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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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Zeng H, Pan W, Xia Q, Shu H, Ji Z. Diagnostic, prognostic, and immunological roles of CDSN in ovarian cancer. Heliyon 2024; 10:e33357. [PMID: 39027431 PMCID: PMC11254609 DOI: 10.1016/j.heliyon.2024.e33357] [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: 01/06/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024] Open
Abstract
Globally, ovarian cancer (OC) ranks as a principal cause of cancer-related mortality in females. Immunotherapy has revolutionized the treatment of OC, but the efficacy of immunotherapy is often limited by different immune microenvironments. The objective of this research was to pinpoint and validate candidate genes with potential value as diagnostic and prognostic biomarkers and therapeutic targets in OC. Data on genes associated with gene mutation, prognostic survival, and immune infiltration in OC were procured from the Cancer Genome Atlas (TCGA). Gene differential analysis, mutation site analysis, prognosis and survival analysis, and functional and signaling pathway enrichment analysis were conducted to identify and evaluate key genes. The genes were further investigated using immune infiltration analysis, receiver operating characteristic curves, and immunohistochemistry. The impact of CDSN on OC cell proliferation was investigated utilizing CCK-8, colony formation, and apoptosis detection assays. We identified a set of genes (CDSN, WARS, and CD38) that were highly expressed in OC and significantly associated with mutations and prognosis. Immune infiltration analysis and immunohistochemistry results indicated a correlation with immune infiltration in the tumor microenvironment, particularly in antigen-presenting cells. Receiver operating characteristic curve analysis demonstrated the diagnostic potential of these three genes in OC, with all three genes showing the area under the curve (AUC) above 0.8. In vitro studies suggested that knocked down CDSN expression resulted in a marked lower in the proliferative capacity of OC cells. The candidate gene CDSN identified through bioinformatics analysis and in vitro experiments is associated with mutation and immune infiltration, showing promise as a diagnostic and prognostic biomarker, as well as a therapeutic objective in OC.
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Affiliation(s)
- Huan Zeng
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Wei Pan
- Lab for Noncoding RNA & Cancer, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Qiuyi Xia
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Hong Shu
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital, Nanning, 530021, China
| | - Zhaodong Ji
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
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3
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Bos J, Groen-van Schooten TS, Brugman CP, Jamaludin FS, van Laarhoven HWM, Derks S. The tumor immune composition of mismatch repair deficient and Epstein-Barr virus-positive gastric cancer: A systematic review. Cancer Treat Rev 2024; 127:102737. [PMID: 38669788 DOI: 10.1016/j.ctrv.2024.102737] [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: 02/13/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Gastric cancer (GC), known for its unfavorable prognosis, has been classified in four distinct molecular subtypes. These subtypes not only exhibit differences in their genome and transcriptome but also in the composition of their tumor immune microenvironment. The microsatellite instable (MSI) and Epstein-Barr virus (EBV) positive GC subtypes show clear clinical benefits from immune checkpoint blockade, likely due to a neoantigen-driven and virus-driven antitumor immune response and high expression of immune checkpoint molecule PD-L1. However, even within these subtypes response to checkpoint inhibition is variable, which is potentially related to heterogeneity in the tumor immune microenvironment (TIME) and expression of co-inhibitory molecules. We conducted a systematic review to outline the current knowledge about the immunological features on the TIME of MSI and EBV + GCs. METHODS A systematic search was performed in PubMed, EMBASE and Cochrane Library. All articles from the year 1990 and onwards addressing immune features of gastric adenocarcinoma were reviewed and included based on predefined in- and exclusion criteria. RESULTS In total 5962 records were screened, of which 139 were included that reported immunological data on molecular GC subtypes. MSI and EBV + GCs were reported to have a more inflamed TIME compared to non-MSI and EBV- GC subtypes. Compared to microsatellite stable (MSS) tumors, MSI tumors were characterized by higher numbers of CD8 + and FoxP3 + T cells, and tumor infiltrating pro- and anti-inflammatory macrophages. HLA-deficiency was most common in MSI tumors compared to other molecular GC subtypes and associated with lower T and B cell infiltrates compared to HLA-proficient tumors. EBV + was associated with a high number of CD8 + T cells, Tregs, NK cells and macrophages. Expression of PD-L1, CTLA-4, Granzyme A and B, Perforin and interferon-gamma was enriched in EBV + tumors. Overall, MSI tumors harbored a more heterogeneous TIME in terms of immune cell composition and immune checkpoints compared to the EBV + tumors. DISCUSSION AND CONCLUSION MSI and EBV + GCs are highly Handbook for Conducting a Literature-Based Health Assessment Using OHAT Approach for Systematic Review and Evidence Integration.; 2019pro-inflammatory immune cell populations. Although studies on the direct comparison of EBV + and MSI tumors are limited, EBV + tumors show less intra-subgroup heterogeneity compared to MSI tumors. More studies are needed to identify how Intra-subgroup heterogeneity impacts response to immunotherapy efficacy.
