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Saha S, Mukherjee B, Banerjee P, Das D. The 'Not-So-Famous Five' in tumorigenesis: tRNAs, tRNA fragments, and tRNA epitranscriptome in concert with AARSs and AIMPs. Biochimie 2024; 222:45-62. [PMID: 38401639 DOI: 10.1016/j.biochi.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
RNA profiling studies have revealed that ∼75% of the human genome is transcribed to RNA but only a meagre fraction of it is translated to proteins. Majority of transcribed RNA constitute a specialized pool of non-coding RNAs. Human genome contains approximately 506 genes encoding a set of 51 different tRNAs, constituting a unique class of non-coding RNAs that not only have essential housekeeping functions as translator molecules during protein synthesis, but have numerous uncharted regulatory functions. Intriguing findings regarding a variety of non-canonical functions of tRNAs, tRNA derived fragments (tRFs), esoteric epitranscriptomic modifications of tRNAs, along with aminoacyl-tRNA synthetases (AARSs) and ARS-interacting multifunctional proteins (AIMPs), envision a 'peripheral dogma' controlling the flow of genetic information in the backdrop of qualitative information wrung out of the long-live central dogma of molecular biology, to drive cells towards either proliferation or differentiation programs. Our review will substantiate intriguing peculiarities of tRNA gene clusters, atypical tRNA-transcription from internal promoters catalysed by another distinct RNA polymerase enzyme, dynamically diverse tRNA epitranscriptome, intricate mechanism of tRNA-charging by AARSs governing translation fidelity, epigenetic regulation of gene expression by tRNA fragments, and the role of tRNAs and tRNA derived/associated molecules as quantitative determinants of the functional proteome, covertly orchestrating the process of tumorigenesis, through a deregulated tRNA-ome mediating selective codon-biased translation of cancer related gene transcripts.
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Affiliation(s)
- Sutapa Saha
- Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata, 700073, WB, India.
| | - Biyas Mukherjee
- Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata, 700064, India
| | - Proma Banerjee
- Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata, 700073, WB, India
| | - Debadrita Das
- Department of Life Sciences, Presidency University, 86/1, College Street, Kolkata, 700073, WB, India
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2
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Ben Toumia I, Bachetti T, Chekir-Ghedira L, Profumo A, Ponassi M, Di Domizio A, Izzotti A, Sciacca S, Puglisi C, Forte S, Giuffrida R, Colarossi C, Milardi D, Grasso G, Lanza V, Fiordoro S, Drago G, Tkachenko K, Cardinali B, Romano P, Iervasi E, Vargas GC, Barboro P, Kohnke FH, Rosano C. Fraisinib: a calixpyrrole derivative reducing A549 cell-derived NSCLC tumor in vivo acts as a ligand of the glycine-tRNA synthase, a new molecular target in oncology. Front Pharmacol 2024; 14:1258108. [PMID: 38235113 PMCID: PMC10791888 DOI: 10.3389/fphar.2023.1258108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/17/2023] [Indexed: 01/19/2024] Open
Abstract
Background and purpose: Lung cancer is the leading cause of death in both men and women, constituting a major public health problem worldwide. Non-small-cell lung cancer accounts for 85%-90% of all lung cancers. We propose a compound that successfully fights tumor growth in vivo by targeting the enzyme GARS1. Experimental approach: We present an in-depth investigation of the mechanism through which Fraisinib [meso-(p-acetamidophenyl)-calix(4)pyrrole] affects the human lung adenocarcinoma A549 cell line. In a xenografted model of non-small-cell lung cancer, Fraisinib was found to reduce tumor mass volume without affecting the vital parameters or body weight of mice. Through a computational approach, we uncovered that glycyl-tRNA synthetase is its molecular target. Differential proteomics analysis further confirmed that pathways regulated by Fraisinib are consistent with glycyl-tRNA synthetase inhibition. Key results: Fraisinib displays a strong anti-tumoral potential coupled with limited toxicity in mice. Glycyl-tRNA synthetase has been identified and validated as a protein target of this compound. By inhibiting GARS1, Fraisinib modulates different key biological processes involved in tumoral growth, aggressiveness, and invasiveness. Conclusion and implications: The overall results indicate that Fraisinib is a powerful inhibitor of non-small-cell lung cancer growth by exerting its action on the enzyme GARS1 while displaying marginal toxicity in animal models. Together with the proven ability of this compound to cross the blood-brain barrier, we can assess that Fraisinib can kill two birds with one stone: targeting the primary tumor and its metastases "in one shot." Taken together, we suggest that inhibiting GARS1 expression and/or GARS1 enzymatic activity may be innovative molecular targets for cancer treatment.
