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Yasar S, Yagin FH, Melekoglu R, Ardigò LP. Integrating proteomics and explainable artificial intelligence: a comprehensive analysis of protein biomarkers for endometrial cancer diagnosis and prognosis. Front Mol Biosci 2024; 11:1389325. [PMID: 38894711 PMCID: PMC11184912 DOI: 10.3389/fmolb.2024.1389325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Endometrial cancer, which is the most common gynaecological cancer in women after breast, colorectal and lung cancer, can be diagnosed at an early stage. The first aim of this study is to classify age, tumor grade, myometrial invasion and tumor size, which play an important role in the diagnosis and prognosis of endometrial cancer, with machine learning methods combined with explainable artificial intelligence. 20 endometrial cancer patients proteomic data obtained from tumor biopsies taken from different regions of EC tissue were used. The data obtained were then classified according to age, tumor size, tumor grade and myometrial invasion. Then, by using three different machine learning methods, explainable artificial intelligence was applied to the model that best classifies these groups and possible protein biomarkers that can be used in endometrial prognosis were evaluated. The optimal model for age classification was XGBoost with AUC (98.8%), for tumor grade classification was XGBoost with AUC (98.6%), for myometrial invasion classification was LightGBM with AUC (95.1%), and finally for tumor size classification was XGBoost with AUC (94.8%). By combining the optimal models and the SHAP approach, possible protein biomarkers and their expressions were obtained for classification. Finally, EWRS1 protein was found to be common in three groups (age, myometrial invasion, tumor size). This article's findings indicate that models have been developed that can accurately classify factors including age, tumor grade, and myometrial invasion all of which are critical for determining the prognosis of endometrial cancer as well as potential protein biomarkers associated with these factors. Furthermore, we were able to provide an analysis of how the quantities of the proteins suggested as biomarkers varied throughout the classes by combining the SHAP values with these ideal models.
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Affiliation(s)
- Seyma Yasar
- Department of Biostatistics, and Medical Informatics, Medicine Faculty, Inonu University, Malatya, Türkiye
| | - Fatma Hilal Yagin
- Department of Biostatistics, and Medical Informatics, Medicine Faculty, Inonu University, Malatya, Türkiye
| | - Rauf Melekoglu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Inonu University, Malatya, Türkiye
| | - Luca Paolo Ardigò
- Department of Teacher Education, NLA University College, Oslo, Norway
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2
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Aragoneses-Cazorla G, Alvarez-Fernandez Garcia R, Martinez-Lopez A, Gomez Gomez M, Vallet-Regí M, Castillo-Lluva S, González B, Luque-Garcia JL. Mechanistic insights into the antitumoral potential and in vivo antiproliferative efficacy of a silver-based core@shell nanosystem. Int J Pharm 2024; 655:124023. [PMID: 38513815 DOI: 10.1016/j.ijpharm.2024.124023] [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: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
This study delves into the biomolecular mechanisms underlying the antitumoral efficacy of a hybrid nanosystem, comprised of a silver core@shell (Ag@MSNs) functionalized with transferrin (Tf). Employing a SILAC proteomics strategy, we identified over 150 de-regulated proteins following exposure to the nanosystem. These proteins play pivotal roles in diverse cellular processes, including mitochondrial fission, calcium homeostasis, endoplasmic reticulum (ER) stress, oxidative stress response, migration, invasion, protein synthesis, RNA maturation, chemoresistance, and cellular proliferation. Rigorous validation of key findings substantiates that the nanosystem elicits its antitumoral effects by activating mitochondrial fission, leading to disruptions in calcium homeostasis, as corroborated by RT-qPCR and flow cytometry analyses. Additionally, induction of ER stress was validated through western blotting of ER stress markers. The cytotoxic action of the nanosystem was further affirmed through the generation of cytosolic and mitochondrial reactive oxygen species (ROS). Finally, in vivo experiments using a chicken embryo model not only confirmed the antitumoral capacity of the nanosystem, but also demonstrated its efficacy in reducing cellular proliferation. These comprehensive findings endorse the potential of the designed Ag@MSNs-Tf nanosystem as a groundbreaking chemotherapeutic agent, shedding light on its multifaceted mechanisms and in vivo applicability.