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Affiliation(s)
- J Bos
- Amsterdam UMC Location University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - T S Groen-van Schooten
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Oncology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - C P Brugman
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Oncology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - F S Jamaludin
- Amsterdam UMC Location University of Amsterdam, Medical Library AMC, Meibergdreef 9, Amsterdam, the Netherlands
| | - H W M van Laarhoven
- Amsterdam UMC Location University of Amsterdam, Department of Medical Oncology, Meibergdreef 9, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands
| | - S Derks
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands; Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Medical Oncology, De Boelelaan 1117, Amsterdam, the Netherlands.
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4
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Li XQ, Cai MP, Wang MY, Shi BW, Yang GY, Wang J, Chu BB, Ming SL. Pseudorabies virus manipulates mitochondrial tryptophanyl-tRNA synthetase 2 for viral replication. Virol Sin 2024; 39:403-413. [PMID: 38636706 PMCID: PMC11279775 DOI: 10.1016/j.virs.2024.04.003] [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: 10/10/2023] [Accepted: 04/11/2024] [Indexed: 04/20/2024] Open
Abstract
The pseudorabies virus (PRV) is identified as a double-helical DNA virus responsible for causing Aujeszky's disease, which results in considerable economic impacts globally. The enzyme tryptophanyl-tRNA synthetase 2 (WARS2), a mitochondrial protein involved in protein synthesis, is recognized for its broad expression and vital role in the translation process. The findings of our study showed an increase in both mRNA and protein levels of WARS2 following PRV infection in both cell cultures and animal models. Suppressing WARS2 expression via RNA interference in PK-15 cells led to a reduction in PRV infection rates, whereas enhancing WARS2 expression resulted in increased infection rates. Furthermore, the activation of WARS2 in response to PRV was found to be reliant on the cGAS/STING/TBK1/IRF3 signaling pathway and the interferon-alpha receptor-1, highlighting its regulation via the type I interferon signaling pathway. Further analysis revealed that reducing WARS2 levels hindered PRV's ability to promote protein and lipid synthesis. Our research provides novel evidence that WARS2 facilitates PRV infection through its management of protein and lipid levels, presenting new avenues for developing preventative and therapeutic measures against PRV infections.
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Affiliation(s)
- Xiu-Qing Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Meng-Pan Cai
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Ming-Yang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Bo-Wen Shi
- School of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Guo-Yu Yang
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China; International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China.
| | - Bei-Bei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China; Longhu Advanced Immunization Laboratory, Zhengzhou 450046, China; International Joint Research Center of National Animal Immunology, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou 450046, China.
| | - Sheng-Li Ming
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou 450046, China; Key Laboratory of Veterinary Biotechnology of Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
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5
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Salnikov MY, MacNeil KM, Mymryk JS. The viral etiology of EBV-associated gastric cancers contributes to their unique pathology, clinical outcomes, treatment responses and immune landscape. Front Immunol 2024; 15:1358511. [PMID: 38596668 PMCID: PMC11002251 DOI: 10.3389/fimmu.2024.1358511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/14/2024] [Indexed: 04/11/2024] Open
Abstract
Epstein-Barr virus (EBV) is a pathogen known to cause a number of malignancies, often taking years for them to develop after primary infection. EBV-associated gastric cancer (EBVaGC) is one such malignancy, and is an immunologically, molecularly and pathologically distinct entity from EBV-negative gastric cancer (EBVnGC). In comparison with EBVnGCs, EBVaGCs overexpress a number of immune regulatory genes to help form an immunosuppressive tumor microenvironment (TME), have improved prognosis, and overall have an "immune-hot" phenotype. This review provides an overview of the histopathology, clinical features and clinical outcomes of EBVaGCs. We also summarize the differences between the TMEs of EBVaGCs and EBVnGCs, which includes significant differences in cell composition and immune infiltration. A list of available EBVaGC and EBVnGC gene expression datasets and computational tools are also provided within this review. Finally, an overview is provided of the various chemo- and immuno-therapeutics available in treating gastric cancers (GCs), with a focus on EBVaGCs.
