Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, Hangzhou 310009, China; Research Center of Diagnosis and Treatment Technology for Hepatocellular Carcinoma of Zhejiang Province, Hangzhou 310009, China; Clinical Medicine Innovation Center of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Disease of Zhejiang University, Hangzhou 310009, China; Clinical Research Center of Hepatobiliary and Pancreatic Diseases of Zhejiang Province, Hangzhou 310009, China; Cancer Center, Zhejiang University, Hangzhou 310009, China
tRNA-derived small RNAs (tsRNAs) are novel non-coding RNAs that are involved in the occurrence and progression of diverse diseases. However, their exact presence and function in hepatocellular carcinoma (HCC) remain unclear. Here, differentially expressed tsRNAs in HCC were profiled. A novel tsRNA, tRNAGln-TTG derived 5′-tiRNA-Gln, is significantly downregulated, and its expression level is correlated with progression in patients. In HCC cells, 5′-tiRNA-Gln overexpression impaired the proliferation, migration, and invasion in vitro and in vivo, while 5′-tiRNA-Gln knockdown yielded opposite results. 5′-tiRNA-Gln exerted its function by binding eukaryotic initiation factor 4A-I (EIF4A1), which unwinds complex RNA secondary structures during translation initiation, causing the partial inhibition of translation. The suppressed downregulated proteins include ARAF, MEK1/2 and STAT3, causing the impaired signaling pathway related to HCC progression. Furthermore, based on the construction of a mutant 5′-tiRNA-Gln, the sequence of forming intramolecular G-quadruplex structure is crucial for 5′-tiRNA-Gln to strongly bind EIF4A1 and repress translation. Clinically, 5′-tiRNA-Gln expression level is negatively correlated with ARAF, MEK1/2, and STAT3 in HCC tissues. Collectively, these findings reveal that 5′-tiRNA-Gln interacts with EIF4A1 to reduce related mRNA binding through the intramolecular G-quadruplex structure, and this process partially inhibits translation and HCC progression.
M Zhou, H Wang, X Zeng, P Yin, J Zhu, W Chen, X Li, L Wang, L Wang, Y Liu, J Liu, M Zhang, J Qi, S Yu, A Afshin, E Gakidou, S Glenn, VS Krish, MK Miller-Petrie, WC Mountjoy-Venning, EC Mullany, SB Redford, H Liu, M Naghavi, SI Hay, L Wang, CJL Murray, X Liang. Mortality, morbidity, and risk factors in China and its provinces, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet 2019; 394(10204): 1145–1158 https://doi.org/10.1016/S0140-6736(19)30427-1
pmid: 31248666
2
H Sung, J Ferlay, RL Siegel, M Laversanne, I Soerjomataram, A Jemal, F Bray. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2021; 71(3): 209–249 https://doi.org/10.3322/caac.21660
pmid: 33538338
3
JD Yang, P Hainaut, GJ Gores, A Amadou, A Plymoth, LR Roberts. A global view of hepatocellular carcinoma: trends, risk, prevention and management. Nat Rev Gastroenterol Hepatol 2019; 16(10): 589–604 https://doi.org/10.1038/s41575-019-0186-y
pmid: 31439937
4
T Kobayashi, H Aikata, T Kobayashi, H Ohdan, K Arihiro, K Chayama. Patients with early recurrence of hepatocellular carcinoma have poor prognosis. Hepatobiliary Pancreat Dis Int 2017; 16(3): 279–288 https://doi.org/10.1016/S1499-3872(16)60181-9
pmid: 28603096
