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Zheng SM, Feng YC, Zhu Q, Li RQ, Yan QQ, Teng L, Yue YM, Han MM, Ye K, Zhang SN, Qi TF, Tang CX, Zhao XH, Zhang YY, Xu L, Xu R, Xing J, Baker M, Liu T, Thorne RF, Jin L, Preiss T, Zhang XD, Cang S, Gao JN. MILIP Binding to tRNAs Promotes Protein Synthesis to Drive Triple-Negative Breast Cancer. Cancer Res 2024; 84:1460-1474. [PMID: 38593213 PMCID: PMC11063688 DOI: 10.1158/0008-5472.can-23-3046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 04/11/2024]
Abstract
Patients with triple-negative breast cancer (TNBC) have a poor prognosis due to the lack of effective molecular targets for therapeutic intervention. Here we found that the long noncoding RNA (lncRNA) MILIP supports TNBC cell survival, proliferation, and tumorigenicity by complexing with transfer RNAs (tRNA) to promote protein production, thus representing a potential therapeutic target in TNBC. MILIP was expressed at high levels in TNBC cells that commonly harbor loss-of-function mutations of the tumor suppressor p53, and MILIP silencing suppressed TNBC cell viability and xenograft growth, indicating that MILIP functions distinctively in TNBC beyond its established role in repressing p53 in other types of cancers. Mechanistic investigations revealed that MILIP interacted with eukaryotic translation elongation factor 1 alpha 1 (eEF1α1) and formed an RNA-RNA duplex with the type II tRNAs tRNALeu and tRNASer through their variable loops, which facilitated the binding of eEF1α1 to these tRNAs. Disrupting the interaction between MILIP and eEF1α1 or tRNAs diminished protein synthesis and cell viability. Targeting MILIP inhibited TNBC growth and cooperated with the clinically available protein synthesis inhibitor omacetaxine mepesuccinate in vivo. Collectively, these results identify MILIP as an RNA translation elongation factor that promotes protein production in TNBC cells and reveal the therapeutic potential of targeting MILIP, alone and in combination with other types of protein synthesis inhibitors, for TNBC treatment. SIGNIFICANCE LncRNA MILIP plays a key role in supporting protein production in TNBC by forming complexes with tRNAs and eEF1α1, which confers sensitivity to combined MILIP targeting and protein synthesis inhibitors.
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Affiliation(s)
- Si Min Zheng
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Yu Chen Feng
- School of Medicine and Public Health, The University of Newcastle, New South Wales, Australia
| | - Qin Zhu
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
| | - Ruo Qi Li
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
| | - Qian Qian Yan
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Liu Teng
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Yi Meng Yue
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Man Man Han
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Kaihong Ye
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Sheng Nan Zhang
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Teng Fei Qi
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Cai Xia Tang
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
| | - Xiao Hong Zhao
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Yuan Yuan Zhang
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Liang Xu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Ran Xu
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Jun Xing
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
| | - Mark Baker
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, New South Wales, Australia
| | - Rick F. Thorne
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Lei Jin
- School of Medicine and Public Health, The University of Newcastle, New South Wales, Australia
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People's Hospital, Academy of Medical Sciences, Zhengzhou University, Henan, P.R. China
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, New South Wales, Australia
| | - Shundong Cang
- Department of Oncology, Henan Provincial International Coalition Laboratory of Oncology Precision Treatment, Henan Provincial Academician Workstation of Non-coding RNA Translational Research, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan, P.R. China
| | - Jin Nan Gao
- General Surgery Department, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, P.R. China
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2
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Ge MK, Zhang C, Zhang N, He P, Cai HY, Li S, Wu S, Chu XL, Zhang YX, Ma HM, Xia L, Yang S, Yu JX, Yao SY, Zhou XL, Su B, Chen GQ, Shen SM. The tRNA-GCN2-FBXO22-axis-mediated mTOR ubiquitination senses amino acid insufficiency. Cell Metab 2023; 35:2216-2230.e8. [PMID: 37979583 DOI: 10.1016/j.cmet.2023.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/26/2023] [Accepted: 10/26/2023] [Indexed: 11/20/2023]
Abstract
Mammalian target of rapamycin complex 1 (mTORC1) monitors cellular amino acid changes for function, but the molecular mediators of this process remain to be fully defined. Here, we report that depletion of cellular amino acids, either alone or in combination, leads to the ubiquitination of mTOR, which inhibits mTORC1 kinase activity by preventing substrate recruitment. Mechanistically, amino acid depletion causes accumulation of uncharged tRNAs, thereby stimulating GCN2 to phosphorylate FBXO22, which in turn accrues in the cytoplasm and ubiquitinates mTOR at Lys2066 in a K27-linked manner. Accordingly, mutation of mTOR Lys2066 abolished mTOR ubiquitination in response to amino acid depletion, rendering mTOR insensitive to amino acid starvation both in vitro and in vivo. Collectively, these data reveal a novel mechanism of amino acid sensing by mTORC1 via a previously unknown GCN2-FBXO22-mTOR pathway that is uniquely controlled by uncharged tRNAs.