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Affiliation(s)
- Mikhail Y. Salnikov
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Katelyn M. MacNeil
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
- Department of Otolaryngology, Western University, London, ON, Canada
- Lawson Health Research Institute, London, ON, Canada
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6
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Luo P, Chen G, Shi Z, Yang J, Wang X, Pan J, Zhu L. Comprehensive multi-omics analysis of tryptophan metabolism-related gene expression signature to predict prognosis in gastric cancer. Front Pharmacol 2023; 14:1267186. [PMID: 37908977 PMCID: PMC10613981 DOI: 10.3389/fphar.2023.1267186] [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: 07/26/2023] [Accepted: 09/18/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction: The 5-year survival of gastric cancer (GC) patients with advanced stage remains poor. Some evidence has indicated that tryptophan metabolism may induce cancer progression through immunosuppressive responses and promote the malignancy of cancer cells. The role of tryptophan and its metabolism should be explored for an in-depth understanding of molecular mechanisms during GC development. Material and methods: We utilized the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) dataset to screen tryptophan metabolism-associated genes via single sample gene set enrichment analysis (ssGSEA) and correlation analysis. Consensus clustering analysis was employed to construct different molecular subtypes. Most common differentially expressed genes (DEGs) were determined from the molecular subtypes. Univariate cox analysis as well as lasso were performed to establish a tryptophan metabolism-associated gene signature. Gene Set Enrichment Analysis (GSEA) was utilized to evaluate signaling pathways. ESTIMATE, ssGSEA, and TIDE were used for the evaluation of the gastric tumor microenvironment. Results: Two tryptophan metabolism-associated gene molecular subtypes were constructed. Compared to the C2 subtype, the C1 subtype showed better prognosis with increased CD4 positive memory T cells as well as activated dendritic cells (DCs) infiltration and suppressed M2-phenotype macrophages inside the tumor microenvironment. The immune checkpoint was downregulated in the C1 subtype. A total of eight key genes, EFNA3, GPX3, RGS2, CXCR4, SGCE, ADH4, CST2, and GPC3, were screened for the establishment of a prognostic risk model. Conclusion: This study concluded that the tryptophan metabolism-associated genes can be applied in GC prognostic prediction. The risk model established in the current study was highly accurate in GC survival prediction.
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Affiliation(s)
| | | | | | | | | | | | - Linghua Zhu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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7
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Gallardo-Gómez M, Rodríguez-Girondo M, Planell N, Moran S, Bujanda L, Etxart A, Castells A, Balaguer F, Jover R, Esteller M, Cubiella J, Gómez-Cabrero D, De Chiara L. Serum methylation of GALNT9, UPF3A, WARS, and LDB2 as noninvasive biomarkers for the early detection of colorectal cancer and advanced adenomas. Clin Epigenetics 2023; 15:157. [PMID: 37794510 PMCID: PMC10552320 DOI: 10.1186/s13148-023-01570-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Early detection has proven to be the most effective strategy to reduce the incidence and mortality of colorectal cancer (CRC). Nevertheless, most current screening programs suffer from low participation rates. A blood test may improve both the adherence to screening and the selection to colonoscopy. In this study, we conducted a serum-based discovery and validation of cfDNA methylation biomarkers for CRC screening in a multicenter cohort of 433 serum samples including healthy controls, benign pathologies, advanced adenomas (AA), and CRC. RESULTS First, we performed an epigenome-wide methylation analysis with the MethylationEPIC array using a sample pooling approach, followed by a robust prioritization of candidate biomarkers for the detection of advanced neoplasia (AN: AA and CRC). Then, candidate biomarkers were validated by pyrosequencing in independent individual cfDNA samples. We report GALNT9, UPF3A, WARS, and LDB2 as new noninvasive biomarkers for the early detection of AN. The combination of GALNT9/UPF3A by logistic regression discriminated AN with 78.8% sensitivity and 100% specificity, outperforming the commonly used fecal immunochemical test and the methylated SEPT9 blood test. CONCLUSIONS Overall, this study highlights the utility of cfDNA methylation for CRC screening. Our results suggest that the combination methylated GALNT9/UPF3A has the potential to serve as a highly specific and sensitive blood-based test for screening and early detection of CRC.
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Affiliation(s)
- María Gallardo-Gómez
- CINBIO, Universidade de Vigo, Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, CINBIO, Universidade de Vigo, Campus As Lagoas-Marcosende s/n. 36310, Vigo, Spain
- Translational Oncology Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Mar Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Núria Planell
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de La Granvia, 199. 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Ane Etxart
- Department of Surgery, Hospital Universitario Donostia, San Sebastián, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Rodrigo Jover
- Department of Gastroenterology, Hospital General Universitario de Alicante, Alicante, Spain
- Servicio de Medicina Digestiva. ISABIAL. Universidad Miguel Hernández, Hospital General Universitario Dr. Balmis, Alicante, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Joaquín Cubiella
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Biomédica Galicia Sur, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - David Gómez-Cabrero
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
- Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
- Mucosal & Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK
| | - Loretta De Chiara
- CINBIO, Universidade de Vigo, Vigo, Spain.
- Department of Biochemistry, Genetics and Immunology, CINBIO, Universidade de Vigo, Campus As Lagoas-Marcosende s/n. 36310, Vigo, Spain.
