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Han Y, Li X, Yan J, Ma C, Wang X, Pan H, Zheng X, Zhang Z, Gao B, Ji XY. Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Melanoma. Front Oncol 2020; 10:581985. [PMID: 33178610 PMCID: PMC7596746 DOI: 10.3389/fonc.2020.581985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/24/2020] [Indexed: 01/19/2023] Open
Abstract
Melanoma is the deadliest skin tumor and is prone to distant metastases. The incidence of melanoma has increased rapidly in the past few decades, and current trends indicate that this growth is continuing. This study was aimed to explore the molecular mechanisms of melanoma pathogenesis and discover underlying pathways and genes associated with melanoma. We used high-throughput expression data to study differential expression profiles of related genes in melanoma. The differentially expressed genes (DEGs) of melanoma in GSE15605, GSE46517, GSE7553, and the Cancer Genome Atlas (TCGA) datasets were analyzed. Differentially expressed genes (DEGs) were identified by paired t-test. Then the DEGs were performed cluster and principal component analyses and protein–protein interaction (PPI) network construction. After that, we analyzed the differential genes through bioinformatics and got hub genes. Finally, the expression of hub genes was confirmed in the TCGA databases and collected patient tissue samples. Total 144 up-regulated DEGs and 16 down-regulated DEGs were identified. A total of 17 gene ontology analysis (GO) terms and 11 pathways were closely related to melanoma. Pathway of pathways in cancer was enriched in 8 DEGs, such as junction plakoglobin (JUP) and epidermal growth factor receptor (EGFR). In the PPI networks, 9 hub genes were obtained, such as loricrin (LOR), filaggrin (FLG), keratin 5 (KRT5), corneodesmosin (CDSN), desmoglein 1 (DSG1), desmoglein 3 (DSG3), keratin 1 (KRT1), involucrin (IVL), and EGFR. The pathway of pathways in cancer and its enriched DEGs may play important roles in the process of melanoma. The hub genes of DEGs may become promising melanoma candidate genes. Five key genes FLG, DSG1, DSG3, IVL, and EGFR were identified in the TCGA database and melanoma tissues. The results suggested that FLG, DSG1, DSG3, IVL, and EGFR might play important roles and potentially be valuable in the prognosis and treatment of melanoma. These hub genes might well have clinical significance as diagnostic markers.
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Affiliation(s)
- Yanjie Han
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xinxin Li
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Jiliang Yan
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Chunyan Ma
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xin Wang
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Hong Pan
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xiaoli Zheng
- Hospital Infection Control Office, First Affiliated Hospital of Henan University, Kaifeng, China
| | - Zhen Zhang
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Biao Gao
- Clinical Laboratory, Functional Laboratory and Department of Stomatology, Kaifeng Central Hospital, Kaifeng, China
| | - Xin-Ying Ji
- Kaifeng Key Laboratory for Infectious Diseases and Biosafety, Henan International Joint Laboratory of Nuclear Protein Regulation, Henan School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, China
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Wolf DA, Lin Y, Duan H, Cheng Y. eIF-Three to Tango: emerging functions of translation initiation factor eIF3 in protein synthesis and disease. J Mol Cell Biol 2020; 12:403-409. [PMID: 32279082 PMCID: PMC7333474 DOI: 10.1093/jmcb/mjaa018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/20/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Studies over the past three years have substantially expanded the involvements of eukaryotic initiation factor 3 (eIF3) in messenger RNA (mRNA) translation. It now appears that this multi-subunit complex is involved in every possible form of mRNA translation, controlling every step of protein synthesis from initiation to elongation, termination, and quality control in positive as well as negative fashion. Through the study of eIF3, we are beginning to appreciate protein synthesis as a highly integrated process coordinating protein production with protein folding, subcellular targeting, and degradation. At the same time, eIF3 subunits appear to have specific functions that probably vary between different tissues and individual cells. Considering the broad functions of eIF3 in protein homeostasis, it comes as little surprise that eIF3 is increasingly implicated in major human diseases and first attempts at therapeutically targeting eIF3 have been undertaken. Much remains to be learned, however, about subunit- and tissue-specific functions of eIF3 in protein synthesis and disease and their regulation by environmental conditions and post-translational modifications.
