tRF-3a-Pro: A Transfer RNA-Derived Small RNA as a Novel Biomarker for Diagnosis of Hepatitis B Virus-Related Hepatocellular Carcinoma

Abstract

Hepatocellular carcinoma (HCC) is one of the most challenging malignancies of the digestive system. Screening for novel biomarkers and therapeutic targets is a promising strategy to enhance HCC prognosis. Recently, liquid biopsy with circulating nucleic acids as the detection targets has attracted much attention in the field of early screening of tumours. However, the diagnostic value and biological functions of transfer RNA-derived small RNAs (tsRNAs) in serum, particularly in HCC, remains unknown. In this study, we characterised the expression profile of tsRNAs in hepatitis B virus (HBV)-related HCC, and confirmed the diagnostic potential of serum tRF-3a-Pro. On this basis, we established a diagnostic model that integrates tRF-3a-Pro with the classic HCC biomarker alpha-fetoprotein (AFP) through logistic regression analysis. Besides, both in vivo and in vitro experiments demonstrated that tRF-3a-Pro, a highly expressed tsRNA, promotes HCC cell proliferation. These findings suggested that tRF-3a-Pro could serve as a novel biomarker for HBV-related HCC.

Keywords

biomarker / hepatocellular carcinoma / transfer RNA-derived small RNAs / tRF-3a-Pro

References

[1] H. Sung, J. Ferlay, R. L. Siegel, et al., “Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries,” CA: A Cancer Journal for Clinicians 71, no. 3 (2021): 209-249.

[2] H. Rumgay, M. Arnold, J. Ferlay, et al., “Global Burden of Primary Liver Cancer in 2020 and Predictions to 2040,” Journal of Hepatology 77, no. 6 (2022): 1598-1606.

[3] T. Akinyemiju, S. Abera, M. Ahmed, et al., “The Burden of Primary Liver Cancer and Underlying Etiologies From 1990 to 2015 at the Global, Regional, and National Level: Results From the Global Burden of Disease Study 2015,” JAMA Oncology 3, no. 12 (2017): 1683-1691.

[4] M. F. Yuen and C. L. Lai, “Screening for Hepatocellular Carcinoma: Survival Benefit and Cost-Effectiveness,” Annals of Oncology 14, no. 10 (2003): 1463-1467.

[5] J. M. Llovet, T. De Baere, L. Kulik, et al., “Locoregional Therapies in the Era of Molecular and Immune Treatments for Hepatocellular Carcinoma,” Nature Reviews. Gastroenterology & Hepatology 18, no. 5 (2021): 293-313.

[6] A. J. Craig, J. Von Felden, T. Garcia-Lezana, S. Sarcognato, and A. Villanueva, “Tumour Evolution in Hepatocellular Carcinoma,” Nature Reviews. Gastroenterology & Hepatology 17, no. 3 (2020): 139-152.

[7] M. Reig, A. Forner, J. Rimola, et al., “BCLC Strategy for Prognosis Prediction and Treatment Recommendation: The 2022 Update,” Journal of Hepatology 76, no. 3 (2022): 681-693.

[8] E. Anastasiadou, L. S. Jacob, and F. J. Slack, “Non-Coding RNA Networks in Cancer,” Nature Reviews. Cancer 18, no. 1 (2018): 5-18.

[9] F. J. Slack and A. M. Chinnaiyan, “The Role of Non-Coding RNAs in Oncology,” Cell 179, no. 5 (2019): 1033-1055.

[10] B. Chen, M. P. Dragomir, C. Yang, Q. Li, D. Horst, and G. A. Calin, “Targeting Non-Coding RNAs to Overcome Cancer Therapy Resistance,” Signal Transduction and Targeted Therapy 7, no. 1 (2022): 121.

[11] M. Shah and D. Sarkar, “HCC-Related lncRNAs: Roles and Mechanisms,” International Journal of Molecular Sciences 25, no. 1 (2024): 597, https://doi.org/10.3390/ijms25010597.

[12] K. Sartorius, J. Makarova, B. Sartorius, et al., “The Regulatory Role of MicroRNA in Hepatitis-B Virus-Associated Hepatocellular Carcinoma (HBV-HCC) Pathogenesis,” Cells 8, no. 12 (2019): 1504, https://doi.org/10.3390/cells8121504.

[13] S. Qin, Y. Mao, X. Chen, J. Xiao, Y. Qin, and L. Zhao, “The Functional Roles, Cross-Talk and Clinical Implications of m6A Modification and circRNA in Hepatocellular Carcinoma,” International Journal of Biological Sciences 17, no. 12 (2021): 3059-3079.

[14] B. Kuhle, Q. Chen, and P. Schimmel, “tRNA Renovatio: Rebirth Through Fragmentation,” Molecular Cell 83, no. 22 (2023): 3953-3971.

[15] Q. Chen, X. Zhang, J. Shi, M. Yan, and T. Zhou, “Origins and Evolving Functionalities of tRNA-Derived Small RNAs,” Trends in Biochemical Sciences 46, no. 10 (2021): 790-804.

[16] J. T. Wen, Z. H. Huang, Q. H. Li, X. Chen, H. L. Qin, and Y. Zhao, “Research Progress on the tsRNA Classification, Function, and Application in Gynecological Malignant Tumors,” Cell Death Discovery 7, no. 1 (2021): 388.