- Translational Oncology Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
- Cancer Genomics Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
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8
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Low YH, Loh CJL, Peh DYY, Chu AJM, Han S, Toh HC. Pathogenesis and therapeutic implications of EBV-associated epithelial cancers. Front Oncol 2023; 13:1202117. [PMID: 37901329 PMCID: PMC10600384 DOI: 10.3389/fonc.2023.1202117] [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: 04/07/2023] [Accepted: 09/07/2023] [Indexed: 10/31/2023] Open
Abstract
Epstein-Barr virus (EBV), one of the most common human viruses, has been associated with both lymphoid and epithelial cancers. Undifferentiated nasopharyngeal carcinoma (NPC), EBV associated gastric cancer (EBVaGC) and lymphoepithelioma-like carcinoma (LELC) are amongst the few common epithelial cancers that EBV has been associated with. The pathogenesis of EBV-associated NPC has been well described, however, the same cannot be said for primary pulmonary LELC (PPLELC) owing to the rarity of the cancer. In this review, we outline the pathogenesis of EBV-associated NPC and EBVaGCs and their recent advances. By drawing on similarities between NPC and PPLELC, we then also postulated the pathogenesis of PPLELC. A deeper understanding about the pathogenesis of EBV enables us to postulate the pathogenesis of other EBV associated cancers such as PPLELC.
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Affiliation(s)
- Yi Hua Low
- Duke-NUS Medical School, Singapore, Singapore
| | | | - Daniel Yang Yao Peh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Axel Jun Ming Chu
- Singapore Health Services Internal Medicine Residency Programme, Singapore, Singapore
| | - Shuting Han
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
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Hirabayashi M, Georges D, Clifford GM, de Martel C. Estimating the Global Burden of Epstein-Barr Virus-Associated Gastric Cancer: A Systematic Review and Meta-Analysis. Clin Gastroenterol Hepatol 2023; 21:922-930.e21. [PMID: 35963539 DOI: 10.1016/j.cgh.2022.07.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Evidence suggests that a fraction of new gastric cancer cases may be etiologically associated with Epstein-Barr virus (EBV), a known carcinogenic agent. We aimed to systematically explore the proportion of EBV-positive gastric cancer. METHODS We did a systematic review (PROSPERO CRD42020164473) from January 1990 to August 2021. For each country and geographical region with available data, pooled prevalence and corresponding 95% confidence intervals (CIs) of EBV in gastric tumors were calculated for 3 subtypes of gastric adenocarcinoma (conventional adenocarcinoma, lymphoepithelioma-like gastric carcinoma, and remnant/stump carcinoma). For conventional adenocarcinoma, prevalence ratios (PRs) were presented for sex, Lauren's classification, gastric cancer stage, and anatomical location of the stomach. RESULTS In 220 eligible studies including over 68,000 cases of conventional gastric adenocarcinoma, EBV prevalence in tumor cells was 7.5% (95% CI, 6.9%-8.1%) and was higher in men compared with women (PR, 2.1; 95% CI, 1.9-2.4), in diffuse type compared with intestinal type (PR, 1.3; 95% CI, 1.1-1.5), and in the proximal region compared with the distal region (PR, 2.5; 95% CI, 2.0-3.1). There was no difference in EBV prevalence by gastric cancer stage. EBV prevalence was 75.9% (95% CI, 62.8%-85.5%) among lymphoepithelioma-like gastric carcinoma and 26.3% (95% CI, 22.2%-32.0%) among remnant or stump carcinoma. CONCLUSIONS Assuming a causal association between EBV and gastric cancer, our findings, when applied to the GLOBOCAN 2020 gastric cancer incidence, suggest that primary prevention such as the development of an effective EBV vaccine might prevent 81,000 EBV-associated gastric cancer cases worldwide annually.
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Affiliation(s)
- Mayo Hirabayashi
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Damien Georges
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Gary M Clifford
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Catherine de Martel
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France.
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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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Atri-Schuller A, Abushukair H, Cavalcante L, Hentzen S, Saeed A, Saeed A. Tumor Molecular and Microenvironment Characteristics in EBV-Associated Malignancies as Potential Therapeutic Targets: Focus on Gastric Cancer. Curr Issues Mol Biol 2022; 44:5756-5767. [PMID: 36421674 PMCID: PMC9689242 DOI: 10.3390/cimb44110390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 09/30/2023] Open
Abstract
Although most people are infected with Epstein-Barr Virus (EBV) during their lifetime, only a minority of them develop an EBV-associated malignancy. EBV acts in both direct and indirect ways to transform infected cells into tumor cells. There are multiple ways in which the EBV, host, and tumor environment interact to promote malignant transformation. This paper focuses on some of the mechanisms that EBV uses to transform the tumor microenvironment (TME) of EBV-associated gastric cancer (EBVaGC) for its benefit, including overexpression of Indoleamine 2,3-Dioxygenase 1 (IDO1), synergism between H. pylori and EBV co-infection, and M1 to M2 switch. In this review, we expand on different modalities and combinatorial approaches to therapeutically target this mechanism.