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Affiliation(s)
- Meng-Kai Ge
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Cheng Zhang
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China
| | - Na Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Ping He
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China
| | - Hai-Yan Cai
- Department of Hematology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Song Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, SJTU-SM, Shanghai 200025, China
| | - Shuai Wu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Xi-Li Chu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Yu-Xue Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Hong-Ming Ma
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Li Xia
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Shuo Yang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Jian-Xiu Yu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China
| | - Shi-Ying Yao
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, SJTU-SM, Shanghai 200025, China.
| | - Guo-Qiang Chen
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China; Hainan Academy of Medical Sciences, Hainan Medical University, Hainan 571199, China.
| | - Shao-Ming Shen
- Institute of Aging & Tissue Regeneration, State Key Laboratory of Systems Medicine for Cancer and Stress and Cancer Research Unit of Chinese Academy of Medical Sciences (No. 2019RU043), Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200127, China; Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, SJTU-SM, Shanghai 200025, China.
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3
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Wu L, Quan W, Zhang Y, Wang M, Ou X, Mao S, Sun D, Yang Q, Wu Y, Wei Y, Jia R, Chen S, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Gao Q, Tian B, Cheng A. Attenuated Duck Hepatitis A Virus Infection Is Associated With High mRNA Maintenance in Duckling Liver via m6A Modification. Front Immunol 2022; 13:839677. [PMID: 35757688 PMCID: PMC9218207 DOI: 10.3389/fimmu.2022.839677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/05/2022] [Indexed: 11/15/2022] Open
Abstract
Host translation is generally modulated by viral infection, including duck hepatitis A virus (DHAV) infection. Previously, we reported that cellular protein synthesis in a cell model of duck embryo fibroblasts is significantly inhibited by DHAV infection but not viral proteins, suggesting that an important viral-host interaction occurs at the translational level. In this study, we aim to further understand the impact of DHAV virulence on cellular N6-methyladenosine (m6A) modification, which is essential to a wide variety of RNA biological processes, such as mRNA stabilization and translation. Using m6A antibody-based immunoprecipitation, m6A-seq, and LC–MS/MS, we observed that m6A-modified mRNA exists in both virulent and attenuated DHAV-infected duckling livers. Importantly, m6A levels in mRNA were much higher in attenuated DHAV-infected livers compared with virulent DHAV-infected livers, suggesting virulence-dependent regulation of m6A modification. Analysis of modification motifs indicated that GAAGAAG is the most enriched motif. Combined m6A-seq and RNA-seq data analysis indicated a generally positive correlation between m6A and mRNA expression levels in DHAV-infected duckling livers. GO analysis of genes with decreased or increased m6A levels showed that these genes were enriched in various terms, including oxidation–reduction processes and antiviral immune responses. Collectively, our work reveals DHAV virulence-dependent coordination between m6A modification and mRNA expression in duckling livers.