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Affiliation(s)
- Guillermo Aragoneses-Cazorla
- Department of Analytical Chemistry, Faculty of Chemical Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Angelica Martinez-Lopez
- Department of Biochemistry and Molecular Biology, Faculty of Chemical Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Milagros Gomez Gomez
- Department of Analytical Chemistry, Faculty of Chemical Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Maria Vallet-Regí
- Department of Chemistry in Pharmaceutical Sciences, Faculty of Pharmacy, Complutense University of Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre (i+12), 28040 Madrid, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Sonia Castillo-Lluva
- Department of Biochemistry and Molecular Biology, Faculty of Chemical Sciences, Complutense University of Madrid, 28040 Madrid, Spain
| | - Blanca González
- Department of Chemistry in Pharmaceutical Sciences, Faculty of Pharmacy, Complutense University of Madrid, Instituto de Investigación Sanitaria Hospital 12 de Octubre (i+12), 28040 Madrid, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Jose L Luque-Garcia
- Department of Analytical Chemistry, Faculty of Chemical Sciences, Complutense University of Madrid, 28040 Madrid, Spain.
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Barai P, Chen J. Beyond protein synthesis: non-translational functions of threonyl-tRNA synthetases. Biochem Soc Trans 2024; 52:661-670. [PMID: 38477373 PMCID: PMC11088916 DOI: 10.1042/bst20230506] [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: 01/21/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
Aminoacyl-tRNA synthetases (AARSs) play an indispensable role in the translation of mRNAs into proteins. It has become amply clear that AARSs also have non-canonical or non-translational, yet essential, functions in a myriad of cellular and developmental processes. In this mini-review we discuss the current understanding of the roles of threonyl-tRNA synthetase (TARS) beyond protein synthesis and the underlying mechanisms. The two proteins in eukaryotes - cytoplasmic TARS1 and mitochondrial TARS2 - exert their non-canonical functions in the regulation of gene expression, cell signaling, angiogenesis, inflammatory responses, and tumorigenesis. The TARS proteins utilize a range of biochemical mechanisms, including assembly of a translation initiation complex, unexpected protein-protein interactions that lead to activation or inhibition of intracellular signaling pathways, and cytokine-like signaling through cell surface receptors in inflammation and angiogenesis. It is likely that new functions and novel mechanisms will continue to emerge for these multi-talented proteins.
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Affiliation(s)
- Pallob Barai
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Jie Chen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
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4
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Izadi M, Ali TA, Shurrab FM, Aharpour E, Pourkarimi E. Tryptophanyl-tRNA synthetase-1 (WARS-1) depletion and high tryptophan concentration lead to genomic instability in Caenorhabditis elegans. Cell Death Discov 2024; 10:165. [PMID: 38575580 PMCID: PMC10995160 DOI: 10.1038/s41420-024-01917-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024] Open
Abstract
The fidelity of translation is ensured by a family of proteins named aminoacyl-tRNA synthetases (ARSs), making them crucial for development and survival. More recently, mutations in the tryptophanyl-tRNA synthetase 1 (WARS1) have been linked to various human diseases, from intellectual disability to various types of cancer. To understand the function of WARS1, we investigated the effect of WARS-1 depletion during the mitotic and meiotic cell cycle in the developing germline of Caenorhabditis elegans (C. elegans) and demonstrated the role of WARS-1 in genome integrity. wars-1 knockdown results in cell cycle arrest of the mitotically active germ cells. Such mitotic arrest is also associated with canonical DNA damage-induced checkpoint signaling in mitotic and meiotic germ cells. Significantly, such DNA checkpoint activation is associated with the morphological anomalies in chromatin structures that are the hallmarks of genome instability, such as the formation of chromatin bridges, micronuclei, and chromatin buds. We demonstrated that knocking down wars-1 results in an elevation of the intracellular concentration of tryptophan and its catabolites, a surprising finding emphasizing the impact of cellular amino acid availability and organismal/individual dietary uptake on genome integrity. Our result demonstrates that exposing C. elegans to a high tryptophan dosage leads to DNA damage checkpoint activation and a significant increase in the tryptophan metabolites. Targeting tryptophan catabolism, the least utilized amino acid in nature, can be important in developing new cancer therapeutic approaches. All in all, we have strong evidence that knocking down wars-1 results in defects in genomic integrity.