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Affiliation(s)
- Aviva Atri-Schuller
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH 45219, USA
| | - Hassan Abushukair
- Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Ludimila Cavalcante
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Stijn Hentzen
- Department of Internal Medicine, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Azhar Saeed
- Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Anwaar Saeed
- Department of Medicine, Division of Medical Oncology, University of Kansas Cancer Center, 2330 Shawnee Mission Pkwy, Kansas City, KS 66205, USA
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12
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Mansorunov D, Apanovich N, Kipkeeva F, Nikulin M, Malikhova O, Stilidi I, Karpukhin A. The Correlation of Ten Immune Checkpoint Gene Expressions and Their Association with Gastric Cancer Development. Int J Mol Sci 2022; 23:ijms232213846. [PMID: 36430322 PMCID: PMC9695628 DOI: 10.3390/ijms232213846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
In the immunotherapy based on immune checkpoint inhibition (IC), additional ICs are being studied to increase its effectiveness. An almost unstudied feature is the possible co-expression of ICs, which can determine the therapeutic efficacy of their inhibition. For the selection of promising ICs, information on the association of their expression with cancer development may be essential. We have obtained data on the expression correlation of ADAM17, PVR, TDO2, CD274, CD276, CEACAM1, IDO1, LGALS3, LGALS9, and HHLA2 genes in gastric cancer (GC). All but one, TDO2, have other IC genes with co-expression at some stage. At the metastatic stage, the expression of the IDO1 does not correlate with any other gene. The correlations are positive, but the expressions of the CD276 and CEACAM1 genes are negatively correlated. The expression of TDO2 and LGALS3 is associated with GC metastasis. The expression of TDO2 four-fold higher in metastatic tumors than in non-metastatic tumors, but LGALS3 was two-fold lower. The differentiation is associated with IDO1. The revealed features of TDO2, with a significant increase in expression at the metastatic stage and the absence of other IC genes with correlated expression indicates that the prospect of inhibiting TDO2 in metastatic GC. IDO1 may be considered for inhibition in low-differentiated tumors.
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Affiliation(s)
- Danzan Mansorunov
- Research Centre for Medical Genetics, 1 Moskvorechye St., 115522 Moscow, Russia
| | - Natalya Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., 115522 Moscow, Russia
| | - Fatimat Kipkeeva
- Research Centre for Medical Genetics, 1 Moskvorechye St., 115522 Moscow, Russia
| | - Maxim Nikulin
- Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, 115478 Moscow, Russia
| | - Olga Malikhova
- Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, 115478 Moscow, Russia
| | - Ivan Stilidi
- Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, 115478 Moscow, Russia
| | - Alexander Karpukhin
- Research Centre for Medical Genetics, 1 Moskvorechye St., 115522 Moscow, Russia
- Correspondence: ; Tel.: +7-499-324-12-39
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13
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Wusiman W, Zhang Z, Ding Q, Liu M. The pathophyiological role of aminoacyl-tRNA synthetases in digestive system diseases. Front Physiol 2022; 13:935576. [PMID: 36017335 PMCID: PMC9396140 DOI: 10.3389/fphys.2022.935576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) catalyze the ligation of amino acids to their cognate transfer RNAs and are indispensable enzymes for protein biosynthesis in all the cells. Previously, ARSs were considered simply as housekeeping enzymes, however, they are now known to be involved in a variety of physiological and pathological processes, such as tumorigenesis, angiogenesis, and immune response. In this review, we summarize the role of ARSs in the digestive system, including the esophagus, stomach, small intestine, colon, as well as the auxiliary organs such as the pancreas, liver, and the gallbladder. Furthermore, we specifically focus on the diagnostic and prognostic value of ARSs in cancers, aiming to provide new insights into the pathophysiological implications of ARSs in tumorigenesis.
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Affiliation(s)
- Wugelanmu Wusiman
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zerui Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Ding
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Liu
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Mei Liu,
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14
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Expression of Immune Checkpoints in Malignant Tumors: Therapy Targets and Biomarkers for the Gastric Cancer Prognosis. Diagnostics (Basel) 2021; 11:diagnostics11122370. [PMID: 34943606 PMCID: PMC8700640 DOI: 10.3390/diagnostics11122370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 02/07/2023] Open
Abstract
To increase the effectiveness of anticancer therapy based on immune checkpoint (IC) inhibition, some ICs are being investigated in addition to those used in clinic. We reviewed data on the relationship between PD-L1, B7-H3, B7-H4, IDO1, Galectin-3 and -9, CEACAM1, CD155, Siglec-15 and ADAM17 expression with cancer development in complex with the results of clinical trials on their inhibition. Increased expression of the most studied ICs—PD-L1, B7-H3, and B7-H4—is associated with poor survival; their inhibition is clinically significant. Expression of IDO1, CD155, and ADAM17 is also associated with poor survival, including gastric cancer (GC). The available data indicate that CD155 and ADAM17 are promising targets for immune therapy. However, the clinical trials of anti-IDO1 antibodies have been unsatisfactory. Expression of Galectin-3 and -9, CEACAM1 and Siglec-15 demonstrates a contradictory relationship with patient survival. The lack of satisfactory results of these IC inhibitor clinical trials additionally indicates the complex nature of their functioning. In conclusion, in many cases it is important to analyze the expression of other participants of the immune response besides target IC. The PD-L1, B7-H3, B7-H4, IDO1 and ADAM17 may be considered as candidates for prognosis markers for GC patient survival.