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Affiliation(s)
| | | | - Leila Chekir-Ghedira
- Unit of Bioactive Natural Substances and Biotechnology, Faculty of Dental Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Aldo Profumo
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Marco Ponassi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Alberto Izzotti
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Stefano Forte
- Istituto Oncologico del Mediterraneo, Viagrande, Italy
| | | | | | - Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Giuseppe Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Valeria Lanza
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Stefano Fiordoro
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Giacomo Drago
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | | | - Paolo Romano
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Erika Iervasi
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Paola Barboro
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Franz Heinrich Kohnke
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Ambientali (CHIBIOFARAM), University of Messina, Messina, Italy
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Pinzaru AM, Tavazoie SF. Transfer RNAs as dynamic and critical regulators of cancer progression. Nat Rev Cancer 2023; 23:746-761. [PMID: 37814109 DOI: 10.1038/s41568-023-00611-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 10/11/2023]
Abstract
Transfer RNAs (tRNAs) have been historically viewed as non-dynamic adaptors that decode the genetic code into proteins. Recent work has uncovered dynamic regulatory roles for these fascinating molecules. Advances in tRNA detection methods have revealed that specific tRNAs can become modulated upon DNA copy number and chromatin alterations and can also be perturbed by oncogenic signalling and transcriptional regulators in cancer cells or the tumour microenvironment. Such alterations in the levels of specific tRNAs have been shown to causally impact cancer progression, including metastasis. Moreover, sequencing methods have identified tRNA-derived small RNAs that influence various aspects of cancer progression, such as cell proliferation and invasion, and could serve as diagnostic and prognostic biomarkers or putative therapeutic targets in various cancers. Finally, there is accumulating evidence, including from genetic models, that specific tRNA synthetases - the enzymes responsible for charging tRNAs with amino acids - can either promote or suppress tumour formation. In this Review, we provide an overview of how deregulation of tRNAs influences cancer formation and progression.
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Affiliation(s)
- Alexandra M Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
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Feng D, Zhu W, Shi X, Wei W, Han P, Wei Q, Yang L. Leucine zipper protein 2 serves as a prognostic biomarker for prostate cancer correlating with immune infiltration and epigenetic regulation. Heliyon 2022; 8:e10750. [PMID: 36217461 PMCID: PMC9547219 DOI: 10.1016/j.heliyon.2022.e10750] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/19/2022] [Accepted: 09/20/2022] [Indexed: 11/04/2022] Open
Abstract
Background We sought to determine whether leucine zipper protein 2 (LUZP2) could benefit men with prostate cancer (PCa) undergoing radical radiotherapy (RT) or prostatectomy (RP). Methods Analysis was done on differentiating expression, clinical prognosis, co-expressed genes, immune infiltration, and epigenetic changes. All of our analyses were done using the R software (version 3.6.3) and the appropriate packages. Results In terms of PCa, tumor samples expressed LUZP2 more than normal samples did. In the TCGA database and GSE116918, we found that LUZP2 was the only independent risk factor for PCa. The shared enriched pathways for patients undergoing RP or RT were cell-cell adhesion, regulation of filopodium assembly, and extracellular matrix containing collagen. With the exception of TNFRSF14, we discovered that LUZP2 was negatively correlated with 21 immune checkpoints in PCa patients receiving RT. We found a significant inverse relationship between LUZP2 expression and the tumor immune environment, which included B cells, CD4+ T cells, neutrophils, macrophages, dendritic cells, stromal score, immune score, and estimate score, in patients receiving RP or RT. Additionally, tumor purity was positively correlated with LUZP2. We found that the drug bortezomib may be susceptible to the LUZP2. DNA methylation was significantly associated with the mRNA expression of LUZP2 in PCa patients from the TCGA database, and LUZP2 methylation was positively correlated with immune cells. The proliferative activity of various PCa cells, which correlated to different stages of this disease, was also found to be significantly reduced by LUZP2 reduction, according to the results of our experimental work. Conclusions We proposed a relatively comprehensive understanding of the roles of LUZP2 on PCa from the fresh perspective of senescence.