CM Wong, FHC Tsang, IOL Ng. Non-coding RNAs in hepatocellular carcinoma: molecular functions and pathological implications. Nat Rev Gastroenterol Hepatol 2018; 15(3): 137–151 https://doi.org/10.1038/nrgastro.2017.169
pmid: 29317776
7
M Klingenberg, A Matsuda, S Diederichs, T Patel. Non-coding RNA in hepatocellular carcinoma: mechanisms, biomarkers and therapeutic targets. J Hepatol 2017; 67(3): 603–618 https://doi.org/10.1016/j.jhep.2017.04.009
pmid: 28438689
HK Kim, JH Yeom, MA Kay. Transfer RNA-derived small RNAs: another layer of gene regulation and novel targets for disease therapeutics. Mol Ther 2020; 28(11): 2340–2357 https://doi.org/10.1016/j.ymthe.2020.09.013
pmid: 32956625
S Yamasaki, P Ivanov, GF Hu, P Anderson. Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 2009; 185(1): 35–42 https://doi.org/10.1083/jcb.200811106
pmid: 19332886
12
S Li, GF Hu. Emerging role of angiogenin in stress response and cell survival under adverse conditions. J Cell Physiol 2012; 227(7): 2822–2826 https://doi.org/10.1002/jcp.23051
pmid: 22021078
13
YS Lee, Y Shibata, A Malhotra, A Dutta. A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 2009; 23(22): 2639–2649 https://doi.org/10.1101/gad.1837609
pmid: 19933153
14
H Goodarzi, X Liu, HC Nguyen, S Zhang, L Fish, SF Tavazoie. Endogenous tRNA-derived fragments suppress breast cancer progression via YBX1 displacement. Cell 2015; 161(4): 790–802 https://doi.org/10.1016/j.cell.2015.02.053
pmid: 25957686
15
LL Zheng, WL Xu, S Liu, WJ Sun, JH Li, J Wu, JH Yang, LH Qu. tRF2Cancer: a web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res 2016; 44(W1): W185–93 https://doi.org/10.1093/nar/gkw414
pmid: 27179031
16
T Zeng, Y Hua, C Sun, Y Zhang, F Yang, M Yang, Y Yang, J Li, X Huang, H Wu, Z Fu, W Li, Y Yin. Relationship between tRNA-derived fragments and human cancers. Int J Cancer 2020; 147(11): 3007–3018 https://doi.org/10.1002/ijc.33107
pmid: 32427348
R Magee, I Rigoutsos. On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res 2020; 48(17): 9433–9448 https://doi.org/10.1093/nar/gkaa657
pmid: 32890397
19
Q Chen, X Zhang, J Shi, M Yan, T Zhou. Origins and evolving functionalities of tRNA-derived small RNAs. Trends Biochem Sci 2021; 46(10): 790–804 https://doi.org/10.1016/j.tibs.2021.05.001
pmid: 34053843
20
MM Emara, P Ivanov, T Hickman, N Dawra, S Tisdale, N Kedersha, GF Hu, P Anderson. Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem 2010; 285(14): 10959–10968 https://doi.org/10.1074/jbc.M109.077560
pmid: 20129916
21
SM Lyons, C Achorn, NL Kedersha, PJ Anderson, P Ivanov. YB-1 regulates tiRNA-induced stress granule formation but not translational repression. Nucleic Acids Res 2016; 44(14): 6949–6960 https://doi.org/10.1093/nar/gkw418
pmid: 27174937
22
HK Kim, G Fuchs, S Wang, W Wei, Y Zhang, H Park, B Roy-Chaudhuri, P Li, J Xu, K Chu, F Zhang, MS Chua, S So, QC Zhang, P Sarnow, MA Kay. A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature 2017; 552(7683): 57–62 https://doi.org/10.1038/nature25005
pmid: 29186115
P Kumar, SB Mudunuri, J Anaya, A Dutta. tRFdb: a database for transfer RNA fragments. Nucleic Acids Res 2015; 43(D1): D141–D145 https://doi.org/10.1093/nar/gku1138
pmid: 25392422
26