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15
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Bermúdez A, Arranz-Salas I, Mercado S, López-Villodres JA, González V, Ríus F, Ortega MV, Alba C, Hierro I, Bermúdez D. Her2-Positive and Microsatellite Instability Status in Gastric Cancer-Clinicopathological Implications. Diagnostics (Basel) 2021; 11:944. [PMID: 34070574 PMCID: PMC8228707 DOI: 10.3390/diagnostics11060944] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related death. The combination of new molecular classifications with clinicopathological data could contribute to the individualization of patients and to the development of new therapeutic strategies. We examined the various associations in two molecular types of GC: HER2-positive (human epidermal growth factor receptor 2) and microsatellite instability (MSI), assessing their influence on treatment and prognosis. A retrospective study of 142 GC patients was performed with molecular characterization through HER2 overexpression and DNA repair protein expression for MSI. The percentage of HER2-positive tumors was 13.4%, predominantly in men. Correlations were found with intestinal type, metastases, advanced stages and chemotherapy. Almost 75% of HER2-positive patients died. MSI occurred in 16.2%, associated with advanced age, female sex, distal location and intestinal type. These patients had few metastases and low stages. The percentage of deaths was higher among MSI patients who received perioperative chemotherapy. The determination of HER2 and MSI status in GC is important for their association with specific clinicopathological features and for their prognostic and predictive value.
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Affiliation(s)
- Ana Bermúdez
- Department of Anesthesiology, Nuestra Señora de Valme University Hospital, 41014 Seville, Spain;
| | - Isabel Arranz-Salas
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
- Unit of Anatomical Pathology, Virgen de la Victoria University Hospital, 29010 Malaga, Spain;
| | - Silvia Mercado
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
| | - Juan A. López-Villodres
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
| | - Virginia González
- Unit of Anatomical Pathology; Montilla Hospital, 14550 Montilla, Spain;
| | - Francisca Ríus
- Department of Public Health and Psychiatry, University of Malaga, 29010 Malaga, Spain;
| | - María V. Ortega
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
- Unit of Anatomical Pathology, Virgen de la Victoria University Hospital, 29010 Malaga, Spain;
| | - Carmen Alba
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
| | - Isabel Hierro
- Unit of Anatomical Pathology, Virgen de la Victoria University Hospital, 29010 Malaga, Spain;
| | - Diego Bermúdez
- Department of Human Physiology, Human Histology, Anatomical Pathology and Physical Education, University of Malaga, 29010 Malaga, Spain; (I.A.-S.); (S.M.); (J.A.L.-V.); (M.V.O.); (C.A.)
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16
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Ahn YH, Oh SC, Zhou S, Kim TD. Tryptophanyl-tRNA Synthetase as a Potential Therapeutic Target. Int J Mol Sci 2021; 22:ijms22094523. [PMID: 33926067 PMCID: PMC8123658 DOI: 10.3390/ijms22094523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Tryptophanyl-tRNA synthetase (WRS) is an essential enzyme that catalyzes the ligation of tryptophan (Trp) to its cognate tRNAtrp during translation via aminoacylation. Interestingly, WRS also plays physiopathological roles in diseases including sepsis, cancer, and autoimmune and brain diseases and has potential as a pharmacological target and therapeutic. However, WRS is still generally regarded simply as an enzyme that produces Trp in polypeptides; therefore, studies of the pharmacological effects, therapeutic targets, and mechanisms of action of WRS are still at an emerging stage. This review summarizes the involvement of WRS in human diseases. We hope that this will encourage further investigation into WRS as a potential target for drug development in various pathological states including infection, tumorigenesis, and autoimmune and brain diseases.
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Affiliation(s)
- Young Ha Ahn
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China;
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
| | - Se-Chan Oh
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China;
- Correspondence: (S.Z.); (T.-D.K.)
| | - Tae-Don Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
- Correspondence: (S.Z.); (T.-D.K.)