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Affiliation(s)
- Liping Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife, Inc., Wuhan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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4
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Li P, Li Y, Wang Y, Liu J, Lavrijsen M, Li Y, Zhang R, Verstegen MMA, Wang Y, Li TC, Ma Z, Kainov DE, Bruno MJ, de Man RA, van der Laan LJW, Peppelenbosch MP, Pan Q. Recapitulating hepatitis E virus-host interactions and facilitating antiviral drug discovery in human liver-derived organoids. SCIENCE ADVANCES 2022; 8:eabj5908. [PMID: 35044825 PMCID: PMC8769558 DOI: 10.1126/sciadv.abj5908] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Hepatotropic viruses naturally have narrow host and tissue tropisms, challenging the development of robust experimental models. The advent of organoid technology provides a unique opportunity for moving the field forward. Here, we demonstrate that three-dimensional cultured organoids from fetal and adult human liver with cholangiocyte or hepatocyte phenotype support hepatitis E virus (HEV) replication. Inoculation with infectious HEV particles demonstrates that human liver–derived organoids support the full life cycle of HEV infection. By directing organoids toward polarized monolayers in a transwell system, we observed predominantly apical secretion of HEV particles. Genome-wide transcriptomic and tRNAome analyses revealed robust host responses triggered by viral replication. Drug screening in organoids identified brequinar and homoharringtonine as potent HEV inhibitors, which are also effective against the ribavirin resistance variant harboring G1634R mutation. Thus, successful recapitulation of HEV infection in liver-derived organoids shall facilitate the study of virus-host interactions and development of antiviral therapies.
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Affiliation(s)
- Pengfei Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Yunlong Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Yijin Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Corresponding author. (Q.P.); (Y.W.)
| | - Jiaye Liu
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Marla Lavrijsen
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Yang Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Ruyi Zhang
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Monique M. A. Verstegen
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Yining Wang
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Tian-Cheng Li
- Department of Virology II, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Zhongren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, PR China
| | - Denis E. Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7028, Norway
- Institute of Technology, University of Tartu, Tartu 50090, Estonia
| | - Marco J. Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Robert A. de Man
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Luc J. W. van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, Netherlands
- Corresponding author. (Q.P.); (Y.W.)
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5
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Zhang R, Noordam L, Ou X, Ma B, Li Y, Das P, Shi S, Liu J, Wang L, Li P, Verstegen MMA, Reddy DS, van der Laan LJW, Peppelenbosch MP, Kwekkeboom J, Smits R, Pan Q. The biological process of lysine-tRNA charging is therapeutically targetable in liver cancer. Liver Int 2021; 41:206-219. [PMID: 33084231 PMCID: PMC7820958 DOI: 10.1111/liv.14692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Mature transfer RNAs (tRNA) charged with amino acids decode mRNA to synthesize proteins. Dysregulation of translational machineries has a fundamental impact on cancer biology. This study aims to map the tRNAome landscape in liver cancer patients and to explore potential therapeutic targets at the interface of charging amino acid with tRNA. METHODS Resected tumour and paired tumour-free (TFL) tissues from hepatocellular carcinoma (HCC) patients (n = 69), and healthy liver tissues from organ transplant donors (n = 21), HCC cell lines, and cholangiocarcinoma (CC) patient-derived tumour organoids were used. RESULTS The expression levels of different mature tRNAs were highly correlated and closely clustered within individual tissues, suggesting that different members of the tRNAome function cooperatively in protein translation. Interestingly, high expression of tRNA-Lys-CUU in HCC tumours was associated with more tumour recurrence (HR 1.1; P = .022) and worse patient survival (HR 1.1; P = .0037). The expression of Lysyl-tRNA Synthetase (KARS), the enzyme catalysing the charge of lysine to tRNA-Lys-CUU, was significantly upregulated in HCC tumour tissues compared to tumour-free liver tissues. In HCC cell lines, lysine deprivation, KARS knockdown or treatment with the KARS inhibitor cladosporin effectively inhibited overall cell growth, single cell-based colony formation and cell migration. This was mechanistically mediated by cell cycling arrest and induction of apoptosis. Finally, these inhibitory effects were confirmed in 3D cultured patient-derived CC organoids. CONCLUSIONS The biological process of charging tRNA-Lys-CUU with lysine sustains liver cancer cell growth and migration, and is clinically relevant in HCC patients. This process can be therapeutically targeted and represents an unexplored territory for developing novel treatment strategies against liver cancer.