V Pliatsika, P Loher, R Magee, AG Telonis, E Londin, M Shigematsu, Y Kirino, I Rigoutsos. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res 2018; 46(D1): D152–D159 https://doi.org/10.1093/nar/gkx1075
pmid: 29186503
RJ Jackson, CUT Hellen, TV Pestova. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 2010; 11(2): 113–127 https://doi.org/10.1038/nrm2838
pmid: 20094052
29
AL Wolfe, K Singh, Y Zhong, P Drewe, VK Rajasekhar, VR Sanghvi, KJ Mavrakis, M Jiang, JE Roderick, der Meulen J Van, JH Schatz, CM Rodrigo, C Zhao, P Rondou, Stanchina E de, J Teruya-Feldstein, MA Kelliher, F Speleman, JA Jr Porco, J Pelletier, G Rätsch, HG Wendel. RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer. Nature 2014; 513(7516): 65–70 https://doi.org/10.1038/nature13485
pmid: 25079319
30
A Modelska, E Turro, R Russell, J Beaton, T Sbarrato, K Spriggs, J Miller, S Gräf, E Provenzano, F Blows, P Pharoah, C Caldas, Quesne J Le. The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape. Cell Death Dis 2015; 6(1): e1603 https://doi.org/10.1038/cddis.2014.542
pmid: 25611378
31
K Singh, J Lin, N Lecomte, P Mohan, A Gokce, VR Sanghvi, M Jiang, O Grbovic-Huezo, A Burčul, SG Stark, PB Romesser, Q Chang, JP Melchor, RK Beyer, M Duggan, Y Fukase, G Yang, O Ouerfelli, A Viale, Stanchina E de, AW Stamford, PT Meinke, G Rätsch, SD Leach, Z Ouyang, HG Wendel. Targeting eIF4A-dependent translation of KRAS signaling molecules. Cancer Res 2021; 81(8): 2002–2014 https://doi.org/10.1158/0008-5472.CAN-20-2929
pmid: 33632898
32
S Iwasaki, W Iwasaki, M Takahashi, A Sakamoto, C Watanabe, Y Shichino, SN Floor, K Fujiwara, M Mito, K Dodo, M Sodeoka, H Imataka, T Honma, K Fukuzawa, T Ito, NT Ingolia. The translation inhibitor rocaglamide targets a bimolecular cavity between eIF4A and polypurine RNA. Mol Cell 2019; 73(4): 738–748.e9 https://doi.org/10.1016/j.molcel.2018.11.026
pmid: 30595437
33
O Kikin, L D’Antonio, PS Bagga. QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res 2006; 34(suppl_2): W676–W682 https://doi.org/10.1093/nar/gkl253
pmid: 16845096
34
DF Calvisi, S Ladu, A Gorden, M Farina, EA Conner, JS Lee, VM Factor, SS Thorgeirsson. Ubiquitous activation of Ras and Jak/Stat pathways in human HCC. Gastroenterology 2006; 130(4): 1117–1128 https://doi.org/10.1053/j.gastro.2006.01.006
pmid: 16618406
35
B Delire, P Stärkel. The Ras/MAPK pathway and hepatocarcinoma: pathogenesis and therapeutic implications. Eur J Clin Invest 2015; 45(6): 609–623 https://doi.org/10.1111/eci.12441
pmid: 25832714
36
M Ranjpour, S Wajid, SK Jain. Elevated expression of A-Raf and FA2H in hepatocellular carcinoma is associated with lipid metabolism dysregulation and cancer progression. Anticancer Agents Med Chem 2019; 19(2): 236–247 https://doi.org/10.2174/1871520618666181015142810
pmid: 30324893
37
M Yu, B Lu, J Zhang, J Ding, P Liu, Y Lu. tRNA-derived RNA fragments in cancer: current status and future perspectives. J Hematol Oncol 2020; 13(1): 121 https://doi.org/10.1186/s13045-020-00955-6
pmid: 32887641
38
L Han, H Lai, Y Yang, J Hu, Z Li, B Ma, W Xu, W Liu, W Wei, D Li, Y Wang, Q Zhai, Q Ji, T Liao. A 5′-tRNA halve, tiRNA-Gly promotes cell proliferation and migration via binding to RBM17 and inducing alternative splicing in papillary thyroid cancer. J Exp Clin Cancer Res 2021; 40(1): 222 https://doi.org/10.1186/s13046-021-02024-3