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17
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Zhou Z, Sun B, Nie A, Yu D, Bian M. Roles of Aminoacyl-tRNA Synthetases in Cancer. Front Cell Dev Biol 2020; 8:599765. [PMID: 33330488 PMCID: PMC7729087 DOI: 10.3389/fcell.2020.599765] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) catalyze the ligation of amino acids to their cognate transfer RNAs (tRNAs), thus playing an important role in protein synthesis. In eukaryotic cells, these enzymes exist in free form or in the form of multi-tRNA synthetase complex (MSC). The latter contains nine cytoplasmic ARSs and three ARS-interacting multifunctional proteins (AIMPs). Normally, ARSs and AIMPs are regarded as housekeeping molecules without additional functions. However, a growing number of studies indicate that ARSs are involved in a variety of physiological and pathological processes, especially tumorigenesis. Here, we introduce the roles of ARSs and AIMPs in certain cancers, such as colon cancer, lung cancer, breast cancer, gastric cancer and pancreatic cancer. Furthermore, we particularly focus on their potential clinical applications in cancer, aiming at providing new insights into the pathogenesis and treatment of cancer.
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Affiliation(s)
- Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bao Sun
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China.,Institution of Clinical Pharmacy, Central South University, Changsha, China
| | - Anzheng Nie
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng Bian
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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18
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Wang J, Vallee I, Dutta A, Wang Y, Mo Z, Liu Z, Cui H, Su AI, Yang XL. Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer. Genes (Basel) 2020; 11:genes11111384. [PMID: 33266490 PMCID: PMC7700366 DOI: 10.3390/genes11111384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/24/2020] [Accepted: 11/20/2020] [Indexed: 12/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are key enzymes in the mRNA translation machinery, yet they possess numerous non-canonical functions developed during the evolution of complex organisms. The aaRSs and aaRS-interacting multi-functional proteins (AIMPs) are continually being implicated in tumorigenesis, but these connections are often limited in scope, focusing on specific aaRSs in distinct cancer subtypes. Here, we analyze publicly available genomic and transcriptomic data on human cytoplasmic and mitochondrial aaRSs across many cancer types. As high-throughput technologies have improved exponentially, large-scale projects have systematically quantified genetic alteration and expression from thousands of cancer patient samples. One such project is the Cancer Genome Atlas (TCGA), which processed over 20,000 primary cancer and matched normal samples from 33 cancer types. The wealth of knowledge provided from this undertaking has streamlined the identification of cancer drivers and suppressors. We examined aaRS expression data produced by the TCGA project and combined this with patient survival data to recognize trends in aaRSs' impact on cancer both molecularly and prognostically. We further compared these trends to an established tumor suppressor and a proto-oncogene. We observed apparent upregulation of many tRNA synthetase genes with aggressive cancer types, yet, at the individual gene level, some aaRSs resemble a tumor suppressor while others show similarities to an oncogene. This study provides an unbiased, overarching perspective on the relationship of aaRSs with cancers and identifies certain aaRS family members as promising therapeutic targets or potential leads for developing biological therapy for cancer.
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Affiliation(s)
- Justin Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
| | - Ingrid Vallee
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
| | - Aditi Dutta
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
| | - Yu Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
| | - Zhongying Mo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
| | - Ze Liu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
| | - Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
| | - Andrew I. Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA;
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA; (J.W.); (I.V.); (A.D.); (Y.W.); (Z.M.); (Z.L.); (H.C.)
- Correspondence: ; Tel.: +1-858-784-8976; Fax: +1-858-784-7250
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19
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Luo H, Ma C. Identification of prognostic genes in uveal melanoma microenvironment. PLoS One 2020; 15:e0242263. [PMID: 33196683 PMCID: PMC7668584 DOI: 10.1371/journal.pone.0242263] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Many previous studies have demonstrated that the infiltrating of immune and stromal cells in the tumor microenvironment contributes significantly to prognosis. Methods Dataset TCGA-UVM, download from TCGA portal, was taken as the training cohort, and GSE22138, obtained from GEO database, was set as the validation cohort. ESTIMATE algorithm was applied to find intersection differentially expressed genes (DEGs) among tumor microenvironment. Kaplan-Meier analysis and univariate Cox regression model were performed on intersection DEGs to initial screen for potential prognostic genes. Then these genes entered into the validation cohort for validation using the same methods as that in the training cohort. Moreover, we conducted correlation analyses between the genes obtained in the validation cohort and the status of chromosome 3, chromosome 8q, and tumor metastasis to get prognosis genes. At last, the immune infiltration analysis was performed between the prognostic genes and 6 main kinds of tumor-infiltrating immune cells (TICs) for understanding the role of the genes in the tumor microenvironment. Results 959 intersection DEGs were found in the UM microenvironment. Kaplan-Meier and Cox analysis was then performed in the training and validation cohorts on these DEGs, and 52 genes were identified with potential prognostic value. After comparing the 52 genes to chromosome 3, chromosome 8q, and metastasis, we obtained 21 genes as the prognostic genes. The immune infiltration analysis showed that Neutrophil had the potential prognostic ability, and almost every prognostic gene we had identified was correlated with abundances of Neutrophil and CD8+ T Cell. Conclusions Identifying 21 prognosis genes (SERPINB9, EDNRB, RAPGEF3, HFE, RNF43, ZNF415, IL12RB2, MTUS1, NEDD9, ZNF667, AZGP1, WARS, GEM, RAB31, CALHM2, CA12, MYEOV, CELF2, SLCO5A1, ISM1, and PAPSS2) could accurately identify patients' prognosis and had close interactions with Neutrophil in the tumor environment, which may provide UM patients with personalized prognosis prediction and new treatment insights.