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Affiliation(s)
- Mahmoud Izadi
- Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar
| | - Tayyiba Akbar Ali
- Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar
| | - Farah M Shurrab
- Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar
| | | | - Ehsan Pourkarimi
- Division of Genomics and Translational Medicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, 34110, Qatar.
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5
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Zhang H, Ling J. Serine mistranslation induces the integrated stress response without accumulation of uncharged tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578812. [PMID: 38370842 PMCID: PMC10871240 DOI: 10.1101/2024.02.04.578812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that support robust and accurate protein synthesis. A rapidly expanding number of studies show that mutations in aaRSs lead to multiple human diseases, including neurological disorders and cancer. Much remains unknown about how aaRS mutations impact human health. In particular, how aminoacylation errors affect stress responses and fitness in eukaryotic cells remains poorly understood. The integrated stress response (ISR) is an adaptive mechanism in response to multiple stresses. However, chronic activation of the ISR contributes to the development of multiple diseases (e.g., neuropathies). Here we show that Ser misincorporation into Ala and Thr codons, resulting from aaRS editing defects or mutations in tRNAs, constitutively active the ISR. Such activation does not appear to depend on the accumulation of uncharged tRNAs, implicating that Ser mistranslation may lead to ribosome stalling and collision.
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Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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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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7
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Yoon I, Kim U, Choi J, Kim S. Disease association and therapeutic routes of aminoacyl-tRNA synthetases. Trends Mol Med 2024; 30:89-105. [PMID: 37949787 DOI: 10.1016/j.molmed.2023.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are enzymes that catalyze the ligation of amino acids to tRNAs for translation. Beyond their traditional role in translation, ARSs have acquired regulatory functions in various biological processes (epi-translational functions). With their dual-edged activities, aberrant expression, secretion, and mutations of ARSs are associated with human diseases, including cancer, autoimmune diseases, and neurological diseases. The increasing numbers of newly unveiled activities and disease associations of ARSs have spurred interest in novel drug development, targeting disease-related catalytic and noncatalytic activities of ARSs as well as harnessing ARSs as sources for biological therapeutics. This review speculates how the translational and epi-translational activities of ARSs can be related and describes how their activities can be linked to diseases and drug discovery.
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Affiliation(s)
- Ina Yoon
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Uijoo Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Jaeyoung Choi
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Sunghoon Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea; College of Medicine, Gangnam Severance Hospital, Yonsei University, Seoul 06273, Republic of Korea; Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Incheon 21983, Republic of Korea.
