disease relevance. Nat. Rev. Mol. Cell Biol. 22, 375–392 (2021).

    Article  CAS  PubMed  Google Scholar 

  12. Wang, L. & Lin, S. Emerging functions of tRNA modifications in mRNA translation and diseases. J. Genet. Genomics 50, 223–232 (2022).

    Article  PubMed  Google Scholar 

  13. Orellana, E. A., Siegal, E. & Gregory, R. I. tRNA dysregulation and disease. Nat. Rev. Genet. 23, 651–664 (2022).

    Article  CAS  PubMed  Google Scholar 

  14. Sloan, K. E. et al. Tuning the ribosome: the influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol. 14, 1138–1152 (2017).

    Article  PubMed  Google Scholar 

  15. Yang, Y. et al. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res. 27, 626–641 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Qian, B., Wang, P., Zhang, D. & Wu, L. m6A modification promotes miR-133a repression during cardiac development and hypertrophy via IGF2BP2. Cell Death Discov. 7, 157 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Desrosiers, R., Friderici, K. & Rottman, F. Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc. Natl Acad. Sci. USA 71, 3971–3975 (1974).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Jia, G. et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).

    Article  CAS  PubMed  Google Scholar 

  20. Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).

    Article  CAS  PubMed  Google Scholar 

  21. Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Yang, Y., Hsu, P. J., Chen, Y. S. & Yang, Y. G. Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism. Cell Res. 28, 616–624 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Wang, X. et al. N6-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Lin, S., Choe, J., Du, P., Triboulet, R. & Gregory, R. I. The m6A methyltransferase METTL3 promotes translation in human cancer cells. Mol. Cell 62, 335–345 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Choe, J. et al. mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis. Nature 561, 556–560 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Meyer, KateD. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zhou, J. et al. Dynamic m6A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Coots, R. A. et al. m6A facilitates eIF4F-independent mRNA translation. Mol. Cell 68, 504–514.e7 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Choi, J. et al. N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nat. Struct. Mol. Biol. 23, 110–115 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Mao, Y. et al. m6A in mRNA coding regions promotes translation via the RNA helicase-containing YTHDC2. Nat. Commun. 10, 5332 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  31. Dominissini, D. et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441–446 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Li, X. et al. Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts. Mol. Cell 68, 993–1005.e9 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Li, Q. et al. NSUN2-mediated m5C methylation and METTL3/METTL14-mediated m6A methylation cooperatively enhance p21 translation. J. Cell. Biochem. 118, 2587–2598 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hoernes, T. P. et al. Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code. Nucleic Acids Res. 44, 852–862 (2016).

    Article  CAS  PubMed  Google Scholar 

  35. Tang, H. et al. NSun2 delays replicative senescence by repressing p27 (KIP1) translation and elevating CDK1 translation. Aging 7, 1143–1158 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Delatte, B. et al. RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 351, 282–285 (2016).

    Article  CAS  PubMed  Google Scholar 

  37. Arango, D. et al. Acetylation of cytidine in mRNA promotes translation efficiency. Cell 175, 1872–1886.e24 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Arango, D. et al. Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. Mol. Cell 82, 2797–2814.e11 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Malbec, L. et al. Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation. Cell Res. 29, 927–941 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Zhang, L. S. et al. Transcriptome-wide mapping of internal N7-methylguanosine methylome in mammalian mRNA. Mol. Cell 74, 1304–1316.e8 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148–162 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143–146 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Svitkin, Y. V. et al. N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density. Nucleic Acids Res. 45, 6023–6036 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Svitkin, Y. V., Gingras, A. C. & Sonenberg, N. Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs. Nucleic Acids Res. 50, 7202–7215 (2022).

    Article  CAS  PubMed  Google Scholar 

  45. Karijolich, J. & Yu, Y. T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature 474, 395–398 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hanson, G. & Coller, J. Codon optimality, bias and usage in translation and mRNA decay. Nat. Rev. Mol. Cell Biol. 19, 20–30 (2018).