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Affiliation(s)
- Huan Luo
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and the Berlin Institute of Health, Berlin, Germany
- Klinik für Augenheilkunde, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Chao Ma
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and the Berlin Institute of Health, Berlin, Germany
- BCRT—Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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20
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Zeng F, Su J, Peng C, Liao M, Zhao S, Guo Y, Chen X, Deng G. Prognostic Implications of Metabolism Related Gene Signature in Cutaneous Melanoma. Front Oncol 2020; 10:1710. [PMID: 33014847 PMCID: PMC7509113 DOI: 10.3389/fonc.2020.01710] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
Metabolic reprogramming is closely related to melanoma. However, the prognostic role of metabolism-related genes (MRGs) remains to be elucidated. We aimed to establish a nomogram by combining MRGs signature and clinicopathological factors to predict melanoma prognosis. Eighteen prognostic MRGs between melanoma and normal samples were identified using The Cancer Genome Atlas (TCGA) and GSE15605. WARS (HR = 0.881, 95% CI = 0.788–0.984, P = 0.025) and MGST1 (HR = 1.124, 95% CI = 1.007–1.255, P = 0.037) were ultimately identified as independent prognostic MRGs with LASSO regression and multivariate Cox regression. The MRGs signature was established according to these two genes and externally validated in the Gene Expression Omnibus (GEO) dataset. Kaplan-Meier survival analysis indicated that patients in the high-risk group had significantly poorer overall survival (OS) than those in the low-risk group. Furthermore, the MRGs signature was identified as an independent prognostic factor for melanoma survival. An MRGs nomogram based on the MRGs signature and clinicopathological factors was developed in TCGA cohort and validated in the GEO dataset. Calibration plots showed good consistency between the prediction of nomogram and actual observation. The receiver operating characteristic curve and decision curve analysis indicated that MRGs nomogram had better OS prediction and clinical net benefit than the stage system. To our knowledge, we are the first to develop a prognostic nomogram based on MRGs signature with better predictive power than the current staging system, which could assist individualized prognosis prediction and improve treatment.
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Affiliation(s)
- Furong Zeng
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Su
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Cong Peng
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Mengting Liao
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Shuang Zhao
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Guo
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Chen
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Guangtong Deng
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Gastric cancer: genome damaged by bugs. Oncogene 2020; 39:3427-3442. [PMID: 32123313 PMCID: PMC7176583 DOI: 10.1038/s41388-020-1241-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022]
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related death worldwide. The role of the microorganisms in gastric tumorigenesis attracts much attention in recent years. These microorganisms include bacteria, virus, and fungi. Among them, Helicobacter pylori (H. pylori) infection is by far the most important risk factor for GC development, with special reference to the early-onset cases. H. pylori targets multiple cellular components by utilizing various virulence factors to modulate the host proliferation, apoptosis, migration, and inflammatory response. Epstein–Barr virus (EBV) serves as another major risk factor in gastric carcinogenesis. The virus protein, EBER noncoding RNA, and EBV miRNAs contribute to the tumorigenesis by modulating host genome methylation and gene expression. In this review, we summarized the related reports about the colonized microorganism in the stomach and discussed their specific roles in gastric tumorigenesis. Meanwhile, we highlighted the therapeutic significance of eradicating the microorganisms in GC treatment.
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22
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Thirty years of Epstein-Barr virus-associated gastric carcinoma. Virchows Arch 2019; 476:353-365. [PMID: 31836926 DOI: 10.1007/s00428-019-02724-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022]
Abstract
Thirty years have passed since a possible association of Epstein-Barr virus (EBV) with gastric carcinoma was reported. We now know EBV-associated gastric carcinoma to be a specific subtype of gastric carcinoma. Global epigenetic methylation and counteraction of the antitumour microenvironment are two major characteristics of this subtype of gastric carcinoma. Recent development of therapeutic modalities for gastric carcinoma, such as endoscopic mucosal dissection and immune checkpoint inhibitor therapy, has made the presence of EBV infection a biomarker for the treatment of gastric carcinoma. This review presents a portrait of EBV-associated gastric carcinoma from initiation to maturity that we define as the 'gastritis-infection-cancer sequence', followed by its molecular abnormalities and interactions with immune checkpoint molecules and the microenvironment. EBV non-coding RNAs (microRNA and circular RNA) and exosomes derived from EBV-infected cells that were previously behind the scenes are now recognized for their roles in EBV-associated gastric carcinoma. The virus utilizes cellular machinery skilfully to control infected cells and their microenvironment. We should thus strive to understand virus-host interactions more fully in the following years to overcome this virus-driven subtype of gastric carcinoma.
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