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Jiang Y, You J, Wu C, Kang Y, Chen F, Chen L, Wu W. High expression of DARS2 indicates poor prognosis in lung adenocarcinoma. J Clin Lab Anal 2022; 36:e24691. [PMID: 36085578 PMCID: PMC9550967 DOI: 10.1002/jcla.24691] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 01/25/2023] Open
Abstract
Background DARS2 was overexpressed in multiple tumor types, but the biological role of DARS2 in lung adenocarcinoma (LUAD) have not been elucidated. Methods Firstly, the DARS2 expression in LUAD was explored using The Cancer Genome Atlas (TCGA). Then, qRT‐PCR and Western blot were performed to confirm DARS2 expression in LUAD. Next, Cox regression and Kaplan–Meier methods were utilized to evaluate whether DARS2 expression can affect the overall survival. The relationships between DARS2 expression and clinicopathological characteristics were investigated by TCGA database. Moreover, we utilized Gene Set Enrichment Analysis (GSEA) to detect DARS2‐related signaling pathways in LUAD. Finally, the special function of DARS2 in cell proliferation, invasion and apoptosis was assessed in vitro. Results The higher expression of DARS2 was found in LUAD compared to para‐carcinoma tissues and significantly related to tumor stage, T stage, and M stage. The survival analysis indicated that DARS2 overexpression was related to poor prognosis in LUAD. Multivariate analysis suggested that DARS2 expression was a prognostic indicator. GSEA revealed that DARS2 was primarily involved in cell cycle‐related pathways. In addition, upregulation of DARS2 facilitated LUAD cell proliferation, migration, invasion and inhabited apoptosis, DARS2 knockdown showed an opposite result. Conclusion DARS2 modulates the proliferation, invasion and apoptosis of LUAD cells, and sever as a promising therapeutic target for LUAD.
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Affiliation(s)
- Yingfeng Jiang
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Jianbin You
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Chuncai Wu
- Department of Clinical Laboratory, Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, China
| | - Yanli Kang
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Falin Chen
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Liangyuan Chen
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Wenbing Wu
- Department of Clinical Laboratory, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
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Chen W, Lin Y, Jiang M, Wang Q, Shu Q. Identification of LARS as an essential gene for osteosarcoma proliferation through large-Scale CRISPR-Cas9 screening database and experimental verification. Lab Invest 2022; 20:355. [PMID: 35962451 PMCID: PMC9373537 DOI: 10.1186/s12967-022-03571-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/04/2022] [Indexed: 11/12/2022]
Abstract
Background Osteosarcoma is one of the most malignant tumors, and it occurs mostly in children and adolescents. Currently, surgery and chemotherapy are the main treatments. The recurrence rate is high and the prognosis is often poor. Finding an effective target gene therapy for osteosarcoma may effectively improve its prognosis. Method In this study, genes essential for the survival of osteosarcoma cells were identified by genome-wide screening of CRISPR-Cas9 based on the DepMap database. The expression of these essential genes in osteosarcoma patients’ tissues and normal tissues was identified in the GSE19276 database. Functional pathway enrichment analysis, protein interaction network construction, and LASSO were performed to construct a prognostic risk model based on these essential genes. CCK8 assay was used to detect the effect of essential gene-LARS (Leucyl-TRNA Synthetase 1) on the proliferation of osteosarcoma. Results In this study, 785 genes critical for osteosarcoma cell proliferation were identified from the DepMap. Among these 785 essential genes, 59 DEGs were identified in osteosarcoma tissues. In the functional enrichment analysis, these 59 essential genes were mainly enriched in cell cycle-related signaling pathways. Furthermore, we established a risk score module, including LARS and DNAJC17, screened from these 59 genes, and this module could divide osteosarcoma patients into the low-risk and high-risk groups. In addition, knockdown of LARS expression inhibited the proliferative ability of osteosarcoma cells. A significant correlation was found between LARS expression and Monocytic lineage, T cells, and Fibroblasts. Conclusion In conclusion, LARS was identified as an essential gene for survival in osteosarcoma based on the DepMap database. Knockdown of LARS expression significantly inhibited the proliferation of osteosarcoma cells, suggesting that it is involved in the formation and development of osteosarcoma. The results are useful as a foundation for further studies to elucidate a potential osteosarcoma diagnostic index and therapeutic targets. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03571-9.