    Article  CAS  PubMed  Google Scholar 

  47. Schaffrath, R. & Leidel, S. A. Wobble uridine modifications – a reason to live, a reason to die?! RNA Biol. 14, 1209–1222 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Nguyen, H. A., Hoffer, E. D. & Dunham, C. M. Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGPro for decoding. J. Biol. Chem. 294, 5281–5291 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Zhou, J. B., Wang, E. D. & Zhou, X. L. Modifications of the human tRNA anticodon loop and their associations with genetic diseases. Cell. Mol. Life Sci. 78, 7087–7105 (2021).

    Article  CAS  PubMed  Google Scholar 

  50. Lin, S. et al. Mettl1/Wdr4-mediated m7G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation. Mol. Cell 71, 244–255.e5 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Liu, F. et al. ALKBH1-mediated tRNA demethylation regulates translation. Cell 167, 816–828.e6 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Liu, Y. et al. tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis. Nat. Immunol. 23, 1433–1444 (2022).

    Article  CAS  PubMed  Google Scholar 

  53. Polikanov, Y. S., Melnikov, S. V., Söll, D. & Steitz, T. A. Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat. Struct. Mol. Biol. 22, 342–344 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Sharma, S. & Lafontaine, D. L. J. ‘View from a bridge’: a new perspective on eukaryotic rRNA base modification. Trends Biochem. Sci. 40, 560–575 (2015).

    Article  CAS  PubMed  Google Scholar 

  55. Erales, J. et al. Evidence for rRNA 2′-O-methylation plasticity: control of intrinsic translational capabilities of human ribosomes. Proc. Natl Acad. Sci. USA 114, 12934–12939 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Jack, K. et al. rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. Mol. Cell 44, 660–666 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Ma, H. et al. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat. Chem. Biol. 15, 88–94 (2019).

    Article  CAS  PubMed  Google Scholar 

  58. Peng, H. et al. N6-methyladenosine (m6A) in 18S rRNA promotes fatty acid metabolism and oncogenic transformation. Nat. Metab. 4, 1041–1054 (2022).

    Article  CAS  PubMed  Google Scholar 

  59. Haag, S., Kretschmer, J. & Bohnsack, M. T. WBSCR22/Merm1 is required for late nuclear pre-ribosomal RNA processing and mediates N7-methylation of G1639 in human 18S rRNA. RNA 21, 180–187 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Cámara, Y. et al. MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. Cell Metab. 13, 527–539 (2011).

    Article  PubMed  Google Scholar 

  61. Barbieri, I. & Kouzarides, T. Role of RNA modifications in cancer. Nat. Rev. Cancer 20, 303–322 (2020).

    Article  CAS  PubMed  Google Scholar 

  62. Chen, M. & Wong, C. M. The emerging roles of N6-methyladenosine (m6A) deregulation in liver carcinogenesis. Mol. Cancer 19, 44 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Qi, L., Chan, T. H., Tenen, D. G. & Chen, L. RNA editome imbalance in hepatocellular carcinoma. Cancer Res. 74, 1301–1306 (2014).

    Article  CAS  PubMed  Google Scholar 

  64. Chen, M. et al. RNA N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of SOCS2. Hepatology 67, 2254–2270 (2018).

    Article  CAS  PubMed  Google Scholar 

  65. Ma, J. Z. et al. METTL14 suppresses the metastatic potential of hepatocellular carcinoma by modulating N6-methyladenosine-dependent primary MicroRNA processing. Hepatology 65, 529–543 (2017).