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8
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Hekmatshoar Y, Rahbar Saadat Y, Ozkan T, Bozkurt S, Karadag Gurel A. Identification of common genes and pathways underlying imatinib and nilotinib treatment in CML: a Bioinformatics Study. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:664-684. [PMID: 38117080 DOI: 10.1080/15257770.2023.2296021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
Imatinib (IMA) and nilotinib are the first and second generations of BCR-ABL tyrosine kinase inhibitors, which widely applied in chronic myeloid leukemia (CML) treatment. Here we aimed to provide new targets for CML treatment by transcriptome analysis. Microarray data GSE19567 was downloaded and analyzed from Gene Expression Omnibus (GEO) to identify common genes, which are downregulated or upregulated in K562-imatinib and K562-nilotinib treated cells. The differentially expressed genes (DEGs) were assessed, and STRING and Cytoscape were used to create the protein-protein interaction (PPI) network. In imatinib and nilotinib treated groups' comparison, there were common 626 upregulated and 268 downregulated genes, which were differentially expressed. The GO analysis represented the enrichment of DEGs in iron ion binding, protein tyrosine kinase activity, transcription factor activity, ATP binding, sequence-specific DNA binding, cytokine activity, the mitochondrion, sequence-specific DNA binding, plasma membrane and cell-cell adherens junction. KEGG pathway analysis revealed that downregulated DEGs were associated with pathways including microRNAs in cancer and PI3K-Akt signaling pathway. Furthermore, upregulated DEGs were involved in hematopoietic cell lineage, lysosome and chemical carcinogenesis. Among the upregulated genes, MYH9, MYH14, MYL10, MYL7, MYL5, RXRA, CYP1A1, FECH, AKR1C3, ALAD, CAT, CITED2, CPT1A, CYP3A5, CYP3A7, FABP1, HBD, HMBS and PPOX genes were found as hub genes. Moreover, 20 downregulated genes, YARS, AARS, SARS, GARS, CARS, IARS, RRP79, CEBPB, RRP12, UTP14A, PNO1, CCND1, DDX10, MYC, WDR43, CEBPG, DDIT3, VEGFA, PIM1 and TRIB3 were identified as hub genes. These genes have the potential to become target genes for diagnosis and therapy of CML patients.
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Affiliation(s)
- Yalda Hekmatshoar
- Department of Medical Biology, School of Medicine, Altinbas University, Istanbul, Turkey
| | | | - Tulin Ozkan
- Department of Medical Biology, School of Medicine, Ankara University, Ankara, Turkey
| | - Sureyya Bozkurt
- Department of Medical Biology, School of Medicine, Istinye University, Istanbul, Turkey
| | - Aynur Karadag Gurel
- Department of Medical Biology, School of Medicine, Usak University, Usak, Turkey
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9
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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: 6] [Impact Index Per Article: 6.0] [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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10
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Feng M, Yang K, Wang J, Li G, Zhang H. First Report of FARSA in the Regulation of Cell Cycle and Survival in Mantle Cell Lymphoma Cells via PI3K-AKT and FOXO1-RAG1 Axes. Int J Mol Sci 2023; 24:ijms24021608. [PMID: 36675119 PMCID: PMC9865697 DOI: 10.3390/ijms24021608] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/26/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
Cancer-associated factors have been largely identified in the understanding of tumorigenesis and progression. However, aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) have so far been neglected in cancer research due to their canonical activities in protein translation and synthesis. FARSA, the alpha subunit of the phenylalanyl-tRNA synthetase is elevated across many cancer types, but its function in mantle cell lymphoma (MCL) remains undetermined. Herein, we found the lowest levels of FARSA in patients with MCL compared with other subtypes of lymphomas, and the same lower levels of FARSA were observed in chemoresistant MCL cell lines. Unexpectedly, despite the essential catalytic roles of FARSA, knockdown of FARSA in MCL cells did not lead to cell death but resulted in accelerated cell proliferation and cell cycle, whereas overexpression of FARSA induced remarkable cell-cycle arrest and overwhelming apoptosis. Further RNA sequencing (RNA-seq) analysis and validation experiments confirmed a strong connection between FARSA and cell cycle in MCL cells. Importantly, FARSA leads to the alteration of cell cycle and survival via both PI3K-AKT and FOXO1-RAG1 axes, highlighting a FARSA-mediated regulatory network in MCL cells. Our findings, for the first time, reveal the noncanonical roles of FARSA in MCL cells, and provide novel insights into understanding the pathogenesis and progression of B-cell malignancies.