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Affiliation(s)
- Ruyi Zhang
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Lisanne Noordam
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Xumin Ou
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands,Institute of Preventive Veterinary MedicineSichuan Agricultural UniversityChengduChina
| | - Buyun Ma
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Yunlong Li
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Pronay Das
- Organic Chemistry DivisionCSIR‐National Chemical LaboratoryPuneIndia
| | - Shaojun Shi
- Department of SurgeryErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Jiaye Liu
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Ling Wang
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Pengfei Li
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | | | | | | | - Maikel P. Peppelenbosch
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Jaap Kwekkeboom
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Ron Smits
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and HepatologyErasmus MC‐University Medical CenterRotterdamThe Netherlands
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6
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Ou X, Peng W, Yang Z, Cao J, Wang M, Peppelenbosch MP, Pan Q, Cheng A. Evolutionarily missing and conserved tRNA genes in human and avian. INFECTION GENETICS AND EVOLUTION 2020; 85:104460. [PMID: 32679345 DOI: 10.1016/j.meegid.2020.104460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 11/29/2022]
Abstract
Viral infection heavily relies on host transfer RNA (tRNA) for viral RNA decoding. Counterintuitively, not all tRNA species based on anticodon are matched to all 64-triplet codons during evolution. Life solves this problem by cognate tRNA species via wobbling decoding. We found that 14 out of 64 tRNA genes in humans and the main avian species (chicken and duck) were parallelly missing, including 8 tRNA-A34NN and 6 tRNA-G34NN species. By analyzing the conservation of key motifs in tRNA genes, we found that box A and B served as intragenic tRNA promoters were evolutionally conserved among human, chicken, and duck. Thus, decoding viral RNA by similar wobbling strategies and tRNA transcripts may be parallelly used by human, chicken, and duck. We envisioned that many basic mechanisms regarding viral RNA decoding were possibly conserved in these hosts and may consequently promote cross-species infection. Transfer RNAs (tRNAs) are essentially required for gene decoding. Despite the universal nature of genetic codon, not all tRNA genes are common to all organisms. Here, we would like to discuss fundamental problems and possible effects arising from the evolutionarily missing and conserved tRNA genes in human, chicken, and duck (Alkatib et al., 2012; Ou et al., 2019; Rogalski et al., 2008). Among these three organisms, viruses especially the avian influenza virus can crossly infect (Pepin et al., 2010). For multi-host viruses, similar viral RNA decoding strategies may be parallelly used by different hosts. Because viral cross-species infection heavily relies on host tRNAs of different species for viral RNA decoding (Ou et al., 2020; van Weringh et al., 2011). We envisioned that many basic mechanisms regarding viral RNA decoding were possibly conserved in these three hosts and may consequently promote cross-species infection.
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Affiliation(s)
- Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China; Postgraduate School Molecular Medicine, Erasmus MC-University Medical Center, 3015 CN Rotterdam, the Netherlands; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China.
| | - Wenjing Peng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China
| | - Zhishuang Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China
| | - Jingyu Cao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China
| | - Maikel P Peppelenbosch
- Postgraduate School Molecular Medicine, Erasmus MC-University Medical Center, 3015 CN Rotterdam, the Netherlands
| | - Qiuwei Pan
- Postgraduate School Molecular Medicine, Erasmus MC-University Medical Center, 3015 CN Rotterdam, the Netherlands
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China; Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China.
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