    Article  CAS  PubMed  Google Scholar 

  66. Zhang, Y. et al. The genomic landscape of cholangiocarcinoma reveals the disruption of post-transcriptional modifiers. Nat. Commun. 13, 3061 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  67. Su, R. et al. METTL16 exerts an m6A-independent function to facilitate translation and tumorigenesis. Nat. Cell Biol. 24, 205–216 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Dai, Y. Z. et al. METTL16 promotes hepatocellular carcinoma progression through downregulating RAB11B-AS1 in an m6A-dependent manner. Cell Mol. Biol. Lett. 27, 41 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Lan, T. et al. KIAA1429 contributes to liver cancer progression through N6-methyladenosine-dependent post-transcriptional modification of GATA3. Mol. Cancer 18, 186 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Cai, X. et al. RBM15 promotes hepatocellular carcinoma progression by regulating N6-methyladenosine modification of YES1 mRNA in an IGF2BP1-dependent manner. Cell Death Discov. 7, 315 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  71. Chen, Y. et al. WTAP facilitates progression of hepatocellular carcinoma via m6A-HuR-dependent epigenetic silencing of ETS1. Mol. Cancer 18, 127 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Ortiz-Barahona, V. et al. Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer. Mol. Cancer 22, 83 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Chen, Y. et al. ALKBH5 suppresses malignancy of hepatocellular carcinoma via m6A-guided epigenetic inhibition of LYPD1. Mol. Cancer 19, 123 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Li, J. et al. m6A demethylase FTO promotes hepatocellular carcinoma tumorigenesis via mediating PKM2 demethylation. Am. J. Transl. Res. 11, 6084–6092 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Liu, X. et al. SIRT1 regulates N6-methyladenosine RNA modification in hepatocarcinogenesis by inducing RANBP2-dependent FTO SUMOylation. Hepatology 72, 2029–2050 (2020).

    Article  CAS  PubMed  Google Scholar 

  76. Rong, Z. X. et al. Downregulation of fat mass and obesity associated (FTO) promotes the progression of intrahepatic cholangiocarcinoma. Front. Oncol. 9, 369 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Qin, S. et al. The comprehensive expression and functional analysis of m6A modification “readers” in hepatocellular carcinoma. Aging 14, 6269–6298 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Li, Q. et al. HIF-1α-induced expression of m6A reader YTHDF1 drives hypoxia-induced autophagy and malignancy of hepatocellular carcinoma by promoting ATG2A and ATG14 translation. Signal. Transduct. Target. Ther. 6, 76 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Zhong, L. et al. YTHDF2 suppresses cell proliferation and growth via destabilizing the EGFR mRNA in hepatocellular carcinoma. Cancer Lett. 442, 252–261 (2019).

    Article  CAS  PubMed  Google Scholar 

  80. Huang, H. et al. Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nat. Cell Biol. 20, 285–295 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Chen, Z. et al. METTL1 promotes hepatocarcinogenesis via m7G tRNA modification-dependent translation control. Clin. Transl. Med. 11, e661 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Dai, Z. et al. N(7)-Methylguanosine tRNA modification enhances oncogenic mRNA translation and promotes intrahepatic cholangiocarcinoma progression. Mol. Cell 81, 3339–3355.e8 (2021).

    Article  CAS  PubMed  Google Scholar 

  83. Tian, Q. H. et al. METTL1 overexpression is correlated with poor prognosis and promotes hepatocellular carcinoma via PTEN. J. Mol. Med. 97, 1535–1545 (2019).

    Article  CAS  PubMed  Google Scholar 

  84. Wang, Y. et al. N1-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism. Nat. Commun. 12, 6314 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Ye, Y. et al. TRMT6 promotes hepatocellular carcinoma progression through the PI3K/AKT signaling pathway. Eur. J. Med. Res. 28, 48 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Ignatova, V. V. et al. METTL6 is a tRNA m3C methyltransferase that regulates pluripotency and tumor cell growth. Sci. Adv. 6, eaaz4551 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Liu, Z. et al. SNORA23 inhibits HCC tumorigenesis by impairing the 2′-O-ribose methylation level of 28S rRNA. Cancer Biol. Med. 19, 104–119 (2021).

    PubMed  Google Scholar 

  88. Lamouille, S., Xu, J. & Derynck, R. Molecular mechanisms of epithelial-mesenchymal transition. Nat. Rev. Mol. Cell Biol. 15, 178–196 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Lin, X. et al. RNA m6A methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail. Nat. Commun. 10, 2065 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  90. Xu, H. et al. SUMO1 modification of methyltransferase-like 3 promotes tumor progression via regulating Snail mRNA homeostasis in hepatocellular carcinoma. Theranostics 10, 5671–5686 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Li, J. et al. RNA m6A methylation regulates dissemination of cancer cells by modulating expression and membrane localization of β-catenin. Mol. Ther. : J. Am. Soc. Gene Ther. 30, 1578–1596 (2022).