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Affiliation(s)
- Wenhao Chen
- Department of Orthopedics, The Children's Hospital, Zhejiang University School of Medicine, National Children's Regional Medical Center, National Clinical Research Center for Child Health, 3333 Bingsheng Road, Hangzhou, 310052, Zhejiang Province, China
| | - Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350001, Fujian Province, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Meichen Jiang
- Department of Pathology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350001, Fujian Province, China
| | - Qingshui Wang
- College of Life Sciences, Fujian Normal University, 8 South Xuefu Road, Fuzhou, 350117, Fujian Province, China.
| | - Qiang Shu
- The Children's Hospital, Zhejiang University School of Medicine, National Children's Regional Medical Center, National Clinical Research Center for Child Health, 3333 Bingsheng Road, Hangzhou, 310052, Zhejiang Province, China.
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Ruan GT, Xie HL, Zhu LC, Ge YZ, Yan L, Liao C, Gong YZ, Shi HP. Immune ULBP1 is Elevated in Colon Adenocarcinoma and Predicts Prognosis. Front Genet 2022; 13:762514. [PMID: 35211154 PMCID: PMC8862730 DOI: 10.3389/fgene.2022.762514] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/10/2022] [Indexed: 01/05/2023] Open
Abstract
Background: Colon adenocarcinoma (COAD) is still the main cause of cancer deaths worldwide. Although immunotherapy has made progress in recent years, there is still a need to improve diagnosis, prognosis, and treatment tools. UL-16 binding protein 1 (ULBP1) is a ligand that activates the receptor natural killer cell group 2 receptor D (NKG2D) and plays an important immunomodulatory role. We aimed to investigate the clinical significance of ULBP1 in COAD. Methods: We obtained the relevant data from The Cancer Genome Atlas (TCGA). A total of 438 patients with COAD were included in this study, with a mean age of 67.1 ± 13.03 years old, of which 234 (53.42%) were male. The diagnostic value of COAD tumor tissues and adjacent tissues was analyzed by ROC curve. Univariate and multivariate survival analysis investigated the prognostic value of ULBP1 gene, and Gene Set Enrichment Analysis (GSEA) curve was performed to analyze the biological process and enriched enrichment pathway of ULBP1 in COAD. Combination survival analysis investigated the combined prognostic effect of prognostic genes. Results:ULBP1 gene had a high diagnostic value in COAD [AUC (TCGA) = 0.959; AUC (Guangxi) = 0.898]. Up-regulated ULBP1 gene of patients with COAD predicted a worse prognosis compared to those patients with down-regulated ULBP1 gene (Adjusted HR = 1.544, 95% CI = 1.020–2.337, p = 0.040). The GSEA showed that ULBP1 was involved in the apoptotic pathway and biological process of T cell mediated cytotoxicity, regulation of natural killer cell activation, and T cell mediated immunity of COAD. The combination survival analysis showed that the combination of high expression of ULBP1, AARS1, and DDIT3 would increase the 2.2-fold death risk of COAD when compared with those of low expression genes. Conclusion: The immune-related ULBP1 gene had diagnostic and prognostic value in COAD. The combination of ULBP1, AARS1, and DDIT3 genes could improve the prognostic prediction performance in COAD.
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Affiliation(s)
- Guo-Tian Ruan
- Department of Gastrointestinal Surgery/Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing International Science and Technology Cooperation Base for Cancer Metabolism and Nutrition, Beijing, China
| | - Hai-Lun Xie
- Department of Gastrointestinal Surgery/Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing International Science and Technology Cooperation Base for Cancer Metabolism and Nutrition, Beijing, China
| | - Li-Chen Zhu
- Department of Immunology, School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - Yi-Zhong Ge
- Department of Gastrointestinal Surgery/Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing International Science and Technology Cooperation Base for Cancer Metabolism and Nutrition, Beijing, China
| | - Lin Yan
- Department of Thoracic Surgery, Affiliated Hospital of Guilin Medical College, Guilin, China
| | - Cun Liao
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yi-Zhen Gong
- Division of Colorectal and Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Han-Ping Shi
- Department of Gastrointestinal Surgery/Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.,Beijing International Science and Technology Cooperation Base for Cancer Metabolism and Nutrition, Beijing, China
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