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Affiliation(s)
- Dieter A Wolf
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Yingying Lin
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Haoran Duan
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
| | - Yabin Cheng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research & Innovation Center for Cell Stress Signaling, Xiamen University, Xiamen 361102, China
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Li J, Yu W, Ge J, Zhang J, Wang Y, Wang P, Shi G. Targeting eIF3f Suppresses the Growth of Prostate Cancer Cells by Inhibiting Akt Signaling. Onco Targets Ther 2020; 13:3739-3750. [PMID: 32440143 PMCID: PMC7210466 DOI: 10.2147/ott.s244345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/10/2020] [Indexed: 01/14/2023] Open
Abstract
Background Eukaryotic initiation factor 3 (eIF3) is the largest translation initiation factor, and oncogenic roles have been discovered for its subunits, including the f subunit (ie, eIF3f), in various human cancers. However, the roles of eIF3f in the development and progression of prostate cancer (PCa) have not been reported. Materials and Methods We performed in silico analysis to screen the expression of eIF3 subunits. Relevant shRNAs were used to knock down eIF3 subunits in 22Rv1 cells and cell proliferation was analyzed. eIF3f expression in PCa specimens was confirmed by immunohistochemistry. eIF3f knockdown was established to evaluate the effects of eIF3f on cell proliferation in vitro and in vivo. RNA‐seq, bioinformatics analysis and Western blotting were applied to explore the molecular details underlying the biological function of eIF3f in PCa cells. shRNA-resistant eIF3f and myristoylated-Akt were used to rescue the effects of eIF3f disturbance on PCa cells. Results Functional analyses confirmed that eIF3f is essential for PCa proliferation. Notably, the expression of eIF3f was found to be elevated in human PCa tissues as well as in PCa cell lines. eIF3f silencing significantly suppressed the growth of PCa cells, both in vitro and in vivo. eIF3f expression was positively correlated with Akt signaling activity in RNA-seq profiles and published prostate cohorts. Knockdown of eIF3f markedly reduced the levels of phosphorylated Akt in PCa cells. Exogenous expression of shRNA-resistant eIF3f in eIF3f knockdown cells restored Akt phosphorylation levels and cell growth. Importantly, rescue experiments revealed that ectopic expression of myristoylated-Akt partially alleviated the suppressive effects of eIF3f disturbance with respect to the growth of PCa cells. Conclusion These results suggested that eIF3f has an oncogenic role in PCa, mediated at least partially through the regulation of Akt signaling, and that eIF3f represents a potential target for the inhibition of PCa growth and progression.
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Affiliation(s)
- Junhong Li
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, People's Republic of China
| | - Wandong Yu
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, People's Republic of China
| | - Jianchao Ge
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, People's Republic of China
| | - Jun Zhang
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, People's Republic of China
| | - Yang Wang
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, People's Republic of China
| | - Pengyu Wang
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, People's Republic of China
| | - Guowei Shi
- Department of Urology, Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, People's Republic of China
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Docquier A, Pavlin L, Raibon A, Bertrand‐Gaday C, Sar C, Leibovitch S, Candau R, Bernardi H. eIF3f depletion impedes mouse embryonic development, reduces adult skeletal muscle mass and amplifies muscle loss during disuse. J Physiol 2019; 597:3107-3131. [DOI: 10.1113/jp277841] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/24/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- Aurélie Docquier
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Laura Pavlin
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Audrey Raibon
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | | | - Chamroeun Sar
- Institut National de la Santé et de la Recherche Médicale, U‐583Institut des Neurosciences de MontpellierHôpital Saint Eloi Montpellier France
| | - Serge Leibovitch
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Robin Candau
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
| | - Henri Bernardi
- INRA, UMR866 Dynamique Musculaire et MétabolismeUniversité de Montpellier Montpellier France
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Targeted release of transcription factors for human cell reprogramming by ZEBRA cell-penetrating peptide. Int J Pharm 2017. [DOI: 10.1016/j.ijpharm.2017.06.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Role of Eukaryotic Initiation Factors during Cellular Stress and Cancer Progression. J Nucleic Acids 2016; 2016:8235121. [PMID: 28083147 PMCID: PMC5204094 DOI: 10.1155/2016/8235121] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis can be segmented into distinct phases comprising mRNA translation initiation, elongation, and termination. Translation initiation is a highly regulated and rate-limiting step of protein synthesis that requires more than 12 eukaryotic initiation factors (eIFs). Extensive evidence shows that the transcriptome and corresponding proteome do not invariably correlate with each other in a variety of contexts. In particular, translation of mRNAs specific to angiogenesis, tumor development, and apoptosis is altered during physiological and pathophysiological stress conditions. In cancer cells, the expression and functions of eIFs are hampered, resulting in the inhibition of global translation and enhancement of translation of subsets of mRNAs by alternative mechanisms. A precise understanding of mechanisms involving eukaryotic initiation factors leading to differential protein expression can help us to design better strategies to diagnose and treat cancer. The high spatial and temporal resolution of translation control can have an immediate effect on the microenvironment of the cell in comparison with changes in transcription. The dysregulation of mRNA translation mechanisms is increasingly being exploited as a target to treat cancer. In this review, we will focus on this context by describing both canonical and noncanonical roles of eIFs, which alter mRNA translation.