    Article  CAS  Google Scholar 

  92. Zhu, S. et al. Targeting N7-methylguanosine tRNA modification blocks hepatocellular carcinoma metastasis after insufficient radiofrequency ablation. Mol. Ther. 31, 1596–1614 (2023).

    Article  CAS  PubMed  Google Scholar 

  93. Fan, Z. et al. METTL3/IGF2BP1/CD47 contributes to the sublethal heat treatment induced mesenchymal transition in HCC. Biochem. Biophys. Res. Commun. 546, 169–177 (2021).

    Article  CAS  PubMed  Google Scholar 

  94. Luo, X., Cao, M., Gao, F. & He, X. YTHDF1 promotes hepatocellular carcinoma progression via activating PI3K/AKT/mTOR signaling pathway and inducing epithelial-mesenchymal transition. Exp. Hematol. Oncol. 10, 35 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Zhang, C. et al. YTHDF2 promotes the liver cancer stem cell phenotype and cancer metastasis by regulating OCT4 expression via m6A RNA methylation. Oncogene 39, 4507–4518 (2020).

    Article  CAS  PubMed  Google Scholar 

  96. Chen, Y. et al. Activation of YAP1 by N6-methyladenosine-modified circCPSF6 drives malignancy in hepatocellular carcinoma. Cancer Res. 82, 599–614 (2022).

    Article  CAS  PubMed  Google Scholar 

  97. Liu, L. et al. CircGPR137B/miR-4739/FTO feedback loop suppresses tumorigenesis and metastasis of hepatocellula\zar carcinoma. Mol. Cancer 21, 149 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Zhang, H. et al. ALKBH5-mediated m6A modification of lincRNA LINC02551 enhances the stability of DDX24 to promote hepatocellular carcinoma growth and metastasis. Cell Death Dis. 13, 926 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. De Matteis, S. et al. Aberrant metabolism in hepatocellular carcinoma provides diagnostic and therapeutic opportunities. Oxid. Med. Cell. Longev. 2018, 7512159 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  100. Shen, X. et al. The m6A methylation landscape stratifies hepatocellular carcinoma into 3 subtypes with distinct metabolic characteristics. Cancer Biol. Med. 17, 937–952 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Li, Z. et al. N6-methyladenosine regulates glycolysis of cancer cells through PDK4. Nat. Commun. 11, 2578 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Lin, Y., Wei, X., Jian, Z. & Zhang, X. METTL3 expression is associated with glycolysis metabolism and sensitivity to glycolytic stress in hepatocellular carcinoma. Cancer Med. 9, 2859–2867 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Gao, J. et al. Methyltransferase like 3 inhibition limits intrahepatic cholangiocarcinoma metabolic reprogramming and potentiates the efficacy of chemotherapy. Oncogene 42, 2507–2520 (2023).

    Article  CAS  PubMed  Google Scholar 

  104. Du, L. et al. USP48 is upregulated by Mettl14 to attenuate hepatocellular carcinoma via regulating SIRT6 stabilization. Cancer Res. 81, 3822–3834 (2021).

    Article  CAS  PubMed  Google Scholar 

  105. Zhao, L. et al. UBR7 inhibits HCC tumorigenesis by targeting Keap1/Nrf2/Bach1/HK2 and glycolysis. J. Exp. Clin. Cancer Res. 41, 330 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Zhou, R. et al. A functional loop between YTH domain family protein YTHDF3 mediated m6A modification and phosphofructokinase PFKL in glycolysis of hepatocellular carcinoma. J. Exp. Clin. Cancer Res. 41, 334 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Yang, Y. et al. Dysregulated m6A modification promotes lipogenesis and development of non-alcoholic fatty liver disease and hepatocellular carcinoma. Mol. Ther. 30, 2342–2353 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Zuo, X. et al. M6A-mediated upregulation of LINC00958 increases lipogenesis and acts as a nanotherapeutic target in hepatocellular carcinoma. J. Hematol. Oncol. 13, 5 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Ben-Haim, M. S. et al. Dynamic regulation of N6,2′-O-dimethyladenosine (m6Am) in obesity. Nat. Commun. 12, 7185 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Donne, R. & Lujambio, A. The liver cancer immune microenvironment: therapeutic implications for hepatocellular carcinoma. Hepatology 77, 1773–1796 (2022).