[17] Y. Zhao, X. Li, C. Ye, C. Huang, X. Lv, and J. Li, “The Biogenesis, Mechanism and Function of the tRNA-Derived Small RNA (tsRNA): A Review Compared With microRNA,” American Journal of Cancer Research 13, no. 5 (2023): 1656-1666.

[18] T. Suzuki, “The Expanding World of tRNA Modifications and Their Disease Relevance,” Nature Reviews. Molecular Cell Biology 22, no. 6 (2021): 375-392.

[19] E. A. Orellana, E. Siegal, and R. I. Gregory, “tRNA Dysregulation and Disease,” Nature Reviews. Genetics 23, no. 11 (2022): 651-664.

[20] M. Gong, Y. Deng, Y. Xiang, and D. Ye, “The Role and Mechanism of Action of tRNA-Derived Fragments in the Diagnosis and Treatment of Malignant Tumors,” Cell Communication and Signaling: CCS 21, no. 1 (2023): 62.

[21] K. Li, Y. Lin, Y. Luo, et al., “A Signature of Saliva-Derived Exosomal Small RNAs as Predicting Biomarker for Esophageal Carcinoma: A Multicenter Prospective Study,” Molecular Cancer 21, no. 1 (2022): 21.

[22] E. W. Tao, H. L. Wang, W. Y. Cheng, Q. Q. Liu, Y. X. Chen, and Q. Y. Gao, “A Specific tRNA Half, 5'tiRNA-His-GTG, Responds to Hypoxia via the HIF1α/ANG Axis and Promotes Colorectal Cancer Progression by Regulating LATS2,” Journal of Experimental & Clinical Cancer Research 40, no. 1 (2021): 67.

[23] R. L. Maute, C. Schneider, P. Sumazin, et al., “tRNA-Derived microRNA Modulates Proliferation and the DNA Damage Response and Is Down-Regulated in B Cell Lymphoma,” Proceedings of the National Academy of Sciences of the United States of America 110, no. 4 (2013): 1404-1409.

[24] G. Fattovich, T. Stroffolini, I. Zagni, and F. Donato, “Hepatocellular Carcinoma in Cirrhosis: Incidence and Risk Factors,” Gastroenterology 127, no. 5 Suppl 1 (2004): S35-S50.

[25] Z. Huang, J. K. Zhou, Y. Peng, W. He, and C. Huang, “The Role of Long Noncoding RNAs in Hepatocellular Carcinoma,” Molecular Cancer 19, no. 1 (2020): 77.

[26] J. Zhou, L. Yu, X. Gao, et al., “Plasma MicroRNA Panel to Diagnose Hepatitis B Virus-Related Hepatocellular Carcinoma,” Journal of Clinical Oncology 29, no. 36 (2011): 4781-4788.

[27] S. Chen, X. Zhang, K. Meng, et al., “Urinary Exosome tsRNAs as Novel Markers for Diagnosis and Prediction of Lupus Nephritis,” Frontiers in Immunology 14 (2023): 1077645.

[28] F. Jin, L. Yang, W. Wang, et al., “A Novel Class of tsRNA Signatures as Biomarkers for Diagnosis and Prognosis of Pancreatic Cancer,” Molecular Cancer 20, no. 1 (2021): 95.

[29] W. Wu, A. Shen, I. Lee, et al., “Changes of tRNA-Derived Fragments by Alzheimer's Disease in Cerebrospinal Fluid and Blood Serum,” Journal of Alzheimer's Disease 96, no. 3 (2023): 1285-1304.

[30] Q. Xiong and Y. Zhang, “Small RNA Modifications: Regulatory Molecules and Potential Applications,” Journal of Hematology & Oncology 16, no. 1 (2023): 64.

[31] Y. Liang, D. Ji, X. Ying, R. Ma, and W. Ji, “tsRNA Modifications: An Emerging Layer of Biological Regulation in Disease,” Journal of Advanced Research S2090-S1232, no. 24 (2024): 00401-6.

[32] Y. Wu, X. Yang, G. Jiang, et al., “5'-tRF-GlyGCC: A tRNA-Derived Small RNA as a Novel Biomarker for Colorectal Cancer Diagnosis,” Genome Medicine 13, no. 1 (2021): 20.

[33] X. Zhang, P. Yang, A. Khan, et al., “Serum tsRNA as a Novel Molecular Diagnostic Biomarker for Lupus Nephritis,” Clinical and Translational Medicine 12, no. 5 (2022): e830.

[34] M. Ding, W. Zhou, W. Chen, et al., “Plasma tsRNAs as Novel Diagnostic Biomarkers for Renal Cell Carcinoma,” Clinical and Translational Medicine 14, no. 2 (2024): e1575, https://doi.org/10.1002/ctm2.1575.

[35] Y. Han, Y. Peng, S. Liu, et al., “tRF3008A Suppresses the Progression and Metastasis of Colorectal Cancer by Destabilizing FOXK1 in an AGO-Dependent Manner,” Journal of Experimental & Clinical Cancer Research 41, no. 1 (2022): 32.

[36] H. Cui, H. Li, H. Wu, et al., “A Novel 3'tRNA-Derived Fragment tRF-Val Promotes Proliferation and Inhibits Apoptosis by Targeting EEF1A1 in Gastric Cancer,” Cell Death & Disease 13, no. 5 (2022): 471.

RIGHTS & PERMISSIONS

2025 The Author(s). Cell Proliferation published by Beijing Institute for Stem Cell and Regenerative Medicine and John Wiley & Sons Ltd.