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Affiliation(s)
- Min Feng
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Kun Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Jia Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
- School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Guilan Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Han Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
- Correspondence: ; Tel.: +86-158-7796-3252
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11
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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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12
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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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13
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The Aminoacyl-tRNA Synthetase and tRNA Expression Levels Are Deregulated in Cancer and Correlate Independently with Patient Survival. Curr Issues Mol Biol 2022; 44:3001-3017. [PMID: 35877431 PMCID: PMC9324904 DOI: 10.3390/cimb44070207] [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: 05/25/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes that load amino acids to their cognate tRNA molecules. The expression of certain ARSs and tRNAs has been shown to be deregulated in cancer, presumably to accommodate elevated protein synthesis requirements. In this work, the expression of cytoplasmic ARSs and tRNAs in ten TCGA cancers has been systematically examined. ARSs were found to be mostly upregulated in tumours and their upregulation often correlated with worse patient survival. tRNAs were found to be either upregulated or downregulated in tumours and their expression sometimes correlated to worse survival outcomes. However, although the expression of most ARSs and tRNAs was deregulated in tumours when compared to healthy adjacent tissues, only in a few cases, and independently, did it correlate to patient survival. These data point to the general uncoupling of concomitant ARS and tRNA expression deregulation and patient survival, highlighting the different ARS and tRNA requirements in cancers.
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14
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Khan K, Gogonea V, Fox PL. Aminoacyl-tRNA synthetases of the multi-tRNA synthetase complex and their role in tumorigenesis. Transl Oncol 2022; 19:101392. [PMID: 35278792 PMCID: PMC8914993 DOI: 10.1016/j.tranon.2022.101392] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, 20 aminoacyl-tRNA synthetases (AARS) catalyze the ligation of amino acids to their cognate tRNAs to generate aminoacylated-tRNAs. In higher eukaryotes, 9 of the 20 AARSs, along with 3 auxiliary proteins, join to form the cytoplasmic multi-tRNA synthetase complex (MSC). The complex is absent in prokaryotes, but evolutionary expansion of MSC constituents, primarily by addition of novel interacting domains, facilitates formation of subcomplexes that join to establish the holo-MSC. In some cases, environmental cues direct the release of constituents from the MSC which enables the execution of non-canonical, i.e., "moonlighting", functions distinct from their essential activities in protein translation. These activities are generally beneficial, but can also be deleterious to the cell. Elucidation of the non-canonical activities of several AARSs residing in the MSC suggest they are potential therapeutic targets for cancer, as well as metabolic and neurologic diseases. Here, we describe the role of MSC-resident AARSs in cancer progression, and the factors that regulate their release from the MSC. Also, we highlight recent developments in therapeutic modalities that target MSC AARSs for cancer prevention and treatment.
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Affiliation(s)
- Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States of America.
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, United States of America
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States of America.
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15
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tRNA modifications and their potential roles in pancreatic cancer. Arch Biochem Biophys 2021; 714:109083. [PMID: 34785212 DOI: 10.1016/j.abb.2021.109083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022]
Abstract
Since the breakthrough discovery of N6-methyladenosine (m6A), the field of RNA epitranscriptomics has attracted increasing interest in the biological sciences. Transfer RNAs (tRNAs) are extensively modified, and various modifications play a crucial role in the formation and stability of tRNA, which is universally required for accurate and efficient functioning of tRNA. Abnormal tRNA modification can lead to tRNA degradation or specific cleavage of tRNA into fragmented derivatives, thus affecting the translation process and frequently accompanying a variety of human diseases. Increasing evidence suggests that tRNA modification pathways are also misregulated in human cancers. In this review, we summarize tRNA modifications and their biological functions, describe the type and frequency of tRNA modification alterations in cancer, and highlight variations in tRNA-modifying enzymes and the multiple functions that they regulate in different types of cancers. Furthermore, the current implications and the potential role of tRNA modifications in the progression of pancreatic cancer are discussed. Collectively, this review describes recent advances in tRNA modification in cancers and its potential significance in pancreatic cancer. Further study of the mechanism of tRNA modifications in pancreatic cancer may provide possibilities for therapies targeting enzymes responsible for regulating tRNA modifications in pancreatic cancer.
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