    Article  Google Scholar 

  111. Zhou, D. et al. m6A regulator-mediated methylation modification highlights immune infiltration patterns for predicting risk in hepatocellular carcinoma. J. Cancer Res. Clin. Oncol. 77, 3661–3680 (2022).

    Google Scholar 

  112. Qiu, X. et al. M6A demethylase ALKBH5 regulates PD-L1 expression and tumor immunoenvironment in intrahepatic cholangiocarcinoma. Cancer Res. 81, 4778–4793 (2021).

    Article  CAS  PubMed  Google Scholar 

  113. You, Y. et al. ALKBH5/MAP3K8 axis regulates PD-L1+ macrophage infiltration and promotes hepatocellular carcinoma progression. Int. J. Biol. Sci. 18, 5001–5018 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Hou, J. et al. YTHDF2 reduction fuels inflammation and vascular abnormalization in hepatocellular carcinoma. Mol. Cancer 18, 163 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  115. Liu, Y. et al. Allosteric regulation of IGF2BP1 as a novel strategy for the activation of tumor immune microenvironment. ACS Cent. Sci. 8, 1102–1115 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Liu, H. et al. Targeting tumour-intrinsic N7-methylguanosine tRNA modification inhibits MDSC recruitment and improves anti-PD-1 efficacy. Gut 72, 1555–1567 (2022).

    Article  PubMed  Google Scholar 

  117. Zeng, X. et al. Eliminating METTL1-mediated accumulation of PMN-MDSCs prevents hepatocellular carcinoma recurrence after radiofrequency ablation. Hepatology 77, 1122–1138 (2022).

    Article  PubMed  Google Scholar 

  118. Kim, G. W. et al. HBV-induced increased N6 methyladenosine modification of PTEN RNA affects innate immunity and contributes to HCC. Hepatology 73, 533–547 (2021).

    Article  CAS  PubMed  Google Scholar 

  119. Jin, Z. et al. Integrative multiomics evaluation reveals the importance of pseudouridine synthases in hepatocellular carcinoma. Front. Genet. 13, 944681 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Li, D. et al. The m6A/m5C/m1A regulated gene signature predicts the prognosis and correlates with the immune status of hepatocellular carcinoma. Front. Immunol. 13, 918140 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Chu, K. F. & Dupuy, D. E. Thermal ablation of tumours: biological mechanisms and advances in therapy. Nat. Rev. Cancer 14, 199–208 (2014).

    Article  CAS  PubMed  Google Scholar 

  122. Su, T. et al. Insufficient radiofrequency ablation promotes hepatocellular carcinoma metastasis through N6-methyladenosine mRNA methylation-dependent mechanism. Hepatology 74, 1339–1356 (2021).

    Article  CAS  PubMed  Google Scholar 

  123. Alexandrov, A., Grayhack, E. J. & Phizicky, E. M. tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. RNA 11, 821–830 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Alexandrov, A. et al. Rapid tRNA decay can result from lack of nonessential modifications. Mol. Cell 21, 87–96 (2006).

    Article  CAS  PubMed  Google Scholar 

  125. Ohri, N. et al. Radiotherapy for hepatocellular carcinoma: new indications and directions for future study. J. Natl Cancer Inst. 108, djw133 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  126. Xiang, M., Liu, W., Tian, W., You, A. & Deng, D. RNA N-6-methyladenosine enzymes and resistance of cancer cells to chemotherapy and radiotherapy. Epigenomics 12, 801–809 (2020).

    Article  CAS  PubMed  Google Scholar 

  127. Chen, Y. et al. ALKBH5-mediated m6A demethylation of TIRAP mRNA promotes radiation-induced liver fibrosis and decreases radiosensitivity of hepatocellular carcinoma. Clin. Transl. Med. 13, e1198 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Liao, J. et al. Methyltransferase 1 is required for nonhomologous end-joining repair and renders hepatocellular carcinoma resistant to radiotherapy. Hepatology 12, 1896–1910 (2022).