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Liu Y, Liu L, Yu T, Lin HC, Chu D, Deng W, Yan MX, Li J, Yao M. Systematic analysis of mRNA expression profiles in NSCLC cell lines to screen metastasis-related genes. Mol Med Rep 2016; 14:5093-5103. [PMID: 27840927 PMCID: PMC5355670 DOI: 10.3892/mmr.2016.5911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/29/2016] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is the most prevalent cancer in humans and has the lowest survival outcomes due to its high metastatic potential. The aim of the present study was to screen for metastasis-related genes (MRGs) by investigating the differential expression genes (DEGs) identified by the mRNA expression profiles in SPC-A-1sci (highly metastatic) and SPC-A-1 (parental) cells. DEGs were screened using Genespring software. Gene Ontology and pathway enrichment analyses of these DEGs were performed. Interaction networks between the proteins encoded by the DEGs were identified using the database BioGRID and were visualized by Cytoscape. Modular analysis of the protein-protein interaction network was performed in CFinder. Among these DEGs, the expression levels of 18 genes were examined in SPC-A-1sci and SPC-A-1 cell lines with reverse transcription-quantitative polymerase chain reaction, and 10 of the 18 genes were assessed by western blotting to validate the results of the microarray. Furthermore, the role of metallothionein 1X (MT1X) in non-small cell lung cancer was explored in functional assays and 72 pairs of clinical samples in vitro. Finally, 4,838 DEGs were screened, including 798 upregulated and 4,040 downregulated genes. The significantly enriched functions included gene expression, cytosol and poly-(A) RNA binding, and the most enriched pathway was biosynthesis of antibiotics. Furthermore, MT1X was revealed to promote the migration and invasion ability in SPC-A-1sci and PC-9 lung cancer cell lines. Therefore, MT1X was identified as a candidate MRG through systematic analysis in the present microarray, which was demonstrated to offer potential reference value in screening MRGs.
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Affiliation(s)
- Ying Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - Lei Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - Tao Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - He-Chun Lin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - Dandan Chu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - Wei Deng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - Ming-Xia Yan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - Jing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, P.R. China
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Yu F, Tan WJ, Lu Y, MacAry PA, Loh KS. The other side of the coin: Leveraging Epstein-Barr virus in research and therapy. Oral Oncol 2016; 60:112-7. [PMID: 27531881 PMCID: PMC7108324 DOI: 10.1016/j.oraloncology.2016.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/09/2016] [Indexed: 12/22/2022]
Abstract
Epstein-Barr virus is (EBV) a ubiquitous virus prevalent in 90% of the human population. Transmitted through infected saliva, EBV is the causative agent of infectious mononucleosis (IM) and is further implicated in malignancies of lymphoid and epithelial origins. In the past few decades, research efforts primarily focused on dissecting the mechanism of EBV-induced oncogenesis. Here, we present an alternate facet of the oncovirus EBV, on its applications in research and therapy. Finally, discussions on the prospective utilization of EBV in nasopharyngeal carcinoma (NPC) diagnosis and therapy will also be presented.
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Affiliation(s)
- Fenggang Yu
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Wei Jian Tan
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yanan Lu
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul A MacAry
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kwok Seng Loh
- Department of Otolaryngology-Head and Neck Surgery, National University Health System, Singapore
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