pmid: 34225773
39
M Saikia, R Jobava, M Parisien, A Putnam, D Krokowski, XH Gao, BJ Guan, Y Yuan, E Jankowsky, Z Feng, GF Hu, M Pusztai-Carey, M Gorla, NB Sepuri, T Pan, M Hatzoglou. Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. Mol Cell Biol 2014; 34(13): 2450–2463 https://doi.org/10.1128/MCB.00136-14
pmid: 24752898
40
P Kumar, J Anaya, SB Mudunuri, A Dutta. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol 2014; 12(1): 78 https://doi.org/10.1186/s12915-014-0078-0
pmid: 25270025
SM Lyons, P Kharel, Y Akiyama, S Ojha, D Dave, V Tsvetkov, W Merrick, P Ivanov, P Anderson. eIF4G has intrinsic G-quadruplex binding activity that is required for tiRNA function. Nucleic Acids Res 2020; 48(11): 6223–6233 https://doi.org/10.1093/nar/gkaa336
pmid: 32374873
45
P Ivanov, E O’Day, MM Emara, G Wagner, J Lieberman, P Anderson. G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments. Proc Natl Acad Sci USA 2014; 111(51): 18201–18206 https://doi.org/10.1073/pnas.1407361111
pmid: 25404306
46
SM Lyons, D Gudanis, SM Coyne, Z Gdaniec, P Ivanov. Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs. Nat Commun 2017; 8(1): 1127 https://doi.org/10.1038/s41467-017-01278-w
pmid: 29066746
47
TM Nguyen, EB Kabotyanski, Y Dou, LC Reineke, P Zhang, XHF Zhang, A Malovannaya, SY Jung, Q Mo, KP Roarty, Y Chen, B Zhang, JR Neilson, RE Lloyd, CM Perou, MJ Ellis, JM Rosen. FGFR1-activated translation of WNT pathway components with structured 5′ UTRs is vulnerable to inhibition of EIF4A-dependent translation initiation. Cancer Res 2018; 78(15): 4229–4240 https://doi.org/10.1158/0008-5472.CAN-18-0631
pmid: 29844125
48
F Raza, JA Waldron, JL Quesne. Translational dysregulation in cancer: eIF4A isoforms and sequence determinants of eIF4A dependence. Biochem Soc Trans 2015; 43(6): 1227–1233 https://doi.org/10.1042/BST20150163
pmid: 26614665
49
G Biffi, M Di Antonio, D Tannahill, S Balasubramanian. Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells. Nat Chem 2014; 6(1): 75–80 https://doi.org/10.1038/nchem.1805
pmid: 24345950
S Zhan, P Yang, S Zhou, Y Xu, R Xu, G Liang, C Zhang, X Chen, L Yang, F Jin, Y Wang. Serum mitochondrial tsRNA serves as a novel biomarker for hepatocarcinoma diagnosis. Front Med 2022; 16(2): 216–226 https://doi.org/10.1007/s11684-022-0920-7
pmid: 35416630
52
L Zhu, J Li, Y Gong, Q Wu, S Tan, D Sun, X Xu, Y Zuo, Y Zhao, YQ Wei, XW Wei, Y Peng. Exosomal tRNA-derived small RNA as a promising biomarker for cancer diagnosis. Mol Cancer 2019; 18(1): 74 https://doi.org/10.1186/s12943-019-1000-8
pmid: 30940133
53
D Mo, P Jiang, Y Yang, X Mao, X Tan, X Tang, D Wei, B Li, X Wang, L Tang, F Yan. A tRNA fragment, 5′-tiRNAVal, suppresses the Wnt/β-catenin signaling pathway by targeting FZD3 in breast cancer. Cancer Lett 2019; 457: 60–73 https://doi.org/10.1016/j.canlet.2019.05.007
pmid: 31078732
54
Y Wu, X Yang, G Jiang, H Zhang, L Ge, F Chen, J Li, H Liu, H Wang. 5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis. Genome Med 2021; 13(1): 20 https://doi.org/10.1186/s13073-021-00833-x
pmid: 33563322
55
M Yu, B Lu, J Zhang, J Ding, P Liu, Y Lu. tRNA-derived RNA fragments in cancer: current status and future perspectives. J Hematol Oncol 2020; 13(1): 121 https://doi.org/10.1186/s13045-020-00955-6
pmid: 32887641