    Google Scholar 

  129. Yang, C. et al. Evolving therapeutic landscape of advanced hepatocellular carcinoma. Nat. Rev. Gastroenterol. Hepatol. 20, 203–222 (2023).

    Article  PubMed  Google Scholar 

  130. Tang, W. et al. The mechanisms of sorafenib resistance in hepatocellular carcinoma: theoretical basis and therapeutic aspects. Signal. Transduct. Target. Ther. 5, 87 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  131. Lin, Z. et al. RNA m6A methylation regulates sorafenib resistance in liver cancer through FOXO3-mediated autophagy. EMBO J. 39, e103181 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Zhou, T. et al. m6A RNA methylation-mediated HNF3γ reduction renders hepatocellular carcinoma dedifferentiation and sorafenib resistance. Signal. Transduct. Target. Ther. 5, 296 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Xu, J. et al. N6-methyladenosine-modified CircRNA-SORE sustains sorafenib resistance in hepatocellular carcinoma by regulating β-catenin signaling. Mol. Cancer 19, 163 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Wang, L. et al. METTL3-m6A-EGFR-axis drives lenvatinib resistance in hepatocellular carcinoma. Cancer Lett. 559, 216122 (2023).

    Article  CAS  PubMed  Google Scholar 

  135. Huang, M. et al. METTL1-mediated m7G tRNA modification promotes lenvatinib resistance in hepatocellular carcinoma. Cancer Res. 83, 89–102 (2023).

    Article  CAS  PubMed  Google Scholar 

  136. Jin, H. et al. EGFR activation limits the response of liver cancer to lenvatinib. Nature 595, 730–734 (2021).

    Article  CAS  PubMed  Google Scholar 

  137. Ke, W., Zhang, L., Zhao, X. & Lu, Z. p53 m6A modulation sensitizes hepatocellular carcinoma to apatinib through apoptosis. Apoptosis 27, 426–440 (2022).

    Article  CAS  PubMed  Google Scholar 

  138. Castaldo, G. et al. Total discrimination of peritoneal malignant ascites from cirrhosis- and hepatocarcinoma-associated ascites by assays of ascitic cholesterol and lactate dehydrogenase. Clin. Chem. 40, 478–483 (1994).

    Article  CAS  PubMed  Google Scholar 

  139. Amuro, Y. et al. Serum pseudouridine as a biochemical marker in patients with hepatocellular carcinoma. Clin. Chim. Acta 178, 151–158 (1988).

    Article  CAS  PubMed  Google Scholar 

  140. Tamura, S. et al. Urinary pseudouridine as a biochemical marker in the diagnosis and monitoring of primary hepatocellular carcinoma. Am. J. Gastroenterol. 83, 841–845 (1988).

    CAS  PubMed  Google Scholar 

  141. Zhang, B. et al. m6A target microRNAs in serum for cancer detection. Mol. Cancer 20, 170 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  142. Liu, P. et al. Constructing and validating of m7G-related genes prognostic signature for hepatocellular carcinoma and immune infiltration: potential biomarkers for predicting the overall survival. J. Gastrointest. Oncol. 13, 3169–3182 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  143. Liu, Y. et al. Identification of the expression patterns and potential prognostic role of 5-methylcytosine regulators in hepatocellular carcinoma. Front. Cell Dev. Biol. 10, 842220 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  144. Tong, C., Wang, W. & He, C. m1A methylation modification patterns and metabolic characteristics in hepatocellular carcinoma. BMC Gastroenterol. 22, 93 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Chang, X. et al. Gene expression profile and prognostic value of m6a RNA methylation regulators in hepatocellular carcinoma. J. Hepatocell. Carcinoma 8, 85–101 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  146. Sun, Z. et al. Aberrant NSUN2-mediated m5C modification of H19 lncRNA is associated with poor differentiation of hepatocellular carcinoma. Oncogene 39, 6906–6919 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Zhang, X. et al. N-acetyltransferase 10 enhances doxorubicin resistance in human hepatocellular carcinoma cell lines by promoting the epithelial-to-mesenchymal transition. Oxid. Med. Cell Longev. 2019, 7561879 (2019).

    PubMed  PubMed Central  Google Scholar 

  148. Zhao, K. et al. M6A regulator-mediated immune infiltration and methylation modification in hepatocellular carcinoma microenvironment and immunotherapy. Front. Pharmacol. 13, 1052177 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Li, J. et al. Structural basis of regulated m7G tRNA modification by METTL1-WDR4. Nature 613, 391–397 (2023).

    Article  CAS  PubMed  Google Scholar 

  150. Ruiz-Arroyo, V. M. et al. Structures and mechanisms of tRNA methylation by METTL1-WDR4. Nature 613, 383–390 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Wang, P., Doxtader, K. A. & Nam, Y. Structural basis for cooperative function of Mettl3 and Mettl14 methyltransferases. Mol. Cell 63, 306–317 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Wang, X. et al. Structural basis of N6-adenosine methylation by the METTL3-METTL14 complex. Nature 534, 575–578 (2016).

    Article  CAS  PubMed  Google Scholar 

  153. Schapira, M. Structural chemistry of human RNA methyltransferases. ACS Chem. Biol. 11, 575–582 (2016).

    Article  CAS  PubMed  Google Scholar 

  154. Yankova, E. et al. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature 593, 597–601 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Xu, Q. C. et al. METTL3 promotes intrahepatic cholangiocarcinoma progression by regulating IFIT2 expression in an m6A-YTHDF2-dependent manner. Oncogene 41, 1622–1633 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Moroz-Omori, E. V. et al. METTL3 inhibitors for epitranscriptomic modulation of cellular processes. ChemMedChem 16, 3035–3043 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Huang, Y. et al. Small-molecule targeting of oncogenic FTO demethylase in acute myeloid leukemia. Cancer Cell 35, 677–691.e10 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Liu, Y. et al. Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance. Cell Metab. 33, 1221–1233.e11 (2021).

    Article  CAS  PubMed  Google Scholar 

  159. Feng, P. et al. Inhibition of the m6A reader IGF2BP2 as a strategy against T-cell acute lymphoblastic leukemia. Leukemia 36, 2180–2188 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Cui, Q. et al. Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis. Nat. Cancer 2, 932–949 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Lucas, M. C. et al. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01743-6 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  162. Sangro, B., Sarobe, P., Hervas-Stubbs, S. & Melero, I. Advances in immunotherapy for hepatocellular carcinoma. Nat. Rev. Gastroenterol. Hepatol. 18, 525–543 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  163. Fabbri, L., Chakraborty, A., Robert, C. & Vagner, S. The plasticity of mRNA translation during cancer progression and therapy resistance. Nat. Rev. Cancer 21, 558–577 (2021).

    Article  CAS  PubMed  Google Scholar 

  164. Jackson, R. J., Hellen, C. U. & Pestova, T. V. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11, 113–127 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Hinnebusch, A. G. Structural insights into the mechanism of scanning and start codon recognition in eukaryotic translation initiation. Trends Biochem. Sci. 42, 589–611 (2017).

    Article  CAS  PubMed  Google Scholar 

  166. Shi, H., Wei, J. & He, C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol. Cell 74, 640–650 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors sincerely thank S. Peng, X. Zeng, H. Han, Z. Dai, S. Guo, H. Liu, S. Zheng, H. Guan, Y. Hou and S. Li for their helpful discussions. S.L. is supported by National Key Research and Development Program (2022YFA1105300 and 2022YFE0138700), National Natural Science Foundation of China (82325036 and 81974435), Distinguished Young Scholars grant from Natural Science Foundation of Guangdong (2019B151502011), and Fundamental Research Funds for the Central Universities, Sun Yat-sen University (23ykzy004). M.K. is supported by the Key Program of National Natural Science Foundation of China (82130083), National Science Fund for Distinguished Young Scholars (81825013), and the Key Research and Development Plan of Guangzhou City (202206080016).

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Lin, S., Kuang, M. RNA modification-mediated mRNA translation regulation in liver cancer: mechanisms and clinical perspectives. Nat Rev Gastroenterol Hepatol 21, 267–281 (2024). https://doi.org/10.1038/s41575-023-00884-y

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